From 0181df537ffb4e4273b2ca005738fdb7bd3d73f5 Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kkebreau@posteo.net>
Date: Sat, 24 Feb 2018 00:01:21 -0500
Subject: gnu: wxmaxima: Update to 18.02.0.

* gnu/packages/maths.scm (wxmaxima): Update to 18.02.0.
[source]: Add patch.
[build-system]: Use the cmake-build-system.
[native-inputs]: Remove autoconf and automake.
[arguments]: Disable tests, remove 'autoconf' phase.
* gnu/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch: New
file.
* gnu/local.mk (dist_patch_DATA): Add it.
---
 gnu/packages/maths.scm                             | 18 +++++++--------
 ...xmaxima-do-not-use-old-gnuplot-parameters.patch | 26 ++++++++++++++++++++++
 2 files changed, 34 insertions(+), 10 deletions(-)
 create mode 100644 gnu/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch

(limited to 'gnu/packages')

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 25e1d5a312..b20cec5440 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -2489,7 +2489,7 @@ point numbers.")
 (define-public wxmaxima
   (package
     (name "wxmaxima")
-    (version "17.10.1")
+    (version "18.02.0")
     (source
      (origin
        (method url-fetch)
@@ -2498,12 +2498,12 @@ point numbers.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0qlzc31cqkwpfgrb9cif9bcnkj3rq487plg4rns7jxv6pq4609v1"))))
-    (build-system gnu-build-system)
+         "03kr2rgfp4hcf3is8m8d8f9hj660c3xgrc50vrrfpixx4syh6wvj"))
+       (patches
+        (search-patches "wxmaxima-do-not-use-old-gnuplot-parameters.patch"))))
+    (build-system cmake-build-system)
     (native-inputs
-     `(("autoconf" ,autoconf)
-       ("automake" ,automake)
-       ("gettext" ,gettext-minimal)))
+     `(("gettext" ,gettext-minimal)))
     (inputs
      `(("wxwidgets" ,wxwidgets)
        ("maxima" ,maxima)
@@ -2512,11 +2512,9 @@ point numbers.")
        ("gtk+" ,gtk+)
        ("shared-mime-info" ,shared-mime-info)))
     (arguments
-     `(#:phases
+     `(#:tests? #f ; no check target
+       #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'autoconf
-           (lambda _
-             (zero? (system* "sh" "bootstrap"))))
          (add-after 'install 'wrap-program
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (wrap-program (string-append (assoc-ref outputs "out")
diff --git a/gnu/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch b/gnu/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch
new file mode 100644
index 0000000000..345101bd3a
--- /dev/null
+++ b/gnu/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch
@@ -0,0 +1,26 @@
+This fixes the wxplot2d plotting issue found at
+https://github.com/andrejv/wxmaxima/issues/973.
+
+From 5a0693c97ceaa4935b908f1e478126896952f399 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Gunter=20K=C3=B6nigsmann?= <gunter@peterpall.de>
+Date: Mon, 19 Feb 2018 05:37:35 +0100
+Subject: [PATCH] Seems I accidentally made wxMaxima to default to parameters
+ for old gnuplots. Resolves #973
+
+---
+ data/wxmathml.lisp.in | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/data/wxmathml.lisp.in b/data/wxmathml.lisp.in
+index a32e3fc3..4e19acaf 100644
+--- a/data/wxmathml.lisp.in
++++ b/data/wxmathml.lisp.in
+@@ -43,7 +43,7 @@
+ (defvar $wxsubscripts t
+   "Recognize TeX-style subscripts")
+ (defvar $wxplot_pngcairo nil "Use gnuplot's pngcairo terminal for new plots?")
+-(defmvar $wxplot_old_gnuplot t)
++(defmvar $wxplot_old_gnuplot nil)
+ 
+ (defun $wxstatusbar (status)
+   (format t "<statusbar>~a</statusbar>~%" status))
-- 
cgit v1.2.3


From 3422e10ededa47ed7e71cc4fd55aab4cf65ea905 Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Sun, 25 Feb 2018 11:45:17 +0100
Subject: gnu: Update java-testng to 6.14.3.

* gnu/packages/java.scm (java-testng): Update to 6.14.3.
---
 gnu/packages/java.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 47220fc75c..94c806b99e 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -6959,7 +6959,7 @@ those in Perl and JavaScript.")
 (define-public java-testng
   (package
     (name "java-testng")
-    (version "6.14.2")
+    (version "6.14.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -6968,7 +6968,7 @@ those in Perl and JavaScript.")
               (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "0ngj88dpbqqdx9084cmiasmn9q3v5dgx45qbvxpip47nxc5x14xy"))))
+                "0y6vq30i5g276kw0v2bhbvci22ijg7ax49ap2611yqlhbs4d6dqv"))))
     (build-system ant-build-system)
     (arguments
      `(#:jdk ,icedtea-8; java.util.function
-- 
cgit v1.2.3


From 3214afabff01f7aae1d4790059a6f40763023711 Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Sat, 10 Feb 2018 21:53:53 +0100
Subject: gnu: Add java-plexus-component-annotations.

* gnu/packages/java.scm (java-plexus-component-annotations): New
variable.
---
 gnu/packages/java.scm | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 94c806b99e..5f8f7fdb55 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -2660,6 +2660,20 @@ archives (jar).")
      `(("archiver" ,java-plexus-archiver)
        ("hamcrest" ,java-hamcrest-core)))))
 
+(define-public java-plexus-component-annotations
+  (package
+    (inherit java-plexus-container-default)
+    (name "java-plexus-component-annotations")
+    (arguments
+     `(#:jar-name "plexus-component-annotations.jar"
+       #:source-dir "plexus-component-annotations/src/main/java"
+       #:tests? #f)); no tests
+    (inputs '())
+    (native-inputs '())
+    (synopsis "Plexus descriptors generator")
+    (description "This package is a Maven plugin to generate Plexus descriptors
+from source tags and class annotations.")))
+
 (define-public java-asm
   (package
     (name "java-asm")
-- 
cgit v1.2.3


From a7ad92ade94d456f991062aedede9fd1ecd64b07 Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Wed, 14 Feb 2018 22:11:34 +0100
Subject: gnu: Make java-plexus-container-default-bootstrap private.

* gnu/packages/java.scm (java-plexus-container-default-bootstrap): Make
private.
---
 gnu/packages/java.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 5f8f7fdb55..7312d4703d 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -2483,7 +2483,7 @@ mechanism of Java.  It is especially useful for dynamic loading of application
 components.")
     (license license:asl2.0)))
 
-(define-public java-plexus-container-default-bootstrap
+(define java-plexus-container-default-bootstrap
   (package
     (name "java-plexus-container-default-bootstrap")
     (version "1.7.1")
-- 
cgit v1.2.3


From 4f77ba17c663881c0657c838fbcb2a98e9137aa5 Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Sat, 10 Feb 2018 22:02:24 +0100
Subject: gnu: Add java-plexus-cipher.

* gnu/packages/java.scm (java-plexus-cipher): New variable.
---
 gnu/packages/java.scm | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 7312d4703d..57370db76e 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -2674,6 +2674,42 @@ archives (jar).")
     (description "This package is a Maven plugin to generate Plexus descriptors
 from source tags and class annotations.")))
 
+(define-public java-plexus-cipher
+  (package
+    (name "java-plexus-cipher")
+    (version "1.7")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/codehaus-plexus/plexus-cipher"
+                                  "/archive/plexus-cipher-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1j3r8xzlxlk340snkjp6lk2ilkxlkn8qavsfiq01f43xmvv8ymk3"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "plexus-cipher.jar"
+       #:source-dir "src/main/java"
+       #:jdk ,icedtea-8
+       #:tests? #f; FIXME: requires sisu-inject-bean
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'copy-resources
+           (lambda _
+             (copy-recursively "src/main/resources" "build/classes")
+             (mkdir-p "build/classes/META-INF/sisu")
+             (with-output-to-file "build/classes/META-INF/sisu/javax.inject.Named"
+               (lambda _
+                 (display "org.sonatype.plexus.components.cipher.DefaultPlexusCipher\n")))
+             #t)))))
+    (inputs
+     `(("java-cdi-api" ,java-cdi-api)
+       ("java-javax-inject" ,java-javax-inject)))
+    (home-page "https://github.com/sonatype/plexus-cipher")
+    (synopsis "Encryption/decryption Component")
+    (description "Plexus-cipher contains a component to deal with encryption
+and decryption.")
+    (license license:asl2.0)))
+
 (define-public java-asm
   (package
     (name "java-asm")
-- 
cgit v1.2.3


From 239126d48b960013cc368a3f3636e760e0adb8fd Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Sat, 10 Feb 2018 23:00:09 +0100
Subject: gnu: Add java-plexus-compiler-api.

* gnu/packages/java.scm (java-plexus-compiler-api): New variable.
---
 gnu/packages/java.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 57370db76e..45904ff84a 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -2710,6 +2710,35 @@ from source tags and class annotations.")))
 and decryption.")
     (license license:asl2.0)))
 
+(define-public java-plexus-compiler-api
+  (package
+    (name "java-plexus-compiler-api")
+    (version "2.8.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/codehaus-plexus/plexus-compiler"
+                                  "/archive/plexus-compiler-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0g3x26pymcdnfnwv2a1i57pd5s26f5zqfi1rdy98z1bn01klx25k"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "plexus-compiler-api.jar"
+       #:source-dir "plexus-compiler-api/src/main/java"
+       #:jdk ,icedtea-8
+       #:test-dir "plexus-compiler-api/src/test"))
+    (inputs
+     `(("java-plexus-container-default" ,java-plexus-container-default)
+       ("java-plexus-util" ,java-plexus-utils)))
+    (native-inputs
+     `(("java-junit" ,java-junit)))
+    (home-page "https://github.com/codehaus-plexus/plexus-compiler")
+    (synopsis "Plexus Compilers component's API to manipulate compilers")
+    (description "This package contains the API used by components to manipulate
+compilers.")
+    (license (list license:asl2.0
+                   license:expat))))
+
 (define-public java-asm
   (package
     (name "java-asm")
-- 
cgit v1.2.3


From f8a519fa3f8af3e3be842d84be49897d0bd9fd06 Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Sat, 10 Feb 2018 23:09:20 +0100
Subject: gnu: Add java-plexus-compiler-javac.

gnu/packages/java.scm (java-plexus-compiler-javac): New variable.
---
 gnu/packages/java.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 45904ff84a..dc8523369a 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -2739,6 +2739,26 @@ compilers.")
     (license (list license:asl2.0
                    license:expat))))
 
+(define-public java-plexus-compiler-javac
+  (package
+    (inherit java-plexus-compiler-api)
+    (name "java-plexus-compiler-javac")
+    (arguments
+     `(#:jar-name "plexus-compiler-javac.jar"
+       #:source-dir "plexus-compilers/plexus-compiler-javac/src/main/java"
+       #:jdk ,icedtea-8
+       #:tests? #f; depends on compiler-test -> maven-core -> ... -> this package.
+       #:test-dir "plexus-compilers/plexus-compiler-javac/src/test"))
+    (inputs
+     `(("java-plexus-compiler-api" ,java-plexus-compiler-api)
+       ("java-plexus-utils" ,java-plexus-utils)
+       ("java-plexus-container-default" ,java-plexus-container-default)))
+    (native-inputs
+     `(("java-junit" ,java-junit)))
+    (synopsis "Javac Compiler support for Plexus Compiler component")
+    (description "This package contains the Javac Compiler support for Plexus
+Compiler component.")))
+
 (define-public java-asm
   (package
     (name "java-asm")
-- 
cgit v1.2.3


From 8f524749bc26601d4dc781978104718adb7addc8 Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Sat, 10 Feb 2018 22:42:43 +0100
Subject: gnu: Add java-sisu-build-api.

* gnu/packages/java.scm (java-sisu-build-api): New variable.
---
 gnu/packages/java.scm | 55 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 55 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index dc8523369a..bbc39831ef 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -2759,6 +2759,61 @@ compilers.")
     (description "This package contains the Javac Compiler support for Plexus
 Compiler component.")))
 
+(define-public java-sisu-build-api
+  (package
+    (name "java-sisu-build-api")
+    (version "0.0.7")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/sonatype/sisu-build-api/"
+                                  "archive/plexus-build-api-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1c3rrpma3x634xp2rm2p5iskfhzdyc7qfbhjzr70agrl1jwghgy2"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "sisu-build-api.jar"
+       #:source-dir "src/main/java"
+       #:jdk ,icedtea-8
+       #:tests? #f; FIXME: how to run the tests?
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'copy-resources
+           (lambda _
+             (copy-recursively "src/main/resources" "build/classes")
+             (substitute* (find-files "build/classes")
+               (("\\$\\{project.version\\}") ,version))
+             #t))
+         (add-before 'build 'generate-plexus-compontent
+           (lambda _
+             (mkdir-p "build/classes/META-INF/plexus")
+             ;; This file is required for plexus to inject this package.
+             ;; FIXME: how is it generated?
+             (with-output-to-file "build/classes/META-INF/plexus/components.xml"
+               (lambda _
+                 (display
+                   "<component-set>\n
+  <components>\n
+    <component>\n
+      <role>org.sonatype.plexus.build.incremental.BuildContext</role>\n
+      <role-hint>default</role-hint>\n
+      <implementation>org.sonatype.plexus.build.incremental.DefaultBuildContext</implementation>\n
+      <description>Filesystem based non-incremental build context implementation\n
+which behaves as if all files were just created.</description>\n
+    </component>\n
+  </components>\n
+</component-set>\n")))
+             #t)))))
+    (inputs
+     `(("java-plexus-utils" ,java-plexus-utils)
+       ("java-plexus-container-default" ,java-plexus-container-default)))
+    (home-page "https://github.com/sonatype/sisu-build-api/")
+    (synopsis "Base build API for maven")
+    (description "This package contains the base build API for maven and
+a default implementation of it.  This API is about scanning files in a
+project and determining what files need to be rebuilt.")
+    (license license:asl2.0)))
+
 (define-public java-asm
   (package
     (name "java-asm")
-- 
cgit v1.2.3


From b26c8b618457943075eaf5d33592af0eabf53cc8 Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Sat, 10 Feb 2018 22:51:17 +0100
Subject: gnu: Add java-modello-core.

* gnu/packages/java.scm (java-modello-core): New variable.
---
 gnu/packages/java.scm | 63 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 63 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index bbc39831ef..d7a1299a7f 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -2814,6 +2814,69 @@ a default implementation of it.  This API is about scanning files in a
 project and determining what files need to be rebuilt.")
     (license license:asl2.0)))
 
+(define-public java-modello-core
+  (package
+    (name "java-modello-core")
+    (version "1.9.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/codehaus-plexus/modello"
+                                  "/archive/modello-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0l2pvns8pmlrmjm3iknp7gpg3654y1m8qhy55b19sdwdchdcyxfh"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "modello-core.jar"
+       #:source-dir "modello-core/src/main/java"
+       #:test-dir "modello-core/src/test"
+       #:main-class "org.codehaus.modello.ModelloCli"
+       #:jdk ,icedtea-8
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'copy-resources
+           (lambda _
+             (mkdir-p "build/classes/META-INF/plexus")
+             (copy-file "modello-core/src/main/resources/META-INF/plexus/components.xml"
+                        "build/classes/META-INF/plexus/components.xml")
+             #t))
+         (add-before 'check 'fix-tests
+           (lambda _
+             (with-directory-excursion "modello-core/src/test/java/org/codehaus"
+               (substitute* '("modello/core/DefaultModelloCoreTest.java"
+                              "modello/core/io/ModelReaderTest.java")
+                 (("src/test") "modello-core/src/test")))
+             #t)))))
+    (inputs
+     `(("java-plexus-utils" ,java-plexus-utils)
+       ("java-plexus-container-default" ,java-plexus-container-default)
+       ("java-sisu-build-api" ,java-sisu-build-api)))
+    (native-inputs
+     `(("java-junit" ,java-junit)
+       ("java-plexus-classworlds" ,java-plexus-classworlds)
+       ("java-geronimo-xbean-reflect" ,java-geronimo-xbean-reflect)
+       ("java-guava" ,java-guava)))
+    (home-page "http://codehaus-plexus.github.io/modello/")
+    (synopsis "Framework for code generation from a simple model")
+    (description "Modello is a framework for code generation from a simple model.
+
+Modello generates code from a simple model format: based on a plugin
+architecture, various types of code and descriptors can be generated from the
+single model, including Java POJOs, XML/JSON/YAML marshallers/unmarshallers,
+XSD and documentation.")
+    (license (list
+               license:expat
+               ;; Although this package uses only files licensed under expat,
+               ;; other parts of the source are licensed under different
+               ;; licenses.  We include them to be inherited by other packages.
+               license:asl2.0
+               ;; Some files in modello-plugin-java are licensed under a
+               ;; 5-clause BSD license.
+               (license:non-copyleft
+                 (string-append "file:///modello-plugins/modello-plugin-java/"
+                                "src/main/java/org/codehaus/modello/plugin/"
+                                "java/javasource/JNaming.java"))))))
+
 (define-public java-asm
   (package
     (name "java-asm")
-- 
cgit v1.2.3


From fc620befd4d4236db8f446dba2e0f3abcd4c0cfb Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Sat, 10 Feb 2018 22:52:22 +0100
Subject: gnu: Add java-modello-plugins-java.

* gnu/packages/java.scm (java-modello-plugins-java): New variable.
---
 gnu/packages/java.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index d7a1299a7f..05cf91999b 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -2877,6 +2877,30 @@ XSD and documentation.")
                                 "src/main/java/org/codehaus/modello/plugin/"
                                 "java/javasource/JNaming.java"))))))
 
+(define-public java-modello-plugins-java
+  (package
+    (inherit java-modello-core)
+    (name "java-modello-plugins-java")
+    (arguments
+     `(#:jar-name "modello-plugins-java.jar"
+       #:source-dir "modello-plugins/modello-plugin-java/src/main/java"
+       #:test-dir "modello-plugins/modello-plugin-java/src/test"
+       #:jdk ,icedtea-8
+       #:tests? #f; requires maven-model, which depends on this package
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'copy-resources
+           (lambda _
+             (mkdir-p "build/classes")
+             (copy-recursively "modello-plugins/modello-plugin-java/src/main/resources"
+                               "build/classes")
+             #t)))))
+    (inputs
+     `(("java-modello-core" ,java-modello-core)
+       ,@(package-inputs java-modello-core)))
+    (synopsis "Modello Java Plugin")
+    (description "Modello Java Plugin generates Java objects for the model.")))
+
 (define-public java-asm
   (package
     (name "java-asm")
-- 
cgit v1.2.3


From a0ce95ba8f6beb79fe77fe4f199dbe49e243bbbc Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Sat, 10 Feb 2018 22:53:12 +0100
Subject: gnu: Add java-modello-plugins-xml.

* gnu/packages/java.scm (java-modello-plugins-xml): New variable.
---
 gnu/packages/java.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 05cf91999b..6d77967de6 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -2901,6 +2901,38 @@ XSD and documentation.")
     (synopsis "Modello Java Plugin")
     (description "Modello Java Plugin generates Java objects for the model.")))
 
+(define-public java-modello-plugins-xml
+  (package
+    (inherit java-modello-core)
+    (name "java-modello-plugins-xml")
+    (arguments
+     `(#:jar-name "modello-plugins-xml.jar"
+       #:source-dir "modello-plugins/modello-plugin-xml/src/main/java"
+       #:test-dir "modello-plugins/modello-plugin-xml/src/test"
+       #:jdk ,icedtea-8
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'copy-resources
+           (lambda _
+             (mkdir-p "build/classes")
+             (copy-recursively
+               "modello-plugins/modello-plugin-xml/src/main/resources"
+               "build/classes")
+             #t))
+         (add-before 'check 'fix-paths
+           (lambda _
+             (with-directory-excursion "modello-plugins/modello-plugin-xml/src/test"
+               (substitute*
+                 "java/org/codehaus/modello/plugins/xml/XmlModelloPluginTest.java"
+                 (("src/test") "modello-plugins/modello-plugin-xml/src/test"))))))))
+    (inputs
+     `(("java-modello-core" ,java-modello-core)
+       ("java-modello-plugins-java" ,java-modello-plugins-java)
+       ,@(package-inputs java-modello-core)))
+    (synopsis "Modello XML Plugin")
+    (description "Modello XML Plugin contains shared code for every plugins
+working on XML representation of the model.")))
+
 (define-public java-asm
   (package
     (name "java-asm")
-- 
cgit v1.2.3


From e470856017a705d4ba1881363717579e62f28671 Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Sat, 10 Feb 2018 23:23:38 +0100
Subject: gnu: Add java-modello-test.

gnu/packages/java.scm (java-modello-test): New variable.
---
 gnu/packages/java.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 6d77967de6..f8bb5e58f7 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -2933,6 +2933,25 @@ XSD and documentation.")
     (description "Modello XML Plugin contains shared code for every plugins
 working on XML representation of the model.")))
 
+(define-public java-modello-test
+  (package
+    (inherit java-modello-core)
+    (name "java-modello-test")
+    (arguments
+     `(#:jar-name "modello-test.jar"
+       #:source-dir "modello-test/src/main/java"
+       #:tests? #f; no tests
+       #:jdk ,icedtea-8))
+    (inputs
+     `(("java-plexus-utils" ,java-plexus-utils)
+       ("java-plexus-compiler-api" ,java-plexus-compiler-api)
+       ("java-plexus-compiler-javac" ,java-plexus-compiler-javac)
+       ("java-plexus-container-default" ,java-plexus-container-default)))
+    (synopsis "Modello test package")
+    (description "The modello test package contains the basis to create
+Modello generator unit-tests, including sample models and xml files to test
+every feature for every plugin.")))
+
 (define-public java-asm
   (package
     (name "java-asm")
-- 
cgit v1.2.3


From 36607d3bfe1f0d26773ffaefd22b4968c6237999 Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Sat, 10 Feb 2018 23:30:59 +0100
Subject: gnu: Add java-modello-plugins-xpp3.

gnu/packages/java.scm (java-modello-plugins-xpp3): New variable.
---
 gnu/packages/java.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index f8bb5e58f7..93b343f62f 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -2952,6 +2952,38 @@ working on XML representation of the model.")))
 Modello generator unit-tests, including sample models and xml files to test
 every feature for every plugin.")))
 
+(define-public java-modello-plugins-xpp3
+  (package
+    (inherit java-modello-core)
+    (name "java-modello-plugins-xpp3")
+    (arguments
+     `(#:jar-name "modello-plugins-xpp3.jar"
+       #:source-dir "modello-plugins/modello-plugin-xpp3/src/main/java"
+       #:test-dir "modello-plugins/modello-plugin-xpp3/src/test"
+       ;; One of the test dependencies is maven-model which depends on this package.
+       #:tests? #f
+       #:jdk ,icedtea-8
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'copy-resources
+           (lambda _
+             (mkdir-p "build/classes")
+             (copy-recursively "modello-plugins/modello-plugin-xpp3/src/main/resources"
+                               "build/classes")
+             #t)))))
+    (inputs
+     `(("java-modello-core" ,java-modello-core)
+       ("java-modello-plugins-java" ,java-modello-plugins-java)
+       ("java-modello-plugins-xml" ,java-modello-plugins-xml)
+       ,@(package-inputs java-modello-core)))
+    (native-inputs
+     `(("java-xmlunit" ,java-xmlunit)
+       ("java-modello-test" ,java-modello-test)
+       ,@(package-native-inputs java-modello-core)))
+    (synopsis "Modello XPP3 Plugin")
+    (description "The modello XPP3 plugin generates XML readers and writers based
+on the XPP3 API (XML Pull Parser).")))
+
 (define-public java-asm
   (package
     (name "java-asm")
-- 
cgit v1.2.3


From 0aa85081d6319b582d53e9113be41cbe1a59f2a8 Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Sat, 10 Feb 2018 23:46:31 +0100
Subject: gnu: Add java-plexus-sec-dispatcher.

* gnu/packages/java.scm (java-plexus-sec-dispatcher): New variable.
---
 gnu/packages/java.scm | 88 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 88 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 93b343f62f..2b7a76fda3 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -2759,6 +2759,94 @@ compilers.")
     (description "This package contains the Javac Compiler support for Plexus
 Compiler component.")))
 
+(define-public java-plexus-sec-dispatcher
+  (package
+    (name "java-plexus-sec-dispatcher")
+    (version "1.4") ;; Newest release listed at the Maven Central Repository.
+    (source (origin
+              ;; This project doesn't tag releases or publish tarballs, so we take
+              ;; the "prepare release plexus-sec-dispatcher-1.4" git commit.
+              (method url-fetch)
+              (uri (string-append "https://github.com/sonatype/plexus-sec-dispatcher/"
+                                  "archive/7db8f88048.tar.gz"))
+              (sha256
+               (base32
+                "1smfrk4n7xbrsxpxcp2j4i0j8q86j73w0w6xg7qz83dp6dagdjgp"))
+              (file-name (string-append name "-" version ".tar.gz"))))
+    (arguments
+     `(#:jar-name "plexus-sec-dispatcher.jar"
+       #:source-dir "src/main/java"
+       #:jdk ,icedtea-8
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'generate-models
+           (lambda* (#:key inputs #:allow-other-keys)
+             (define (modello-single-mode file version mode)
+               (zero? (system* "java"
+                               "org.codehaus.modello.ModelloCli"
+                               file mode "src/main/java" version
+                               "false" "true")))
+             (let ((file "src/main/mdo/settings-security.mdo"))
+               (and
+               (modello-single-mode file "1.0.0" "java")
+               (modello-single-mode file "1.0.0" "xpp3-reader")
+               (modello-single-mode file "1.0.0" "xpp3-writer")))))
+         (add-before 'build 'generate-components.xml
+           (lambda _
+             (mkdir-p "build/classes/META-INF/plexus")
+             (with-output-to-file "build/classes/META-INF/plexus/components.xml"
+               (lambda _
+                 (display
+                   "<component-set>\n
+  <components>\n
+    <component>\n
+      <role>org.sonatype.plexus.components.sec.dispatcher.SecDispatcher</role>\n
+      <role-hint>default</role-hint>\n
+      <implementation>org.sonatype.plexus.components.sec.dispatcher.DefaultSecDispatcher</implementation>\n
+      <description></description>\n
+      <requirements>\n
+        <requirement>\n
+          <role>org.sonatype.plexus.components.cipher.PlexusCipher</role>\n
+          <field-name>_cipher</field-name>\n
+        </requirement>\n
+        <requirement>\n
+          <role>org.sonatype.plexus.components.sec.dispatcher.PasswordDecryptor</role>\n
+          <field-name>_decryptors</field-name>\n
+        </requirement>\n
+      </requirements>\n
+      <configuration>\n
+        <_configuration-file>~/.settings-security.xml</_configuration-file>\n
+      </configuration>\n
+    </component>\n
+  </components>\n
+</component-set>\n")))))
+         (add-before 'check 'fix-paths
+           (lambda _
+             (copy-recursively "src/test/resources" "target"))))))
+    (inputs
+     `(("java-plexus-cipher" ,java-plexus-cipher)))
+    (native-inputs
+     `(("java-modello-core" ,java-modello-core)
+       ;; for modello:
+       ("java-plexus-container-default" ,java-plexus-container-default)
+       ("java-plexus-classworlds" ,java-plexus-classworlds)
+       ("java-plexus-utils" ,java-plexus-utils)
+       ("java-guava" ,java-guava)
+       ("java-geronimo-xbean-reflect" ,java-geronimo-xbean-reflect)
+       ("java-sisu-build-api" ,java-sisu-build-api)
+       ;; modello plugins:
+       ("java-modellop-plugins-java" ,java-modello-plugins-java)
+       ("java-modellop-plugins-xml" ,java-modello-plugins-xml)
+       ("java-modellop-plugins-xpp3" ,java-modello-plugins-xpp3)
+       ;; for tests
+       ("java-junit" ,java-junit)))
+    (build-system ant-build-system)
+    (home-page "https://github.com/sonatype/plexus-sec-dispatcher")
+    (synopsis "Plexus Security Dispatcher Component")
+    (description "This package is the Plexus Security Dispatcher Component.
+This component decrypts a string passed to it.")
+    (license license:asl2.0)))
+
 (define-public java-sisu-build-api
   (package
     (name "java-sisu-build-api")
-- 
cgit v1.2.3


From 9d2749f62f1479d2d88cb8270fb20ba2bb146b33 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sun, 25 Feb 2018 16:56:06 +0100
Subject: gnu: kodi: Update to 18.0_alpha-8.ec16dbc.

* gnu/packages/kodi.scm (libdvdnav/kodi): Update to 6.0.0-Leia-Alpha-1.
(libdvdread/kodi): Update to 6.0.0-Leia-Alpha-1.
(libdvdcss/kodi): Update to 1.4.1-Leia-Alpha-1.
(kodi): Update to 18.0_alpha-8.ec16dbc.
[version]: Use GIT-VERSION.
[source](file-name): Use GIT-FILE-NAME.
[arguments]: Adjust substitution.
[home-page]: Use HTTPS.
---
 gnu/packages/kodi.scm | 27 +++++++++++++--------------
 1 file changed, 13 insertions(+), 14 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/kodi.scm b/gnu/packages/kodi.scm
index dab2a7c692..ad66a846d4 100644
--- a/gnu/packages/kodi.scm
+++ b/gnu/packages/kodi.scm
@@ -128,7 +128,7 @@ generator library for C++.")
 ;; of the standard build process. To make things easier, we bootstrap
 ;; and patch shebangs here, so we don't have to worry about it later.
 (define libdvdnav/kodi
-  (let ((commit "981488f7f27554b103cca10c1fbeba027396c94a"))
+  (let ((commit "6.0.0-Leia-Alpha-1"))
     (package
       (name "libdvdnav-bootstrapped")
       (version commit)
@@ -140,7 +140,7 @@ generator library for C++.")
                 (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
-                  "089pswc51l3avh95zl4cpsh7gh1innh7b2y4xgx840mcmy46ycr8"))))
+                  "1xiyfgf8v8aknlxlzsvk6pbzkhclz0hbh3s1b0w6ivkng2k310j9"))))
       (build-system gnu-build-system)
       (arguments
        '(#:tests? #f
@@ -165,7 +165,7 @@ generator library for C++.")
       (license license:gpl2+))))
 
 (define libdvdread/kodi
-  (let ((commit "17d99db97e7b8f23077b342369d3c22a6250affd"))
+  (let ((commit "6.0.0-Leia-Alpha-1"))
     (package
       (name "libdvdread-bootstrapped")
       (version commit)
@@ -177,7 +177,7 @@ generator library for C++.")
                 (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
-                  "1gr5aq1cjr3as9mnwrw29cxn4m6f6pfrxdahkdcjy70q3ldg90sl"))))
+                  "1c3g18n2vwhgcfz3dka1pmw58bnv2ram7xjvizfiykb3sgi9zfwp"))))
       (build-system gnu-build-system)
       (arguments
        '(#:tests? #f
@@ -202,7 +202,7 @@ generator library for C++.")
       (license (list license:gpl2+ license:lgpl2.1+)))))
 
 (define libdvdcss/kodi
-  (let ((commit "2f12236bc1c92f73c21e973363f79eb300de603f"))
+  (let ((commit "1.4.1-Leia-Alpha-1"))
     (package
       (name "libdvdcss-bootstrapped")
       (version commit)
@@ -214,7 +214,7 @@ generator library for C++.")
                 (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
-                  "198r0q73i55ga1dvyqq9nfcri0zq08b94hy8671lg14i3izx44dd"))))
+                  "0adafwsawxssj3nilkql447v0l4a2584rdpmy5rfjmznh91lykgh"))))
       (build-system gnu-build-system)
       (arguments
        '(#:tests? #f
@@ -241,20 +241,20 @@ generator library for C++.")
 (define-public kodi
   ;; We package the git version because the current released
   ;; version was cut while the cmake transition was in turmoil.
-  (let ((commit "67fd70f01a363002881f3519b50765b756716e3b")
-        (revision "7"))
+  (let ((commit "ec16dbca4dcf2923f53f819695a6d47c52e68d74")
+        (revision "8"))
   (package
     (name "kodi")
-    (version (string-append "18.0_alpha-" revision "-" (string-take commit 7)))
+    (version (git-version "18.0_alpha" revision commit))
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/xbmc/xbmc.git")
                     (commit commit)))
-              (file-name (string-append name "-" version "-checkout"))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "12975n4r982kmxc0r9w24n3lrj7aj3cs4fjkdjnn0r9jbnvfxhs3"))
+                "1rxg752cl59124cfpfwmyjldn6qpq5jginxddpzvgagfadf10i4d"))
               (snippet
                '(begin
                   (use-modules (guix build utils))
@@ -267,7 +267,6 @@ generator library for C++.")
                               ;; "tools/depend/native/TexturePacker"
                               ;; "lib/gtest"
                               ;; "lib/cpluff"
-                              ;; "lib/libexif"
                               ;; "lib/libUPnP"
                               "lib/libUPnP/Neptune/ThirdParty"
                               "project/Win32BuildSetup/tools/7z"))
@@ -318,7 +317,7 @@ generator library for C++.")
                ;; to make them writable before the build process starts.
                (("autoreconf -vif") "chmod -R u+w ."))
 
-             (substitute* "xbmc/linux/LinuxTimezone.cpp"
+             (substitute* "xbmc/platform/linux/LinuxTimezone.cpp"
                (("/usr/share/zoneinfo")
                 (string-append (assoc-ref inputs "tzdata")
                                "/share/zoneinfo")))
@@ -420,7 +419,7 @@ generator library for C++.")
     (description "Kodi is a media center application for playing videos,
 music, games, etc.  Kodi is highly customizable and features a theme and
 plug-in system.")
-    (home-page "http://kodi.tv")
+    (home-page "https://kodi.tv")
     ;; XBMC is largely GPL2+, with some library components as LGPL2.1+, but
     ;; there are some other licenses spread throughout.
     (license (list license:gpl2+ license:lgpl2.1+
-- 
cgit v1.2.3


From a2f0b01221c7256ca0bbb2ad9895c53168176a60 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sun, 25 Feb 2018 17:56:21 +0100
Subject: gnu: fribidi: Update to 1.0.1.

* gnu/packages/fribidi.scm (fribidi): Update to 1.0.1.
[source](uri): Change to new GitHub URI.
[home-page]: Update to redirected URL.
---
 gnu/packages/fribidi.scm | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/fribidi.scm b/gnu/packages/fribidi.scm
index 735fdab8e8..c8a91be4ef 100644
--- a/gnu/packages/fribidi.scm
+++ b/gnu/packages/fribidi.scm
@@ -26,15 +26,16 @@
 (define-public fribidi
   (package
     (name "fribidi")
-    (version "0.19.7")
+    (version "1.0.1")
     (source
       (origin
         (method url-fetch)
         (uri
-          (string-append "http://fribidi.org/download/" name "-" version
+         (string-append "https://github.com/fribidi/fribidi/releases"
+                        "/download/v" version "/fribidi-" version
                          ".tar.bz2"))
         (sha256
-          (base32 "13jsb5qadlhsaxkbrb49nqslmbh904vvzhsm5mm2ghmv29i2l8h8"))))
+          (base32 "1r3ll7apx4b8bhvdkwi71y06df9kvr4q3asvajswvdlh0pbq5cf1"))))
 
     (build-system gnu-build-system)
     (synopsis "Implementation of the Unicode bidirectional algorithm")
@@ -42,5 +43,5 @@
      "GNU FriBidi is an implementation of the Unicode Bidirectional
 Algorithm.  This algorithm is used to properly display text in left-to-right
 or right-to-left ordering as necessary.")
-    (home-page "http://fribidi.org/")
+    (home-page "https://github.com/fribidi/fribidi")
     (license lgpl2.1+)))
-- 
cgit v1.2.3


From 20a792b5536e26a9545435df26336fb882e10bc9 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sat, 24 Feb 2018 22:27:43 +0200
Subject: gnu: recode: Update to 3.7.

* gnu/packages/textutils.scm (recode): Update to 3.7.
[source]: Update source uri and download type. Add snippet to remove
cythonized source.
[native-inputs]: Add python2-cython.
[arguments]: Remove custom phases.
[home-page]: Update to new upstream.
[license]: Update license.
---
 gnu/packages/textutils.scm | 41 +++++++++++++++++------------------------
 1 file changed, 17 insertions(+), 24 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm
index 3284be243e..7e001ed493 100644
--- a/gnu/packages/textutils.scm
+++ b/gnu/packages/textutils.scm
@@ -5,7 +5,7 @@
 ;;; Copyright © 2015 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2016 Jelle Licht <jlicht@fsfe.org>
 ;;; Copyright © 2016 Alex Griffin <a@ajgrf.com>
-;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 ng0 <ng0@we.make.ritual.n0.is>
 ;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org>
@@ -83,32 +83,25 @@ to DOS format and vice versa.")
 (define-public recode
   (package
     (name "recode")
-    ;; Last beta release (3.7-beta2) is from 2008; last commit from Feb 2014.
-    ;; So we use that commit instead.
-    (version "3.7.0.201402")
+    (version "3.7")
     (source
      (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/pinard/Recode.git")
-             (commit "2d7092a9999194fc0e9449717a8048c8d8e26c18")))
+       (method url-fetch)
+       (uri (string-append "https://github.com/rrthomas/recode/releases/"
+                           "download/v" version "/" name "-" version ".tar.gz"))
        (sha256
-        (base32 "1wssv8z6g3ryrw33sksz4rjhlnhgvvdqszw1ggl4rcwks34n86zm"))
-       (file-name (string-append name "-" version "-checkout"))))
+        (base32
+         "0r4yhf7i7zp2nl2apyzz7r3i2in12n385hmr8zcfr18ly0ly530q"))
+       (modules '((guix build utils)))
+       (snippet
+        `(begin
+           (delete-file "tests/Recode.c")
+           #t))))
     (build-system gnu-build-system)
-    (native-inputs `(("python" ,python-2)))
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (add-before 'check 'pre-check
-           (lambda _
-             (substitute* "tests/setup.py"
-               (("([[:space:]]*)include_dirs=.*" all space)
-                (string-append all space "library_dirs=['../src/.libs'],\n")))
-             ;; The test extension 'Recode.so' lacks RUNPATH for 'librecode.so'.
-             (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/src/.libs"))
-             #t)))))
-    (home-page "https://github.com/pinard/Recode")
+    (native-inputs
+     `(("python" ,python-2)
+       ("python2-cython" ,python2-cython)))
+    (home-page "https://github.com/rrthomas/recode")
     (synopsis "Text encoding converter")
     (description "The Recode library converts files between character sets and
 usages.  It recognises or produces over 200 different character sets (or about
@@ -116,7 +109,7 @@ usages.  It recognises or produces over 200 different character sets (or about
 any pair.  When exact transliteration are not possible, it gets rid of
 offending characters or falls back on approximations.  The recode program is a
 handy front-end to the library.")
-    (license license:gpl2+)))
+    (license license:gpl3+)))
 
 (define-public enca
   (package
-- 
cgit v1.2.3


From 1462b456577ca315dd910f52baaf1e7750d9f281 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sat, 24 Feb 2018 23:59:45 +0200
Subject: gnu: enca: Update to 1.19.

* gnu/packages/textutils.scm (enca): Update to 1.19.
[inputs]: Remove recode.
[arguments]: Allow parallel tests.
---
 gnu/packages/textutils.scm | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm
index 7e001ed493..1417bea4e5 100644
--- a/gnu/packages/textutils.scm
+++ b/gnu/packages/textutils.scm
@@ -114,22 +114,18 @@ handy front-end to the library.")
 (define-public enca
   (package
     (name "enca")
-    (version "1.16")
+    (version "1.19")
     (source
      (origin
        (method url-fetch)
        (uri (string-append
              "https://github.com/nijel/enca/archive/" version ".tar.gz"))
        (sha256
-        (base32 "1xik00x0yvhswsw2isnclabhv536xk1s42cf5z54gfbpbhc7ni8l"))
+        (base32 "099z526i7qgij7q1w3lvhl88iv3jc3nqxca2i09h6s08ghyrmzf4"))
        (file-name (string-append name "-" version ".tar.gz"))))
     (build-system gnu-build-system)
-    (inputs `(("recode" ,recode)))
-
-    ;; Both 'test-convert-64.sh' and 'test-convert-filter.sh' manipulate a
-    ;; 'test.tmp' file, so they have to run in sequence.
-    (arguments '(#:parallel-tests? #f))
-
+    ;; enca-1.19 tests fail with recent recode.
+    ;(inputs `(("recode" ,recode)))
     (home-page "https://github.com/nijel/enca")
     (synopsis "Text encoding detection tool")
     (description "Enca (Extremely Naive Charset Analyser) consists of libenca,
-- 
cgit v1.2.3


From 04ab38b7ee11bd6497fce6ce4bf4ebc689c1cff6 Mon Sep 17 00:00:00 2001
From: Andy Patterson <ajpatter@uwaterloo.ca>
Date: Sun, 18 Feb 2018 22:08:15 -0500
Subject: gnu: ccl: Update to 1.11.5.

* gnu/packages/lisp.scm (ccl): Update to 1.11.5.
[inputs]: Update ccl to its new hosting location.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
---
 gnu/packages/lisp.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 020abc7494..5f9a24500c 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -435,7 +435,7 @@ statistical profiler, a code coverage tool, and many other extensions.")
 (define-public ccl
   (package
     (name "ccl")
-    (version "1.11")
+    (version "1.11.5")
     (source #f)
     (build-system gnu-build-system)
     ;; CCL consists of a "lisp kernel" and "heap image", both of which are
@@ -448,7 +448,7 @@ statistical profiler, a code coverage tool, and many other extensions.")
         ,(origin
            (method url-fetch)
            (uri (string-append
-                 "ftp://ftp.clozure.com/pub/release/" version
+                 "https://github.com/Clozure/ccl/releases/download/v" version
                  "/ccl-" version "-"
                  (match (%current-system)
                    ((or "i686-linux" "x86_64-linux") "linuxx86")
@@ -461,9 +461,9 @@ statistical profiler, a code coverage tool, and many other extensions.")
             (base32
              (match (%current-system)
                ((or "i686-linux" "x86_64-linux")
-                "0w3dmj7q9kqyra3yrf1lxclnjz151yvf5s5q8ayllvmvqbl8bs08")
+                "0hs1f3z7crgzvinpj990kv9gvbsipxvcvwbmk54n51nasvc5025q")
                ("armhf-linux"
-                "1x487aaz2rqcb6k301sy2p39a1m4qdhg6z9p9fb76ssipqgr38b4")
+                "0p0l1dzsygb6i1xxgbipjpxkn46xhq3jm41a34ga1qqp4x8lkr62")
                (_ ""))))))))
     (native-inputs
      `(("m4" ,m4)
-- 
cgit v1.2.3


From 543cf6fd3729b81c4ea939d93d563a70490793c1 Mon Sep 17 00:00:00 2001
From: Andy Patterson <ajpatter@uwaterloo.ca>
Date: Sun, 18 Feb 2018 22:20:06 -0500
Subject: gnu: cl-bordeaux-threads: Update to commit 354abb0a.

This commit includes a fix which makes the package compatible asdf 3.3.1.

* gnu/packages/lisp.scm (sbcl-bordeaux-threads): Update to commit 354abb0a.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
---
 gnu/packages/lisp.scm | 40 +++++++++++++++++++++-------------------
 1 file changed, 21 insertions(+), 19 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 5f9a24500c..f05d7eec78 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -726,27 +726,29 @@ interactive development model in mind.")
   (sbcl-package->ecl-package sbcl-fiveam))
 
 (define-public sbcl-bordeaux-threads
-  (package
-    (name "sbcl-bordeaux-threads")
-    (version "0.8.5")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/sionescu/bordeaux-threads/archive/v"
-                    version ".tar.gz"))
-              (sha256
-               (base32 "10ryrcx832fwqdawb6jmknymi7wpdzhi30qzx7cbrk0cpnka71w2"))
-              (file-name
-               (string-append "bordeaux-threads-" version ".tar.gz"))))
-    (inputs `(("alexandria" ,sbcl-alexandria)))
-    (native-inputs `(("fiveam" ,sbcl-fiveam)))
-    (build-system asdf-build-system/sbcl)
-    (synopsis "Portable shared-state concurrency library for Common Lisp")
-    (description "BORDEAUX-THREADS is a proposed standard for a minimal
+  (let ((commit "354abb0ae9f1d9324001e1a8abab3128d7420e0e")
+        (revision "1"))
+    (package
+      (name "sbcl-bordeaux-threads")
+      (version (git-version "0.8.5" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/sionescu/bordeaux-threads.git")
+                      (commit commit)))
+                (sha256
+                 (base32 "1hcfp21l6av1xj6z7r77sp6h4mwf9vvx4s745803sysq2qy2mwnq"))
+                (file-name
+                 (git-file-name "bordeaux-threads" version))))
+      (inputs `(("alexandria" ,sbcl-alexandria)))
+      (native-inputs `(("fiveam" ,sbcl-fiveam)))
+      (build-system asdf-build-system/sbcl)
+      (synopsis "Portable shared-state concurrency library for Common Lisp")
+      (description "BORDEAUX-THREADS is a proposed standard for a minimal
 MP/Threading interface.  It is similar to the CLIM-SYS threading and lock
 support.")
-    (home-page "https://common-lisp.net/project/bordeaux-threads/")
-    (license license:x11)))
+      (home-page "https://common-lisp.net/project/bordeaux-threads/")
+      (license license:x11))))
 
 (define-public cl-bordeaux-threads
   (sbcl-package->cl-source-package sbcl-bordeaux-threads))
-- 
cgit v1.2.3


From e5f9540691b2ea5cace3d1d03aeb53f9a14381d7 Mon Sep 17 00:00:00 2001
From: Alex Vong <alexvong1995@gmail.com>
Date: Wed, 21 Feb 2018 17:04:54 +0800
Subject: gnu: emacs-ahungry-theme: Update to 1.10.0.

* gnu/packages/emacs.scm (emacs-ahungry-theme): Update to 1.10.0.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
---
 gnu/packages/emacs.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 81e6885f66..b7b088d42e 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -2990,14 +2990,14 @@ package provides a light and a dark variant.")
 (define-public emacs-ahungry-theme
   (package
     (name "emacs-ahungry-theme")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin (method url-fetch)
              (uri (string-append "https://elpa.gnu.org/packages/ahungry-theme-"
                                  version ".tar"))
              (sha256
               (base32
-               "14dhnrlbjzrxk5ligf0z2im5bgnxpjqqzqcrmqg5355xrgpbpb7v"))))
+               "14q5yw56n82qph09bk7wmj5b1snhh9w0nk5s1l7yn9ldg71xq6pm"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/ahungry/color-theme-ahungry")
     (synopsis "Ahungry color theme for Emacs")
-- 
cgit v1.2.3


From 9f29ecc1b1d1da57afea71cf1a028a84a9399003 Mon Sep 17 00:00:00 2001
From: Alex ter Weele <alex.ter.weele@gmail.com>
Date: Tue, 20 Feb 2018 18:49:41 -0600
Subject: gnu: ghc-edit-distance: Allow newer version of QuickCheck.

* gnu/packages/haskell.scm (ghc-edit-distance)[arguments]: Allow running tests
  with newer version of QuickCheck.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
---
 gnu/packages/haskell.scm | 2 ++
 1 file changed, 2 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index e62c405ab7..737b7a4cd1 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -5755,6 +5755,8 @@ representations of current time.")
        (sha256
         (base32 "0jkca97zyv23yyilp3jydcrzxqhyk27swhzh82llvban5zp8b21y"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:configure-flags (list "--allow-newer=QuickCheck")))
     (inputs
      `(("ghc-random" ,ghc-random)
        ("ghc-test-framework" ,ghc-test-framework)
-- 
cgit v1.2.3


From abfec9b375a78144ece06b36a033412a105dccaf Mon Sep 17 00:00:00 2001
From: Alex ter Weele <alex.ter.weele@gmail.com>
Date: Tue, 20 Feb 2018 18:51:16 -0600
Subject: gnu: ghc-hashtables: Allow newer version of vector.

* gnu/packages/haskell.scm (ghc-hashtables)[arguments]: Allow newer version of
  vector.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
---
 gnu/packages/haskell.scm | 2 ++
 1 file changed, 2 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 737b7a4cd1..dbb9ebc808 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -7360,6 +7360,8 @@ Haskell, using gnuplot for rendering.")
        (sha256
         (base32 "1b6w9xznk42732vpd8ili60k12yq190xnajgga0iwbdpyg424lgg"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:configure-flags (list "--allow-newer=vector")))
     (inputs
      `(("ghc-hashable" ,ghc-hashable)
        ("ghc-primitive" ,ghc-primitive)
-- 
cgit v1.2.3


From 7df5669f3903b58cd5587ee8660dd12a18756bd0 Mon Sep 17 00:00:00 2001
From: Alex ter Weele <alex.ter.weele@gmail.com>
Date: Tue, 20 Feb 2018 18:53:26 -0600
Subject: gnu: Add ghc-uri-encode.

* gnu/packages/haskell-web.scm (ghc-uri-encode): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
---
 gnu/packages/haskell-web.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index a24ee4b7c0..f1b50b29bd 100644
--- a/gnu/packages/haskell-web.scm
+++ b/gnu/packages/haskell-web.scm
@@ -866,3 +866,26 @@ of a JSON value into a @code{Data.Aeson.Value}.")
     (description
      "HTTP multipart split out of the cgi package, for Haskell.")
     (license license:bsd-3)))
+
+(define-public ghc-uri-encode
+  (package
+    (name "ghc-uri-encode")
+    (version "1.5.0.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://hackage.haskell.org/package/uri-encode/uri-encode-"
+             version ".tar.gz"))
+       (sha256
+        (base32
+         "11miwb5vvnn17m92ykz1pzg9x6s8fbpz3mmsyqs2s4b3mn55haz8"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-text" ,ghc-text)
+       ("ghc-utf8-string" ,ghc-utf8-string)
+       ("ghc-network-uri" ,ghc-network-uri)))
+    (home-page "https://hackage.haskell.org/package/uri-encode")
+    (synopsis "Unicode aware uri-encoding")
+    (description "Unicode aware uri-encoding for Haskell.")
+    (license license:bsd-3)))
-- 
cgit v1.2.3


From f61682e7ea87db3eed7e67adacd1d3f8c1b7c119 Mon Sep 17 00:00:00 2001
From: Alex ter Weele <alex.ter.weele@gmail.com>
Date: Tue, 20 Feb 2018 18:55:06 -0600
Subject: gnu: Add agda.

* gnu/packages/agda.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add adga.scm.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
---
 gnu/local.mk          |  1 +
 gnu/packages/agda.scm | 86 +++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 87 insertions(+)
 create mode 100644 gnu/packages/agda.scm

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index 2f8f7b7e3a..8acb3cea47 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -52,6 +52,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/acl.scm				\
   %D%/packages/admin.scm			\
   %D%/packages/adns.scm				\
+  %D%/packages/agda.scm				\
   %D%/packages/algebra.scm			\
   %D%/packages/aidc.scm				\
   %D%/packages/android.scm			\
diff --git a/gnu/packages/agda.scm b/gnu/packages/agda.scm
new file mode 100644
index 0000000000..6aa230116c
--- /dev/null
+++ b/gnu/packages/agda.scm
@@ -0,0 +1,86 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2018 Alex ter Weele <alex.ter.weele@gmail.com>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages agda)
+  #:use-module (gnu packages haskell)
+  #:use-module (gnu packages haskell-check)
+  #:use-module (gnu packages haskell-web)
+  #:use-module (guix build-system haskell)
+  #:use-module (guix build-system trivial)
+  #:use-module (guix download)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages))
+
+(define-public agda
+  (package
+    (name "agda")
+    (version "2.5.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://hackage.haskell.org/package/Agda/Agda-"
+             version ".tar.gz"))
+       (sha256
+        (base32
+         "0r80vw7vnvbgq47y50v050malv7zvv2p2kg6f47i04r0b2ix855a"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("cpphs" ,cpphs)
+       ("ghc-alex" ,ghc-alex)
+       ("ghc-async" ,ghc-async)
+       ("ghc-blaze-html" ,ghc-blaze-html)
+       ("ghc-boxes" ,ghc-boxes)
+       ("ghc-data-hash" ,ghc-data-hash)
+       ("ghc-edisoncore" ,ghc-edisoncore)
+       ("ghc-edit-distance" ,ghc-edit-distance)
+       ("ghc-equivalence" ,ghc-equivalence)
+       ("ghc-geniplate-mirror" ,ghc-geniplate-mirror)
+       ("ghc-gitrev" ,ghc-gitrev)
+       ("ghc-happy" ,ghc-happy)
+       ("ghc-hashable" ,ghc-hashable)
+       ("ghc-hashtables" ,ghc-hashtables)
+       ("ghc-ieee754" ,ghc-ieee754)
+       ("ghc-monadplus" ,ghc-monadplus)
+       ("ghc-mtl" ,ghc-mtl)
+       ("ghc-murmur-hash" ,ghc-murmur-hash)
+       ("ghc-uri-encode" ,ghc-uri-encode)
+       ("ghc-parallel" ,ghc-parallel)
+       ("ghc-regex-tdfa" ,ghc-regex-tdfa)
+       ("ghc-stm" ,ghc-stm)
+       ("ghc-strict" ,ghc-strict)
+       ("ghc-text" ,ghc-text)
+       ("ghc-unordered-containers" ,ghc-unordered-containers)
+       ("ghc-zlib" ,ghc-zlib)))
+    (home-page "http://wiki.portal.chalmers.se/agda/")
+    (synopsis
+     "Dependently typed functional programming language and proof assistant")
+    (description
+     "Agda is a dependently typed functional programming language: it has
+inductive families, which are similar to Haskell's GADTs, but they can be
+indexed by values and not just types.  It also has parameterised modules,
+mixfix operators, Unicode characters, and an interactive Emacs interface (the
+type checker can assist in the development of your code).  Agda is also a
+proof assistant: it is an interactive system for writing and checking proofs.
+Agda is based on intuitionistic type theory, a foundational system for
+constructive mathematics developed by the Swedish logician Per Martin-Löf.  It
+has many similarities with other proof assistants based on dependent types,
+such as Coq, Epigram and NuPRL.")
+    ;; Agda is distributed under the MIT license, and a couple of
+    ;; source files are BSD-3.  See LICENSE for details.
+    (license (list license:expat license:bsd-3))))
-- 
cgit v1.2.3


From f58764d8ed633a8ad1c9f2578be7bbde36ed7ce7 Mon Sep 17 00:00:00 2001
From: ng0 <ng0@crash.cx>
Date: Sun, 25 Feb 2018 13:34:28 +0000
Subject: gnu: neomutt: Update to 20180223.

* gnu/packages/mail.scm (neomutt): Update to 20180223.
[native-inputs]: Use 'docbook-xml-4.2'.
[arguments]: Remove 'fix-docbook' phases.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
---
 gnu/packages/mail.scm | 18 +++---------------
 1 file changed, 3 insertions(+), 15 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index 6e8f9a74ae..9fbfddbec1 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -296,7 +296,7 @@ operating systems.")
 (define-public neomutt
   (package
     (name "neomutt")
-    (version "20171215")
+    (version "20180223")
     (source
      (origin
        (method url-fetch)
@@ -304,7 +304,7 @@ operating systems.")
                            "/archive/" name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1df1c2ynvivna42ifj1lxmgb0bbfih0ggn1afyniadzjm6cnxdvz"))))
+         "1fr7158xhrhasylyxp709g9mdbggdmni3qn3baxvczfg2w003fhh"))))
     (build-system gnu-build-system)
     (inputs
      `(("cyrus-sasl" ,cyrus-sasl)
@@ -325,7 +325,7 @@ operating systems.")
        ("gettext-minimal" ,gettext-minimal)
        ("pkg-config" ,pkg-config)
        ("docbook-xsl" ,docbook-xsl)
-       ("docbook-xml" ,docbook-xml)
+       ("docbook-xml" ,docbook-xml-4.2)
        ("w3m" ,w3m)
        ("tcl" ,tcl)))
     (arguments
@@ -368,18 +368,6 @@ operating systems.")
        (modify-phases %standard-phases
          ;; TODO: autosetup is meant to be included in the source,
          ;; but we should package autosetup and use our own version of it.
-         (add-before 'configure 'fix-docbook
-           (lambda* (#:key inputs #:allow-other-keys)
-             (substitute* '("doc/chunk.xsl" "doc/manual.xml.tail"
-                            "doc/html.xsl" "doc/manual.xml.head")
-               (("http://docbook.sourceforge.net/release/xsl/current/")
-                (string-append (assoc-ref inputs "docbook-xsl")
-                               "/xml/xsl/docbook-xsl-"
-                               ,(package-version docbook-xsl) "/"))
-               (("http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd")
-                (string-append (assoc-ref inputs "docbook-xml")
-                               "/xml/dtd/docbook/docbookx.dtd")))
-             #t))
          (add-before 'configure 'fix-sasl-test
            (lambda _
              ;; Upstream suggestion to fix the failing sasl autosetup test.
-- 
cgit v1.2.3


From 2115bde3024b685087af70a20d7846498d6c9985 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Mon, 26 Feb 2018 02:39:15 +0100
Subject: gnu: python-parse: Update to 1.8.2.

* gnu/packages/patches/python-parse-too-many-fields.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/python.scm (python-parse): Update to 1.8.2.
[source](patches): Remove.
[arguments]: Use INVOKE instead of SYSTEM*.
---
 gnu/local.mk                                       |  1 -
 .../patches/python-parse-too-many-fields.patch     | 52 ----------------------
 gnu/packages/python.scm                            |  7 ++-
 3 files changed, 3 insertions(+), 57 deletions(-)
 delete mode 100644 gnu/packages/patches/python-parse-too-many-fields.patch

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index 8acb3cea47..72fbf90f83 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1031,7 +1031,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/python2-larch-coverage-4.0a6-compatibility.patch \
   %D%/packages/patches/python-networkx2-reproducible-build.patch	\
   %D%/packages/patches/python-nose-timer-drop-ordereddict.patch \
-  %D%/packages/patches/python-parse-too-many-fields.patch	\
   %D%/packages/patches/python-pillow-fix-failing-tests.patch	\
   %D%/packages/patches/python2-rdflib-drop-sparqlwrapper.patch	\
   %D%/packages/patches/python-statsmodels-fix-tests.patch	\
diff --git a/gnu/packages/patches/python-parse-too-many-fields.patch b/gnu/packages/patches/python-parse-too-many-fields.patch
deleted file mode 100644
index 9db6b91a7f..0000000000
--- a/gnu/packages/patches/python-parse-too-many-fields.patch
+++ /dev/null
@@ -1,52 +0,0 @@
-From 32f15cfefb7c7b6476360ac65cba807aa3dfccfa Mon Sep 17 00:00:00 2001
-From: David King <dking@redhat.com>
-Date: Mon, 14 Dec 2015 09:58:19 +0000
-Subject: [PATCH] Fix test_too_many_fields with Python 3.5
-
-taken from https://github.com/r1chardj0n3s/parse/pull/34
-
-Python versions before 3.5 had a limit of 100 groups in regular
-expressions. This limit was removed during 3.5 development:
-
-http://bugs.python.org/issue22437
-https://hg.python.org/cpython/rev/0b85ea4bd1af
-
-The test_too_many_fields test asserts that the limit exists by
-attempting to parse a string with 15 fields, which triggers the 100
-named groups limit.
-
-Adjust the test so that if first checks to see whether the limit of 100
-named groups exists, and only assert that parsing 15 fields fails if
-that is the case.
----
- test_parse.py | 10 ++++++++--
- 1 file changed, 8 insertions(+), 2 deletions(-)
-
-diff --git a/test_parse.py b/test_parse.py
-index c524349..1d50568 100755
---- a/test_parse.py
-+++ b/test_parse.py
-@@ -6,6 +6,7 @@
- 
- import unittest
- from datetime import datetime, time
-+import re
- 
- import parse
- 
-@@ -624,8 +625,13 @@ def test_mixed_type_variant(self):
-         self.assertEqual(r.fixed[21], 'spam')
- 
-     def test_too_many_fields(self):
--        p = parse.compile('{:ti}' * 15)
--        self.assertRaises(parse.TooManyFields, p.parse, '')
-+        # Python 3.5 removed the limit of 100 named groups in a regular expression,
-+        # so only test for the exception if the limit exists.
-+        try:
-+            re.compile("".join("(?P<n{n}>{n}-)".format(n=i) for i in range(101)))
-+        except AssertionError:
-+            p = parse.compile('{:ti}' * 15)
-+            self.assertRaises(parse.TooManyFields, p.parse, '')
- 
- 
- class TestSearch(unittest.TestCase):
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 3c816cda53..14a79a9b22 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -1431,21 +1431,20 @@ backported for previous versions of Python from 2.4 to 3.3.")
 (define-public python-parse
   (package
     (name "python-parse")
-    (version "1.6.6")
+    (version "1.8.2")
     (source
      (origin
       (method url-fetch)
       (uri (pypi-uri "parse" version))
       (sha256
        (base32
-        "0y31i3mwgv35qn0kzzjn9q8jqfdqmbi6sr6yfvn8rq4lqjm5lhvi"))
-      (patches (search-patches "python-parse-too-many-fields.patch"))))
+        "1lj9v1q4imszyhvipb6drsm3xdl35nan011mqxxas1yaypixsj40"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
          (replace 'check
-           (lambda _ (zero? (system* "python" "test_parse.py")))))))
+           (lambda _ (invoke "python" "test_parse.py"))))))
     (home-page "https://github.com/r1chardj0n3s/parse")
     (synopsis "Parse strings")
     (description
-- 
cgit v1.2.3


From 557f8f212e9bfc28ce689a2ccbcc91c8dafe01b2 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Mon, 26 Feb 2018 02:42:17 +0100
Subject: gnu: python-parse-type: Update to 0.4.2.

* gnu/packages/python.scm (python-parse-type): Update to 0.4.2.
[source](uri): Use PYPI-URI.
[arguments]: Remove field.
---
 gnu/packages/python.scm | 17 +++--------------
 1 file changed, 3 insertions(+), 14 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 14a79a9b22..2129cbec07 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -1386,26 +1386,15 @@ backported for previous versions of Python from 2.4 to 3.3.")
 (define-public python-parse-type
   (package
     (name "python-parse-type")
-    (version "0.3.4")
+    (version "0.4.2")
     (source
      (origin
       (method url-fetch)
-      (uri (string-append "https://pypi.python.org/packages/source/p/"
-                          "parse_type/parse_type-" version ".tar.gz"))
+      (uri (pypi-uri "parse_type" version))
       (sha256
        (base32
-        "0iv1c34npr4iynwpgv1vkjx9rjd18a85ir8c01gc5f7wp8iv7l1x"))))
+        "0g3b6gsdwnm8dpkh2vn34q6dzxm9gl908ggyzcv31n9xbp3vv5pm"))))
     (build-system python-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'patch-tests
-           (lambda _
-             (substitute* "tests/test_parse_type_parse.py"
-               ;; Newer Python versions don't have the problem this test tests.
-               (("self[.]assertRaises[(]parse.TooManyFields, p.parse, ''[)]")
-                ""))
-             #t)))))
     (propagated-inputs
      `(("python-six" ,python-six)
        ("python-parse" ,python-parse)))
-- 
cgit v1.2.3


From b8509387d1e303b24204213c09fe82f35899ebff Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Mon, 26 Feb 2018 03:01:48 +0100
Subject: gnu: python-pathpy: Update to 11.0.

* gnu/packages/python.scm (python-pathpy): Update to 11.0.
[source](uri): Use PYPI-URI.
[outputs]: Remove field.
[arguments]: Set #:tests? #f.  Remove #:phases.
---
 gnu/packages/python.scm | 43 ++++++++++++++++++++++---------------------
 1 file changed, 22 insertions(+), 21 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 2129cbec07..1b5e3836d9 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -4270,15 +4270,14 @@ them as the version argument or in a SCM managed file.")
 (define-public python-pathpy
   (package
     (name "python-pathpy")
-    (version "8.1.1")
+    (version "11.0")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://pypi.python.org/packages/source/p/"
-                           "path.py/path.py-" version ".tar.gz"))
+       (uri (pypi-uri "path.py" version))
        (sha256
-        (base32 "1p8s1l2vfkqhqxdhqlj0g1jjw4f1as2frr35sjcpjjpd5a89y41f"))))
-    (outputs '("out" "doc"))
+        (base32 "12s84maimiz61980q065rjgi8ang6xw2wwm64m0lmfks51dlw4qn"))))
+    ;; (outputs '("out" "doc"))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-appdirs" ,python-appdirs)))
@@ -4289,22 +4288,24 @@ them as the version argument or in a SCM managed file.")
        ("python-pytest" ,python-pytest)
        ("python-pytest-runner" ,python-pytest-runner)))
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'build 'build-doc
-           (lambda _
-             (setenv "LANG" "en_US.UTF-8")
-             (zero? (system* "python" "setup.py" "build_sphinx"))))
-         (add-after 'install 'install-doc
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
-                    (doc (string-append data "/doc/" ,name "-" ,version))
-                    (html (string-append doc "/html")))
-               (mkdir-p html)
-               (for-each (lambda (file)
-                           (copy-file file (string-append doc "/" file)))
-                         '("README.rst" "CHANGES.rst"))
-               (copy-recursively "build/sphinx/html" html)))))))
+     ;; FIXME: Documentation and tests require "jaraco.packaging".
+     `(#:tests? #f))
+    ;;    #:phases
+    ;;    (modify-phases %standard-phases
+    ;;      (add-after 'build 'build-doc
+    ;;        (lambda _
+    ;;          (setenv "LANG" "en_US.UTF-8")
+    ;;          (zero? (system* "python" "setup.py" "build_sphinx"))))
+    ;;      (add-after 'install 'install-doc
+    ;;        (lambda* (#:key outputs #:allow-other-keys)
+    ;;          (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
+    ;;                 (doc (string-append data "/doc/" ,name "-" ,version))
+    ;;                 (html (string-append doc "/html")))
+    ;;            (mkdir-p html)
+    ;;            (for-each (lambda (file)
+    ;;                        (copy-file file (string-append doc "/" file)))
+    ;;                      '("README.rst" "CHANGES.rst"))
+    ;;            (copy-recursively "build/sphinx/html" html)))))))
     (home-page "https://github.com/jaraco/path.py")
     (synopsis "Python module wrapper for built-in os.path")
     (description
-- 
cgit v1.2.3


From eddb9dacd2943301c7d1bc3cbad8df6ddab09c5a Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Mon, 26 Feb 2018 03:05:58 +0100
Subject: gnu: behave: Update to 1.2.6.

* gnu/packages/check.scm (behave): Update to 1.2.6.
[source](uri): Adjust file extension.
[native-inputs]: Add PYTHON-PATHPY and PYTHON-PYTEST.
---
 gnu/packages/check.scm | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 8e1eb127b2..fbd2ac4f80 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -1629,18 +1629,20 @@ backported from Python 2.7 for Python 2.4+.")
 (define-public behave
   (package
     (name "behave")
-    (version "1.2.5")
+    (version "1.2.6")
     (source (origin
              (method url-fetch)
-             (uri (pypi-uri "behave" version ".tar.bz2"))
+             (uri (pypi-uri "behave" version))
              (sha256
               (base32
-               "1iypp6z46r19n4xmgx6m1lwmlpfjh8vapq8izigrqlaarvp2y64c"))))
+               "11hsz365qglvpp1m1w16239c3kiw15lw7adha49lqaakm8kj6rmr"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-mock" ,python-mock)
        ("python-nose" ,python-nose)
-       ("python-pyhamcrest" ,python-pyhamcrest)))
+       ("python-pathpy" ,python-pathpy)
+       ("python-pyhamcrest" ,python-pyhamcrest)
+       ("python-pytest" ,python-pytest)))
     (propagated-inputs
      `(("python-six" ,python-six)
        ("python-parse" ,python-parse)
-- 
cgit v1.2.3


From ed519b3c1fc8b3a57d86318018e93ff8822fcccd Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Mon, 26 Feb 2018 04:23:46 +0100
Subject: gnu: python-pickleshare: Update to 0.7.4.

* gnu/packages/databases.scm (python-pickleshare): Update to 0.7.4.
[source](uri): Use PYPI-URI.
[propagated-inputs]: Remove.
[properties]: Delay python2 variant.
(python2-pickleshare)[propagated-inputs]: Add PYTHON2-PATHLIB2.
---
 gnu/packages/databases.scm | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 29b6ca1698..98686910d1 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -2240,17 +2240,14 @@ SQLAlchemy Database Toolkit for Python.")
 (define-public python-pickleshare
   (package
     (name "python-pickleshare")
-    (version "0.5")
+    (version "0.7.4")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://pypi.python.org/packages/source/p/"
-                           "pickleshare/pickleshare-" version ".tar.gz"))
+       (uri (pypi-uri "pickleshare" version))
        (sha256
-        (base32 "11ljr90j3p6qswdrbl7p4cjb2i93f6vn0vx9anzpshsx0d2mggn0"))))
+        (base32 "0yvk14dzxk7g6qpr7iw23vzqbsr0dh4ij4xynkhnzpfz4xr2bac4"))))
     (build-system python-build-system)
-    (propagated-inputs
-     `(("python-pathpy" ,python-pathpy)))
     (home-page "https://github.com/vivainio/pickleshare")
     (synopsis "Tiny key value database with concurrency support")
     (description
@@ -2261,10 +2258,15 @@ value in database is immediately visible to other processes accessing the same
 database.  Concurrency is possible because the values are stored in separate
 files.  Hence the “database” is a directory where all files are governed by
 PickleShare.")
+    (properties `((python2-variant . ,(delay python2-pickleshare))))
     (license license:expat)))
 
 (define-public python2-pickleshare
-  (package-with-python2 python-pickleshare))
+  (let ((pickleshare (package-with-python2
+                      (strip-python2-variant python-pickleshare))))
+    (package (inherit pickleshare)
+      (propagated-inputs `(("python2-pathlib2" ,python2-pathlib2)
+                           ,@(package-propagated-inputs pickleshare))))))
 
 (define-public python-apsw
   (package
-- 
cgit v1.2.3


From 76397e12ada2832279fbd37dc89d1484adb5b4b1 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Mon, 26 Feb 2018 04:35:38 +0100
Subject: gnu: python2-pathlib2: Propagate python2-six.

* gnu/packages/python.scm (python2-pathlib2)[native-inputs]: Move to ...
[propagated-inputs] ... here.
---
 gnu/packages/python.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 1b5e3836d9..82108baed1 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -8074,7 +8074,7 @@ anymore.")
     ;; standard library.
     (arguments
      `(#:python ,python-2))
-    (native-inputs
+    (propagated-inputs
      `(("python2-six" ,python2-six)))
     (home-page "https://pypi.python.org/pypi/pathlib2/")
     (synopsis "Object-oriented file system paths - backport of standard
-- 
cgit v1.2.3


From ff856cfdccd544394740fc5826cc0ef9ea54d247 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Mon, 26 Feb 2018 04:40:40 +0100
Subject: gnu: python-pickleshare: Run the tests.

* gnu/packages/databases.scm (python-pickleshare)[arguments]: Replace CHECK-PHASE.
[native-inputs]: Add PYTHON-PYTEST.
---
 gnu/packages/databases.scm | 7 +++++++
 1 file changed, 7 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 98686910d1..56984af6e2 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -2248,6 +2248,13 @@ SQLAlchemy Database Toolkit for Python.")
        (sha256
         (base32 "0yvk14dzxk7g6qpr7iw23vzqbsr0dh4ij4xynkhnzpfz4xr2bac4"))))
     (build-system python-build-system)
+    (arguments
+     `(#:phases (modify-phases %standard-phases
+                  (replace 'check
+                    (lambda _
+                      (invoke "pytest"))))))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)))
     (home-page "https://github.com/vivainio/pickleshare")
     (synopsis "Tiny key value database with concurrency support")
     (description
-- 
cgit v1.2.3


From f160557b955a27c681d4482e7b541966e31e3c78 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Mon, 26 Feb 2018 04:47:22 +0100
Subject: gnu: python-ipython: Update to 5.5.0.

* gnu/packages/python.scm (python-ipython): Update to 5.5.0.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 82108baed1..19f43dc27c 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -4496,13 +4496,13 @@ installing @code{kernelspec}s for use with Jupyter frontends.")
 (define-public python-ipython
   (package
     (name "python-ipython")
-    (version "5.3.0")
+    (version "5.5.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "ipython" version ".tar.gz"))
        (sha256
-        (base32 "079wyjir4a9qx6kvx096b1asm63djbidk65z3ykcbnlngmg62pmz"))))
+        (base32 "03qmzpfy00if10i9k8fjkam1s4xg22j73f933x5d228z9n4rwik6"))))
     (build-system python-build-system)
     (outputs '("out" "doc"))
     (propagated-inputs
-- 
cgit v1.2.3


From ea3f45a5a0d9f55ca1df2c7f9d9fd45d624dd1a1 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Mon, 26 Feb 2018 04:47:44 +0100
Subject: gnu: python2-pathlib2: Update to 2.3.0.

* gnu/packages/python.scm (python2-pathlib2): Update to 2.3.0.
[propagated-inputs]: Add PYTHON2-SCANDIR.
---
 gnu/packages/python.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 19f43dc27c..5b8c5081fc 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -8061,13 +8061,13 @@ anymore.")
 (define-public python2-pathlib2
   (package
     (name "python2-pathlib2")
-    (version "2.1.0")
+    (version "2.3.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "pathlib2" version))
               (sha256
                (base32
-                "0p050msg5c8d0kadv702jnfshaxrb0il765cpkgnhn6mq5hakcyy"))))
+                "1cx5gs2v9j2vnzmcrbq5l8fq2mwrr1h6pyf1sjdji2w1bavm09fk"))))
     (build-system python-build-system)
     ;; We only need the the Python 2 variant, since for Python 3 our minimum
     ;; version is 3.4 which already includes this package as part of the
@@ -8075,7 +8075,8 @@ anymore.")
     (arguments
      `(#:python ,python-2))
     (propagated-inputs
-     `(("python2-six" ,python2-six)))
+     `(("python2-scandir" ,python2-scandir)
+       ("python2-six" ,python2-six)))
     (home-page "https://pypi.python.org/pypi/pathlib2/")
     (synopsis "Object-oriented file system paths - backport of standard
 pathlib module")
-- 
cgit v1.2.3


From 71a2d4176bdf7d88fd9d342b95ae74ed9685ec8d Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Mon, 26 Feb 2018 05:01:16 +0100
Subject: gnu: python-scandir: Update to 1.7.

* gnu/packages/python.scm (python-scandir): Update to 1.7.
[description]: Mention that the Python3 variant is obsolete.
---
 gnu/packages/python.scm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 5b8c5081fc..64f48fd352 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -11083,13 +11083,13 @@ It supports both normal and Unicode strings.")
 (define-public python-scandir
   (package
     (name "python-scandir")
-    (version "1.4")
+    (version "1.7")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "scandir" version))
        (sha256
-        (base32 "0yjrgp0mxp3d8bjkq2m1ac2ys8n76wykksvgyjrnil9gr3fx7a5d"))))
+        (base32 "0gbnhjzg42rj87ljv9kb648rfxph69ly3c8r9841dxy4d7l5pmdj"))))
     (build-system python-build-system)
     (home-page "https://github.com/benhoyt/scandir")
     (synopsis "Directory iteration function")
@@ -11098,7 +11098,9 @@ It supports both normal and Unicode strings.")
 returning a list of bare filenames, it yields DirEntry objects that include
 file type and stat information along with the name.  Using scandir() increases
 the speed of os.walk() by 2-20 times (depending on the platform and file
-system) by avoiding unnecessary calls to os.stat() in most cases.")
+system) by avoiding unnecessary calls to os.stat() in most cases.
+
+This package is part of the Python standard library since version 3.5.")
     (license license:bsd-3)))
 
 (define-public python2-scandir
-- 
cgit v1.2.3


From cb723be5b98a57ae4f909022d1ce2b5d3bcdaabf Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Mon, 26 Feb 2018 05:03:22 +0100
Subject: gnu: python-scandir: Run the test suite.

* gnu/packages/python.scm (python-scandir)[arguments]: Replace CHECK-PHASE.
---
 gnu/packages/python.scm | 5 +++++
 1 file changed, 5 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 64f48fd352..4946d9afd7 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -11091,6 +11091,11 @@ It supports both normal and Unicode strings.")
        (sha256
         (base32 "0gbnhjzg42rj87ljv9kb648rfxph69ly3c8r9841dxy4d7l5pmdj"))))
     (build-system python-build-system)
+    (arguments
+     `(#:phases (modify-phases %standard-phases
+                  (replace 'check
+                    (lambda _
+                      (invoke "python" "test/run_tests.py"))))))
     (home-page "https://github.com/benhoyt/scandir")
     (synopsis "Directory iteration function")
     (description
-- 
cgit v1.2.3


From ecbea1bcb1e349eb66140cb3b83329f9699c357a Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Mon, 26 Feb 2018 19:47:54 +0100
Subject: gnu: automake: Add 1.16.

* gnu/packages/autotools.scm (automake-1.16): New variable.
---
 gnu/packages/autotools.scm | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/autotools.scm b/gnu/packages/autotools.scm
index 355e66f42a..846e318aa1 100644
--- a/gnu/packages/autotools.scm
+++ b/gnu/packages/autotools.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2012 Nikita Karetnikov <nikita@karetnikov.org>
-;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015 Mathieu Lirzin <mthl@openmailbox.org>
 ;;; Copyright © 2014 Manolis Fragkiskos Ragkousis <manolis837@gmail.com>
 ;;; Copyright © 2015, 2017 Mark H Weaver <mhw@netris.org>
@@ -315,6 +315,21 @@ intuitive format and then Automake works with Autoconf to produce a robust
 Makefile, simplifying the entire process for the developer.")
     (license gpl2+)))                      ; some files are under GPLv3+
 
+(define-public automake-1.16
+  ;; Make this the default on the next rebuild cycle.
+  (package
+    (inherit automake)
+    (version "1.16")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://gnu/automake/automake-"
+                                  version ".tar.xz"))
+              (sha256
+               (base32
+                "12jvcmkcmd5p14b41w9f7ixd3sca97pymd6lqbkwnl8qn6bjv3zr"))
+              (patches
+               (search-patches "automake-skip-amhello-tests.patch"))))))
+
 (define-public libtool
   (package
     (name "libtool")
-- 
cgit v1.2.3


From 54d82c81d558b593f1f515ac6c735fd48e5929ca Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 24 Feb 2018 13:51:13 +0100
Subject: gnu: libfilezilla: Update to 0.12.1.

* gnu/packages/ftp.scm (libfilezilla): Update to 0.12.1.
---
 gnu/packages/ftp.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/ftp.scm b/gnu/packages/ftp.scm
index a70398f678..4ad6bcbf1b 100644
--- a/gnu/packages/ftp.scm
+++ b/gnu/packages/ftp.scm
@@ -173,7 +173,7 @@ as required.")
 (define-public libfilezilla
   (package
     (name "libfilezilla")
-    (version "0.12.0")
+    (version "0.12.1")
     (source
      (origin
        (method url-fetch)
@@ -181,7 +181,7 @@ as required.")
                            name "/" name "-" version ".tar.bz2"))
        (sha256
         (base32
-         "14zag4mhwp5mbir63j1k01jys973kmrivznmm78v6qa92l64jn0a"))))
+         "1gbqm42dd0m3fvqz3bk53889479dvn8679zp6ba8a9q2br2wkvv0"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("cppunit" ,cppunit)
-- 
cgit v1.2.3


From d5a352937aad9e1afbf042889d5134a5bea30423 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 24 Feb 2018 15:00:27 +0100
Subject: gnu: youtube-dl: Update to 2018.02.22.

* gnu/packages/video.scm (youtube-dl): Update to 2018.02.22.
---
 gnu/packages/video.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index bf7a3960d4..8008cdd608 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -1157,7 +1157,7 @@ access to mpv's powerful playback capabilities.")
 (define-public youtube-dl
   (package
     (name "youtube-dl")
-    (version "2018.02.11")
+    (version "2018.02.22")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://yt-dl.org/downloads/"
@@ -1165,7 +1165,7 @@ access to mpv's powerful playback capabilities.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0zg34spkfiwjq55jrk417ifdcyvrj80gdbc338rdpfw2s6ibggv8"))))
+                "112qmwrkd0cpyx2h20k6y07lw7iixvj8yya7r97h3k1y1py9vbz8"))))
     (build-system python-build-system)
     (arguments
      ;; The problem here is that the directory for the man page and completion
-- 
cgit v1.2.3


From 7ed1abfa81ff87cfeb2043b953f79b4b894e8de6 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 24 Feb 2018 15:10:44 +0100
Subject: gnu: gource: Update to 0.48.

* gnu/packages/version-control.scm (gource): Update to 0.48.
---
 gnu/packages/version-control.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index 91698b5f7f..7a0f37b4e7 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -1768,7 +1768,7 @@ network protocols, and core version control algorithms.")
 (define-public gource
   (package
     (name "gource")
-    (version "0.47")
+    (version "0.48")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1776,7 +1776,7 @@ network protocols, and core version control algorithms.")
                     "/gource-" version "/gource-" version ".tar.gz"))
               (sha256
                (base32
-                "1llqwdnfa1pff8bxk27qsqff1fcg0a9kfdib0rn7p28vl21n1cgj"))))
+                "04qxcm05qiyr9rg2kv6abfy7kkzqr8ziw4iyp1d14lniv93m61dp"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
-- 
cgit v1.2.3


From 383ad03e832ec52c3e24780cb188e5ec71ae7620 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 24 Feb 2018 15:02:22 +0100
Subject: gnu: tinc: Update to 1.0.33.

* gnu/packages/vpn.scm (tinc): Update to 1.0.33.
---
 gnu/packages/vpn.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm
index d7f5dc6597..952f12ce55 100644
--- a/gnu/packages/vpn.scm
+++ b/gnu/packages/vpn.scm
@@ -4,7 +4,7 @@
 ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015 Jeff Mickey <j@codemac.net>
 ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2016, 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2016, 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -272,14 +272,14 @@ traversing network address translators (NATs) and firewalls.")
 (define-public tinc
   (package
     (name "tinc")
-    (version "1.0.28")
+    (version "1.0.33")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://tinc-vpn.org/packages/"
                                   name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0i5kx3hza359nclyhb60kxlzqyx0phmg175350hww28g6scjcl0b"))))
+                "1x0hpfz13vn4pl6dcpnls6xq3rfcbdsg90awcfn53ijb8k35svvz"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags
-- 
cgit v1.2.3


From 74b977d7259db7684dad52d4f01635df5ac80873 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 24 Feb 2018 15:30:50 +0100
Subject: gnu: libdvbpsi: Update to 1.3.2.

* gnu/packages/video.scm (libdvbpsi): Update to 1.3.2.
---
 gnu/packages/video.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 8008cdd608..a1ead1d609 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -2475,7 +2475,7 @@ RTSP or SIP clients and servers.")
 (define-public libdvbpsi
   (package
     (name "libdvbpsi")
-    (version "1.3.1")
+    (version "1.3.2")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2483,7 +2483,7 @@ RTSP or SIP clients and servers.")
                     version "/libdvbpsi-" version ".tar.bz2"))
               (sha256
                (base32
-                "0824r08kaspbrrg2dd5d46s475zb7j59brqkm2y6x3mdsnpng0yn"))))
+                "1zn5hfv4qbahmydbwh59a3b480s3m5ss27r6ml35gqdip7r3jkmc"))))
     (build-system gnu-build-system)
     (home-page "https://www.videolan.org/developers/libdvbpsi.html")
     (synopsis "Library for decoding and generation of MPEG TS and DVB PSI
-- 
cgit v1.2.3


From 24a300b1bde7099b482bb4b8b7ecc27a5249a1e0 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 26 Feb 2018 01:15:57 +0100
Subject: gnu: dvdstyler: Remove hard-coded version string.

* gnu/packages/cdrom.scm (dvdstyler)[arguments]: Remove a hard-coded
version string from the docbook-xsl search path.
---
 gnu/packages/cdrom.scm | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cdrom.scm b/gnu/packages/cdrom.scm
index 598b584cb3..672064db12 100644
--- a/gnu/packages/cdrom.scm
+++ b/gnu/packages/cdrom.scm
@@ -8,7 +8,7 @@
 ;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017 John Darrington <jmd@gnu.org>
 ;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be>
-;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 ng0 <ng0@n0.is>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -360,14 +360,15 @@ capacity is user-selectable.")
          "0lwc0hn94m9r8fi07sjqz3fr618l6lnw3zsakxw7nlgnxbjsk7pi"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:configure-flags (list (string-append "XMLTO="
-                                              (assoc-ref %build-inputs "xmlto")
-                                              "/bin/xmlto"
-                                              " --searchpath "
-                                              (assoc-ref %build-inputs "docbook-xsl")
-                                              "/xml/xsl/docbook-xsl-1.79.1/htmlhelp:"
-                                              (assoc-ref %build-inputs "docbook-xml")
-                                              "/xml/dtd/docbook"))
+     `(#:configure-flags
+       (list (string-append "XMLTO="
+                            (assoc-ref %build-inputs "xmlto")
+                            "/bin/xmlto --searchpath "
+                            (assoc-ref %build-inputs "docbook-xsl")
+                            "/xml/xsl/docbook-xsl-" ,(package-version docbook-xsl)
+                            "/htmlhelp:"
+                            (assoc-ref %build-inputs "docbook-xml")
+                            "/xml/dtd/docbook"))
        #:phases
        (modify-phases %standard-phases
          (add-after 'install 'wrap-program
-- 
cgit v1.2.3


From 6f8d1f72743e2faa44b28a80fafb35254279fd1b Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 26 Feb 2018 06:49:41 +0100
Subject: gnu: perl-http-server-simple: Update to 0.52.

* gnu/packages/web.scm (perl-http-server-simple): Update to 0.52.
---
 gnu/packages/web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 801741dd22..5bcdf28f7d 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -2848,7 +2848,7 @@ environment from an HTTP::Request.")
 (define-public perl-http-server-simple
   (package
     (name "perl-http-server-simple")
-    (version "0.51")
+    (version "0.52")
     (source
      (origin
        (method url-fetch)
@@ -2856,7 +2856,7 @@ environment from an HTTP::Request.")
                            "HTTP-Server-Simple-" version ".tar.gz"))
        (sha256
         (base32
-         "1yvd2g57z2kq00q5i3zzfi15k98qgbif3vghjsda6v612agmrp5r"))))
+         "0k6bg7k6mjixfzxdkkdrhqvaqmdhjszx0zsk8g0bimiby6j9z4yq"))))
     (build-system perl-build-system)
     (propagated-inputs
      `(("perl-cgi" ,perl-cgi)))
-- 
cgit v1.2.3


From 12505baed9dfa179a8cb47e128a8e028d1699d3d Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 26 Feb 2018 06:50:17 +0100
Subject: gnu: perl-net-smtp-ssl: Update to 1.04.

* gnu/packages/web.scm (perl-net-smtp-ssl): Update to 1.04.
---
 gnu/packages/web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 5bcdf28f7d..d597d2bfb6 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -3208,7 +3208,7 @@ or to multiple server ports.")
 (define-public perl-net-smtp-ssl
   (package
     (name "perl-net-smtp-ssl")
-    (version "1.03")
+    (version "1.04")
     (source
      (origin
        (method url-fetch)
@@ -3216,7 +3216,7 @@ or to multiple server ports.")
                            "Net-SMTP-SSL-" version ".tar.gz"))
        (sha256
         (base32
-         "05y94mb1vdw32mvwb0cp2h4ggh32f8j8nwwfjb8kjwxvfkfhyp9h"))))
+         "001a6dcfahf7kkyirqkc8jd4fh4fkal7n7vm9c4dblqrvmdc8abv"))))
     (build-system perl-build-system)
     (propagated-inputs
      `(("perl-io-socket-ssl" ,perl-io-socket-ssl)))
-- 
cgit v1.2.3


From 73a3e98f01973b1f92fe9a1b905c6d14c4d8f5ae Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 25 Feb 2018 15:48:36 +0100
Subject: gnu: perl-xml-libxslt: Update to 1.96.

* gnu/packages/xml.scm (perl-xml-libxslt): Update to 1.96.
---
 gnu/packages/xml.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm
index cc5e19af27..820083e7cb 100644
--- a/gnu/packages/xml.scm
+++ b/gnu/packages/xml.scm
@@ -425,7 +425,7 @@ XML parser and the high performance DOM implementation.")
 (define-public perl-xml-libxslt
   (package
     (name "perl-xml-libxslt")
-    (version "1.95")
+    (version "1.96")
     (source
      (origin
        (method url-fetch)
@@ -433,7 +433,7 @@ XML parser and the high performance DOM implementation.")
                            "XML-LibXSLT-" version ".tar.gz"))
        (sha256
         (base32
-         "0dggycql18kfxzkb1kw3yc7gslxlrrgyyn2r2ygsylycb89j3jpi"))))
+         "0wyl8klgr65j8y8fzgwz9jlvfjwvxazna8j3dg9gksd2v973fpia"))))
     (build-system perl-build-system)
     (inputs
      `(("libxslt" ,libxslt)))
-- 
cgit v1.2.3


From 3c4bbb4c52418c8daf8b0e4605e3912685c9f44a Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 24 Feb 2018 13:33:42 +0100
Subject: gnu: polkit: Update phase & snippet style.

* gnu/packages/polkit.scm (polkit)[source]: End snippet with #t.
[arguments]: Substitute INVOKE for SYSTEM* and end phases with #t.
---
 gnu/packages/polkit.scm | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/polkit.scm b/gnu/packages/polkit.scm
index 0e38dd61ee..8fe37097e1 100644
--- a/gnu/packages/polkit.scm
+++ b/gnu/packages/polkit.scm
@@ -4,6 +4,7 @@
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Huang Ying <huang.ying.caritas@gmail.com>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -77,7 +78,8 @@
                  ;; Set the setuid helper's real location.
                  (substitute* "src/polkitagent/polkitagentsession.c"
                    (("PACKAGE_PREFIX \"/lib/polkit-1/polkit-agent-helper-1\"")
-                    "\"/run/setuid-programs/polkit-agent-helper-1\""))))))
+                    "\"/run/setuid-programs/polkit-agent-helper-1\""))
+                 #t))))
     (build-system gnu-build-system)
     (inputs
      `(("expat" ,expat)
@@ -105,7 +107,8 @@
                 (("@INTROSPECTION_GIRDIR@")
                  (string-append out "/share/gir-1.0/"))
                 (("@INTROSPECTION_TYPELIBDIR@")
-                 (string-append out "/lib/girepository-1.0/"))))))
+                 (string-append out "/lib/girepository-1.0/")))
+              #t)))
          (replace
           'install
           (lambda* (#:key outputs (make-flags '()) #:allow-other-keys)
@@ -113,12 +116,12 @@
             ;; to install in /etc, and to instead install the skeletons in the
             ;; output directory.
             (let ((out (assoc-ref outputs "out")))
-             (zero? (apply system*
-                           "make" "install"
+             (invoke "make" "install"
                            (string-append "sysconfdir=" out "/etc")
                            (string-append "polkit_actiondir="
                                           out "/share/polkit-1/actions")
-                           make-flags))))))))
+                           make-flags)
+             #t))))))
     (home-page "http://www.freedesktop.org/wiki/Software/polkit/")
     (synopsis "Authorization API for privilege management")
     (description "Polkit is an application-level toolkit for defining and
-- 
cgit v1.2.3


From 57e7d7486ba17d7b5407ebc429ce8553460371ea Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 24 Feb 2018 13:44:26 +0100
Subject: gnu: Use HTTPS for supported freedesktop.org home pages.

* gnu/packages/fontutils.scm (fontconfig)[home-page]: Use HTTPS.
* gnu/packages/freedesktop.scm (python-pyxdg, accountsservice)
(modem-manager, telepathy-mission-control, telepathy-mission-control)
(colord-gtk, desktop-file-utils)[home-page]: Likewise.
* gnu/packages/ghostscript.scm (libspectre)[home-page]: Likewise.
* gnu/packages/glib.scm (dbus, dbus-glib, telepathy-glib)[home-page]:
Likewise.
* gnu/packages/gnome.scm (shared-mime-info, hicolor-icon-theme)
(libxklavier, colord, upower)[home-page]: Likewise.
* gnu/packages/gstreamer.scm (orc, python-gst)[home-page]: Likewise.
* gnu/packages/libcanberra.scm (sound-theme-freedesktop)[home-page]:
Likewise.
* gnu/packages/libreoffice.scm (libexttextcat)[home-page]: Likewise.
* gnu/packages/polkit.scm (polkit-gnome, polkit-gnome)[home-page]:
Likewise.
* gnu/packages/pulseaudio.scm (pavucontrol)[home-page]: Likewise.
* gnu/packages/python.scm (python-dbus)[home-page]: Likewise.
* gnu/packages/xdisorg.scm (startup-notification)[home-page]: Likewise.
---
 gnu/packages/fontutils.scm   |  2 +-
 gnu/packages/freedesktop.scm | 14 +++++++-------
 gnu/packages/ghostscript.scm |  2 +-
 gnu/packages/glib.scm        |  6 +++---
 gnu/packages/gnome.scm       | 10 +++++-----
 gnu/packages/gstreamer.scm   |  4 ++--
 gnu/packages/libcanberra.scm |  2 +-
 gnu/packages/libreoffice.scm |  2 +-
 gnu/packages/polkit.scm      |  4 ++--
 gnu/packages/pulseaudio.scm  |  2 +-
 gnu/packages/python.scm      |  2 +-
 gnu/packages/xdisorg.scm     |  2 +-
 12 files changed, 26 insertions(+), 26 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/fontutils.scm b/gnu/packages/fontutils.scm
index a04441a005..a5e8c79371 100644
--- a/gnu/packages/fontutils.scm
+++ b/gnu/packages/fontutils.scm
@@ -290,7 +290,7 @@ high quality, anti-aliased and subpixel rendered text on a display.")
    ; The exact license is more X11-style than BSD-style.
    (license (license:non-copyleft "file://COPYING"
                        "See COPYING in the distribution."))
-   (home-page "http://www.freedesktop.org/wiki/Software/fontconfig")))
+   (home-page "https://www.freedesktop.org/wiki/Software/fontconfig")))
 
 (define-public t1lib
   (package
diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm
index 63adb4d076..3c83e668b0 100644
--- a/gnu/packages/freedesktop.scm
+++ b/gnu/packages/freedesktop.scm
@@ -409,7 +409,7 @@ manager for the current system.")
      `(("shared-mime-info" ,shared-mime-info) ;for tests
        ("hicolor-icon-theme" ,hicolor-icon-theme) ;for tests
        ("python-nose" ,python-nose)))
-    (home-page "http://freedesktop.org/wiki/Software/pyxdg")
+    (home-page "https://www.freedesktop.org/wiki/Software/pyxdg")
     (synopsis "Implementations of freedesktop.org standards in Python")
     (description
      "PyXDG is a collection of implementations of freedesktop.org standards in
@@ -740,7 +740,7 @@ message bus.")
     (inputs
      `(("shadow" ,shadow)
        ("polkit" ,polkit)))
-    (home-page "http://www.freedesktop.org/wiki/Software/AccountsService/")
+    (home-page "https://www.freedesktop.org/wiki/Software/AccountsService/")
     (synopsis "D-Bus interface for user account query and manipulation")
     (description
      "The AccountService project provides a set of D-Bus interfaces for querying
@@ -840,7 +840,7 @@ which speak the Qualcomm MSM Interface (QMI) protocol.")
        ("libqmi" ,libqmi)
        ("polkit" ,polkit)))
     (synopsis "Mobile broadband modems manager")
-    (home-page "http://www.freedesktop.org/wiki/Software/ModemManager/")
+    (home-page "https://www.freedesktop.org/wiki/Software/ModemManager/")
     (description
      "ModemManager is a DBus-activated daemon which controls mobile
 broadband (2G/3G/4G) devices and connections.  Whether built-in devices, USB
@@ -882,7 +882,7 @@ modems and setup connections with them.")
        ("sqlite" ,sqlite)
        ("telepathy-glib" ,telepathy-glib)))
     (synopsis "Telepathy logger library")
-    (home-page "http://telepathy.freedesktop.org/")
+    (home-page "https://telepathy.freedesktop.org/")
     (description
      "Telepathy logger is a headless observer client that logs information
 received by the Telepathy framework.  It features pluggable backends to log
@@ -909,7 +909,7 @@ different sorts of messages in different formats.")
        ("python-dbus" ,python2-dbus)))
     (propagated-inputs
      `(("telepathy-glib" ,telepathy-glib)))
-    (home-page "http://telepathy.freedesktop.org/")
+    (home-page "https://telepathy.freedesktop.org/")
     (synopsis "Telepathy IRC connection manager")
     (description
      "Idle is an IRC connection manager for the Telepathy framework.  This
@@ -971,7 +971,7 @@ share connections to real-time communication services without conflicting.")
      `(("colord" ,colord)
        ("gtk+" ,gtk+)))
     (synopsis "GTK integration for libcolord")
-    (home-page "http://www.freedesktop.org/software/colord/")
+    (home-page "https://www.freedesktop.org/software/colord/")
     (description
      "This is a GTK+ convenience library for interacting with colord.  It is
 useful for both applications which need colour management and applications that
@@ -1068,7 +1068,7 @@ to applications simultaneously competing for fingerprint readers.")
      `(("pkg-config" ,pkg-config)))
     (inputs
      `(("glib" ,glib)))
-    (home-page "http://www.freedesktop.org/wiki/Software/desktop-file-utils/")
+    (home-page "https://www.freedesktop.org/wiki/Software/desktop-file-utils/")
     (synopsis "Utilities for working with desktop entries")
     (description
      "This package contains a few command line utilities for working with
diff --git a/gnu/packages/ghostscript.scm b/gnu/packages/ghostscript.scm
index 0561387931..6d2dd4c008 100644
--- a/gnu/packages/ghostscript.scm
+++ b/gnu/packages/ghostscript.scm
@@ -362,4 +362,4 @@ Ghostscript.  It currently includes the 35 standard PostScript fonts.")
 It provides a convenient easy to use API for handling and rendering
 Postscript documents.")
    (license license:gpl2+)
-   (home-page "http://www.freedesktop.org/wiki/Software/libspectre")))
+   (home-page "https://www.freedesktop.org/wiki/Software/libspectre")))
diff --git a/gnu/packages/glib.scm b/gnu/packages/glib.scm
index d32472b85e..45d0d891c4 100644
--- a/gnu/packages/glib.scm
+++ b/gnu/packages/glib.scm
@@ -124,7 +124,7 @@
        ;; '--autolaunch'.
        ("libx11" ,libx11)))
 
-    (home-page "http://dbus.freedesktop.org/")
+    (home-page "https://www.freedesktop.org/wiki/Software/dbus/")
     (synopsis "Message bus for inter-process communication (IPC)")
     (description
      "D-Bus is a message bus system, a simple way for applications to
@@ -461,7 +461,7 @@ translated.")
     (native-inputs
      `(("glib" ,glib "bin")
        ("pkg-config" ,pkg-config)))
-    (home-page "http://dbus.freedesktop.org/doc/dbus-glib/")
+    (home-page "https://dbus.freedesktop.org/doc/dbus-glib/")
     (synopsis "D-Bus GLib bindings")
     (description
      "GLib bindings for D-Bus.  The package is obsolete and superseded
@@ -662,7 +662,7 @@ useful for C++.")
      `(("dbus" ,dbus)
        ("dbus-glib" ,dbus-glib)
        ("glib" ,glib)))
-    (home-page "http://telepathy.freedesktop.org/wiki/")
+    (home-page "https://telepathy.freedesktop.org/wiki/")
     (synopsis "GLib Real-time communications framework over D-Bus")
     (description "Telepathy is a flexible, modular communications framework
 that enables real-time communication over D-Bus via pluggable protocol
diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 43a3489021..f52f3227d1 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -947,7 +947,7 @@ guidelines.")
     (native-inputs
      `(("intltool" ,intltool)
        ("pkg-config" ,pkg-config)))
-    (home-page "http://freedesktop.org/wiki/Software/shared-mime-info")
+    (home-page "https://www.freedesktop.org/wiki/Software/shared-mime-info")
     (synopsis "Database of common MIME types")
     (description
      "The shared-mime-info package contains the core database of common types
@@ -972,7 +972,7 @@ database is translated at Transifex.")
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f)) ; no check target
-    (home-page "http://icon-theme.freedesktop.org/releases/")
+    (home-page "https://icon-theme.freedesktop.org/releases/")
     (synopsis
      "Freedesktop icon theme")
     (description
@@ -2322,7 +2322,7 @@ and objects.")
        ("libxkbfile"       ,libxkbfile)
        ("xkbcomp"          ,xkbcomp)
        ("xkeyboard-config" ,xkeyboard-config)))
-    (home-page "http://www.freedesktop.org/wiki/Software/LibXklavier/")
+    (home-page "https://www.freedesktop.org/wiki/Software/LibXklavier/")
     (synopsis "High-level API for X Keyboard Extension")
     (description
      "LibXklavier is a library providing high-level API for X Keyboard
@@ -2828,7 +2828,7 @@ keyboard shortcuts.")
        ("sqlite" ,sqlite)
        ("polkit" ,polkit)
        ("sane-backends" ,sane-backends)))
-    (home-page "http://www.freedesktop.org/software/colord/")
+    (home-page "https://www.freedesktop.org/software/colord/")
     (synopsis "Color management service")
     (description "Colord is a system service that makes it easy to manage,
 install and generate color profiles to accurately color manage input and
@@ -2964,7 +2964,7 @@ faster results and to avoid unnecessary server load.")
      `(("dbus-glib" ,dbus-glib)
        ("libgudev" ,libgudev)
        ("libusb" ,libusb)))
-    (home-page "http://upower.freedesktop.org/")
+    (home-page "https://upower.freedesktop.org/")
     (synopsis "System daemon for managing power devices")
     (description
      "UPower is an abstraction for enumerating power devices,
diff --git a/gnu/packages/gstreamer.scm b/gnu/packages/gstreamer.scm
index 5fad28952b..4ec5765bb1 100644
--- a/gnu/packages/gstreamer.scm
+++ b/gnu/packages/gstreamer.scm
@@ -87,7 +87,7 @@
                             "testsuite/exec_opcodes_sys.c")
                (("if \\(error\\) return 1;")
                 "if (error) return 77;")))))))
-    (home-page "http://gstreamer.freedesktop.org/modules/orc.html")
+    (home-page "https://gstreamer.freedesktop.org/modules/orc.html")
     (synopsis "Oil runtime compiler")
     (description
      "Orc is a just-in-time compiler implemented as a library and set of
@@ -405,7 +405,7 @@ distribution problems in some jurisdictions, e.g. due to patent threats.")
        ("ffmpeg" ,ffmpeg)
        ("orc" ,orc)
        ("zlib" ,zlib)))
-    (home-page "http://gstreamer.freedesktop.org/")
+    (home-page "https://gstreamer.freedesktop.org/")
     (synopsis "Plugins for the GStreamer multimedia library")
     (description
      "This GStreamer plugin supports a large number of audio and video
diff --git a/gnu/packages/libcanberra.scm b/gnu/packages/libcanberra.scm
index b4ed90ebb4..e9d6ce594c 100644
--- a/gnu/packages/libcanberra.scm
+++ b/gnu/packages/libcanberra.scm
@@ -130,7 +130,7 @@ sounds for various system events.")
     ;; The license of the various sounds is given in the 'CREDITS' file.
     (license (list cc-by-sa4.0 cc-by3.0 gpl2 gpl2+))
 
-    (home-page "http://www.freedesktop.org/wiki/Specifications/sound-theme-spec/")))
+    (home-page "https://www.freedesktop.org/wiki/Specifications/sound-theme-spec/")))
 
 (define-public python-pycanberra
   (package
diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm
index 9b60c06a8d..b7c675d274 100644
--- a/gnu/packages/libreoffice.scm
+++ b/gnu/packages/libreoffice.scm
@@ -428,7 +428,7 @@ standard 21.0.2.")
       (sha256 (base32
                "1j6sjwkyhqvsgyw938bxxfwkzzi1mahk66g5342lv6j89jfvrz8k"))))
     (build-system gnu-build-system)
-    (home-page "http://www.freedesktop.org/wiki/Software/libexttextcat/")
+    (home-page "https://www.freedesktop.org/wiki/Software/libexttextcat/")
     (synopsis "Text Categorization library")
     (description "Libexttextcat is an N-Gram-Based Text Categorization
 library primarily intended for language guessing.")
diff --git a/gnu/packages/polkit.scm b/gnu/packages/polkit.scm
index 8fe37097e1..76a1aa21c4 100644
--- a/gnu/packages/polkit.scm
+++ b/gnu/packages/polkit.scm
@@ -122,7 +122,7 @@
                                           out "/share/polkit-1/actions")
                            make-flags)
              #t))))))
-    (home-page "http://www.freedesktop.org/wiki/Software/polkit/")
+    (home-page "https://www.freedesktop.org/wiki/Software/polkit/")
     (synopsis "Authorization API for privilege management")
     (description "Polkit is an application-level toolkit for defining and
 handling the policy that allows unprivileged processes to speak to
@@ -186,5 +186,5 @@ easily with PolicyKit.")
     (description "PolicyKit-gnome provides a D-Bus session bus service
 that is used to bring up authentication dialogs used for obtaining
 privileges.")
-    (home-page "http://www.freedesktop.org/wiki/Software/polkit/")
+    (home-page "https://www.freedesktop.org/wiki/Software/polkit/")
     (license lgpl2.0+)))
diff --git a/gnu/packages/pulseaudio.scm b/gnu/packages/pulseaudio.scm
index 249afd3f68..903b22529d 100644
--- a/gnu/packages/pulseaudio.scm
+++ b/gnu/packages/pulseaudio.scm
@@ -229,7 +229,7 @@ sound server.")
     (native-inputs
      `(("intltool" ,intltool)
        ("pkg-config" ,pkg-config)))
-    (home-page "http://freedesktop.org/software/pulseaudio/pavucontrol/")
+    (home-page "https://www.freedesktop.org/software/pulseaudio/pavucontrol/")
     (synopsis "PulseAudio volume control")
     (description
      "PulseAudio Volume Control (pavucontrol) provides a GTK+
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 4946d9afd7..4ccd6a7359 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -4762,7 +4762,7 @@ toolkit.  Use it to build trees of widgets.")
     (synopsis "Python bindings for D-bus")
     (description "python-dbus provides bindings for libdbus, the reference
 implementation of D-Bus.")
-    (home-page "http://www.freedesktop.org/wiki/Software/DBusBindings/")
+    (home-page "https://www.freedesktop.org/wiki/Software/DBusBindings/")
     (license license:expat)))
 
 (define-public python2-dbus
diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm
index be2ee2d086..a3630b3cb9 100644
--- a/gnu/packages/xdisorg.scm
+++ b/gnu/packages/xdisorg.scm
@@ -406,7 +406,7 @@ tracking.")
     (inputs
      `(("libx11" ,libx11)
        ("xcb-util" ,xcb-util)))
-    (home-page "http://www.freedesktop.org/wiki/Software/startup-notification/")
+    (home-page "https://www.freedesktop.org/wiki/Software/startup-notification/")
     (synopsis "Application startup notification and feedback library")
     (description
      "Startup-notification contains a reference implementation of the startup
-- 
cgit v1.2.3


From 4ff3484f1e7d0dccd67a94ae805d4ea41cdf675c Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 25 Feb 2018 16:31:50 +0100
Subject: gnu: libpsl: Update to 0.20.0.

* gnu/packages/web.scm (libpsl): Update to 0.20.0.
---
 gnu/packages/web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index d597d2bfb6..b5a54f686b 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -796,7 +796,7 @@ for efficient socket-like bidirectional reliable communication channels.")
 (define-public libpsl
   (package
     (name "libpsl")
-    (version "0.19.1")
+    (version "0.20.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/rockdaboot/libpsl/"
@@ -804,7 +804,7 @@ for efficient socket-like bidirectional reliable communication channels.")
                                   "/libpsl-" version ".tar.gz"))
               (sha256
                (base32
-                "0ydwi9m39qv6k7zagqx2kzxzf59ipxj9r0c71xmwngdx3fslclbk"))))
+                "0rsjm6mb71nnj6ikr2dq5qmny314v3j7m07zz1i7m6v8hxxm98i7"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
-- 
cgit v1.2.3


From 9de33cc726cb4d050ea722ec6a8ceb7613d676a2 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 24 Feb 2018 14:45:38 +0100
Subject: gnu: ruby-ffi: Update to 1.9.22.

* gnu/packages/libffi.scm (ruby-ffi): Update to 1.9.22.
---
 gnu/packages/libffi.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/libffi.scm b/gnu/packages/libffi.scm
index 948dabb41e..e5e4023450 100644
--- a/gnu/packages/libffi.scm
+++ b/gnu/packages/libffi.scm
@@ -5,6 +5,7 @@
 ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -152,13 +153,13 @@ conversions for values passed between the two languages.")
 (define-public ruby-ffi
   (package
     (name "ruby-ffi")
-    (version "1.9.18")
+    (version "1.9.22")
     (source (origin
               (method url-fetch)
               (uri (rubygems-uri "ffi" version))
               (sha256
                (base32
-                "034f52xf7zcqgbvwbl20jwdyjwznvqnwpbaps9nk18v9lgb1dpx0"))))
+                "17lvnpmllg4mlzf25lxbmfzk4l6rsddlxwwdkbs4d9v5gv154529"))))
     (build-system ruby-build-system)
     ;; FIXME: Before running tests the build system attempts to build libffi
     ;; from sources.
-- 
cgit v1.2.3


From 0ae079ec2abdd64a937b80dcd59d6a75545ac3b0 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 25 Feb 2018 17:46:16 +0100
Subject: gnu: Add nghttp2.

* gnu/packages/web.scm (nghttp2): New public variable.
---
 gnu/packages/web.scm | 84 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 84 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index b5a54f686b..26768ccc1e 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -60,6 +60,7 @@
   #:use-module (guix build-system ant)
   #:use-module (guix build-system scons)
   #:use-module (gnu packages)
+  #:use-module (gnu packages adns)
   #:use-module (gnu packages apr)
   #:use-module (gnu packages check)
   #:use-module (gnu packages cran)
@@ -83,8 +84,10 @@
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages java)
   #:use-module (gnu packages javascript)
+  #:use-module (gnu packages jemalloc)
   #:use-module (gnu packages image)
   #:use-module (gnu packages imagemagick)
+  #:use-module (gnu packages libevent)
   #:use-module (gnu packages libidn)
   #:use-module (gnu packages libunistring)
   #:use-module (gnu packages lisp)
@@ -6343,3 +6346,84 @@ derivation by David Revoy from the original MonsterID by Andreas Gohr.")
     ;; expat for the code, CC-BY 4.0 for the artwork
     (license (list l:expat
                    l:cc-by4.0))))
+
+(define-public nghttp2
+  (package
+    (name "nghttp2")
+    (version "1.30.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/nghttp2/nghttp2/"
+                           "releases/download/v" version "/"
+                           name "-" version ".tar.xz"))
+       (sha256
+        (base32
+         "1b2j7il0wp8hi4jl3cah7fkshmg29cchdski9cw74gx5496gp6h8"))))
+    (build-system gnu-build-system)
+    (outputs (list "out"
+                   "lib"))              ; only libnghttp2
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+
+       ;; Required by tests.
+       ("cunit" ,cunit)
+       ("tzdata" ,tzdata)))
+    (inputs
+     ;; Required to build the tools (i.e. without ‘--enable-lib-only’).
+     `(("c-ares" ,c-ares)
+       ("jansson" ,jansson)             ; for HPACK tools
+       ("jemalloc" ,jemalloc)           ; fight nghttpd{,x} heap fragmentation
+       ("libev" ,libev)
+       ("libxml2" ,libxml2)             ; for ‘nghttp -a’
+       ("openssl" ,openssl)))
+    (arguments
+     `(#:configure-flags
+       (list (string-append "--libdir=" (assoc-ref %outputs "lib") "/lib")
+             "--enable-app"             ; build all the tools
+             "--enable-hpack-tools"     ; ...all the tools
+             "--disable-examples"
+             "--disable-static")        ; don't bother building .a files
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'break-circular-reference
+           ;; libnghttp2.pc by default retains a reference to the ‘out’ output,
+           ;; which is not allowed.  Break this cycle.  While we could install
+           ;; only the library to ‘out’ and move everything else to a separate
+           ;; output, this would inconvenience the majority of (human) users.
+           (lambda* (#:key outputs #:allow-other-keys)
+             (substitute* "lib/libnghttp2.pc.in"
+               (("@prefix@")
+                (assoc-ref outputs "lib")))
+             #t))
+         (add-before 'check 'set-timezone-directory
+           (lambda* (#:key inputs #:allow-other-keys)
+             (setenv "TZDIR" (string-append (assoc-ref inputs "tzdata")
+                                            "/share/zoneinfo"))
+             #t)))))
+    (home-page "https://nghttp2.org/")
+    (synopsis "HTTP/2 protocol client, proxy, server, and library")
+    (description
+     "nghttp2 implements the Hypertext Transfer Protocol, version
+2 (@dfn{HTTP/2}).
+
+A reusable C library provides the HTTP/2 framing layer, with several tools built
+on top of it:
+
+@itemize
+@item @command{nghttp}, a command-line HTTP/2 client.  It exposes many advanced
+and low-level aspects of the protocol and is useful for debugging.
+@item @command{nghttpd}, a fast, multi-threaded HTTP/2 static web server that
+serves files from a local directory.
+@item @command{nghttpx}, a fast, multi-threaded HTTP/2 reverse proxy that can be
+deployed in front of existing web servers that don't support HTTP/2.
+Both @command{nghttpd} and @command{nghttpx} can fall back to HTTP/1.1 for
+backwards compatibilty with clients that don't speak HTTP/2.
+@item @command{h2load} for benchmarking (only!) your own HTTP/2 servers.
+@item HTTP/2 uses a header compression method called @dfn{HPACK}.
+nghttp2 provides a HPACK encoder and decoder as part of its public API.
+@item @command{deflatehd} converts JSON data or HTTP/1-style header fields to
+compressed JSON header blocks.
+@item @command{inflatehd} converts such compressed headers back to JSON pairs.
+@end itemize\n")
+    (license l:expat)))
-- 
cgit v1.2.3


From 4e501d064204d059d9d0e5af0533c055433f7b63 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 25 Feb 2018 19:28:36 +0100
Subject: gnu: perl-scalar-list-utils: Update to 1.50.

* gnu/packages/perl.scm (perl-scalar-list-utils): Update to 1.50.
---
 gnu/packages/perl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index cef42847c6..7512dfaf1f 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -8961,7 +8961,7 @@ files, using JSON::PP and/or CPAN::Meta::YAML.")
 (define-public perl-scalar-list-utils
   (package
     (name "perl-scalar-list-utils")
-    (version "1.47")
+    (version "1.50")
     (source
      (origin
        (method url-fetch)
@@ -8969,7 +8969,7 @@ files, using JSON::PP and/or CPAN::Meta::YAML.")
                            "Scalar-List-Utils-" version ".tar.gz"))
        (sha256
         (base32
-         "1qgg6zxqwziva5j1k5gjks4xmhmgklm551ni3zb74sd9f9rk90y4"))))
+         "0x9n0617gjjcqa4nk5biiwkxdi90xpdfg6z07gjr009qjg3bkah6"))))
     (build-system perl-build-system)
     (home-page "http://search.cpan.org/dist/Scalar-List-Utils/")
     (synopsis "Common Scalar and List utility subroutines")
-- 
cgit v1.2.3


From b737530569844d1538a45f209460fedc0edf7497 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 24 Feb 2018 14:12:20 +0100
Subject: gnu: python-cffi: Update to 1.11.4.

* gnu/packages/libffi.scm (python-cffi): Update to 1.11.4.
---
 gnu/packages/libffi.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/libffi.scm b/gnu/packages/libffi.scm
index e5e4023450..e5e93eb916 100644
--- a/gnu/packages/libffi.scm
+++ b/gnu/packages/libffi.scm
@@ -80,13 +80,13 @@ conversions for values passed between the two languages.")
 (define-public python-cffi
   (package
     (name "python-cffi")
-    (version "1.11.2")
+    (version "1.11.4")
     (source
      (origin
       (method url-fetch)
       (uri (pypi-uri "cffi" version))
       (sha256
-       (base32 "19h0wwz9cww74gw8cyq0izj8zkhjyzjw2d3ks1c3f1y4q28xv1xb"))))
+       (base32 "07fiy4wqg8g08x38r04ydjr8n6g0g74gb8si8b6jhymijalq746z"))))
     (build-system python-build-system)
     (outputs '("out" "doc"))
     (inputs
-- 
cgit v1.2.3


From fc38e317cde56897b575c5af2d7787d889323193 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 24 Feb 2018 14:36:48 +0100
Subject: gnu: python-cffi: Update phase style.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/libffi.scm (python-cffi)[arguments]: Substitute INVOKE
for SYSTEM*, end phases with #t, and remove unneeded bits from the
‘install-doc’ phase.
---
 gnu/packages/libffi.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/libffi.scm b/gnu/packages/libffi.scm
index e5e93eb916..dd6b2237f9 100644
--- a/gnu/packages/libffi.scm
+++ b/gnu/packages/libffi.scm
@@ -122,7 +122,8 @@ conversions for values passed between the two languages.")
                                "linker_so='gcc -shared')")))
              (substitute* "testing/cffi0/test_ownlib.py"
                (("'cc testownlib") "'gcc testownlib"))
-             (zero? (system* "py.test" "-v" "c/" "testing/"))))
+             (invoke "py.test" "-v" "c/" "testing/")
+             #t))
          (add-before 'check 'disable-failing-test
            ;; This is assumed to be a libffi issue:
            ;; https://bitbucket.org/cffi/cffi/issues/312/tests-failed-with-armv8
@@ -131,15 +132,14 @@ conversions for values passed between the two languages.")
                (("ret.left") "ownlib.left"))
              #t))
          (add-after 'install 'install-doc
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
-                    (doc (string-append data "/doc/" ,name "-" ,version))
+           (lambda* (#:key outputs (make-flags '())  #:allow-other-keys)
+             (let* ((doc (string-append (assoc-ref outputs "doc")
+                                        "/share/doc/" ,name "-" ,version))
                     (html (string-append doc "/html")))
                (with-directory-excursion "doc"
-                 (system* "make" "html")
+                 (apply invoke "make" "html" make-flags)
                  (mkdir-p html)
                  (copy-recursively "build/html" html))
-               (copy-file "LICENSE" (string-append doc "/LICENSE"))
                #t))))))
     (home-page "https://cffi.readthedocs.org")
     (synopsis "Foreign function interface for Python")
-- 
cgit v1.2.3


From d504de2655e553e7b826af63fe9a66516ddf2ea5 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 26 Feb 2018 20:11:56 +0100
Subject: gnu: assword: Update to 0.11.

* gnu/packages/password-utils.scm (assword): Update to 0.11.
---
 gnu/packages/password-utils.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm
index f83c05a25b..e8639c02e1 100644
--- a/gnu/packages/password-utils.scm
+++ b/gnu/packages/password-utils.scm
@@ -9,7 +9,7 @@
 ;;; Copyright © 2016 Alex Griffin <a@ajgrf.com>
 ;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2017, 2018 Clément Lassieur <clement@lassieur.org>
-;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Jelle Licht <jlicht@fsfe.org>
 ;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2017 Nicolas Goaziou <mail@nicolasgoaziou.fr>
@@ -271,7 +271,7 @@ random passwords that pass the checks.")
 (define-public assword
   (package
     (name "assword")
-    (version "0.10")
+    (version "0.11")
     (source (origin
               (method url-fetch)
               (uri (list
@@ -280,7 +280,7 @@ random passwords that pass the checks.")
                      "assword_" version ".orig.tar.gz")))
               (sha256
                (base32
-                "0l6170y6my1gprqkazvzabgjkrkr9v2q7z48vjflna4r323yqira"))))
+                "03gkb6kvsghznbcw5l7nmrc6mn3ixkjd5jcs96ni4zs9l47jf7yp"))))
     (arguments
      `(;; irritatingly, tests do run but not there are two problems:
        ;;  - "import gtk" fails for unknown reasons here despite it the
-- 
cgit v1.2.3


From c74b8b41cf18ecb52f17bb069980aa7ba46661fb Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Sat, 24 Feb 2018 11:51:27 +0100
Subject: gnu: Add emacs-esxml.

* gnu/packages/emacs.scm (emacs-esxml): New variable.
---
 gnu/packages/emacs.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index b7b088d42e..4a56325e4f 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -3559,6 +3559,28 @@ The purpose of this library is to wrap all the quirks and hassle of
 @code{package.el} into a sane API.")
     (license license:gpl3+)))
 
+(define-public emacs-esxml
+  (package
+    (name "emacs-esxml")
+    (version "0.3.4")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/tali713/esxml/archive/"
+                    version ".tar.gz"))
+              (sha256
+               (base32
+                "01yk4ibbln3ykrin2124hfdi53fsp9gv7j49qw93s2ls52c9zb2f"))))
+    (build-system emacs-build-system)
+    (home-page "https://github.com/tali713/esxml")
+    (synopsis "Elisp library for working with XML, ESXML and SXML")
+    (description
+     "This library provides two formats for XML code generation.  The primary
+form is esxml.  This is the form that is returned by such functions as
+@code{libxml-parse-xml-region} and it is used internally by emacs in many
+xml-related libraries.")
+    (license license:gpl3+)))
+
 (define-public emacs-queue
   (package
     (name "emacs-queue")
-- 
cgit v1.2.3


From 5815e3bc943b380b647ecb6c147cef0c015f853c Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Sat, 24 Feb 2018 11:52:21 +0100
Subject: gnu: Add emacs-nov.

* gnu/packages/emacs.scm (emacs-nov): New variable.
---
 gnu/packages/emacs.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 4a56325e4f..e96dca66b2 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -3581,6 +3581,41 @@ form is esxml.  This is the form that is returned by such functions as
 xml-related libraries.")
     (license license:gpl3+)))
 
+(define-public emacs-nov
+  (package
+    (name "emacs-nov")
+    (version "0.2.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/wasamasa/nov.el/archive/"
+                    version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0pc07cr2qfa66pxyxhvgrxiwssykisj25yjxvx3qr4v7bp5qmms7"))))
+    (build-system emacs-build-system)
+    (propagated-inputs
+     `(("emacs-dash" ,emacs-dash)
+       ("emacs-esxml" ,emacs-esxml)))
+    (home-page "https://github.com/wasamasa/nov.el")
+    (synopsis "Major mode for reading EPUB files in Emacs")
+    (description
+     "This package provides a major mode for reading EPUB documents.
+Features:
+@itemize
+@item Basic navigation (jump to table of contents (TOC), previous/next chapter)
+@item Remembering and restoring the last read position
+@item Jump to next chapter when scrolling beyond end
+@item Renders EPUB2 (.ncx) and EPUB3 (<nav>) TOCs
+@item Hyperlinks to internal and external targets
+@item Supports textual and image documents
+@item View source of document files
+@item Metadata display
+@item Image rescaling
+@end itemize\n")
+    (license license:gpl3+)))
+
 (define-public emacs-queue
   (package
     (name "emacs-queue")
-- 
cgit v1.2.3


From bc806b0c122a80d2df2e0b7ad7dae9b4160a2647 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Mon, 26 Feb 2018 17:01:54 -0500
Subject: gnu: Add libiptcdata.

* gnu/packages/image.scm (libiptcdata): New variable.
---
 gnu/packages/image.scm | 24 ++++++++++++++++++++++--
 1 file changed, 22 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm
index 5943457f94..e3e3a3ccc7 100644
--- a/gnu/packages/image.scm
+++ b/gnu/packages/image.scm
@@ -7,8 +7,7 @@
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2015 Amirouche Boubekki <amirouche@hypermove.net>
 ;;; Copyright © 2014, 2017 John Darrington <jmd@gnu.org>
-;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
-;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2016, 2017, 2018 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
@@ -1230,3 +1229,24 @@ medical image data, e.g. magnetic resonance image (MRI) and functional MRI
     (synopsis "Color picker")
     (description "Gpick is an advanced color picker and palette editing tool.")
     (license license:bsd-3)))
+
+(define-public libiptcdata
+  (package
+    (name "libiptcdata")
+    (version "1.0.4")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/" name "/" name "/"
+                                  version "/" name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "03pfvkmmx762iydq0q207x2028d275pbdysfsgpmrr0ywy63pxkr"))))
+    (build-system gnu-build-system)
+    (home-page "http://libiptcdata.sourceforge.net/")
+    (synopsis "IPTC metadata manipulation library")
+    (description "Libiptcdata is a C library for manipulating the International
+Press Telecommunications Council (IPTC) metadata stored within multimedia files
+such as images.  This metadata can include captions and keywords, often used by
+popular photo management applications.  The library provides routines for
+parsing, viewing, modifying, and saving this metadata.")
+    (license license:lgpl2.0+)))
-- 
cgit v1.2.3


From 13d9794d8fcbe4b1bab0060594f6d52058db0cb0 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Mon, 26 Feb 2018 17:01:54 -0500
Subject: gnu: Add RawTherapee.

* gnu/packages/photo.scm (rawtherapee): New variable.
---
 gnu/packages/photo.scm | 56 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 56 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/photo.scm b/gnu/packages/photo.scm
index 788dcf36fc..758ed3f6f1 100644
--- a/gnu/packages/photo.scm
+++ b/gnu/packages/photo.scm
@@ -5,6 +5,7 @@
 ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -46,6 +47,7 @@
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages image)
   #:use-module (gnu packages imagemagick)
+  #:use-module (gnu packages libcanberra)
   #:use-module (gnu packages libusb)
   #:use-module (gnu packages llvm)
   #:use-module (gnu packages man)
@@ -465,3 +467,57 @@ user interface.  It can be used to assemble a mosaic of photographs into
 a complete panorama and stitch any series of overlapping pictures.")
     (license license:gpl2+)))
 
+(define-public rawtherapee
+  (package
+    (name "rawtherapee")
+    (version "5.3")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://rawtherapee.com/shared/source/"
+                                  "rawtherapee-" version ".tar.xz"))
+              (sha256
+               (base32
+                "1y1ygxqmqfp4zg8rcgrlfdc1597cyr5zqgp5zjpldhvwdfa9r5cp"))))
+    (build-system cmake-build-system)
+    (arguments
+     '(#:tests? #f ; no test suite
+       #:configure-flags
+       (list (string-append "-DLENSFUNDBDIR="
+                            (assoc-ref %build-inputs "lensfun")
+                            "/share/lensfun")
+             "-DCMAKE_BUILD_TYPE=release"
+             ; Don't optimize the build for the host machine. See the file
+             ; 'ProcessorTargets.cmake' in the source distribution for more
+             ; information.
+             "-DPROC_TARGET_NUMBER=1"
+             ; These flags are recommended by upstream for distributed packages.
+             ; See the file 'RELEASE_NOTES.txt' in the source distribution.
+             "-O3"
+             "-DCACHE_NAME_SUFFIX=\"\"")))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("expat" ,expat)
+       ("fftw" ,fftwf)
+       ("glib" ,glib)
+       ("glibmm" ,glibmm)
+       ("gtk+" ,gtk+)
+       ("gtkmm" ,gtkmm)
+       ("lcms" ,lcms)
+       ("lensfun" ,lensfun)
+       ("libcanberra" ,libcanberra)
+       ("libiptcdata" ,libiptcdata)
+       ("libjpeg" ,libjpeg)
+       ("libpng" ,libpng)
+       ("libsigc++" ,libsigc++)
+       ("libtiff" ,libtiff)
+       ("zlib" ,zlib)))
+    (home-page "http://rawtherapee.com")
+    (synopsis "Raw image developing and processing")
+    (description "RawTherapee is a raw image processing suite.  It comprises a
+subset of image editing operations specifically aimed at non-destructive raw
+photo post-production and is primarily focused on improving a photographer's
+workflow by facilitating the handling of large numbers of images.  Most raw
+formats are supported, including Pentax Pixel Shift, Canon Dual-Pixel, and those
+from Foveon and X-Trans sensors.")
+    (license license:gpl3+)))
-- 
cgit v1.2.3


From fcbb8461a4c733cbfb5ba25cb90f97116cf1e8bc Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Thu, 22 Feb 2018 00:02:08 -0500
Subject: gnu: Add go@1.10.

Building Go 1.10 with the Go 1.4 bootstrap, Thread Sanitizer from GCC 5
finds a data race during the the test suite of Go 1.10. With GCC 6, the
race doesn't seem to be present.

.##### ../misc/cgo/testsanitizers
--- FAIL: TestShared (0.03s)
    --- FAIL: TestShared/tsan_shared (2.54s)
        cshared_test.go:71: `/tmp/guix-build-go-1.10.drv-0/TestShared367937240/tsan_shared` exited with exit status 66
                ==================
                WARNING: ThreadSanitizer: data race (pid=28778)
                  Write of size 8 at 0x7ffff5495c30 by thread T1:
                    #0 pthread_attr_getstacksize <null> (tsan_shared+0x00000041be82)
                    #1 x_cgo_init <null> (libtsan_shared.so+0x00000008aeaf)
                    #2 runtime.rt0_go /tmp/guix-build-go-1.10.drv-0/go/src/runtime/asm_amd64.s:199 (libtsan_shared.so+0x000000081586)

                  Previous write of size 8 at 0x7ffff5495c30 by main thread:
                    #0 <null> <null> (0x000000000001)

                  Location is stack of thread T1.

                  Thread T1 (tid=28786, running) created by main thread at:
                    #0 pthread_create <null> (tsan_shared+0x00000040c794)
                    #1 _cgo_try_pthread_create <null> (libtsan_shared.so+0x00000008ad70)
                    #2 x_cgo_sys_thread_create <null> (libtsan_shared.so+0x00000008ab12)
                    #3 _rt0_amd64_lib /tmp/guix-build-go-1.10.drv-0/go/src/runtime/asm_amd64.s:56 (libtsan_shared.so+0x0000000813b6)

                SUMMARY: ThreadSanitizer: data race ??:0 __interceptor_pthread_attr_getstacksize

* gnu/packages/golang.scm (go-1.10): New variable.
(go-1.4)[native-inputs]: Use gcc:lib version 6.
---
 gnu/packages/golang.scm | 119 +++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 118 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index f11cc76d9c..e201ac8e4c 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -187,7 +187,11 @@
     (inputs
      `(("tzdata" ,tzdata)
        ("pcre" ,pcre)
-       ("gcc:lib" ,gcc "lib")))
+       ;; Building Go 1.10 with the Go 1.4 bootstrap, Thread Sanitizer from GCC
+       ;; 5 finds a data race during the the test suite of Go 1.10. With GCC 6,
+       ;; the race doesn't seem to be present:
+       ;; https://github.com/golang/go/issues/24046
+       ("gcc:lib" ,gcc-6 "lib")))
     (native-inputs
      `(("pkg-config" ,%pkg-config)
        ("which" ,which)
@@ -372,6 +376,119 @@ in the style of communicating sequential processes (@dfn{CSP}).")
        ,@(package-native-inputs go-1.4)))
     (supported-systems %supported-systems)))
 
+(define-public go-1.10
+  (package
+    (inherit go-1.9)
+    (name "go")
+    (version "1.10")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://storage.googleapis.com/golang/"
+                           name version ".src.tar.gz"))
+       (sha256
+        (base32
+         "093z1h0gmi458kv7smpx0ph6jm7ss9mzxa432kysbz85jhl4kppk"))))
+    (arguments
+     (substitute-keyword-arguments (package-arguments go-1.9)
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (replace 'prebuild
+             (lambda* (#:key inputs outputs #:allow-other-keys)
+               (let* ((gcclib (string-append (assoc-ref inputs "gcc:lib") "/lib"))
+                      (ld (string-append (assoc-ref inputs "libc") "/lib"))
+                      (loader (car (find-files ld "^ld-linux.+")))
+                      (net-base (assoc-ref inputs "net-base"))
+                      (tzdata-path
+                       (string-append (assoc-ref inputs "tzdata") "/share/zoneinfo"))
+                      (output (assoc-ref outputs "out")))
+
+                 ;; Removing net/ tests, which fail when attempting to access
+                 ;; network resources not present in the build container.
+                 (for-each delete-file
+                           '("net/listen_test.go"
+                             "net/parse_test.go"
+                             "net/cgo_unix_test.go"))
+
+                 (substitute* "os/os_test.go"
+                   (("/usr/bin") (getcwd))
+                   (("/bin/pwd") (which "pwd"))
+                   (("/bin/sh") (which "sh")))
+
+                 ;; Add libgcc to runpath
+                 (substitute* "cmd/link/internal/ld/lib.go"
+                   (("!rpath.set") "true"))
+                 (substitute* "cmd/go/internal/work/gccgo.go"
+                   (("cgoldflags := \\[\\]string\\{\\}")
+                    (string-append "cgoldflags := []string{"
+                                   "\"-rpath=" gcclib "\""
+                                   "}"))
+                   (("\"-lgcc_s\", ")
+                    (string-append
+                     "\"-Wl,-rpath=" gcclib "\", \"-lgcc_s\", ")))
+                 (substitute* "cmd/go/internal/work/gc.go"
+                   (("ldflags = setextld\\(ldflags, compiler\\)")
+                    (string-append
+                     "ldflags = setextld(ldflags, compiler)\n"
+                     "ldflags = append(ldflags, \"-r\")\n"
+                     "ldflags = append(ldflags, \"" gcclib "\")\n")))
+
+                 ;; Disable failing tests: these tests attempt to access
+                 ;; commands or network resources which are neither available
+                 ;; nor necessary for the build to succeed.
+                 (for-each
+                  (match-lambda
+                    ((file regex)
+                     (substitute* file
+                       ((regex all before test_name)
+                        (string-append before "Disabled" test_name)))))
+                  '(("net/net_test.go" "(.+)(TestShutdownUnix.+)")
+                    ("net/dial_test.go" "(.+)(TestDialTimeout.+)")
+                    ("os/os_test.go" "(.+)(TestHostname.+)")
+                    ("time/format_test.go" "(.+)(TestParseInSydney.+)")
+                    ("time/format_test.go" "(.+)(TestParseInLocation.+)")
+                    ("os/exec/exec_test.go" "(.+)(TestEcho.+)")
+                    ("os/exec/exec_test.go" "(.+)(TestCommandRelativeName.+)")
+                    ("os/exec/exec_test.go" "(.+)(TestCatStdin.+)")
+                    ("os/exec/exec_test.go" "(.+)(TestCatGoodAndBadFile.+)")
+                    ("os/exec/exec_test.go" "(.+)(TestExitStatus.+)")
+                    ("os/exec/exec_test.go" "(.+)(TestPipes.+)")
+                    ("os/exec/exec_test.go" "(.+)(TestStdinClose.+)")
+                    ("os/exec/exec_test.go" "(.+)(TestIgnorePipeErrorOnSuccess.+)")
+                    ("syscall/syscall_unix_test.go" "(.+)(TestPassFD\\(.+)")
+                    ("os/exec/exec_test.go" "(.+)(TestExtraFiles/areturn.+)")
+                    ("cmd/go/go_test.go" "(.+)(TestCoverageWithCgo.+)")
+                    ("os/exec/exec_test.go" "(.+)(TestOutputStderrCapture.+)")
+                    ("os/exec/exec_test.go" "(.+)(TestExtraFiles.+)")
+                    ("os/exec/exec_test.go" "(.+)(TestExtraFilesRace.+)")
+                    ("net/lookup_test.go" "(.+)(TestLookupPort.+)")
+                    ("syscall/exec_linux_test.go"
+                     "(.+)(TestCloneNEWUSERAndRemapNoRootDisableSetgroups.+)")))
+
+                 ;; fix shebang for testar script
+                 ;; note the target script is generated at build time.
+                 (substitute* "../misc/cgo/testcarchive/carchive_test.go"
+                   (("#!/usr/bin/env") (string-append "#!" (which "env"))))
+
+                 (substitute* "net/lookup_unix.go"
+                   (("/etc/protocols") (string-append net-base "/etc/protocols")))
+                 (substitute* "net/port_unix.go"
+                   (("/etc/services") (string-append net-base "/etc/services")))
+                 (substitute* "time/zoneinfo_unix.go"
+                   (("/usr/share/zoneinfo/") tzdata-path))
+                 (substitute* (find-files "cmd" "\\.go")
+                   (("/lib(64)?/ld-linux.*\\.so\\.[0-9]") loader))
+                 #t)))
+           (replace 'set-bootstrap-variables
+             (lambda* (#:key outputs inputs #:allow-other-keys)
+               ;; Tell the build system where to find the bootstrap Go.
+               (let ((go  (assoc-ref inputs "go")))
+                 (setenv "GOROOT_BOOTSTRAP" go)
+                 (setenv "GOGC" "400")
+                 ;; Go 1.10 tries to write to $HOME in a test
+                 (setenv "HOME" "/tmp")
+                 #t)))))))))
+
 (define-public go go-1.9)
 
 (define-public go-github-com-alsm-ioprogress
-- 
cgit v1.2.3


From 7ad05d8526388fec47b98d00fc04e7da38eb046d Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Tue, 27 Feb 2018 00:32:06 +0100
Subject: gnu: emacs-org, emacs-org-contrib: Update to 20180226

* gnu/packages/emacs.scm (emacs-org):
(emacs-org-contrib): Update to 20180226, aka Org 9.1.7.
---
 gnu/packages/emacs.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index e96dca66b2..bb3bf1cf8a 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -14,7 +14,7 @@
 ;;; Copyright © 2016, 2017 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2016, 2017 ng0 <ng0@infotropique.org>
 ;;; Copyright © 2016 Alex Griffin <a@ajgrf.com>
-;;; Copyright © 2016, 2017 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2016, 2017, 2018 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2016, 2017 Alex Vong <alexvong1995@gmail.com>
 ;;; Copyright © 2016, 2017, 2018 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2017 Christopher Baines <mail@cbaines.net>
@@ -4549,14 +4549,14 @@ passive voice.")
     (name "emacs-org")
     ;; emacs-org-contrib inherits from this package.  Please update its sha256
     ;; checksum as well.
-    (version "20180103")
+    (version "20180226")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://orgmode.org/elpa/org-"
                                   version ".tar"))
               (sha256
                (base32
-                "1hyw9sigcv9wn37y2icmhf1czf0s3dgvsmn36355l95zsw7hnvgj"))))
+                "0jqvry6gah1bwnryha4asynj13jyds3qim0xcy7s01rxk99m2ziy"))))
     (build-system emacs-build-system)
     (home-page "https://orgmode.org/")
     (synopsis "Outline-based notes management and organizer")
@@ -4576,7 +4576,7 @@ reproducible research.")
                                   (package-version emacs-org) ".tar"))
               (sha256
                (base32
-                "164i2asqh34p1g3iqsn7rziyxbi1ys8fwdmn7nsw5xph8qszv9zj"))))
+                "034wp70hcqnpidji5k1k80mj35iyyy098nbvc2sl7i2aca4m03zc"))))
     (arguments
      `(#:modules ((guix build emacs-build-system)
                   (guix build utils)
-- 
cgit v1.2.3


From 26204b81f9f401da10a86d191ea30780607908da Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Mon, 26 Feb 2018 21:30:16 -0500
Subject: gnu: linux-libre@4.4: Update to 4.4.118.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.118.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 6f0ef369f7..6b0920a9a6 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -408,8 +408,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.4
-  (make-linux-libre "4.4.117"
-                    "1mlq9npyriwj0wpj24zah55bkxil31l182ypbn6b3x4yvmr8lhz0"
+  (make-linux-libre "4.4.118"
+                    "0di91awl8ii1fxrfyqbpfpn134apcc98fas7yisjg87f16bn4azl"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
-- 
cgit v1.2.3


From 5de50beda350a5de70ec8e86ce45c475f88dbd1c Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Mon, 26 Feb 2018 21:31:07 -0500
Subject: gnu: linux-libre@4.9: Update to 4.9.84.

* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.84.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 6b0920a9a6..70c86d8441 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -402,8 +402,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.83"
-                    "09mw2r2fbn0g6xfhyxk0n54c7sg0vk9nlp7k2ca3v0v24n7lrfza"
+  (make-linux-libre "4.9.84"
+                    "08bgdcysva2igz4rc55slyz7nbzwz5skakh5c2iahsklg343pwbw"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
-- 
cgit v1.2.3


From cd2bcc9bdaa3ef00af13eaf63a1144a6a9ff0990 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Mon, 26 Feb 2018 21:31:46 -0500
Subject: gnu: linux-libre@4.14: Update to 4.14.22.

* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.22.
(%linux-libre-4.14-hash): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 70c86d8441..4eb2f98621 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -392,8 +392,8 @@ It has been modified to remove all non-free binary blobs.")
                     %linux-compatible-systems
                     #:configuration-file kernel-config))
 
-(define %linux-libre-4.14-version "4.14.21")
-(define %linux-libre-4.14-hash "07d27mph514jxxkzil4b3c848ywfd4r4js0wl5wsfy7a3j757278")
+(define %linux-libre-4.14-version "4.14.22")
+(define %linux-libre-4.14-hash "1lhswcvgl077kzsln3nxmrdbnlc3b8mphjjmkqz0f2663wa6rhcv")
 
 (define-public linux-libre-4.14
   (make-linux-libre %linux-libre-4.14-version
-- 
cgit v1.2.3


From 701cfb9b333973f242043497b3231b5ea296282b Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Mon, 26 Feb 2018 21:32:34 -0500
Subject: gnu: linux-libre: Update to 4.15.6.

* gnu/packages/linux.scm (%linux-libre-version): Update to 4.15.6.
(%linux-libre-hash): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 4eb2f98621..420bdf5a47 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -383,8 +383,8 @@ It has been modified to remove all non-free binary blobs.")
 ;; supports qemu "virt" machine and possibly a large number of ARM boards.
 ;; See : https://wiki.debian.org/DebianKernel/ARMMP.
 
-(define %linux-libre-version "4.15.5")
-(define %linux-libre-hash "1vrqya5zkhzl37fpj5v0v1igm7jf2gi13apkpak90l51xiw592cs")
+(define %linux-libre-version "4.15.6")
+(define %linux-libre-hash "13mv6wrhwjw2wll918c1r9l872wzzanvyi8rk6gv0k6cg0f56jal")
 
 (define-public linux-libre
   (make-linux-libre %linux-libre-version
-- 
cgit v1.2.3


From a1df45e904caf4d26f6e44d07ce74881bb25ecd9 Mon Sep 17 00:00:00 2001
From: Chris Marusich <cmmarusich@gmail.com>
Date: Tue, 27 Feb 2018 05:25:47 +0100
Subject: gnu: commencement: Add commentary regarding grafts.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/commencement.scm: Add comments that were originally
  included only in the Git commit message of
  f00b85ff8d34df0a1879e593d4a85629b8586af7.

Co-Authored-By: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/commencement.scm | 9 +++++++++
 1 file changed, 9 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/commencement.scm b/gnu/packages/commencement.scm
index 7286e954c5..c38f40f618 100644
--- a/gnu/packages/commencement.scm
+++ b/gnu/packages/commencement.scm
@@ -66,6 +66,15 @@
 ;;; To avoid circular dependencies, this module should not be imported
 ;;; directly from anywhere.
 ;;;
+;;; Below, we frequently use "inherit" to create modified packages.  The
+;;; reason why we use "inherit" instead of "package/inherit" is because we do
+;;; not want these commencement packages to inherit grafts.  By definition,
+;;; these packages are not depended on at run time by any of the packages we
+;;; use.  Thus it does not make sense to inherit grafts.  Furthermore, those
+;;; grafts would often lead to extra overhead for users who would end up
+;;; downloading those "-boot0" packages just to build package replacements
+;;; that are in fact not going to be used.
+;;;
 ;;; Code:
 
 (define gnu-make-boot0
-- 
cgit v1.2.3


From 87b6305e72a0d96260716719b041bd7ae84ca230 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Tue, 27 Feb 2018 09:21:27 +0100
Subject: gnu: polkit: Fix 'invoke' call.

* gnu/packages/polkit.scm (polkit)[arguments] <'install>: Add 'apply'.
Fixes a regression introduced in 3c4bbb4c52418c8daf8b0e4605e3912685c9f44a.
---
 gnu/packages/polkit.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/polkit.scm b/gnu/packages/polkit.scm
index 76a1aa21c4..a3dbc4ff79 100644
--- a/gnu/packages/polkit.scm
+++ b/gnu/packages/polkit.scm
@@ -116,7 +116,7 @@
             ;; to install in /etc, and to instead install the skeletons in the
             ;; output directory.
             (let ((out (assoc-ref outputs "out")))
-             (invoke "make" "install"
+             (apply invoke "make" "install"
                            (string-append "sysconfdir=" out "/etc")
                            (string-append "polkit_actiondir="
                                           out "/share/polkit-1/actions")
-- 
cgit v1.2.3


From 36d48a536e0bd86f1fdb7f41038db4aa4e0507cb Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kkebreau@posteo.net>
Date: Mon, 26 Feb 2018 14:47:15 -0500
Subject: gnu: mbedtls-apache: Fix upstream typo.

A typo was introduced in version 2.7.0 that caused the hiawatha package to
fail to build. See https://github.com/ARMmbed/mbedtls/pull/1362.

* gnu/packages/tls.scm (mbedtls-apache)[source]: Add snippet to fix typo.
---
 gnu/packages/tls.scm | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm
index 9e06e675f4..2233b5974c 100644
--- a/gnu/packages/tls.scm
+++ b/gnu/packages/tls.scm
@@ -797,7 +797,15 @@ then ported to the GNU / Linux environment.")
                            version "-apache.tgz"))
        (sha256
         (base32
-         "1vsmgxnw7dpvma51896n63yaf9sncmf885ax2jfcg89ssin6vdmf"))))
+         "1vsmgxnw7dpvma51896n63yaf9sncmf885ax2jfcg89ssin6vdmf"))
+       ;; An RFC 5114 constant was accidentally renamed in version 2.7.0.
+       ;; See https://github.com/ARMmbed/mbedtls/pull/1362.
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           (substitute* "include/mbedtls/dhm.h"
+             (("#define MBEDTLS_DHM_RFC5114_MODP_P")
+              "#define MBEDTLS_DHM_RFC5114_MODP_2048_P"))))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags
-- 
cgit v1.2.3


From 63f931cf82460cecdeef2d147add07e5b671cc73 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 27 Feb 2018 01:46:58 +0100
Subject: gnu: gcab: Update to 1.1.

* gnu/packages/package-management.scm (gcab): Update to 1.1.
[source]: Remove git dependency in a snippet.
---
 gnu/packages/package-management.scm | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 32a7a30e7a..6ec70b12fe 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -791,14 +791,23 @@ on top of GNU Guix.")
 (define-public gcab
   (package
     (name "gcab")
-    (version "1.0")
+    (version "1.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/" name "/"
                                   version "/" name "-" version ".tar.xz"))
               (sha256
                (base32
-                "1ji8j8pnxqaycbp9ydi2zq7gcr02c2vw4qnc198i6jwy9zkh2x19"))))
+                "0l19sr6pg0cfcddmi5n79d08mjjbhn427ip5jlsy9zddq9r24aqr"))
+              ;; gcab 1.1 has a hard dependency on git — even when building
+              ;; from a tarball.  Remove it early so ‘guix environment gcab’
+              ;; can actually build what ‘guix build --source gcab’ returns.
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  (substitute* "meson.build"
+                    (("git_version = .*$") "git_version = []\n"))
+                  #t))))
     (build-system meson-build-system)
     (native-inputs
      `(("glib:bin" ,glib "bin")         ; for glib-mkenums
-- 
cgit v1.2.3


From 4f3506a48a120ace07a3e0c85f02381b305be6a0 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 26 Feb 2018 21:47:20 +0100
Subject: gnu: thermald: Update to 1.7.1.

* gnu/packages/admin.scm (thermald): Update to 1.7.1.
[arguments]: Substitute INVOKE for SYSTEM* and end phase with #t.
---
 gnu/packages/admin.scm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index cf9524eb5f..80cf8c391c 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -2373,7 +2373,7 @@ make it a perfect utility on modern distros.")
 (define-public thermald
   (package
     (name "thermald")
-    (version "1.6")
+    (version "1.7.1")
     (source
      (origin
       (method url-fetch)
@@ -2381,7 +2381,7 @@ make it a perfect utility on modern distros.")
                           version ".tar.gz"))
       (file-name (string-append name "-" version ".tar.gz"))
       (sha256 (base32
-               "14klz9fnvi9jdlaqwrp61xa5nh051n8ykrs1fh1wxd7j66qf2fn6"))))
+               "0isgmav3z3nb5bsdya8m3haqhzj1lyfjx7i812cqfjrh2a9msin4"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases
@@ -2389,6 +2389,7 @@ make it a perfect utility on modern distros.")
                    'unpack 'autogen.sh-and-fix-paths
                    (lambda* (#:key outputs #:allow-other-keys)
                      (let ((out (assoc-ref outputs "out")))
+                       ;; XXX this can probably be removed after version 1.7.1.
                        ;; upstartconfir is hardcoded to /etc/init and the build
                        ;; system tries to mkdir that.  We don't even need upstart
                        ;; files at all; this is a fast and kludgy workaround
@@ -2397,7 +2398,8 @@ make it a perfect utility on modern distros.")
                           (string-append "upstartconfdir = "
                                          out "/etc/init")))
                        ;; Now run autogen
-                       (zero? (system* "sh" "autogen.sh"))))))
+                       (invoke "sh" "autogen.sh")
+                       #t))))
        #:configure-flags
        (let ((out      (assoc-ref %outputs "out")))
          (list (string-append "--sysconfdir="
-- 
cgit v1.2.3


From 0c548d9875df9f099aff0b8158003c63436376de Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 27 Feb 2018 13:01:55 +0100
Subject: gnu: youtube-dl: Update to 2018.02.26.

* gnu/packages/video.scm (youtube-dl): Update to 2018.02.26.
---
 gnu/packages/video.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index a1ead1d609..0d939ab6d3 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -1157,7 +1157,7 @@ access to mpv's powerful playback capabilities.")
 (define-public youtube-dl
   (package
     (name "youtube-dl")
-    (version "2018.02.22")
+    (version "2018.02.26")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://yt-dl.org/downloads/"
@@ -1165,7 +1165,7 @@ access to mpv's powerful playback capabilities.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "112qmwrkd0cpyx2h20k6y07lw7iixvj8yya7r97h3k1y1py9vbz8"))))
+                "0ijjnx8qjxk07v5dbz3n5z3cvz8dlkmh7jkyvgng7inl74c29zq5"))))
     (build-system python-build-system)
     (arguments
      ;; The problem here is that the directory for the man page and completion
-- 
cgit v1.2.3


From 713b519eaad39f5fd29cc5ad6e3cad0f089f9bbb Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 26 Feb 2018 22:44:24 +0100
Subject: gnu: fluidsynth: Update to 1.1.10.

* gnu/packages/audio.scm (fluidsynth): Update to 1.1.10.
---
 gnu/packages/audio.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index b1a15ed34d..d4d2636614 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -1030,7 +1030,7 @@ follower.")
 (define-public fluidsynth
   (package
     (name "fluidsynth")
-    (version "1.1.9")
+    (version "1.1.10")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1039,14 +1039,15 @@ follower.")
               (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "0krvmb1idnf95l2ydzfcb08ayyx3n4m71hf9fgwv3srzaikvpf3q"))))
+                "04jlgq1d1hd8r9cnmkl3lgf1fgm7kgy4hh9nfddap41fm1wp121p"))))
     (build-system cmake-build-system)
     (arguments
-     '(#:tests? #f  ; no check phase
+     '(#:tests? #f                      ; no check target
        #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'fix-libdir
            (lambda _
+             ;; Install libraries to /lib, not /lib64.
              (substitute* "CMakeLists.txt"
                (("LIB_SUFFIX \\$\\{_init_lib_suffix\\}")
                 "LIB_SUFFIX \"\""))
-- 
cgit v1.2.3


From 9e9a211f9d2b24cdbda5ddcddc3df5f8e725277e Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 26 Feb 2018 22:25:32 +0100
Subject: gnu: soxr: Update to 0.1.3.

* gnu/packages/audio.scm (soxr): Update to 0.1.3.
---
 gnu/packages/audio.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index d4d2636614..369af141fa 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -2537,7 +2537,7 @@ can play and record audio files.")
 (define-public soxr
   (package
     (name "soxr")
-    (version "0.1.2")
+    (version "0.1.3")
     (source
      (origin
        (method url-fetch)
@@ -2545,7 +2545,7 @@ can play and record audio files.")
         (string-append "mirror://sourceforge/soxr/soxr-" version
                        "-Source.tar.xz"))
        (sha256
-        (base32 "0xf2w3piwz9gfr1xqyrj4k685q5dy53kq3igv663i4f4y4sg9rjl"))))
+        (base32 "12aql6svkplxq5fjycar18863hcq84c5kx8g6f4rj0lcvigw24di"))))
     (build-system cmake-build-system)
     (arguments '(#:tests? #f))          ;no 'check' target
     (home-page "https://sourceforge.net/p/soxr/wiki/Home/")
-- 
cgit v1.2.3


From c26d74dde67316c6c01646ed07a29b035d73e15b Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 26 Feb 2018 22:52:39 +0100
Subject: gnu: phonon: Update to 4.10.0.

* gnu/packages/kde-frameworks.scm (phonon): Update to 4.10.0.
---
 gnu/packages/kde-frameworks.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm
index 84b45961b5..246860e3f3 100644
--- a/gnu/packages/kde-frameworks.scm
+++ b/gnu/packages/kde-frameworks.scm
@@ -4,6 +4,7 @@
 ;;; Copyright © 2016,2017 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2016 David Craven <david@craven.ch>
 ;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -140,7 +141,7 @@ common build settings used in software produced by the KDE community.")
 (define-public phonon
   (package
     (name "phonon")
-    (version "4.9.1")
+    (version "4.10.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -149,7 +150,7 @@ common build settings used in software produced by the KDE community.")
                     name "-" version ".tar.xz"))
               (sha256
                (base32
-                "177647r2jqfm32hqcz2nqfqv6v48hn5ab2vc31svba2wz23fkgk7"))))
+                "0gyhlnwamzfw31kw4qh0v6rj0m47k9wfygd6h07klg9ggp60xhg2"))))
     (build-system cmake-build-system)
     (native-inputs
      ;; TODO: Think about adding pulseaudio. Is it required for sound?
-- 
cgit v1.2.3


From 2504fd3794e9a6fa6fba0fbce4bec2e97652154b Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 26 Feb 2018 23:04:26 +0100
Subject: gnu: xfburn: Update to 0.5.5.

* gnu/packages/xfce.scm (xfburn): Update to 0.5.5.
---
 gnu/packages/xfce.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xfce.scm b/gnu/packages/xfce.scm
index 035e9c5f20..ba749c9989 100644
--- a/gnu/packages/xfce.scm
+++ b/gnu/packages/xfce.scm
@@ -912,7 +912,7 @@ sending standard messages over D-Bus using the
 (define-public xfburn
   (package
     (name "xfburn")
-    (version "0.5.4")
+    (version "0.5.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://archive.xfce.org/src/apps/xfburn/"
@@ -920,7 +920,7 @@ sending standard messages over D-Bus using the
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "1xn1kwxa3dl5r9bfj90a5322ynkwbn6k5v9b3a3pbr3a23zm604s"))))
+                "1qdd8prnsfilsprg36p95cz3z50ffr9kgvka4d5pm260lsl3l5xa"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("intltool" ,intltool)
-- 
cgit v1.2.3


From d5d7d26df7c424a9cffee27f1210b59ef8682d5c Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 27 Feb 2018 01:21:27 +0100
Subject: gnu: perl-gd: Update to 2.68.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/gd.scm (perl-gd): Update to 2.68.
[source]: Remove obsolete patch.
[native-inputs]: Remove perl-module-build.
[inputs]: Use canonical package names and order alphabetically.
[arguments]: Replace #:module-build-flags with fewer #:make-maker-flags,
enable #:tests?, and remove ‘clear-autogenerated-files’ phase.
* gnu/packages/patches/perl-gd-options-passthrough-and-fontconfig.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/local.mk                                       |  1 -
 gnu/packages/gd.scm                                | 43 ++++++------------
 ...erl-gd-options-passthrough-and-fontconfig.patch | 53 ----------------------
 3 files changed, 13 insertions(+), 84 deletions(-)
 delete mode 100644 gnu/packages/patches/perl-gd-options-passthrough-and-fontconfig.patch

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index 72fbf90f83..bae3df5a6d 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -972,7 +972,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/perl-dbd-mysql-CVE-2017-10788.patch	\
   %D%/packages/patches/perl-deterministic-ordering.patch	\
   %D%/packages/patches/perl-finance-quote-unuse-mozilla-ca.patch \
-  %D%/packages/patches/perl-gd-options-passthrough-and-fontconfig.patch \
   %D%/packages/patches/perl-io-socket-ssl-openssl-1.0.2f-fix.patch \
   %D%/packages/patches/perl-net-amazon-s3-moose-warning.patch	\
   %D%/packages/patches/perl-net-dns-resolver-programmable-fix.patch	\
diff --git a/gnu/packages/gd.scm b/gnu/packages/gd.scm
index 3b1def55e1..c815cdd7ea 100644
--- a/gnu/packages/gd.scm
+++ b/gnu/packages/gd.scm
@@ -5,6 +5,7 @@
 ;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -93,45 +94,27 @@ most common applications of GD involve website development.")
 (define-public perl-gd
   (package
     (name "perl-gd")
-    (version "2.56")
+    (version "2.68")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "mirror://cpan/authors/id/L/LD/LDS/"
+       (uri (string-append "mirror://cpan/authors/id/R/RU/RURBAN/"
                            "GD-" version ".tar.gz"))
        (sha256
         (base32
-         "1ya8f9hpiax8j29vwaiwlvvgah0vkyvpzva28r8231nyk0f3s40z"))
-       (patches (search-patches
-                 "perl-gd-options-passthrough-and-fontconfig.patch"))))
+         "0p2ya641nl5cvcqgw829xgabh835qijfd6vq2ba12862946xx8va"))))
     (build-system perl-build-system)
-    (native-inputs
-     `(("perl-module-build" ,perl-module-build))) ;needs Module::Build >= 0.42
     (inputs
-     `(("gd" ,gd)
-       ("zlib" ,zlib)
-       ("png" ,libpng)
-       ("ft" ,freetype)
-       ("jpeg" ,libjpeg)
-       ("fontconfig" ,fontconfig)))
+     `(("fontconfig" ,fontconfig)
+       ("freetype" ,freetype)
+       ("gd" ,gd)
+       ("libpng" ,libpng)
+       ("libjpeg" ,libjpeg)
+       ("zlib" ,zlib)))
     (arguments
-     ;; We must use Build.PL for building because Makefile.PL fails to build
-     ;; the XS source.
-     `(#:module-build-flags (map (lambda (i)
-                                   (string-append "--lib_" i "_path="
-                                                  (assoc-ref %build-inputs i)))
-                                 '("zlib" "png" "ft" "jpeg" "fontconfig"))
-       #:tests? #f ;; Failed 1/2 test programs. 1/12 subtests failed.
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'configure 'clear-autogenerated-files
-           (lambda _
-             ;; This file is autogenerated by its .PLS script at build
-             ;; time, but file creation fails because that file already
-             ;; exists in the distribution with non-writable
-             ;; permissions, so delete it first.
-             (delete-file "bdf_scripts/bdf2gdfont.pl")
-             #t)))))
+     `(#:make-maker-flags
+       (list (string-append "--lib_jpeg_path="
+                            (assoc-ref %build-inputs "libjpeg")))))
     (home-page "http://search.cpan.org/dist/GD")
     (synopsis "Perl interface to the GD graphics library")
     (description "GD.pm is an autoloadable interface module for libgd, a
diff --git a/gnu/packages/patches/perl-gd-options-passthrough-and-fontconfig.patch b/gnu/packages/patches/perl-gd-options-passthrough-and-fontconfig.patch
deleted file mode 100644
index b2ff43c0d3..0000000000
--- a/gnu/packages/patches/perl-gd-options-passthrough-and-fontconfig.patch
+++ /dev/null
@@ -1,53 +0,0 @@
-This patch (adapted from nixpkgs for Build.PL) configures Getopt::Long to pass
-options so they will be available at the second GetOptions call.
-
-Also an option to specify the search path for libfontconfig is added.
-
---- GD-2.56/Build.PL	2014-10-27 20:34:54.000000000 -0500
-+++ GD-2.56/Build.PL	2015-02-22 10:08:12.569973657 -0600
-@@ -2,14 +2,14 @@
- 
- use strict;
- use Module::Build;
--use Getopt::Long;
-+use Getopt::Long qw(:config pass_through);
- use Config;
- 
- # =====> PATHS: CHECK AND ADJUST <=====
- my (@INC,@LIBPATH,@LIBS);
- my $AUTOCONFIG = 0;      # global set by try_to_autoconfigure() below
- 
--my ($options,$lib_gd_path,$lib_ft_path,$lib_png_path,$lib_jpeg_path,$lib_xpm_path,$lib_zlib_path);
-+my ($options,$lib_gd_path,$lib_ft_path,$lib_png_path,$lib_jpeg_path,$lib_xpm_path,$lib_zlib_path,$lib_fontconfig_path);
- 
- unless (try_to_autoconfigure(\$options,\$lib_gd_path,\@INC,\@LIBPATH,\@LIBS)) {
-     die <<END;
-@@ -38,6 +38,7 @@
- 			"lib_jpeg_path=s" => \$lib_jpeg_path,
- 			"lib_xpm_path=s"  => \$lib_xpm_path,
- 			"lib_zlib_path=s" => \$lib_zlib_path,
-+			"lib_fontconfig_path=s" => \$lib_fontconfig_path,
- 		       );
- unless ($result) {
-   die <<END;
-@@ -53,6 +54,7 @@
-      -lib_jpeg_path path            path to libjpeg
-      -lib_xpm_path  path            path to libxpm
-      -lib_zlib_path path            path to libpng
-+     -lib_fontconfig_path path      path to fontconfig
-      -ignore_missing_gd             Ignore missing or old libgd installations and try to compile anyway
- 
- If no options are passed on the command line.  The program will
-@@ -100,6 +102,12 @@
-     @INC     = ("-I$lib_zlib_path/include", @INC);
-     @LIBPATH = ("-L$lib_zlib_path/lib", @LIBPATH); 
- }
-+if( defined($lib_fontconfig_path) ) 
-+{
-+    print "Fontconfig library used from:     $lib_fontconfig_path\n";
-+    @INC     = ("-I$lib_fontconfig_path/include", @INC);
-+    @LIBPATH = ("-L$lib_fontconfig_path/lib", @LIBPATH); 
-+}
- #############################################################################################
- 
- if ($^O eq 'VMS'){
-- 
cgit v1.2.3


From 130acf72f78feaf008c148a22680e15725b9112a Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 12 Feb 2018 11:08:54 +0100
Subject: gnu: love: Fix build with luajit@2.1.0-beta3.

* gnu/packages/game-development.scm (love)[source]: Add snippet fixing Lua version detection.
---
 gnu/packages/game-development.scm | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index ffc3522919..5deb5a3d91 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -547,7 +547,15 @@ archive on a per-file basis.")
                                  "love-" version "-linux-src.tar.gz"))
              (sha256
               (base32
-               "11x346pw0gqad8nmkmywzx4xpcbfc3dslbrdw5x94n1i25mk0sxj"))))
+               "11x346pw0gqad8nmkmywzx4xpcbfc3dslbrdw5x94n1i25mk0sxj"))
+             (modules '((guix build utils)))
+             (snippet
+              '(begin
+                 ;; Build with luajit 2.1.0-beta3.  Fixed in love 0.11.
+                 ;; See <https://bitbucket.org/rude/love/issues/1277>.
+                 (substitute* "src/libraries/luasocket/libluasocket/lua.h"
+                   (("> 501") ">= 501"))
+                 #t))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
-- 
cgit v1.2.3


From 7da5db8e45850a798258db092e0028b9ca52e351 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 27 Feb 2018 02:01:44 +0100
Subject: gnu: godot: Update to 3.0.1.

* gnu/packages/game-development.scm (godot): Update to 3.0.1.
[arguments]: End phases with #t and remove redundant MKDIR-P.
---
 gnu/packages/game-development.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index 5deb5a3d91..3025a68ec1 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -8,7 +8,7 @@
 ;;; Copyright © 2016, 2017 Kei Kebreau <kkebreau@posteo.net>
 ;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017 Julian Graham <joolean@gmail.com>
-;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Manolis Fragkiskos Ragkousis <manolis837@gmail.com>
 ;;; Copyright © 2017 Peter Mikkelsen <petermikkelsen10@gmail.com>
 ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
@@ -1064,7 +1064,7 @@ games.")
 (define-public godot
   (package
     (name "godot")
-    (version "3.0")
+    (version "3.0.1")
     (source (origin
               (method url-fetch)
               (uri
@@ -1073,7 +1073,7 @@ games.")
               (file-name (string-append name "-" version))
               (sha256
                (base32
-                "1jhp269n1a7c663v2555444icbjwzscj4r8cq4rrrap7r7dr4hyc"))))
+                "0k8c12nzhl98i9il9s3awbwdamkrwxk0s47jr7n8a3z93rpszd2p"))))
     (build-system scons-build-system)
     (arguments
      `(#:scons ,scons-python2
@@ -1116,16 +1116,16 @@ games.")
                  (if (file-exists? "godot.x11.tools.64")
                      (rename-file "godot.x11.tools.64" "godot")
                      (rename-file "godot.x11.tools.32" "godot"))
-                 (install-file "godot" bin)))))
+                 (install-file "godot" bin))
+               #t)))
          (add-after 'install 'install-godot-desktop
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
                     (desktop (string-append out "/share/applications"))
                     (icon-dir (string-append out "/share/pixmaps")))
-               (mkdir-p desktop)
-               (mkdir-p icon-dir)
                (rename-file "icon.png" "godot.png")
                (install-file "godot.png" icon-dir)
+               (mkdir-p desktop)
                (with-output-to-file
                    (string-append desktop "/godot.desktop")
                  (lambda _
-- 
cgit v1.2.3


From 4886d5b23c031b790cb0f3f36a30315306504b44 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 27 Feb 2018 04:46:57 +0100
Subject: gnu: spin2cpp: Update to 3.6.4.

* gnu/packages/embedded.scm (spin2cpp): Update to 3.6.4.
---
 gnu/packages/embedded.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/embedded.scm b/gnu/packages/embedded.scm
index b2e33ea10b..6f09c8f353 100644
--- a/gnu/packages/embedded.scm
+++ b/gnu/packages/embedded.scm
@@ -3,6 +3,7 @@
 ;;; Copyright © 2016, 2017 Theodoros Foradis <theodoros@foradis.org>
 ;;; Copyright © 2016 David Craven <david@craven.ch>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -696,7 +697,7 @@ upload binaries to a Parallax Propeller micro-controller.")
 (define-public spin2cpp
   (package
     (name "spin2cpp")
-    (version "3.6.3")
+    (version "3.6.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/totalspectrum/spin2cpp/"
@@ -704,7 +705,7 @@ upload binaries to a Parallax Propeller micro-controller.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0v5vzh69bp1r2byrpz12rql1w24ff2v9msr31596zq6hd6n82lnh"))))
+                "05qak187sn0xg7vhrxw27b19xhmid1b8ab8kax3gv0faavzablfw"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ;; The tests assume that a micro-controller is connected.
-- 
cgit v1.2.3


From 5cacd3144e52044f2b2c0e3fae873aa92f2ef6d8 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 27 Feb 2018 13:47:32 +0100
Subject: gnu: tig: Update to 2.3.3.

* gnu/packages/version-control.scm (tig): Update to 2.3.3.
[arguments]: Substitute INVOKE for SYSTEM*.
---
 gnu/packages/version-control.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index 7a0f37b4e7..229dab5f35 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -1389,7 +1389,7 @@ from Subversion to any supported Distributed Version Control System (DVCS).")
 (define-public tig
   (package
     (name "tig")
-    (version "2.3.0")
+    (version "2.3.3")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1397,7 +1397,7 @@ from Subversion to any supported Distributed Version Control System (DVCS).")
                     version "/tig-" version ".tar.gz"))
               (sha256
                (base32
-                "1vf02snz8qiiqiyqss1z63rzzmwbrc9agcgh21jdq13rja306vv8"))))
+                "1skbhhj1narsnsff1azdylcy6xghxb18mzqysmipcyyvlv2i17fk"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("asciidoc" ,asciidoc)
@@ -1410,7 +1410,7 @@ from Subversion to any supported Distributed Version Control System (DVCS).")
        (modify-phases %standard-phases
          (add-after 'install 'install-doc
            (lambda _
-             (zero? (system* "make" "install-doc")))))
+             (invoke "make" "install-doc"))))
        #:tests? #f)) ; tests require access to /dev/tty
     ;; #:test-target "test"))
     (home-page "https://jonas.github.io/tig/")
-- 
cgit v1.2.3


From fa964e96e636fb9815a756f937698696962fbbf0 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 27 Feb 2018 13:58:20 +0100
Subject: gnu: perl-xml-sax-base: Update to 1.09.

* gnu/packages/xml.scm (perl-xml-sax-base): Update to 1.09.
---
 gnu/packages/xml.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm
index 820083e7cb..67e1ca7427 100644
--- a/gnu/packages/xml.scm
+++ b/gnu/packages/xml.scm
@@ -538,7 +538,7 @@ building Perl SAX2 XML parsers, filters, and drivers.")
 (define-public perl-xml-sax-base
   (package
     (name "perl-xml-sax-base")
-    (version "1.08")
+    (version "1.09")
     (source
      (origin
        (method url-fetch)
@@ -546,7 +546,7 @@ building Perl SAX2 XML parsers, filters, and drivers.")
                            "XML-SAX-Base-" version ".tar.gz"))
        (sha256
         (base32
-         "17i161rq1ngjlk0c8vdkrkkc56y1pf51k1g54y28py0micqp0qk6"))))
+         "1l1ai9g1z11ja7mvnfl5mj346r13jyckbg9qlw6c2izglidkbjv6"))))
     (build-system perl-build-system)
     (home-page "http://search.cpan.org/dist/XML-SAX-Base")
     (synopsis "Base class for SAX Drivers and Filters")
-- 
cgit v1.2.3


From 7349fed5918e284ae5014c3bf3a230fc62a9e13b Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 27 Feb 2018 16:46:13 +0100
Subject: gnu: perl-x11-xcb: Update to 0.17.

* gnu/packages/xorg.scm (perl-x11-xcb): Update to 0.17.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index 3a488ce74e..78f99f334a 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -5813,7 +5813,7 @@ programs that cannot use the window system directly.")
 (define-public perl-x11-xcb
   (package
     (name "perl-x11-xcb")
-    (version "0.16")
+    (version "0.17")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -5821,7 +5821,7 @@ programs that cannot use the window system directly.")
                     "X11-XCB-" version ".tar.gz"))
               (sha256
                (base32
-                "14mnvr1001py2z1n43l18yaw0plwvjg5pcsyc7k81sa0amw8ahzw"))))
+                "12qyf98s5hbybmh0mblpz50c00i68srq73w5rw31m2dhclj8n96q"))))
     (build-system perl-build-system)
     (arguments
      '(;; Disable parallel build to prevent a race condition.
-- 
cgit v1.2.3


From 29d37e999c495431eafde90027d2b97b16d0db4e Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Tue, 27 Feb 2018 22:46:04 +0100
Subject: gnu: make-bootstrap: Build grep without PCRE support.

Partly fixes <https://bugs.gnu.org/24841>.
Reported by Chris Marusich <cmmarusich@gmail.com>.

This fixes cross-compilation of the statically-linked grep.

* gnu/packages/make-bootstrap.scm (%static-inputs): Add 'inputs' field
for grep.
---
 gnu/packages/make-bootstrap.scm | 24 +++++++++++++-----------
 1 file changed, 13 insertions(+), 11 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/make-bootstrap.scm b/gnu/packages/make-bootstrap.scm
index 07ac93686a..f1c4bf7bc5 100644
--- a/gnu/packages/make-bootstrap.scm
+++ b/gnu/packages/make-bootstrap.scm
@@ -197,6 +197,18 @@ for `sh' in $PATH, and without nscd, and with static NSS modules."
 				   (("/bin/sh") "sh")
 				   (("execv ") "execvp "))
 				 #t)))))))
+        ;; We don't want to retain a reference to /gnu/store in the bootstrap
+        ;; versions of egrep/fgrep, so we remove the custom phase added since
+        ;; grep@2.25. The effect is 'egrep' and 'fgrep' look for 'grep' in
+        ;; $PATH.
+        (grep (package
+                (inherit grep)
+                (inputs '())                   ;remove PCRE, which is optional
+                (arguments
+                 (substitute-keyword-arguments (package-arguments grep)
+                   ((#:phases phases)
+                    `(modify-phases ,phases
+                       (delete 'fix-egrep-and-fgrep)))))))
         (finalize (compose static-package
                            package-with-relocatable-glibc)))
     `(,@(map (match-lambda
@@ -209,17 +221,7 @@ for `sh' in $PATH, and without nscd, and with static NSS modules."
                ("patch" ,patch)
                ("coreutils" ,coreutils)
                ("sed" ,sed)
-               ;; We don't want to retain a reference to /gnu/store in the
-               ;; bootstrap versions of egrep/fgrep, so we remove the custom
-               ;; phase added since grep@2.25. The effect is 'egrep' and
-               ;; 'fgrep' look for 'grep' in $PATH.
-               ("grep" ,(package
-                          (inherit grep)
-                          (arguments
-                            (substitute-keyword-arguments (package-arguments grep)
-                              ((#:phases phases)
-                               `(modify-phases ,phases
-                                  (delete 'fix-egrep-and-fgrep)))))))
+               ("grep" ,grep)
                ("gawk" ,gawk)))
       ("bash" ,static-bash))))
 
-- 
cgit v1.2.3


From e87ab2e8953ef2c9e5ce7d22d5c8ff581da519d1 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 27 Feb 2018 17:04:05 +0100
Subject: gnu: perl-data-optlist: Update to 0.110.

* gnu/packages/perl.scm (perl-data-optlist): Update to 0.110.
---
 gnu/packages/perl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 7512dfaf1f..f5f39add9c 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -1720,7 +1720,7 @@ indentation and newlines plus sub deparsing.")
 (define-public perl-data-optlist
   (package
     (name "perl-data-optlist")
-    (version "0.109")
+    (version "0.110")
     (source
      (origin
        (method url-fetch)
@@ -1729,7 +1729,7 @@ indentation and newlines plus sub deparsing.")
              version ".tar.gz"))
        (sha256
         (base32
-         "1j44rm2spprlq3bc80cxni3dzs3gfjiqv1qc9q7820n1qj0wgmqw"))))
+         "1hzmgr2imdg1fc3hmwx0d56fhsdfyrgmgx7jb4jkyiv6575ifq9n"))))
     (build-system perl-build-system)
     (propagated-inputs
      `(("perl-sub-install" ,perl-sub-install)
-- 
cgit v1.2.3


From 92a37fd22489b8e9a98605c92ba3e10c081de29e Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 12 Feb 2018 11:08:54 +0100
Subject: gnu: perl-config-autoconf: Update to 0.315.

* gnu/packages/perl.scm (perl-config-autoconf): Update to 0.315.
---
 gnu/packages/perl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index f5f39add9c..52925f8667 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -1341,7 +1341,7 @@ supports XML, YAML, JSON, Apache-style configuration, and Perl code.")
 (define-public perl-config-autoconf
   (package
     (name "perl-config-autoconf")
-    (version "0.309")
+    (version "0.315")
     (source
      (origin
        (method url-fetch)
@@ -1349,7 +1349,7 @@ supports XML, YAML, JSON, Apache-style configuration, and Perl code.")
                            "Config-AutoConf-" version ".tar.gz"))
        (sha256
         (base32
-         "1nqc7calfny12dwfhz7ylsvx55nf69kirdc5dbyvh3sjsqj8yvdq"))))
+         "0h39x9rzrhhilpg8yxlzpka269qrzsjg0iy0c1b9xflqlvhx2g2b"))))
     (build-system perl-build-system)
     (propagated-inputs
      `(("perl-capture-tiny" ,perl-capture-tiny)))
-- 
cgit v1.2.3


From 63651b8057ffe98a5da1d77f9e7f19bb11ceee38 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 12 Feb 2018 11:08:54 +0100
Subject: gnu: perl-devel-globaldestruction: Update to 0.14.

* gnu/packages/perl.scm (perl-devel-globaldestruction): Update to 0.14.
---
 gnu/packages/perl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 52925f8667..11d8fa01ee 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -2585,7 +2585,7 @@ based memory management, circular references will cause memory leaks.")
 (define-public perl-devel-globaldestruction
   (package
     (name "perl-devel-globaldestruction")
-    (version "0.13")
+    (version "0.14")
     (source
      (origin
        (method url-fetch)
@@ -2593,7 +2593,7 @@ based memory management, circular references will cause memory leaks.")
                            "Devel-GlobalDestruction-" version ".tar.gz"))
        (sha256
         (base32
-         "0qn4iszgylnxjdkb6430f6a3ci7bcx9ih1az6bd5cbij1pf2965j"))))
+         "1aslj6myylsvzr0vpqry1cmmvzbmpbdcl4v9zrl18ccik7rabf1l"))))
     (build-system perl-build-system)
     (propagated-inputs
      `(("perl-sub-exporter-progressive" ,perl-sub-exporter-progressive)))
-- 
cgit v1.2.3


From a32f1365478288ffb738144bf55410c9cb10b1b0 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 12 Feb 2018 11:08:54 +0100
Subject: gnu: perl-extutils-installpaths: Update to 0.011.

* gnu/packages/perl.scm (perl-extutils-installpaths): Update to 0.011.
---
 gnu/packages/perl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 11d8fa01ee..a076b905f4 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -3104,7 +3104,7 @@ extensions")
 (define-public perl-extutils-installpaths
   (package
     (name "perl-extutils-installpaths")
-    (version "0.010")
+    (version "0.011")
     (source
      (origin
        (method url-fetch)
@@ -3112,7 +3112,7 @@ extensions")
                            "ExtUtils-InstallPaths-" version ".tar.gz"))
        (sha256
         (base32
-         "0mi1px42in7i442jqncg3gmxd5zn7sw5b2s85h690rz433qvyk6i"))))
+         "0z06y0fhx9hy9x01abb7s2xdbqrh9x4ps7avmlf4bwfwih2gl2bn"))))
     (build-system perl-build-system)
     (propagated-inputs
      `(("perl-extutils-config" ,perl-extutils-config)))
-- 
cgit v1.2.3


From 89badfbcc304b82f974f4d244ffc5f11220fc93d Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 12 Feb 2018 11:08:54 +0100
Subject: gnu: perl-import-into: Update to 1.002005.

* gnu/packages/perl.scm (perl-import-into): Update to 1.002005.
[source]: Update origin URI.
---
 gnu/packages/perl.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index a076b905f4..55c01a1f0a 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -3913,15 +3913,15 @@ variables.")
 (define-public perl-import-into
   (package
     (name "perl-import-into")
-    (version "1.002004")
+    (version "1.002005")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "mirror://cpan/authors/id/E/ET/ETHER/"
+       (uri (string-append "mirror://cpan/authors/id/H/HA/HAARG/"
                            "Import-Into-" version ".tar.gz"))
        (sha256
         (base32
-         "110hifk3cj14lxgjq2vaa2qfja21gll4lpn8vbimy0gzqadjbjyy"))))
+         "0rq5kz7c270q33jq6hnrv3xgkvajsc62ilqq7fs40av6zfipg7mx"))))
     (build-system perl-build-system)
     (propagated-inputs
      `(("perl-module-runtime" ,perl-module-runtime)))
-- 
cgit v1.2.3


From 24397ab1a31614c636931e89ff86b1144fd88750 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 12 Feb 2018 11:08:54 +0100
Subject: gnu: perl-list-moreutils-xs: Update to 0.428.

* gnu/packages/perl.scm (perl-list-moreutils-xs): Update to 0.428.
---
 gnu/packages/perl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 55c01a1f0a..597f45835a 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -4580,7 +4580,7 @@ functionality on lists which is not going to go into List::Util.")
 (define-public perl-list-moreutils-xs
   (package
     (name "perl-list-moreutils-xs")
-    (version "0.426")
+    (version "0.428")
     (source
      (origin
        (method url-fetch)
@@ -4588,7 +4588,7 @@ functionality on lists which is not going to go into List::Util.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "0ss0a0f9yqs7gd9qamhaxq27mvn573ljg28ry1gy2pxbz56byzbc"))))
+         "0bfndmnkqaaf3gffprak143bzplxd69c368jxgr7rzlx88hyd7wx"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-config-autoconf" ,perl-config-autoconf)
-- 
cgit v1.2.3


From b0821f6b8de4c3f172387e58468eb330d0994a8a Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 12 Feb 2018 11:08:54 +0100
Subject: gnu: perl-path-class: Update to 0.37.

* gnu/packages/perl.scm (perl-path-class): Update to 0.37.
---
 gnu/packages/perl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 597f45835a..b05f73ee8d 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -6557,7 +6557,7 @@ up inheritance from those modules at the same time.")
 (define-public perl-path-class
   (package
     (name "perl-path-class")
-    (version "0.35")
+    (version "0.37")
     (source
      (origin
        (method url-fetch)
@@ -6565,7 +6565,7 @@ up inheritance from those modules at the same time.")
                            "Path-Class-" version ".tar.gz"))
        (sha256
         (base32
-         "1viaj8jyshcj135la0kgfgzalaw06xnbsg9h54jx09v1342v69lj"))))
+         "1kj8q8dmd8jci94w5arav59nkp0pkxrkliz4n8n6yf02hsa82iv5"))))
     (build-system perl-build-system)
     (native-inputs `(("perl-module-build" ,perl-module-build)))
     (home-page "http://search.cpan.org/dist/Path-Class/")
-- 
cgit v1.2.3


From 1d4e6e1756e0a91c814653b56eb13ebca9914c1f Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 12 Feb 2018 11:08:54 +0100
Subject: gnu: perl-text-diff: Update to 1.45.

* gnu/packages/perl.scm (perl-text-diff): Update to 1.45.
---
 gnu/packages/perl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index b05f73ee8d..8dd60666ea 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -7861,7 +7861,7 @@ and escapes.")
 (define-public perl-text-diff
   (package
     (name "perl-text-diff")
-    (version "1.44")
+    (version "1.45")
     (source
      (origin
        (method url-fetch)
@@ -7869,7 +7869,7 @@ and escapes.")
                            "Text-Diff-" version ".tar.gz"))
        (sha256
         (base32
-         "041v92zla2acdc433f47giridf6p820sdczs7x5d71fhsyza1xsp"))))
+         "013g13prdghxvrp5754gyc7rmv1syyxrhs33yc5f0lrz3dxs1fp8"))))
     (build-system perl-build-system)
     (propagated-inputs
      `(("perl-algorithm-diff" ,perl-algorithm-diff)))
-- 
cgit v1.2.3


From 91b73dba9d0434eacbc93e5fd69c222d7ac1b193 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 12 Feb 2018 11:08:54 +0100
Subject: gnu: perl-throwable: Update to 0.200013.

* gnu/packages/perl.scm (perl-throwable): Update to 0.200013.
---
 gnu/packages/perl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 8dd60666ea..05052b1b72 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -8041,7 +8041,7 @@ system.")
 (define-public perl-throwable
   (package
     (name "perl-throwable")
-    (version "0.200012")
+    (version "0.200013")
     (source
      (origin
        (method url-fetch)
@@ -8049,7 +8049,7 @@ system.")
                            "Throwable-" version ".tar.gz"))
        (sha256
         (base32
-         "0cy8kza9pd9y5m7k5385asf4xqm54vdqnqm0am10z6j2mrxwr527"))))
+         "184gdcwxqwnkrx5md968v1ny70pq6blzpkihccm3bpdxnpgd11wr"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-devel-stacktrace" ,perl-devel-stacktrace)))
-- 
cgit v1.2.3


From 047cd2be078d8bc136021e50f1ba1f3b44c64ccf Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 12 Feb 2018 11:08:54 +0100
Subject: gnu: perl-variable-magic: Update to 0.62.

* gnu/packages/perl.scm (perl-variable-magic): Update to 0.62.
---
 gnu/packages/perl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 05052b1b72..0aa96e6b55 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -8647,7 +8647,7 @@ built-in.")
 (define-public perl-variable-magic
   (package
     (name "perl-variable-magic")
-    (version "0.61")
+    (version "0.62")
     (source
      (origin
        (method url-fetch)
@@ -8655,7 +8655,7 @@ built-in.")
                            "Variable-Magic-" version ".tar.gz"))
        (sha256
         (base32
-         "1mx6z36c3wk61x6lag6kyws5g1cba68cw20vrb92wan7ahpfkbxq"))))
+         "0p31dclnj47k4hj35rzay9pzxasl3gq46kzwqalhdw1kgr8ii6iz"))))
     (build-system perl-build-system)
     (home-page "http://search.cpan.org/dist/Variable-Magic/")
     (synopsis "Associate user-defined magic to variables from Perl")
-- 
cgit v1.2.3


From 3199acb2cf5cae1f1d20d03fa3fa32bd7fff5bd9 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 12 Feb 2018 11:08:54 +0100
Subject: gnu: perl-yaml: Update to 1.24.

* gnu/packages/perl.scm (perl-yaml): Update to 1.24.
[source]: Update origin URI.
---
 gnu/packages/perl.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 0aa96e6b55..a188891e95 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -8721,15 +8721,15 @@ neither visible nor modifiable from Perl space).")
 (define-public perl-yaml
   (package
     (name "perl-yaml")
-    (version "1.23")
+    (version "1.24")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "mirror://cpan/authors/id/I/IN/INGY/"
+       (uri (string-append "mirror://cpan/authors/id/T/TI/TINITA/"
                            "YAML-" version ".tar.gz"))
        (sha256
         (base32
-         "0kf8mllrgnrmlvjijxc6srjj1y9i8rik5jpjvm8jh4yx70h9gn1a"))))
+         "1dpzgnjbd8yvf94vf45cmyj5bc6vrm6bchhx9xqwxqd5f9d093dm"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-test-yaml" ,perl-test-yaml)))
-- 
cgit v1.2.3


From bf5e7189dc4311cf1db25c95cf6c996990f7095d Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 12 Feb 2018 11:08:54 +0100
Subject: gnu: perl-yaml-libyaml: Update to 0.69.

* gnu/packages/perl.scm (perl-yaml-libyaml): Update to 0.69.
---
 gnu/packages/perl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index a188891e95..556d8d31b4 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -8742,7 +8742,7 @@ on the YAML 1.0 specification.")
 (define-public perl-yaml-libyaml
   (package
     (name "perl-yaml-libyaml")
-    (version "0.65")
+    (version "0.69")
     (source
      (origin
        (method url-fetch)
@@ -8752,7 +8752,7 @@ on the YAML 1.0 specification.")
              ".tar.gz"))
        (sha256
         (base32
-         "0izhvz8f29x1f50hhwfgm0iq1lz7apjjvg77lmky949jr07hnwfv"))))
+         "06msvj3vmjszl5zj1k7g47ll0kkds9gdb5sky0q27lh4zw1vlj33"))))
     (build-system perl-build-system)
     (home-page
      "http://search.cpan.org/dist/YAML-LibYAML/")
-- 
cgit v1.2.3


From 1143450c14edfd91a27f73844d9e46eb376d1b64 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 12 Feb 2018 11:08:54 +0100
Subject: gnu: dblatex: Update to 0.3.10.

* gnu/packages/docbook.scm (dblatex): Update to 0.3.10.
[source]: Remove patch.
* gnu/packages/patches/dblatex-remove-multirow.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/local.mk                                       |  1 -
 gnu/packages/docbook.scm                           |  6 ++---
 gnu/packages/patches/dblatex-remove-multirow.patch | 30 ----------------------
 3 files changed, 3 insertions(+), 34 deletions(-)
 delete mode 100644 gnu/packages/patches/dblatex-remove-multirow.patch

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index 94ffbe1b53..68f3a20f6d 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -610,7 +610,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/cursynth-wave-rand.patch			\
   %D%/packages/patches/cvs-2017-12836.patch			\
   %D%/packages/patches/cyrus-sasl-CVE-2013-4122.patch		\
-  %D%/packages/patches/dblatex-remove-multirow.patch		\
   %D%/packages/patches/dbus-helper-search-path.patch		\
   %D%/packages/patches/deja-dup-use-ref-keyword-for-iter.patch	\
   %D%/packages/patches/dfu-programmer-fix-libusb.patch		\
diff --git a/gnu/packages/docbook.scm b/gnu/packages/docbook.scm
index ed1e60a7a3..d56dc49198 100644
--- a/gnu/packages/docbook.scm
+++ b/gnu/packages/docbook.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2014 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2016 Mathieu Lirzin <mthl@gnu.org>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -176,7 +177,7 @@ by no means limited to these applications.)  This package provides XML DTDs.")
 (define-public dblatex
   (package
     (name "dblatex")
-    (version "0.3.9")
+    (version "0.3.10")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/dblatex/dblatex/"
@@ -184,8 +185,7 @@ by no means limited to these applications.)  This package provides XML DTDs.")
                                   version ".tar.bz2"))
               (sha256
                (base32
-                "0pdizc5rjywwzxa1qqhdmba5zr35pbmdwbysalsid7xw87w3kq06"))
-              (patches (search-patches "dblatex-remove-multirow.patch"))))
+                "1yicd861rqz78i2khl35j7nvc0ccv4jx4hzqrbhll17082vrdmkg"))))
     (build-system python-build-system)
     ;; TODO: Add xfig/transfig for fig2dev utility
     (inputs
diff --git a/gnu/packages/patches/dblatex-remove-multirow.patch b/gnu/packages/patches/dblatex-remove-multirow.patch
deleted file mode 100644
index 62d1c64e08..0000000000
--- a/gnu/packages/patches/dblatex-remove-multirow.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-This patch is needed to fix dblatex with newer versions of TeX Live.
-It was taken from https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=840189
-
---- a/latex/style/dbk_table.sty	Sun Oct 02 23:21:03 2016 +0200
-+++ b/latex/style/dbk_table.sty	Mon Oct 10 21:31:00 2016 +0200
-@@ -9,7 +9,6 @@
- \usepackage{longtable}
- \usepackage{lscape}
- \usepackage{colortbl}
--\usepackage{multirow}
- \usepackage{calc}
- \usepackage{hhline}
-
-@@ -21,16 +20,6 @@
-   \expandafter[\expandafter3\expandafter]\expandafter{%
-   \multicolumn{#1}{#2}{#3}}
-
--% Make \@xmultirow long
--\expandafter\long\expandafter\def%
--\expandafter\@xmultirow%
--\expandafter#\expandafter1%
--\expandafter[\expandafter#\expandafter2\expandafter]%
--\expandafter#\expandafter3%
--\expandafter[\expandafter#\expandafter4\expandafter]%
--\expandafter#\expandafter5%
--\expandafter{\@xmultirow{#1}[#2]{#3}[#4]{#5}}
--
- % For the newtbl code
- \newdimen\newtblstarfactor%
- \newdimen\newtblsparewidth%
-- 
cgit v1.2.3


From 971d232b27099f86194a69b616bc33f292e0edeb Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 28 Feb 2018 02:10:48 +0100
Subject: gnu: r-httpuv: Update to 1.3.6.

* gnu/packages/web.scm (r-httpuv): Update to 1.3.6.
---
 gnu/packages/web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 26768ccc1e..4876918b53 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -3780,13 +3780,13 @@ CDF, Atom 0.3, and Atom 1.0 feeds.")
 (define-public r-httpuv
   (package
     (name "r-httpuv")
-    (version "1.3.5")
+    (version "1.3.6")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "httpuv" version))
               (sha256
                (base32
-                "1sg4f223zfyd265b28rlhsn3b6mqflcpnmya98cjmjncmy9vjdj3"))))
+                "1nzbcw1dm4l5qc9156kz95rdb8bwnpdr57wfc87w8arv7m0i40bc"))))
     (build-system r-build-system)
     (native-inputs `(("r-rcpp" ,r-rcpp)))
     (home-page "https://github.com/rstudio/httpuv")
-- 
cgit v1.2.3


From bd041e7fd3dbae04d5182afa8e4be4e96cfd8b3e Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Wed, 28 Feb 2018 14:41:42 +0200
Subject: gnu: dionysus: Update to 1.4.0.

* gnu/packages/maths.scm (dionysus): Update to 1.4.0.
---
 gnu/packages/maths.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index b20cec5440..8d0c10697f 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -8,7 +8,7 @@
 ;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2016 Kei Kebreau <kkebreau@posteo.net>
@@ -259,14 +259,14 @@ routines that have been extracted from the V8 JavaScript engine.")
 (define-public dionysus
   (package
     (name "dionysus")
-    (version "1.3.0")
+    (version "1.4.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnu/dionysus/dionysus-" version
-                                  ".tar.gz"))
+                                  ".tar.xz"))
               (sha256
                (base32
-                "1aqnvw6z33bzqgd1ga571pnx6vq2zrkckm1cz91grv45h4jr9vgs"))))
+                "194pzs1mlsj4ww6v37qq3961h5hckm5h805cv0r14xj3g9wfx2sk"))))
     (build-system gnu-build-system)
     (inputs `(("tcl" ,tcl)))                      ;for 'tclsh'
     (synopsis "Local search for universal constants and scientific values")
-- 
cgit v1.2.3


From 335c9e39024302476edb35b139ba2350a5d76437 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 27 Feb 2018 16:21:12 +0100
Subject: gnu: python-fixtures: Propagate python-pbr.

* gnu/packages/check.scm (python-fixtures-bootstrap,
python2-fixtures-bootstrap, python-testrepository-bootstrap,
python2-testrepository-bootstrap): New public variables.
(python-fixtures): Adjust accordingly.
(python-testrepository): Likewise.
[native-inputs]: Remove PYTHON-PBR-MINIMAL.
* gnu/packages/python.scm (python-pbr)[native-inputs]: Replace PYTHON-FIXTURES
and PYTHON-TESTREPOSITORY WITH PYTHON-FIXTURES-BOOTSTRAP and
PYTHON-TESTREPOSITORY-BOOTSTRAP.
---
 gnu/packages/check.scm  | 81 ++++++++++++++++++++++++++++++++++---------------
 gnu/packages/python.scm |  4 +--
 2 files changed, 59 insertions(+), 26 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index fbd2ac4f80..20845f82f6 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -962,18 +962,37 @@ protocol.")
 (define-public python2-subunit
   (package-with-python2 python-subunit))
 
-(define-public python-fixtures
+;; Fixtures requires python-pbr at runtime, but pbr uses fixtures for its
+;; own tests.  Hence this bootstrap variant.
+(define-public python-fixtures-bootstrap
   (package
-    (name "python-fixtures")
+    (name "python-fixtures-bootstrap")
     (version "1.4.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "fixtures" version))
-       (sha256
-        (base32
-         "0djxvdwm8s60dbfn7bhf40x6g818p3b3mlwijm1c3bqg7msn271y"))))
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "fixtures" version))
+              (sha256
+               (base32
+                "0djxvdwm8s60dbfn7bhf40x6g818p3b3mlwijm1c3bqg7msn271y"))))
     (build-system python-build-system)
+    (arguments `(#:tests? #f))
+    (propagated-inputs
+     `(("python-pbr-minimal" ,python-pbr-minimal)
+       ("python-six" ,python-six)))
+    (home-page "https://launchpad.net/python-fixtures")
+    (synopsis "Python test fixture library")
+    (description
+     "This package is only used for bootstrapping.  Use the regular
+python-fixtures package instead.")
+    (license (list license:bsd-3 license:asl2.0)))) ; at user's option
+
+(define-public python2-fixtures-bootstrap
+  (package-with-python2 python-fixtures-bootstrap))
+
+(define-public python-fixtures
+  (package
+    (inherit python-fixtures-bootstrap)
+    (name "python-fixtures")
     (arguments
      '(#:phases
        (modify-phases %standard-phases
@@ -982,25 +1001,23 @@ protocol.")
              (zero? (system* "python" "-m" "testtools.run"
                              "fixtures.test_suite")))))))
     (propagated-inputs
-     `(("python-six" ,python-six)))
+     ;; Fixtures uses pbr at runtime to check versions, etc.
+     `(("python-pbr" ,python-pbr)
+       ("python-six" ,python-six)))
     (native-inputs
      `(("python-mock" ,python-mock)
-       ("python-pbr-minimal" ,python-pbr-minimal)
        ("python-testtools" ,python-testtools)))
-    (home-page "https://launchpad.net/python-fixtures")
-    (synopsis "Python test fixture library")
     (description
      "Fixtures provides a way to create reusable state, useful when writing
-Python tests.")
-    (license (list license:bsd-3 license:asl2.0)))) ; at user's option
+Python tests.")))
 
 (define-public python2-fixtures
   (package-with-python2 python-fixtures))
 
-(define-public python-testrepository
+(define-public python-testrepository-bootstrap
   (package
-    (name "python-testrepository")
-    (version "0.0.20")
+    (name "python-testrepository-bootstrap")
+     (version "0.0.20")
     (source
      (origin
        (method url-fetch)
@@ -1011,6 +1028,26 @@ Python tests.")
         (base32
          "1ssqb07c277010i6gzzkbdd46gd9mrj0bi0i8vn560n2k2y4j93m"))))
     (build-system python-build-system)
+    (arguments '(#:tests? #f))
+    (propagated-inputs
+     `(("python-fixtures" ,python-fixtures-bootstrap)
+       ("python-subunit" ,python-subunit)
+       ("python-testtools" ,python-testtools)))
+    (native-inputs
+     `(("python-mimeparse" ,python-mimeparse)))
+    (home-page "https://launchpad.net/testrepository")
+    (synopsis "Database for Python test results")
+    (description
+     "Bootstrap package for python-testrepository.  Don't use this.")
+    (license (list license:bsd-3 license:asl2.0)))) ; at user's option
+
+(define-public python2-testrepository-bootstrap
+  (package-with-python2 python-testrepository-bootstrap))
+
+(define-public python-testrepository
+  (package
+    (inherit python-testrepository-bootstrap)
+    (name "python-testrepository")
     (arguments
      ;; FIXME: Many tests are failing.
      '(#:tests? #f))
@@ -1019,14 +1056,10 @@ Python tests.")
        ("python-subunit" ,python-subunit)
        ("python-testtools" ,python-testtools)))
     (native-inputs
-     `(("python-pbr-minimal" ,python-pbr-minimal) ;; same as for building fixture
-       ("python-mimeparse" ,python-mimeparse)))
-    (home-page "https://launchpad.net/testrepository")
-    (synopsis "Database for Python test results")
+     `(("python-mimeparse" ,python-mimeparse)))
     (description "Testrepository provides a database of test results which can
 be used as part of a developer's workflow to check things such as what tests
-have failed since the last commit or what tests are currently failing.")
-    (license (list license:bsd-3 license:asl2.0)))) ; at user's option
+have failed since the last commit or what tests are currently failing.")))
 
 (define-public python2-testrepository
   (package-with-python2 python-testrepository))
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 4ccd6a7359..efe8e8c638 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -1689,12 +1689,12 @@ code introspection, and logging.")
     (propagated-inputs
       `(("git" ,git))) ;; pbr actually uses the "git" binary.
     (native-inputs
-      `(("python-fixtures" ,python-fixtures)
+      `(("python-fixtures" ,python-fixtures-bootstrap)
         ;; discover, coverage, hacking, subunit
         ("python-mock" ,python-mock)
         ("python-six" ,python-six)
         ("python-sphinx" ,python-sphinx)
-        ("python-testrepository" ,python-testrepository)
+        ("python-testrepository" ,python-testrepository-bootstrap)
         ("python-testresources" ,python-testresources)
         ("python-testscenarios" ,python-testscenarios)
         ("python-testtools" ,python-testtools)
-- 
cgit v1.2.3


From 151f32a74bb50461f701fce8b4ac233ca311fdc4 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 27 Feb 2018 16:37:38 +0100
Subject: gnu: python-subunit: Update to 1.2.0.

* gnu/packages/check.scm (python-subunit): Update to 1.2.0.
[source](uri): Use PYPI-URI.
[propagated-inputs]: Remove PYTHON-MIMEPARSE.  Add PYTHON-TESTTOOLS.
[native-inputs]: Add PYTHON-FIXTURES and PYTHON-TESTSCENARIOS.
---
 gnu/packages/check.scm | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 20845f82f6..fbb89ce496 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -936,22 +936,22 @@ use of resources by test cases.")
 (define-public python-subunit
   (package
     (name "python-subunit")
-    (version "0.0.21")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append
-             "https://pypi.python.org/packages/source/p/python-subunit/python-subunit-"
-             version ".tar.gz"))
+       (uri (pypi-uri name version))
        (sha256
         (base32
-         "1nkw9wfbvizmpajbj3in8ns07g7lwkiv8hip14jjlwk3cacls6jv"))))
+         "1yii2gx3z6323as3iraj1yphj76dy7i3h6kj63pnc5y0hwjs5sgx"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-extras" ,python-extras)
-       ("python-mimeparse" ,python-mimeparse)))
+       ("python-testtools" ,python-testtools)))
     (native-inputs
-     `(("python-testscenarios" ,python-testscenarios)))
+     `(("python-fixtures" ,python-fixtures-bootstrap)
+       ("python-hypothesis" ,python-hypothesis)
+       ("python-testscenarios" ,python-testscenarios)))
     (home-page "http://launchpad.net/subunit")
     (synopsis "Python implementation of the subunit protocol")
     (description
-- 
cgit v1.2.3


From bc69104a442e1dd2338397a54a3a80eff170e78f Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 27 Feb 2018 17:09:43 +0100
Subject: gnu: python-testresources: Update to 2.0.1.

* gnu/packages/check.scm (python-testresources-bootstrap,
python2-testresources-bootstrap): New public variables.
(python-testresources): Adjust accordingly.
[propagated-inputs]: Add PYTHON-PBR.
[native-inputs]: Add PYTHON-FIXTURES and PYTHON-TESTTOOLS.
* gnu/packages/python.scm (python-pbr)[native-inputs]: Replace
PYTHON-TESTRESOURCES with PYTHON-TESTRESOURCES-BOOTSTRAP.
---
 gnu/packages/check.scm  | 47 +++++++++++++++++++++++++++++++++--------------
 gnu/packages/python.scm |  2 +-
 2 files changed, 34 insertions(+), 15 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index fbb89ce496..0a7d888d46 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -908,28 +908,47 @@ style tests.")
 (define-public python2-testscenarios
   (package-with-python2 python-testscenarios))
 
-(define-public python-testresources
+;; Testresources requires python-pbr at runtime, but pbr needs it for its
+;; own tests.  Hence this bootstrap variant.
+(define-public python-testresources-bootstrap
   (package
-    (name "python-testresources")
-    (version "0.2.7")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://pypi.python.org/packages/source/t/testresources/testresources-"
-             version ".tar.gz"))
-       (sha256
-        (base32
-         "0cbj3plbllyz42c4b5xxgwaa7mml54lakslrn4kkhinxhdri22md"))))
+    (name "python-testresources-bootstrap")
+    (version "2.0.1")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "testresources" version))
+              (sha256
+               (base32
+                "05s4dsli9g17m1r3b1gvwicbbgq011hnpb2b9qnj27ja2n11k7gf"))))
     (build-system python-build-system)
+    (arguments '(#:tests? #f))
+    (propagated-inputs
+     `(("python-pbr" ,python-pbr-minimal)))
     (home-page "https://launchpad.net/testresources")
     (synopsis
      "Pyunit extension for managing test resources")
     (description
-     "Testresources is an extension to Python's unittest to allow declarative
-use of resources by test cases.")
+     "This package is only here for bootstrapping purposes.  Use the regular
+testresources package instead.")
     (license (list license:bsd-3 license:asl2.0)))) ; at the user's option
 
+(define-public python2-testresources-bootstrap
+  (package-with-python2 python-testresources-bootstrap))
+
+(define-public python-testresources
+  (package
+    (inherit python-testresources-bootstrap)
+    (name "python-testresources")
+    (propagated-inputs
+     `(("python-pbr" ,python-pbr)))
+    (arguments '())
+    (native-inputs
+     `(("python-fixtures" ,python-fixtures)
+       ("python-testtols" ,python-testtools)))
+    (description
+     "Testresources is an extension to Python's unittest to allow declarative
+use of resources by test cases.")))
+
 (define-public python2-testresources
   (package-with-python2 python-testresources))
 
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index efe8e8c638..22160bcfaa 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -1695,7 +1695,7 @@ code introspection, and logging.")
         ("python-six" ,python-six)
         ("python-sphinx" ,python-sphinx)
         ("python-testrepository" ,python-testrepository-bootstrap)
-        ("python-testresources" ,python-testresources)
+        ("python-testresources" ,python-testresources-bootstrap)
         ("python-testscenarios" ,python-testscenarios)
         ("python-testtools" ,python-testtools)
         ("python-virtualenv" ,python-virtualenv)))
-- 
cgit v1.2.3


From 881ed3f8680a42327ce4efe7aaab04a2f3e65c6e Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 27 Feb 2018 18:20:07 +0100
Subject: gnu: python-extras: Update to 1.0.0.

* gnu/packages/python.scm (python-extras): Update to 1.0.0.
[source](uri): Use PYPI-URI.
---
 gnu/packages/python.scm | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 22160bcfaa..f08d93dc78 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -1500,19 +1500,17 @@ software.")
 (define-public python-extras
   (package
     (name "python-extras")
-    (version "0.0.3")
+    (version "1.0.0")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append
-             "https://pypi.python.org/packages/source/e/extras/extras-"
-             version ".tar.gz"))
+       (uri (pypi-uri "extras" version))
        (sha256
         (base32
-         "1h7zx4dfyclalg0fqnfjijpn0f793a9mx8sy3b27gd31nr6dhq3s"))))
+         "0khvm08rcwm62wc47j8niyl6h13f8w51c8669ifivjdr23g3cbhk"))))
     (build-system python-build-system)
     (arguments
-     ;; error in setup.cfg: command 'test' has no such option 'buffer'
+     ;; FIXME: Circular dependency on testtools.
      '(#:tests? #f))
     (home-page "https://github.com/testing-cabal/extras")
     (synopsis "Useful extensions to the Python standard library")
-- 
cgit v1.2.3


From 8b93f7e4371ac53d56314f8a6a4061566b92e28c Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 27 Feb 2018 18:33:09 +0100
Subject: gnu: python-testtools: Update to 2.3.0.

* gnu/packages/check.scm (python-testtools-bootstrap,
python2-testtools-bootstrap): New public variables.
(python-testtools): Inherit.
[arguments]: Remove old.  Replace CHECK-PHASE with custom command.
[propagated-inputs]: Add PYTHON-FIXTURES, PYTHON-PBR, PYTHON-SIX,
PYTHON-TRACEBACK2 and PYTHON-UNITTEST2.
[native-inputs]: Add PYTHON-TESTSCENARIOS-BOOTSTRAP.
(python-testscenarios-bootstrap, python2-testscenarios-bootstrap): New public
variables.
(python-testscenarios): Adjust accordingly.
[propagated-inputs]: Replace PYTHON-TESTTOOLS with PYTHON-TESTTOOLS-BOOTSTRAP.
(python-subunit-bootstrap, python2-subunit-bootstrap): New public variables.
(python-subunit): Inherit.
(python-fixtures-bootstrap)[native-inputs]: Replace PYTHON-TESTTOOLS with
PYTHON-TESTTOOLS-BOOTSTRAP.
(python-testrepository-bootstrap)[native-inputs]: Replace PYTHON-SUBUNIT and
PYTHON-TESTTOOLS with PYTHON-SUBUNIT-BOOTSTRAP and PYTHON-TESTTOOLS-BOOTSTRAP.
* gnu/packages/python.scm (python-pbr)[native-inputs]: Replace
PYTHON-TESTSCENARIOS and PYTHON-TESTTOOLS with
PYTHON-TESTSCENARIOS-BOOTSTRAP and PYTHON-TESTTOOLS-BOOTSTRAP.
---
 gnu/packages/check.scm  | 129 +++++++++++++++++++++++++++++++-----------------
 gnu/packages/python.scm |   4 +-
 2 files changed, 87 insertions(+), 46 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 0a7d888d46..6b6d0376e8 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -834,57 +834,68 @@ subprocess and see the output as well as any file modifications.")
 (define-public python2-scripttest
   (package-with-python2 python-scripttest))
 
-(define-public python-testtools
+(define-public python-testtools-bootstrap
   (package
-    (name "python-testtools")
-    (version "1.4.0")
+    (name "python-testtools-bootstrap")
+    (version "2.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "testtools" version))
        (sha256
         (base32
-         "1vw8yljnd75d396hhw6s2hrf4cclzy845ifd5am0lxsl235z3i8c"))))
+         "0n8519lk8aaa91vymz842831181wf7fss98hyllhygi3z1nfq9sq"))))
     (build-system python-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'fix-module-imports
-           (lambda _
-             (substitute* "setup.py"
-               (("'unittest2>=0.8.0',") ""))
-             (substitute* '("testtools/testcase.py"
-                            "testtools/testsuite.py"
-                            "testtools/run.py"
-                            "testtools/tests/test_run.py"
-                            "testtools/tests/test_testsuite.py"
-                            "testtools/tests/test_deferredruntest.py")
-               ;; unittest2 is a backport of Python2.7 features to Python 2.4.
-               (("import unittest2 as unittest") "import unittest")
-               (("import unittest2") "import unittest as unittest2")
-               (("from unittest2 import") "from unittest import"))
-             (substitute* "testtools/tests/test_testresult.py"
-               ;; NUL in source code is not allowed (raises ValueError).
-               (("\\x00\\x04") "\\x04"))
-             #t)))))
+    (arguments '(#:tests? #f))
     (propagated-inputs
-     `(("python-mimeparse" ,python-mimeparse)
-       ("python-extras" ,python-extras)))
+     `(("python-extras" ,python-extras)
+       ("python-fixtures" ,python-fixtures-bootstrap)
+       ("python-mimeparse" ,python-mimeparse)
+       ("python-pbr" ,python-pbr-minimal)
+       ("python-six" ,python-six)
+       ("python-traceback2" ,python-traceback2)
+       ("python-unittest2" ,python-unittest2)))
     (home-page "https://github.com/testing-cabal/testtools")
     (synopsis
      "Extensions to the Python standard library unit testing framework")
+    (description
+     "This package is only for bootstrapping.  Do not use this.")
+    (license license:psfl)))
+
+(define-public python2-testtools-bootstrap
+  (package-with-python2 python-testtools-bootstrap))
+
+(define-public python-testtools
+  (package
+    (inherit python-testtools-bootstrap)
+    (name "python-testtools")
+    (arguments
+     `(#:phases (modify-phases %standard-phases
+                  (replace 'check
+                    (lambda _
+                      (invoke "python" "-m" "testtools.run"
+                              "testtools.tests.test_suite"))))))
+    (propagated-inputs
+     `(("python-extras" ,python-extras)
+       ("python-fixtures" ,python-fixtures)
+       ("python-mimeparse" ,python-mimeparse)
+       ("python-pbr" ,python-pbr)
+       ("python-six" ,python-six)
+       ("python-traceback2" ,python-traceback2)
+       ("python-unittest2" ,python-unittest2)))
+    (native-inputs
+     `(("python-testscenarios" ,python-testscenarios-bootstrap)))
     (description
      "Testtools extends the Python standard library unit testing framework to
 provide matchers, more debugging information, and cross-Python
-compatibility.")
-    (license license:psfl)))
+compatibility.")))
 
 (define-public python2-testtools
   (package-with-python2 python-testtools))
 
-(define-public python-testscenarios
+(define-public python-testscenarios-bootstrap
   (package
-    (name "python-testscenarios")
+    (name "python-testscenarios-bootstrap")
     (version "0.4")
     (source
      (origin
@@ -897,14 +908,26 @@ compatibility.")
          "1671jvrvqlmbnc42j7pc5y6vc37q44aiwrq0zic652pxyy2fxvjg"))))
     (build-system python-build-system)
     (propagated-inputs
-     `(("python-testtools" ,python-testtools)))
+     `(("python-testtools" ,python-testtools-bootstrap)))
     (home-page "https://launchpad.net/testscenarios")
     (synopsis "Pyunit extension for dependency injection")
     (description
-     "Testscenarios provides clean dependency injection for Python unittest
-style tests.")
+     "This package is only for bootstrapping.  Don't use this.")
     (license (list license:bsd-3 license:asl2.0)))) ; at the user's option
 
+(define-public python2-testscenarios-bootstrap
+  (package-with-python2 python-testscenarios-bootstrap))
+
+(define-public python-testscenarios
+  (package
+    (inherit python-testscenarios-bootstrap)
+    (name "python-testscenarios")
+    (propagated-inputs
+     `(("python-testtools" ,python-testtools)))
+    (description
+     "Testscenarios provides clean dependency injection for Python unittest
+style tests.")))
+
 (define-public python2-testscenarios
   (package-with-python2 python-testscenarios))
 
@@ -952,32 +975,50 @@ use of resources by test cases.")))
 (define-public python2-testresources
   (package-with-python2 python-testresources))
 
-(define-public python-subunit
+(define-public python-subunit-bootstrap
   (package
-    (name "python-subunit")
+    (name "python-subunit-bootstrap")
     (version "1.2.0")
     (source
      (origin
        (method url-fetch)
-       (uri (pypi-uri name version))
+       (uri (pypi-uri "python-subunit" version))
        (sha256
         (base32
          "1yii2gx3z6323as3iraj1yphj76dy7i3h6kj63pnc5y0hwjs5sgx"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-extras" ,python-extras)
-       ("python-testtools" ,python-testtools)))
+       ("python-testtools" ,python-testtools-bootstrap)))
     (native-inputs
      `(("python-fixtures" ,python-fixtures-bootstrap)
        ("python-hypothesis" ,python-hypothesis)
-       ("python-testscenarios" ,python-testscenarios)))
+       ("python-testscenarios" ,python-testscenarios-bootstrap)))
     (home-page "http://launchpad.net/subunit")
     (synopsis "Python implementation of the subunit protocol")
     (description
-     "Python-subunit is a Python implementation of the subunit test streaming
-protocol.")
+     "This package is here for bootstrapping purposes only.  Use the regular
+python-subunit package instead.")
     (license (list license:bsd-3 license:asl2.0)))) ; at the user's option
 
+(define-public python2-subunit-bootstrap
+  (package-with-python2 python-subunit-bootstrap))
+
+(define-public python-subunit
+  (package
+    (inherit python-subunit-bootstrap)
+    (name "python-subunit")
+    (propagated-inputs
+     `(("python-extras" ,python-extras)
+       ("python-testtools" ,python-testtools)))
+    (native-inputs
+     `(("python-fixtures" ,python-fixtures)
+       ("python-hypothesis" ,python-hypothesis)
+       ("python-testscenarios" ,python-testscenarios)))
+    (description
+     "Python-subunit is a Python implementation of the subunit test streaming
+protocol.")))
+
 (define-public python2-subunit
   (package-with-python2 python-subunit))
 
@@ -1025,7 +1066,7 @@ python-fixtures package instead.")
        ("python-six" ,python-six)))
     (native-inputs
      `(("python-mock" ,python-mock)
-       ("python-testtools" ,python-testtools)))
+       ("python-testtools" ,python-testtools-bootstrap)))
     (description
      "Fixtures provides a way to create reusable state, useful when writing
 Python tests.")))
@@ -1050,8 +1091,8 @@ Python tests.")))
     (arguments '(#:tests? #f))
     (propagated-inputs
      `(("python-fixtures" ,python-fixtures-bootstrap)
-       ("python-subunit" ,python-subunit)
-       ("python-testtools" ,python-testtools)))
+       ("python-subunit" ,python-subunit-bootstrap)
+       ("python-testtools" ,python-testtools-bootstrap)))
     (native-inputs
      `(("python-mimeparse" ,python-mimeparse)))
     (home-page "https://launchpad.net/testrepository")
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index f08d93dc78..8285a4ea3c 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -1694,8 +1694,8 @@ code introspection, and logging.")
         ("python-sphinx" ,python-sphinx)
         ("python-testrepository" ,python-testrepository-bootstrap)
         ("python-testresources" ,python-testresources-bootstrap)
-        ("python-testscenarios" ,python-testscenarios)
-        ("python-testtools" ,python-testtools)
+        ("python-testscenarios" ,python-testscenarios-bootstrap)
+        ("python-testtools" ,python-testtools-bootstrap)
         ("python-virtualenv" ,python-virtualenv)))
     (synopsis "Enhance the default behavior of Python’s setuptools")
     (description
-- 
cgit v1.2.3


From ae565a9a6d3329a0be11fa021f046260b35a4958 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 27 Feb 2018 18:51:44 +0100
Subject: gnu: python-testscenarios: Update to 0.5.0.

* gnu/packages/check.scm (python-testscenarios-bootstrap): Update to 0.5.0.
[source](uri): Use PYPI-URI.
[arguments]: Replace CHECK-PHASE.
[propagated-inputs]: Add PYTHON-PBR-MINIMAL.
(python-testscenarios)[propagated-inputs]: Add PYTHON-PBR.
---
 gnu/packages/check.scm | 20 +++++++++++++-------
 1 file changed, 13 insertions(+), 7 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 6b6d0376e8..19d7dec393 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -896,19 +896,24 @@ compatibility.")))
 (define-public python-testscenarios-bootstrap
   (package
     (name "python-testscenarios-bootstrap")
-    (version "0.4")
+    (version "0.5.0")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append
-             "https://pypi.python.org/packages/source/t/testscenarios/testscenarios-"
-             version ".tar.gz"))
+       (uri (pypi-uri "testscenarios" version))
        (sha256
         (base32
-         "1671jvrvqlmbnc42j7pc5y6vc37q44aiwrq0zic652pxyy2fxvjg"))))
+         "1dm2aydqpv76vnsk1pw7k8n42hq58cfi4n1ixy7nyzpaj1mwnmy2"))))
     (build-system python-build-system)
+    (arguments
+     `(#:phases (modify-phases %standard-phases
+                  (replace 'check
+                    (lambda _
+                      (invoke "python" "-m" "testtools.run"
+                              "testscenarios.test_suite"))))))
     (propagated-inputs
-     `(("python-testtools" ,python-testtools-bootstrap)))
+     `(("python-pbr" ,python-pbr-minimal)
+       ("python-testtools" ,python-testtools-bootstrap)))
     (home-page "https://launchpad.net/testscenarios")
     (synopsis "Pyunit extension for dependency injection")
     (description
@@ -923,7 +928,8 @@ compatibility.")))
     (inherit python-testscenarios-bootstrap)
     (name "python-testscenarios")
     (propagated-inputs
-     `(("python-testtools" ,python-testtools)))
+     `(("python-pbr" ,python-pbr)
+       ("python-testtools" ,python-testtools)))
     (description
      "Testscenarios provides clean dependency injection for Python unittest
 style tests.")))
-- 
cgit v1.2.3


From be3f88c29c0f729dab5744957d321ab6a5a4d001 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 27 Feb 2018 19:49:42 +0100
Subject: gnu: python-oslotest: Update to 3.2.0.

* gnu/packages/openstack.scm (python-oslotest): Update to 3.2.0.
[source](uri): Use PYPI-URI.
[native-inputs]: Move PYTHON-OS-CLIENT-CONFIG, PYTHON-SIX, PYTHON-SUBUNIT,
PYTHON-TESTREPOSITORY and PYTHON-TESTTOOLS ...
[propagated-inputs]: ... here.
[properties]: Remove field.
(python2-oslotest)[arguments]: Remove.
---
 gnu/packages/openstack.scm | 25 ++++++++-----------------
 1 file changed, 8 insertions(+), 17 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index 2a55a80842..1fb0cabb3b 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -623,45 +623,36 @@ from the OpenStack project.")
 (define-public python-oslotest
   (package
     (name "python-oslotest")
-    (version "1.10.0")
+    (version "3.2.0")
     (source
       (origin
         (method url-fetch)
-        (uri (string-append
-               "https://pypi.python.org/packages/source/o/oslotest/oslotest-"
-               version
-               ".tar.gz"))
+        (uri (pypi-uri "oslotest" version))
         (sha256
           (base32
-            "0l3ny48ddz5xbf0v4r0jv1yhbdzinc2vy0lybhdkmx3xy0b886fs"))))
+            "1xay6wjxzqm4bg87fahqas84dhvhgf1gghzldkcczsfx897mqdkh"))))
     (build-system python-build-system)
     (propagated-inputs
       `(("python-fixtures" ,python-fixtures)
         ("python-mock" ,python-mock)
         ("python-mox3" ,python-mox3)
-        ("python-six" ,python-six)))
-    (native-inputs
-      `(("python-pbr" ,python-pbr)
         ("python-os-client-config" ,python-os-client-config)
+        ("python-six" ,python-six)
         ("python-subunit" ,python-subunit)
         ("python-testrepository" ,python-testrepository)
-        ("python-testscenarios" ,python-testscenarios)
         ("python-testtools" ,python-testtools)))
+    (native-inputs
+      `(("python-pbr" ,python-pbr)
+        ("python-testscenarios" ,python-testscenarios)))
     (home-page "https://launchpad.net/oslo")
     (synopsis "Oslo test framework")
     (description
       "The Oslo Test framework provides common fixtures, support for debugging,
 and better support for mocking results.")
-    (properties `((python2-variant . ,(delay python2-oslotest))))
     (license asl2.0)))
 
 (define-public python2-oslotest
-  (package (inherit (package-with-python2
-                     (strip-python2-variant python-oslotest)))
-           (arguments
-            `(#:python ,python-2
-              ;; FIXME: 'subunit.run discover: error: no such option: --list'
-              #:tests? #f))))
+  (package-with-python2 python-oslotest))
 
 (define-public python-oslo.utils
   (package
-- 
cgit v1.2.3


From d2ae66b756dbf9f505be9185b2646a8b3feb79dc Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 27 Feb 2018 20:07:00 +0100
Subject: gnu: python-reno: Update to 2.7.0.

* gnu/packages/openstack.scm (python-reno): Update to 2.7.0.
[propagated-inputs]: Remove PYTHON-BABEL.  Add PYTHON-PBR.
[native-inputs]: Remove PYTHON-PBR and PYTHON-OSLOTEST.  Add PYTHON-DOCUTILS
and PYTHON-SPHINX.
---
 gnu/packages/openstack.scm | 20 +++++++-------------
 1 file changed, 7 insertions(+), 13 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index 1fb0cabb3b..f1dffcf33e 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -538,13 +538,13 @@ in transmittable and storable formats, such as JSON and MessagePack.")
 (define-public python-reno
   (package
     (name "python-reno")
-    (version "2.0.3")
+    (version "2.7.0")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "reno" version))
         (sha256
-          (base32 "1i2wnn5fnm3jm5774pahg000q0lma5i913hml91bbbm2mybphndd"))))
+          (base32 "0gwzi5dvacqx43smxl3rd1z33npn7gfhm50bvgmq90fib2q431wc"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -554,33 +554,27 @@ in transmittable and storable formats, such as JSON and MessagePack.")
              ;; reno expects a git repo
              (zero? (system* "git" "init")))))))
     (propagated-inputs
-      `(("python-babel" ,python-babel)
-        ("python-dulwich" ,python-dulwich)
+      `(("python-dulwich" ,python-dulwich)
+        ("python-pbr" ,python-pbr)
         ("python-pyyaml" ,python-pyyaml)
         ("python-six" ,python-six)))
     (native-inputs
       `(("python-testtools" ,python-testtools)
-        ("python-pbr" ,python-pbr)
         ("python-testscenarios" ,python-testscenarios)
         ("python-testrepository" ,python-testrepository)
         ("python-mock" ,python-mock)
-        ("python-oslotest" ,python-oslotest)
+        ("python-docutils" ,python-docutils)
+        ("python-sphinx" ,python-sphinx)
         ("gnupg" ,gnupg)
         ("git" ,git)))
     (home-page "http://docs.openstack.org/developer/reno/")
     (synopsis "Release notes manager")
     (description "Reno is a tool for storing release notes in a git repository
 and building documentation from them.")
-    (properties `((python2-variant . ,(delay python2-reno))))
     (license asl2.0)))
 
 (define-public python2-reno
-  (package (inherit (package-with-python2
-                     (strip-python2-variant python-reno)))
-           (arguments
-            `(#:python ,python-2
-              ;; FIXME: 'subunit.run discover: error: no such option: --list'
-              #:tests? #f))))
+  (package-with-python2 python-reno))
 
 (define-public python-oslosphinx
   (package
-- 
cgit v1.2.3


From 9c77852e1948f21b62932e073bad49c7bc65b614 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 27 Feb 2018 20:22:36 +0100
Subject: gnu: python-fixtures: Update to 3.0.0.

* gnu/packages/check.scm (python-fixtures-bootstrap): Update to 3.0.0.
---
 gnu/packages/check.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 19d7dec393..50b4afcaf0 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -1033,13 +1033,13 @@ protocol.")))
 (define-public python-fixtures-bootstrap
   (package
     (name "python-fixtures-bootstrap")
-    (version "1.4.0")
+    (version "3.0.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "fixtures" version))
               (sha256
                (base32
-                "0djxvdwm8s60dbfn7bhf40x6g818p3b3mlwijm1c3bqg7msn271y"))))
+                "1vxj29bzz3rd4pcy51d05wng9q9dh4jq6wx92yklsm7i6h1ddw7w"))))
     (build-system python-build-system)
     (arguments `(#:tests? #f))
     (propagated-inputs
-- 
cgit v1.2.3


From 3719d0edf2ecbcad7cb155548927004bc64cfc97 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 27 Feb 2018 20:44:16 +0100
Subject: gnu: python-sphinx@1.6: Add python2 variant.

* gnu/packages/python.scm (python-sphinx-1.6)[properties]: Declare python2 variant.
(python2-sphinx-1.6): New public variable.
---
 gnu/packages/python.scm | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 8285a4ea3c..5c6bc7f04e 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -2412,7 +2412,17 @@ sources.")
      `(("python-pytest" ,python-pytest)
        ("imagemagick" ,imagemagick) ; for "convert"
        ,@(package-native-inputs python-sphinx)))
-    (properties '())))
+    (properties `((python2-variant . ,(delay python2-sphinx-1.6))))))
+
+(define-public python2-sphinx-1.6
+  (let ((base (package-with-python2 (strip-python2-variant python-sphinx-1.6))))
+    (package
+      (inherit base)
+      (propagated-inputs
+       `(("python2-typing" ,python2-typing)
+         ,@(package-propagated-inputs base)))
+      (native-inputs `(("python2-enum34" ,python2-enum34)
+                       ,@(package-native-inputs base))))))
 
 (define-public python-sphinx-1.5.3
   (package
-- 
cgit v1.2.3


From 7a565dc9ec7c2b904cf3a82975b947cd736d0b3a Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 27 Feb 2018 22:04:00 +0100
Subject: gnu: Add python-openstackdocstheme.

* gnu/packages/openstack.scm (python-openstackdocstheme,
python2-openstackdocstheme): New public variables.
---
 gnu/packages/openstack.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index f1dffcf33e..0d1d69945e 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -3,6 +3,7 @@
 ;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2017 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -185,6 +186,36 @@ tested on Python versions 3.2, 2.7, and 2.6.")
 (define-public python2-mox3
   (package-with-python2 python-mox3))
 
+(define-public python-openstackdocstheme
+  (package
+    (name "python-openstackdocstheme")
+    (version "1.18.1")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "openstackdocstheme" version))
+              (sha256
+               (base32
+                "1ki5204rjdqjvr8xr9w2qc1z6b6d2i5jas0i70xzkf9njlzjzv2r"))))
+    (build-system python-build-system)
+    (arguments
+     ;; FIXME: Tests require an old version of python-hacking, which in
+     ;; turn depends on mox3 which depends on this package.
+     `(#:tests? #f))
+    (propagated-inputs
+     `(("python-dulwich" ,python-dulwich)
+       ("python-pbr" ,python-pbr)))
+    (native-inputs
+     `(("python-sphinx" ,python-sphinx-1.6)))
+    (home-page "https://docs.openstack.org/openstackdocstheme/latest/")
+    (synopsis "OpenStack Docs Theme")
+    (description
+     "This package provides themes and extensions for Sphinx for publishing
+to docs.openstack.org and developer.openstack.org.")
+    (license asl2.0)))
+
+(define-public python2-openstackdocstheme
+  (package-with-python2 python-openstackdocstheme))
+
 (define-public python-os-client-config
   (package
     (name "python-os-client-config")
-- 
cgit v1.2.3


From b39667cdcb2cbcf98d9fa94101c47731ca7b6394 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 27 Feb 2018 22:19:31 +0100
Subject: gnu: python-mox3: Update to 0.24.0.

* gnu/packages/openstack.scm (python-mox3): Update to 0.24.0.
[source](patches): New field.
[arguments]: Remove.
[native-inputs]: Add PYTHON-OPENSTACKDOCSTHEME and PYTHON-SUBUNIT.  Replace
PYTHON-SPHINX with PYTHON-SPHINX-1.6.  Move PYTHON-PBR and PYTHON-FIXTURES ...
[propagated-inputs]: ... here.  New field.
[description]: Don't mention explicit Python versions.
* gnu/packages/patches/python-mox3-python3.6-compat.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
---
 gnu/local.mk                                       |  1 +
 gnu/packages/openstack.scm                         | 23 ++++++------
 .../patches/python-mox3-python3.6-compat.patch     | 43 ++++++++++++++++++++++
 3 files changed, 56 insertions(+), 11 deletions(-)
 create mode 100644 gnu/packages/patches/python-mox3-python3.6-compat.patch

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index 68f3a20f6d..24368727f2 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1036,6 +1036,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-scikit-learn-fix-test-non-determinism.patch	\
   %D%/packages/patches/python-configobj-setuptools.patch	\
   %D%/packages/patches/python-faker-fix-build-32bit.patch	\
+  %D%/packages/patches/python-mox3-python3.6-compat.patch	\
   %D%/packages/patches/python-paste-remove-website-test.patch	\
   %D%/packages/patches/python-paste-remove-timing-test.patch	\
   %D%/packages/patches/python-pygit2-disable-network-tests.patch	\
diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index 0d1d69945e..be1927dbe8 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -21,6 +21,7 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages openstack)
+  #:use-module (gnu packages)
   #:use-module (gnu packages check)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages python)
@@ -156,31 +157,31 @@ guidelines}.")
 (define-public python-mox3
   (package
     (name "python-mox3")
-    (version "0.14.0")
+    (version "0.24.0")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "mox3" version))
+        (patches (search-patches "python-mox3-python3.6-compat.patch"))
         (sha256
           (base32
-           "0njmh40i1lg5mzn9hc2ax83adj6dli455j6xifilrw27c4wlkjzx"))))
+           "0w58adwv7q9wzvmq9mlrk2asfk73myq9fpwy7mjkzsz3baa95zf5"))))
     (build-system python-build-system)
-    (arguments
-     ;; TODO: Resolve dependency cycle and re-enable.
-     '(#:tests? #f))
+    (propagated-inputs
+     `(("python-fixtures" ,python-fixtures)
+       ("python-pbr" ,python-pbr)))
     (native-inputs
-      `(("python-fixtures" ,python-fixtures)
-        ; TODO re-add ("python-oslosphinx" ,python-oslosphinx)
-        ("python-pbr" ,python-pbr)
-        ("python-sphinx" ,python-sphinx)
+      `(("python-openstackdocstheme" ,python-openstackdocstheme)
+        ("python-sphinx" ,python-sphinx-1.6)
+        ("python-subunit" ,python-subunit)
+        ("python-testrepository" ,python-testrepository)
         ("python-testtools" ,python-testtools)))
     (home-page "https://www.openstack.org/")
     (synopsis "Mock object framework for Python")
     (description
       "Mox3 is an unofficial port of the @uref{https://code.google.com/p/pymox/,
 Google mox framework} to Python 3.  It was meant to be as compatible
-with mox as possible, but small enhancements have been made.  The library was
-tested on Python versions 3.2, 2.7, and 2.6.")
+with mox as possible, but small enhancements have been made.")
     (license asl2.0)))
 
 (define-public python2-mox3
diff --git a/gnu/packages/patches/python-mox3-python3.6-compat.patch b/gnu/packages/patches/python-mox3-python3.6-compat.patch
new file mode 100644
index 0000000000..0426d07cf9
--- /dev/null
+++ b/gnu/packages/patches/python-mox3-python3.6-compat.patch
@@ -0,0 +1,43 @@
+Fix regex so that it works with Python 3.6.
+
+See <https://docs.python.org/3/library/re.html#re.LOCALE>.
+
+Copied from upstream bug report:
+https://bugs.launchpad.net/python-mox3/+bug/1665266
+
+From 05064cdb6ea7a16450c6beae2b6f7c6074212a69 Mon Sep 17 00:00:00 2001
+From: Zac Medico <zmedico@gentoo.org>
+Date: Thu, 16 Feb 2017 00:24:10 -0800
+Subject: [PATCH] RegexTest: python3.6 compatibility
+
+These fixes are backward-compatible with older python versions:
+
+* raw strings fix invalid escape sequences
+* flags=8 fixes ValueError: cannot use LOCALE flag with a str pattern
+---
+ mox3/tests/test_mox.py | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/mox3/tests/test_mox.py b/mox3/tests/test_mox.py
+index 15ac565..3a1af17 100644
+--- a/mox3/tests/test_mox.py
++++ b/mox3/tests/test_mox.py
+@@ -312,12 +312,12 @@ class RegexTest(testtools.TestCase):
+     def testReprWithoutFlags(self):
+         """repr should return the regular expression pattern."""
+         self.assertTrue(
+-            repr(mox.Regex(r"a\s+b")) == "<regular expression 'a\s+b'>")
++            repr(mox.Regex(r"a\s+b")) == r"<regular expression 'a\s+b'>")
+ 
+     def testReprWithFlags(self):
+         """repr should return the regular expression pattern and flags."""
+-        self.assertTrue(repr(mox.Regex(r"a\s+b", flags=4)) ==
+-                        "<regular expression 'a\s+b', flags=4>")
++        self.assertTrue(repr(mox.Regex(r"a\s+b", flags=8)) ==
++                        r"<regular expression 'a\s+b', flags=8>")
+ 
+ 
+ class IsTest(testtools.TestCase):
+-- 
+2.10.2
+
-- 
cgit v1.2.3


From 0ab4c3928502dd3621c9a4592295a48ad7cee4ee Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 27 Feb 2018 23:27:58 +0100
Subject: gnu: python2-swiftclient: Enable tests.

* gnu/packages/openstack.scm (python-swiftclient)[properties]: Declare python2
variant.
(python2-swiftclient): Use STRIP-PYTHON2-VARIANT.
[propagated-inputs]: Remove PYTHON2-REQUESTS.
[arguments]: Remove.
[native-inputs]: Delete.
---
 gnu/packages/openstack.scm | 19 +++++--------------
 1 file changed, 5 insertions(+), 14 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index be1927dbe8..bcd075424d 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -844,25 +844,16 @@ data that best fit this type of storage model are virtual machine images, photo
 storage, email storage and backup archiving.  Having no central \"brain\" or
 master point of control provides greater scalability, redundancy and
 permanence.")
-  (license asl2.0)))
+    (properties `((python2-variant . ,(delay python2-swiftclient))))
+    (license asl2.0)))
 
 (define-public python2-swiftclient
-  (let ((swiftclient (package-with-python2 python-swiftclient)))
+  (let ((swiftclient (package-with-python2
+                      (strip-python2-variant python-swiftclient))))
     (package (inherit swiftclient)
-      (arguments
-       `(#:python ,python-2
-         ;; FIXME: subunit.run discover: error: no such option: --list
-         #:tests? #f))
       (propagated-inputs
        `(("python2-futures" ,python2-futures)
-         ("python2-requests" ,python2-requests)
-         ,@(alist-delete "python-requests"
-                         (package-propagated-inputs swiftclient))))
-      (native-inputs
-       `(("python2-keystoneclient" ,python2-keystoneclient)
-         ("python2-oslosphinx" ,python2-oslosphinx)
-         ,@(fold alist-delete (package-native-inputs swiftclient)
-            '("python-keystoneclient" "python-oslosphinx")))))))
+         ,@(package-propagated-inputs swiftclient))))))
 
 (define-public python-git-review
   (package
-- 
cgit v1.2.3


From 39033c8f5719d85736798f3101022cca8ea92e5d Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 27 Feb 2018 23:40:30 +0100
Subject: gnu: python2-bandit: Enable tests.

* gnu/packages/openstack.scm (python-bandit)[properties]: Remove.
(python2-bandit): Don't use STRIP-PYTHON2-VARIANT.
---
 gnu/packages/openstack.scm | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index bcd075424d..2767d6d58a 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -72,16 +72,10 @@
 To do this Bandit processes each file, builds an AST from it, and runs
 appropriate plugins against the AST nodes.  Once Bandit has finished scanning
 all the files it generates a report.")
-    (properties `((python2-variant . ,(delay python2-bandit))))
     (license asl2.0)))
 
 (define-public python2-bandit
-  (package (inherit (package-with-python2
-                     (strip-python2-variant python-bandit)))
-           (arguments
-            `(#:python ,python-2
-              ;; FIXME: 'subunit.run discover: error: no such option: --list'
-              #:tests? #f))))
+  (package-with-python2 python-bandit))
 
 (define-public python-debtcollector
   (package
-- 
cgit v1.2.3


From 8fa28808a6d26200e915a3f0f32c63e85f70f7b9 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 27 Feb 2018 23:43:20 +0100
Subject: gnu: python-oslo.context: Enable tests.

* gnu/packages/openstack.scm (python-oslo.context)[arguments]: Remove.
---
 gnu/packages/openstack.scm | 2 --
 1 file changed, 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index 2767d6d58a..ce32e108ef 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -422,8 +422,6 @@ common features used in Tempest.")
         (base32
          "0kvha0rs9295njyl2z6n6zm5dapi5mrl5zwjm0m6ldqrvccyf8c3"))))
     (build-system python-build-system)
-    (arguments
-     '(#:tests? #f)) ; FIXME: Requires python-mock >= 1.2.
     (native-inputs
       `(("python-babel" ,python-babel)
         ("python-pbr" ,python-pbr)
-- 
cgit v1.2.3


From 79d9effa51cd8a68cc0afbf3a9c2bfb4bddbeb64 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 27 Feb 2018 23:46:33 +0100
Subject: gnu: python2-stevedore: Enable tests.

* gnu/packages/openstack.scm (python-stevedore)[properties]: Remove.
(python2-stevedore)[arguments]: Remove.
---
 gnu/packages/openstack.scm | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index ce32e108ef..461006fc7b 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -315,16 +315,10 @@ mechanism by building on top of setuptools entry points.  The code for managing
 entry points tends to be repetitive, though, so stevedore provides manager
 classes for implementing common patterns for using dynamically loaded
 extensions.")
-    (properties `((python2-variant . ,(delay python2-stevedore))))
     (license asl2.0)))
 
 (define-public python2-stevedore
-  (package (inherit (package-with-python2
-                     (strip-python2-variant python-stevedore)))
-           (arguments
-            `(#:python ,python-2
-              ;; FIXME: 'subunit.run discover: error: no such option: --list'
-              #:tests? #f))))
+  (package-with-python2 python-stevedore))
 
 (define-public python-tempest-lib
   (package
-- 
cgit v1.2.3


From 3e3302acc51aca4415b394b067e69249d3f11e06 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 00:02:53 +0100
Subject: gnu: Add python-rfc3986.

* gnu/packages/python.scm (python-rfc3986, python2-rfc3986): New public
variables.
---
 gnu/packages/python.scm | 42 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 5c6bc7f04e..ee867517fc 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -11500,6 +11500,48 @@ applying JSON Patches according to RFC 6902.")
 (define-public python2-jsonpatch-0.4
   (package-with-python2 python-jsonpatch-0.4))
 
+(define-public python-rfc3986
+  (package
+    (name "python-rfc3986")
+    (version "1.1.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "rfc3986" version))
+              (sha256
+               (base32
+                "06wlmysw83f75ff84zr1yr6n0shvc2xn1n1sb4iwzqap9hf5fn44"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:modules ((guix build utils)
+                  (guix build python-build-system)
+                  (ice-9 ftw)
+                  (srfi srfi-1)
+                  (srfi srfi-26))
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda _
+             (let ((cwd (getcwd)))
+               (setenv "PYTHONPATH"
+                       (string-append cwd "/build/"
+                                      (find (cut string-prefix? "lib" <>)
+                                            (scandir (string-append cwd "/build")))
+                                      ":"
+                                      (getenv "PYTHONPATH")))
+             (invoke "pytest" "-v")))))))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)))
+    (home-page "https://rfc3986.readthedocs.io/")
+    (synopsis "Parse and validate URI references")
+    (description
+     "@code{rfc3986} is a Python implementation of RFC@tie{}3986 including
+validation and authority parsing.  This module also supports RFC@tie{}6874
+which adds support for zone identifiers to IPv6 addresses.")
+    (license license:asl2.0)))
+
+(define-public python2-rfc3986
+  (package-with-python2 python-rfc3986))
+
 (define-public python-rfc3987
   (package
     (name "python-rfc3987")
-- 
cgit v1.2.3


From 1cccdca2310adbc0932ae2fbf0a7fe064851a5d5 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 01:18:54 +0100
Subject: gnu: python-stevedore: Update to 1.28.0.

* gnu/packages/openstack.scm (python-stevedore): Update to 1.28.0.
[propagated-inputs]: Add PYTHON-PBR.
[native-inputs]: Remove PYTHON-PBR, PYTHON-DISCOVER, PYTHON-DOCUTILS,
PYTHON-OSLOSPHINX and PYTHON-OSLOTEST.  Replace PYTHON-SPHINX with
PYTHON-SPHINX-1.6.
---
 gnu/packages/openstack.scm | 21 ++++++++-------------
 1 file changed, 8 insertions(+), 13 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index 461006fc7b..be858e17c3 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -283,27 +283,22 @@ to docs.openstack.org and developer.openstack.org.")
 (define-public python-stevedore
   (package
     (name "python-stevedore")
-    (version "1.12.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "stevedore" version))
        (sha256
-         (base32
-          "0999zvawaapzg6givjhn7vjscdwblcs73wf28wq1wb4g5mbb5phv"))))
+        (base32
+         "02ynfgwma84g59834dmvzr39mcppy5s229zf1w23c0qngf753izi"))))
     (build-system python-build-system)
     (propagated-inputs
-      `(("python-six" ,python-six)))
+     `(("python-pbr" ,python-pbr)
+       ("python-six" ,python-six)))
     (native-inputs
-      `(("python-pbr" ,python-pbr)
-        ;; Tests
-        ("python-discover" ,python-discover)
-        ("python-docutils" ,python-docutils)
-        ("python-mock" ,python-mock)
-        ("python-oslosphinx" ,python-oslosphinx)
-        ("python-oslotest" ,python-oslotest)
-        ("python-sphinx" ,python-sphinx)
-        ("python-testrepository" ,python-testrepository)))
+     `(("python-mock" ,python-mock)
+       ("python-sphinx" ,python-sphinx-1.6)
+       ("python-testrepository" ,python-testrepository)))
     (home-page "https://github.com/dreamhost/stevedore")
     (synopsis "Manage dynamic plugins for Python applications")
     (description
-- 
cgit v1.2.3


From ea4be20af07ded69670b38fb321e3f5874f7ad41 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 02:29:39 +0100
Subject: gnu: Add python-gitdb.

* gnu/packages/version-control.scm (python-gitdb, python2-gitdb): New public
variables.
---
 gnu/packages/version-control.scm | 60 +++++++++++++++++++++++++++++++++++++++-
 1 file changed, 59 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index 229dab5f35..adf28ed1ed 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -15,7 +15,7 @@
 ;;; Copyright © 2017 Vasile Dumitrascu <va511e@yahoo.com>
 ;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2017 André <eu@euandre.org>
-;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2017, 2018 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017 Stefan Reichör <stefan@xsteve.at>
 ;;; Copyright © 2017 Oleg Pykhalov <go.wigust@gmail.com>
 ;;;
@@ -52,6 +52,7 @@
   #:use-module (gnu packages base)
   #:use-module (gnu packages bison)
   #:use-module (gnu packages boost)
+  #:use-module (gnu packages check)
   #:use-module (gnu packages cook)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages docbook)
@@ -633,6 +634,63 @@ default) of the repository.")
   (package-with-python2
    (strip-python2-variant python-ghp-import)))
 
+(define-public python-gitdb
+  (package
+    (name "python-gitdb")
+    (version "2.0.3")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "gitdb2" version))
+              (sha256
+               (base32
+                "02azg62mr99b7cllyjrly77np3vw32y8nrxpa2xjapiyaga2j3mn"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases (modify-phases %standard-phases
+                  (add-before 'check 'create-test-repository
+                    (lambda _
+                      (mkdir "/tmp/testrepo")
+                      ;; Some tests require a git repository, so create one.
+                      (with-directory-excursion "/tmp/testrepo"
+                        (do ((filecount 1 (1+ filecount)))
+                            ((> filecount 1000))
+                          (call-with-output-file (string-append
+                                                  "file" (number->string filecount))
+                            (lambda (port)
+                              (format port "~a" filecount))))
+                        (and
+                         (invoke "git" "init")
+                         (invoke "git" "config" "user.name" "Total Git")
+                         (invoke "git" "config" "user.email" "git@localhost")
+                         (invoke "git" "add" "-A")
+                         (invoke "git" "commit" "-q" "-m" "dummy commit")))
+
+                      ;; The repository checkout must be a "bare" clone.
+                      (invoke "git" "clone" "--bare" "/tmp/testrepo"
+                              "/tmp/testrepo.git")))
+                  (replace 'check
+                    (lambda _
+                      (setenv "GITDB_TEST_GIT_REPO_BASE" "/tmp/testrepo.git")
+                      ;; Skip tests that must be run from the gitdb repository.
+                      (setenv "TRAVIS" "1")
+                      (invoke "nosetests" "-v"))))))
+    (propagated-inputs
+     `(("python-smmap2" ,python-smmap2)))
+    (native-inputs
+     `(("git" ,git)
+       ("python-nose" ,python-nose)))
+    (home-page "https://github.com/gitpython-developers/gitdb")
+    (synopsis "Python implementation of the Git object database")
+    (description
+     "GitDB allows you to access @dfn{bare} Git repositories for reading and
+writing.  It aims at allowing full access to loose objects as well as packs
+with performance and scalability in mind.  It operates exclusively on streams,
+allowing to handle large objects with a small memory footprint.")
+    (license license:bsd-3)))
+
+(define-public python2-gitdb
+  (package-with-python2 python-gitdb))
+
 (define-public shflags
   (package
     (name "shflags")
-- 
cgit v1.2.3


From 8e6177204e9f3cb5ff2651153a7388796ebccbb8 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 02:54:41 +0100
Subject: gnu: Add python-gitpython.

* gnu/packages/version-control.scm (python-gitpython, python2-gitpython): New
public variables.
---
 gnu/packages/version-control.scm | 44 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index adf28ed1ed..ef19382365 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -691,6 +691,50 @@ allowing to handle large objects with a small memory footprint.")
 (define-public python2-gitdb
   (package-with-python2 python-gitdb))
 
+(define-public python-gitpython
+  (package
+    (name "python-gitpython")
+    (version "2.1.8")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "GitPython" version))
+              (sha256
+               (base32
+                "1sbn018mn3y2r58ix5z12na1s02ccprhckb88yq3bdddvqjvqqdd"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f ;XXX: Tests can only be run within the GitPython repository.
+       #:phases (modify-phases %standard-phases
+                  (add-after 'unpack 'embed-git-reference
+                    (lambda* (#:key inputs #:allow-other-keys)
+                      (substitute* "git/cmd.py"
+                        (("git_exec_name = \"git\"")
+                         (string-append "git_exec_name = \""
+                                        (assoc-ref inputs "git")
+                                        "/bin/git\"")))
+                      #t)))))
+    (inputs
+     `(("git" ,git)))
+    (propagated-inputs
+     `(("python-gitdb" ,python-gitdb)))
+    (native-inputs
+     `(("python-ddt" ,python-ddt)
+       ("python-nose" ,python-nose)))
+    (home-page "https://github.com/gitpython-developers/GitPython")
+    (synopsis "Python library for interacting with Git repositories")
+    (description
+     "GitPython is a python library used to interact with Git repositories,
+high-level like git-porcelain, or low-level like git-plumbing.
+
+It provides abstractions of Git objects for easy access of repository data,
+and additionally allows you to access the Git repository more directly using
+either a pure Python implementation, or the faster, but more resource intensive
+@command{git} command implementation.")
+    (license license:bsd-3)))
+
+(define-public python2-gitpython
+  (package-with-python2 python-gitpython))
+
 (define-public shflags
   (package
     (name "shflags")
-- 
cgit v1.2.3


From 231bd07e8d4b0a7cb68e2db4ed6893add759d9c6 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 03:11:43 +0100
Subject: gnu: python-bandit: Update to 1.4.0.

* gnu/packages/openstack.scm (python-bandit): Update to 1.4.0.
[source](uri): Use PYPI-URI.
[arguments]: Run CHECK-PHASE after INSTALL-PHASE.
[propagated-inputs]: Remove PYTHON-APPDIRS.  Add PYTHON-GITPYTHON.
[native-inputs]: Remove PYTHON-PBR.  Add PYTHON-BEAUTIFULSOUP4,
PYTHON-OSLOTEST and PYTHON-SUBUNIT.
---
 gnu/packages/openstack.scm | 26 ++++++++++++++++++--------
 1 file changed, 18 insertions(+), 8 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index be858e17c3..efb305ea04 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -41,27 +41,37 @@
 (define-public python-bandit
   (package
     (name "python-bandit")
-    (version "0.13.2")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append
-             "https://pypi.python.org/packages/source/b/bandit/bandit-"
-             version ".tar.gz"))
+       (uri (pypi-uri "bandit" version))
        (sha256
         (base32
-         "03g3cflvrc99ncjd611iy5nnnscsc2vgnrx4mjaqyx8glbfw8y7g"))))
+         "1m5bm42120zyazky4k0lp3d9r0jwhjmp6sb108xfr0vz952p15yb"))))
     (build-system python-build-system)
+    (arguments
+     `(#:phases (modify-phases %standard-phases
+                  (delete 'check)
+                  (add-after 'install 'check
+                    (lambda* (#:key inputs outputs #:allow-other-keys)
+                      ;; Tests require the 'bandit' executable in PATH.
+                      ;; It's only built during install time.
+                      (add-installed-pythonpath inputs outputs)
+                      (setenv "PATH" (string-append (assoc-ref outputs "out")
+                                                    "/bin:" (getenv "PATH")))
+                      (invoke "python" "setup.py" "testr"))))))
     (propagated-inputs
-      `(("python-appdirs" ,python-appdirs)
+      `(("python-gitpython" ,python-gitpython)
         ("python-pyyaml" ,python-pyyaml)
         ("python-six" ,python-six)
         ("python-stevedore" ,python-stevedore)))
     (native-inputs
-      `(("python-pbr" ,python-pbr)
-        ;; Tests
+      `(;; Tests.
+        ("python-beautifulsoup4" ,python-beautifulsoup4)
         ("python-fixtures" ,python-fixtures)
         ("python-mock" ,python-mock)
+        ("python-subunit" ,python-subunit)
         ("python-testrepository" ,python-testrepository)
         ("python-testscenarios" ,python-testscenarios)
         ("python-testtools" ,python-testtools)))
-- 
cgit v1.2.3


From c822e880fede683e35c4340a9cc0a28ba5c63f0e Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 03:23:30 +0100
Subject: gnu: python-oslo.i18n: Update to 3.19.0.

* gnu/packages/openstack.scm (python-oslo.i18n): Update to 3.19.0.
[arguments]: Remove field.
---
 gnu/packages/openstack.scm | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index efb305ea04..d1c2374b07 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -446,17 +446,15 @@ pipeline and used by various modules such as logging.")
 (define-public python-oslo.i18n
   (package
     (name "python-oslo.i18n")
-    (version "3.0.0")
+    (version "3.19.0")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "oslo.i18n" version))
         (sha256
           (base32
-           "0bpb1c20sm8my650gl824nzaip83bfn8hr91s65k5ncmyh8hb6pl"))))
+           "18lbfq55cqrbmwm5p6vci9mkjfzr0zwz54ax3ysa463wba5m84cp"))))
     (build-system python-build-system)
-    (arguments
-     '(#:tests? #f)) ; FIXME: Circular dependency on python-oslo.config.
     (propagated-inputs
       `(("python-babel" ,python-babel)
         ("python-six" ,python-six)))
-- 
cgit v1.2.3


From a2803e206b4e61727e7b74c39f9a395d37545cfd Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 03:38:00 +0100
Subject: gnu: python-debtcollector: Update to 1.19.0.

* gnu/packages/openstack.scm (python-debtcollector): Update to 1.19.0.
[arguments]: Remove field.
[propagated-inputs]: Add PYTHON-PBR.
[native-inputs]: Remove PYTHON-PBR and PYTHON-BABEL.  Add PYTHON-SUBUNIT,
PYTHON-TESTREPOSITORY and PYTHON-TESTTOOLS.
[properties]: Declare python2 variant.
(python2-debtcollector)[propaged-inputs]: Add PYTHON-FUNCSIGS.
---
 gnu/packages/openstack.scm | 28 +++++++++++++++++-----------
 1 file changed, 17 insertions(+), 11 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index d1c2374b07..0c4c6eb759 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -90,36 +90,42 @@ all the files it generates a report.")
 (define-public python-debtcollector
   (package
     (name "python-debtcollector")
-    (version "1.0.0")
+    (version "1.19.0")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "debtcollector" version))
         (sha256
           (base32
-           "0g4dfskaiy47rhsh4gh66l5vmdsrgq0qk68pl3ix1cj3ffvfndzv"))))
+           "06c7vyn184y9f0lsrwaz13aq63hdz5fjrd191b8nifx6acsni42f"))))
     (build-system python-build-system)
-    (arguments
-     '(#:tests? #f)) ;FIXME: Requires packaging python-doc8.
     (propagated-inputs
-     `(("python-six" ,python-six)
+     `(("python-pbr" ,python-pbr)
+       ("python-six" ,python-six)
        ("python-wrapt" ,python-wrapt)))
     (native-inputs
-      `(("python-babel" ,python-babel)
-        ("python-pbr" ,python-pbr)
-        ;; Tests.
-        ("python-oslotest" ,python-oslotest)))
+     `(;; Tests.
+       ("python-subunit" ,python-subunit)
+       ("python-testrepository" ,python-testrepository)
+       ("python-testtools" ,python-testtools)))
     (home-page "https://www.openstack.org/")
     (synopsis
-      "Find deprecated patterns and strategies in Python code")
+     "Find deprecated patterns and strategies in Python code")
     (description
       "This package provides a collection of Python deprecation patterns and
 strategies that help you collect your technical debt in a non-destructive
 manner.")
+    (properties `((python2-variant . ,(delay python2-debtcollector))))
     (license asl2.0)))
 
 (define-public python2-debtcollector
-  (package-with-python2 python-debtcollector))
+  (let ((base (package-with-python2 (strip-python2-variant
+                                     python-debtcollector))))
+    (package
+      (inherit base)
+      (propagated-inputs
+       `(("python2-funcsigs" ,python2-funcsigs)
+         ,@(package-propagated-inputs base))))))
 
 (define-public python-hacking
   (package
-- 
cgit v1.2.3


From 9e4546a2be4d91cc8bb498340923ef01ae94971b Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 03:48:18 +0100
Subject: gnu: python-oslo.config: Update to 5.2.0.

* gnu/packages/openstack.scm (python-oslo.config): Update to 5.2.0.
[source](uri): Use PYPI-URI.
[arguments]: Remove field.
[propagated-inputs]: Add PYTHON-DEBTCOLLECTOR, PYTHON-OSLO.I18N, PYTHON-PBR,
PYTHON-RFC3986 and PYTHON-PYYAML.
[native-inputs]: Remove PYTHON-PBR and PYTHON-I18N.  Add PYTHON-BANDIT,
PYTHON-COVERAGE, PYTHON-OPENSTACKDOCSTHEME, PYTHON-RENO, PYTHON-SPHINX-1.6,
PYTHON-TESTREPOSITORY and PYTHON-TESTTOOLS.
---
 gnu/packages/openstack.scm | 38 +++++++++++++++++++++-----------------
 1 file changed, 21 insertions(+), 17 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index 0c4c6eb759..e49fe8e903 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -380,31 +380,35 @@ common features used in Tempest.")
 (define-public python-oslo.config
   (package
     (name "python-oslo.config")
-    (version "2.4.0")
+    (version "5.2.0")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append
-             "https://pypi.python.org/packages/source/o/oslo.config/oslo.config-"
-             version
-             ".tar.gz"))
+       (uri (pypi-uri "oslo.config" version))
        (sha256
          (base32
-          "13r778jfb0fhna37c2pd1f2xipnsbd7zli7qhn96acrzymrwj5k1"))))
+          "0ymf7jxbq29fifyvkwhfiys1qvljqfxdw8ajwzwaf3yiqidgpxqd"))))
     (build-system python-build-system)
-    (arguments
-     '(#:tests? #f)) ; FIXME: Requires packaging python-argparse.
     (propagated-inputs
-      `(("python-netaddr" ,python-netaddr)
-        ("python-six" ,python-six)
-        ("python-stevedore" ,python-stevedore)))
+     `(("python-debtcollector" ,python-debtcollector)
+       ("python-netaddr" ,python-netaddr)
+       ("python-oslo.i18n" ,python-oslo.i18n)
+       ("python-pbr" ,python-pbr)
+       ("python-rfc3986" ,python-rfc3986)
+       ("python-six" ,python-six)
+       ("python-stevedore" ,python-stevedore)
+       ("python-pyyaml" ,python-pyyaml)))
     (native-inputs
-      `(("python-pbr" ,python-pbr)
-        ;; Tests
-        ("python-oslo.i18n" ,python-oslo.i18n)
-        ("python-mock" ,python-mock)
-        ("python-oslotest" ,python-oslotest)
-        ("python-testscenarios" ,python-testscenarios)))
+     `(("python-bandit" ,python-bandit)
+       ("python-coverage" ,python-coverage)
+       ("python-mock" ,python-mock)
+       ("python-openstackdocstheme" ,python-openstackdocstheme)
+       ("python-oslotest" ,python-oslotest)
+       ("python-reno" ,python-reno)
+       ("python-sphinx" ,python-sphinx-1.6)
+       ("python-testrepository" ,python-testrepository)
+       ("python-testscenarios" ,python-testscenarios)
+       ("python-testtools" ,python-testtools)))
     (home-page "https://launchpad.net/oslo")
     (synopsis "Oslo Configuration API")
     (description
-- 
cgit v1.2.3


From b51fbd6d6e67cc947c1c2977e08511930e7f7648 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 03:59:22 +0100
Subject: gnu: python-oslo.utils: Update to 3.35.0.

* gnu/packages/openstack.scm (python-oslo.utils): Update to 3.35.0.
[source](snippet): Remove.
[propagated-inputs]: Add PYTHON-PYPARSING.
[native-inputs]: Add PYTHON-DDT, PYTHON-FIXTURES, PYTHON-TESTREPOSITORY and
PYTHON-TESTTOOLS.  Remove PYTHON-MOX3.
---
 gnu/packages/openstack.scm | 22 +++++++++-------------
 1 file changed, 9 insertions(+), 13 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index e49fe8e903..0802e93eea 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -682,22 +682,15 @@ and better support for mocking results.")
 (define-public python-oslo.utils
   (package
     (name "python-oslo.utils")
-    (version "3.0.0")
+    (version "3.35.0")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "oslo.utils" version))
         (sha256
           (base32
-           "1c4jrbvfs4hs37fics8frqlyhmsv7v92ncv2cpbm0av9x0ic6pnj"))
-        (snippet
-         '(begin
-            ;; FIXME: setuptools fails to import this file during the test
-            ;; phase.
-            (delete-file "oslo_utils/tests/test_netutils.py")))))
+           "1ai9yyasyh1563khsri6ryk6iqdprmyiashg377m9h4nmv700ybx"))))
     (build-system python-build-system)
-    (arguments
-     '(#:tests? #f)) ; FIXME: Requires oslo.config >= 2.7.0.
     (propagated-inputs
       `(("python-debtcollector" ,python-debtcollector)
         ("python-oslo.i18n" ,python-oslo.i18n)
@@ -705,18 +698,21 @@ and better support for mocking results.")
         ("python-monotonic" ,python-monotonic)
         ("python-netaddr" ,python-netaddr)
         ("python-netifaces" ,python-netifaces)
+        ("python-pyparsing" ,python-pyparsing)
         ("python-pytz" ,python-pytz)
         ("python-six" ,python-six)))
     (native-inputs
-      `(("python-babel" ,python-babel)
-        ("python-pbr" ,python-pbr)
+      `(("python-pbr" ,python-pbr)
         ;; Tests.
         ("python-bandit" ,python-bandit)
+        ("python-ddt" ,python-ddt)
+        ("python-fixtures" ,python-fixtures)
         ("python-oslo.config" ,python-oslo.config)
         ("python-oslotest" ,python-oslotest)
         ("python-mock" ,python-mock)
-        ("python-mox3" ,python-mox3)
-        ("python-testscenarios" ,python-testscenarios)))
+        ("python-testrepository" ,python-testrepository)
+        ("python-testscenarios" ,python-testscenarios)
+        ("python-testtools" ,python-testtools)))
     (home-page "https://launchpad.net/oslo")
     (synopsis "Oslo utility library")
     (description
-- 
cgit v1.2.3


From 24f4400aa69925635c229d7f494eabf37e980cae Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 8 Oct 2016 09:55:51 +0100
Subject: gnu: Add python-pyinotify.

* gnu/packages/python.scm (python-pyinotify, python2-pyinotify): New
variables.
---
 gnu/packages/python.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index ee867517fc..a44c3a0fd0 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -12896,3 +12896,25 @@ interpreter. bpython's main features are
                  (("^(\\s+'bpython)(-\\S+)?(\\s+=.*',?)\\s*?$" _ name sub rest)
                   (string-append name "2" (or sub "") rest "\n")))
                #t))))))))
+
+(define-public python-pyinotify
+  (package
+    (name "python-pyinotify")
+    (version "0.9.6")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "pyinotify" version))
+              (sha256
+               (base32
+                "1x3i9wmzw33fpkis203alygfnrkcmq9w1aydcm887jh6frfqm6cw"))))
+    (build-system python-build-system)
+    (arguments `(#:tests? #f))          ;no tests
+    (home-page "https://github.com/seb-m/pyinotify")
+    (synopsis "Python library for monitoring inotify events")
+    (description
+     "@code{pyinotify} provides a Python interface for monitoring
+filesystem events on Linux.")
+    (license license:expat)))
+
+(define-public python2-pyinotify
+  (package-with-python2 python-pyinotify))
-- 
cgit v1.2.3


From 32bb0c617b12a3a937097922e4dfc819490d3f13 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 04:37:23 +0100
Subject: gnu: python-oslo.context: Update to 2.20.0.

* gnu/packages/openstack.scm (python-oslo.context): Update to 2.20.0.
[propagated-inputs]: Add PYTHON-DEBTCOLLECTOR and PYTHON-PBR.
[native-inputs]: Remove PYTHON-PBR, PYTHON-COVERAGE, PYTHON-MOCK,
PYTHON-OS-CLIENT-CONFIG, PYTHON-OSLOSPHINX and PYTHON-SPHINX.  Add
PYTHON-FIXTURES.
---
 gnu/packages/openstack.scm | 20 ++++++++------------
 1 file changed, 8 insertions(+), 12 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index 0802e93eea..c990fb929b 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -422,26 +422,22 @@ common features used in Tempest.")
 (define-public python-oslo.context
   (package
     (name "python-oslo.context")
-    (version "1.0.0")
+    (version "2.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "oslo.context" version))
        (sha256
         (base32
-         "0kvha0rs9295njyl2z6n6zm5dapi5mrl5zwjm0m6ldqrvccyf8c3"))))
+         "0iiq9rpwg6wrdqnhf3d8z8g0g7fjhs5zn6qw6igvxplz2c3rbvvx"))))
     (build-system python-build-system)
+    (propagated-inputs
+     `(("python-debtcollector" ,python-debtcollector)
+       ("python-pbr" ,python-pbr)))
     (native-inputs
-      `(("python-babel" ,python-babel)
-        ("python-pbr" ,python-pbr)
-        ;; Tests.
-        ("python-coverage" ,python-coverage)
-        ("python-hacking" ,python-hacking)
-        ("python-mock" ,python-mock)
-        ("python-os-client-config" ,python-os-client-config)
-        ("python-oslotest" ,python-oslotest)
-        ("python-oslosphinx" ,python-oslosphinx)
-        ("python-sphinx" ,python-sphinx)))
+     `(("python-fixtures" ,python-fixtures)
+       ("python-hacking" ,python-hacking)
+       ("python-oslotest" ,python-oslotest)))
     (home-page "https://launchpad.net/oslo")
     (synopsis "Oslo context library")
     (description
-- 
cgit v1.2.3


From caf3713ad580126d18094ead081a7ed65399b699 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 04:48:41 +0100
Subject: gnu: python-oslo.serialization: Update to 2.24.0.

* gnu/packages/openstack.scm (python-oslo.serialization): Update to 2.24.0.
[arguments]: Remove field.
[propagated-inputs]: Remove PYTHON-ISO8601 and PYTHON-SIMPLEJSON.  Add
PYTHON-MSGPACK.
[native-inputs]: Remove PYTHON-BABEL.
[properties]: New field.
(python2-oslo.serialization)[native-inputs]: Add PYTHON2-IPADDRESS.
---
 gnu/packages/openstack.scm | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index c990fb929b..dfcd1e3a81 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -527,27 +527,23 @@ handlers and support for context specific logging (like resource id’s etc).")
 (define-public python-oslo.serialization
   (package
     (name "python-oslo.serialization")
-    (version "2.2.0")
+    (version "2.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "oslo.serialization" version))
        (sha256
         (base32
-         "00s03krhf833gs76aw5ns32w9m1i4hx6x6d9g82m0j5wyqk0sci4"))))
+         "08bxkp98c617y58x630xq44iiffm7f0f3cwh6zbnlkgq0zgh7jk1"))))
     (build-system python-build-system)
-    (arguments
-     '(#:tests? #f)) ; FIXME: Requires python-oslo.utils >= 3.2.0.
     (propagated-inputs
-      `(("python-iso8601" ,python-iso8601)
+      `(("python-msgpack" ,python-msgpack)
         ("python-netaddr" ,python-netaddr)
         ("python-oslo.utils" ,python-oslo.utils)
-        ("python-simplejson" ,python-simplejson)
         ("python-six" ,python-six)
         ("python-pytz" ,python-pytz)))
     (native-inputs
-      `(("python-babel" ,python-babel)
-        ("python-pbr" ,python-pbr)
+      `(("python-pbr" ,python-pbr)
         ;; Tests.
         ("python-mock" ,python-mock)
         ("python-oslo.i18n" ,python-oslo.i18n)
@@ -557,10 +553,17 @@ handlers and support for context specific logging (like resource id’s etc).")
     (description
       "The oslo.serialization library provides support for representing objects
 in transmittable and storable formats, such as JSON and MessagePack.")
+    (properties `((python2-variant . ,(delay python2-oslo.serialization))))
     (license asl2.0)))
 
 (define-public python2-oslo.serialization
-  (package-with-python2 python-oslo.serialization))
+  (let ((base (package-with-python2 (strip-python2-variant
+                                     python-oslo.serialization))))
+    (package
+      (inherit base)
+      (native-inputs
+       `(("python2-ipaddress" ,python2-ipaddress)
+         ,@(package-native-inputs base))))))
 
 (define-public python-reno
   (package
-- 
cgit v1.2.3


From 0075644662acf58287f9ad825c5b8386b216a1fc Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 04:59:32 +0100
Subject: gnu: python-msgpack: Update to 0.5.6.

* gnu/packages/python.scm (python-msgpack): Update to 0.5.6.
[source, home-page]: Adjust to msgpack-python->msgpack rename.
---
 gnu/packages/python.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index a44c3a0fd0..32fcea480b 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -5832,19 +5832,19 @@ should be stored on various operating systems.")
 (define-public python-msgpack
   (package
     (name "python-msgpack")
-    (version "0.4.8")
+    (version "0.5.6")
     (source (origin
               (method url-fetch)
-              (uri (pypi-uri "msgpack-python" version))
+              (uri (pypi-uri "msgpack" version))
               (sha256
                (base32
-                "11pqk5braa6wndpnr1dhg64js82vjgxnm0lzy73rwl831zgijaqs"))))
+                "1hz2dba1nvvn52afg34liijsm7kn65cmn06dl0xbwld6bb4cis0f"))))
     (build-system python-build-system)
     (synopsis "MessagePack (de)serializer")
     (description "MessagePack is a fast, compact binary serialization format,
 suitable for similar data to JSON.  This package provides CPython bindings for
 reading and writing MessagePack data.")
-    (home-page "https://pypi.python.org/pypi/msgpack-python/")
+    (home-page "https://pypi.python.org/pypi/msgpack/")
     (license license:asl2.0)))
 
 (define-public python2-msgpack
-- 
cgit v1.2.3


From 2441239842fa6f786008e8c75651342b2c0172d2 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 05:04:26 +0100
Subject: gnu: python-msgpack: Run the tests.

* gnu/packages/python.scm (python-msgpack)[arguments]: Add #:modules.  Replace
CHECK-PHASE with pytest invocation.
[native-inputs]: Add PYTHON-PYTEST.
---
 gnu/packages/python.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 32fcea480b..80ea4caf76 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -5840,6 +5840,26 @@ should be stored on various operating systems.")
                (base32
                 "1hz2dba1nvvn52afg34liijsm7kn65cmn06dl0xbwld6bb4cis0f"))))
     (build-system python-build-system)
+    (arguments
+     `(#:modules ((guix build utils)
+                  (guix build python-build-system)
+                  (ice-9 ftw)
+                  (srfi srfi-1)
+                  (srfi srfi-26))
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda _
+             (let ((cwd (getcwd)))
+               (setenv "PYTHONPATH"
+                       (string-append cwd "/build/"
+                                      (find (cut string-prefix? "lib" <>)
+                                            (scandir (string-append cwd "/build")))
+                                      ":"
+                                      (getenv "PYTHONPATH")))
+             (invoke "pytest" "-v" "test")))))))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)))
     (synopsis "MessagePack (de)serializer")
     (description "MessagePack is a fast, compact binary serialization format,
 suitable for similar data to JSON.  This package provides CPython bindings for
-- 
cgit v1.2.3


From db3e631db8fe0d6c833974ed556bddd5d13ee0f8 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 05:18:33 +0100
Subject: gnu: python-monotonic: Update to 1.4.

* gnu/packages/time.scm (python-monotonic): Update to 1.4.
[source]: Use PYPI-URI.
[arguments]: Explicitly disable tests.
---
 gnu/packages/time.scm | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/time.scm b/gnu/packages/time.scm
index a54524087f..59414f6d7c 100644
--- a/gnu/packages/time.scm
+++ b/gnu/packages/time.scm
@@ -264,18 +264,16 @@ ISO 8601 dates, time and duration.")
 (define-public python-monotonic
   (package
     (name "python-monotonic")
-    (version "0.3")
+    (version "1.4")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append
-             "https://pypi.python.org/packages/source/m/monotonic/monotonic-"
-             version
-             ".tar.gz"))
+       (uri (pypi-uri "monotonic" version))
        (sha256
         (base32
-         "0yz0bcbwx8r2c01czzfpbrxddynxyk9k95jj8h6sgcb7xmfvl998"))))
+         "110zd5ld3nchdjds34r95lzs1csmmv81pli2px8l1k8qnpai29m0"))))
     (build-system python-build-system)
+    (arguments '(#:tests? #f))          ;no tests
     (home-page "https://github.com/atdt/monotonic")
     (synopsis "Implementation of time.monotonic() for Python 2 & < 3.3")
     (description
-- 
cgit v1.2.3


From f8a4547c2973d91389f0b468133ea1de45e592a4 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 05:39:45 +0100
Subject: gnu: python-oslo.log: Update to 3.36.0.

* gnu/packages/openstack.scm (python-oslo.log): Update to 3.36.0.
[source](uri): Use PYPI-URI.
[arguments]: Remove.
[propagated-inputs]: Add PYTHON-DATEUTIL, PYTHON-MONOTONIC, PYTHON-PBR and
PYTHON-PYINOTIFY.
[native-inputs]: Remove PYTHON-BABEL, PYTHON-ISO8601 and PYTHON-PBR.  Add
PYTHON-SUBUNIT, PYTHON-TESTREPOSITORY and PYTHON-TESTTOOLS.
---
 gnu/packages/openstack.scm | 25 ++++++++++++-------------
 1 file changed, 12 insertions(+), 13 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index dfcd1e3a81..f0147bab59 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -485,34 +485,33 @@ in an application or library.")
 (define-public python-oslo.log
   (package
   (name "python-oslo.log")
-  (version "1.6.0")
+  (version "3.36.0")
   (source
     (origin
       (method url-fetch)
-      (uri (string-append
-             "https://pypi.python.org/packages/source/o/oslo.log/oslo.log-"
-             version
-             ".tar.gz"))
+      (uri (pypi-uri "oslo.log" version))
       (sha256
         (base32
-          "1fhy6yvbd565nv4x4i3ppyrlbmz3yy9d0xsvw5nkqsa7g43nmf8z"))))
+          "0h7hplf1h8k24v75m3mq1jlrl74x5ynyr4hwgffsg5campxnza4x"))))
   (build-system python-build-system)
-  (arguments
-   '(#:tests? #f)) ; FIXME: Requires oslo.utils >= 3.2.0.
   (propagated-inputs
-   `(("python-debtcollector" ,python-debtcollector)
+   `(("python-dateutil" ,python-dateutil)
+     ("python-debtcollector" ,python-debtcollector)
+     ("python-monotonic" ,python-monotonic)
      ("python-oslo.config" ,python-oslo.config)
      ("python-oslo.context" ,python-oslo.context)
      ("python-oslo.i18n" ,python-oslo.i18n)
      ("python-oslo.utils" ,python-oslo.utils)
      ("python-oslo.serialization" ,python-oslo.serialization)
+     ("python-pbr" ,python-pbr)
+     ("python-pyinotify" ,python-pyinotify)
      ("python-six" ,python-six)))
   (native-inputs
-    `(("python-babel" ,python-babel)
-      ("python-iso8601" ,python-iso8601)
-      ("python-mock" ,python-mock)
+    `(("python-mock" ,python-mock)
       ("python-oslotest" ,python-oslotest)
-      ("python-pbr" ,python-pbr)))
+      ("python-subunit" ,python-subunit)
+      ("python-testrepository" ,python-testrepository)
+      ("python-testtools" ,python-testtools)))
   (home-page "https://launchpad.net/oslo")
   (synopsis "Python logging library of the Oslo project")
   (description
-- 
cgit v1.2.3


From 836de07a47aa4a982fe99b774da2db53e235f2ca Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 13:54:08 +0100
Subject: gnu: python-wrapt: Update to 1.10.11.

* gnu/packages/python.scm (python-wrapt): Update to 1.10.11.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 80ea4caf76..fc906e6858 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -5896,14 +5896,14 @@ and MAC network addresses.")
 (define-public python-wrapt
   (package
     (name "python-wrapt")
-    (version "1.10.8")
+    (version "1.10.11")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "wrapt" version))
         (sha256
           (base32
-            "0wrcm1mydvfivbkzz0h81ygzdchnscshi6xvy5n3r21r9s0px8af"))))
+            "1ip3dwib39xhp79kblskgvz3fjzcwxgx3fs3ahdixhpjg7a61mfl"))))
     (build-system python-build-system)
     (arguments
      ;; Tests are not included in the tarball, they are only available in the
-- 
cgit v1.2.3


From fb2477f6d2fc9e41b226dae1f88723fd92b03c1c Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 14:17:55 +0100
Subject: gnu: python-psutil: Update to 5.4.3.

* gnu/packages/python.scm (python-psutil): Update to 5.4.3.
[properties]: Declare python2 variant.
(python2-psutil): Propagate PYTHON2-ENUM34.
---
 gnu/packages/python.scm | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index fc906e6858..fa8f4902d2 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -448,14 +448,14 @@ instead of @command{python3}.")))
 (define-public python-psutil
   (package
     (name "python-psutil")
-    (version "4.3.0")
+    (version "5.4.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "psutil" version))
        (sha256
         (base32
-         "1w4r09fvn6kd80m5mx4ws1wz100brkaq6hzzpwrns8cgjzjpl6c6"))))
+         "063v69x7spyclyaxrd3gmzj3p16q5ayg97xqhwb1kyn22a9pwip2"))))
     (build-system python-build-system)
     (arguments
      ;; FIXME: some tests does not return and times out.
@@ -470,10 +470,16 @@ limiting process resources and management of running processes.  It implements
 many functionalities offered by command line tools such as: ps, top, lsof,
 netstat, ifconfig, who, df, kill, free, nice, ionice, iostat, iotop, uptime,
 pidof, tty, taskset, pmap.")
+    (properties `((python2-variant . ,(delay python2-psutil))))
     (license license:bsd-3)))
 
 (define-public python2-psutil
-  (package-with-python2 python-psutil))
+  (let ((base (package-with-python2 (strip-python2-variant python-psutil))))
+    (package
+      (inherit base)
+      (propagated-inputs
+       `(("python2-enum34" ,python2-enum34)         ;optional
+         ,@(package-propagated-inputs base))))))
 
 (define-public python-shapely
   (package
-- 
cgit v1.2.3


From a846f29dfff9c7420f44c577bd556f34ac9c6c56 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 15:26:01 +0100
Subject: gnu: python-netifaces: Update to 0.10.6.

* gnu/packages/python.scm (python-netifaces): Update to 0.10.6.
[source](uri): Use PYPI-URI.
[home-page]: Update.
---
 gnu/packages/python.scm | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index fa8f4902d2..064d79002d 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -4862,20 +4862,16 @@ converts incoming documents to Unicode and outgoing documents to UTF-8.")
 (define-public python-netifaces
   (package
     (name "python-netifaces")
-    (version "0.10.4")
+    (version "0.10.6")
     (source
       (origin
         (method url-fetch)
-        (uri (string-append
-              "https://pypi.python.org/packages/source/n/netifaces/netifaces-"
-              version
-              ".tar.gz"))
+        (uri (pypi-uri "netifaces" version))
         (sha256
           (base32
-            "1plw237a4zib4z8s62g0mrs8gm3kjfrp5sxh6bbk9nl3rdls2mln"))))
+            "1q7bi5k2r955rlcpspx4salvkkpk28jky67fjbpz2dkdycisak8c"))))
     (build-system python-build-system)
-    (home-page
-      "https://bitbucket.org/al45tair/netifaces")
+    (home-page "https://github.com/al45tair/netifaces")
     (synopsis
       "Python module for portable network interface information")
     (description
-- 
cgit v1.2.3


From 4ef80b2f585f414410b003296b6846582a0801e4 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 16:01:43 +0100
Subject: gnu: python-html5lib: Update to 1.0.1.

* gnu/packages/python-web.scm (python-html5lib): Update to 1.0.1.
---
 gnu/packages/python-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 219b7f9fe2..f9cdbeef02 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -165,14 +165,14 @@ both of which are installed automatically if you install this library.")
 (define-public python-html5lib
   (package
     (name "python-html5lib")
-    (version "1.0b10")
+    (version "1.0.1")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "html5lib" version))
         (sha256
           (base32
-            "1yd068a5c00wd0ajq0hqimv7fd82lhrw0w3s01vbhy9bbd6xapqd"))))
+            "0dipzfrycv6j1jw82v9b7d8lzggx3x8xngx6l4xrqkxwvg7hvjv6"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-six" ,python-six)
-- 
cgit v1.2.3


From b0a2c9cbe9959613f2ddcf1a9030a32f0362bc85 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 16:02:55 +0100
Subject: gnu: python-webencodings: Update to 0.5.1.

* gnu/packages/python-web.scm (python-webencodings): Update to 0.5.1.
---
 gnu/packages/python-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index f9cdbeef02..47fc5cd63a 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -241,13 +241,13 @@ C, yielding parse times that can be a thirtieth of the html5lib parse times.")
 (define-public python-webencodings
   (package
     (name "python-webencodings")
-    (version "0.5")
+    (version "0.5.1")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "webencodings" version))
               (sha256
                (base32
-                "015rw7662lkpb9aqiqah2hbizk6w531badqwjpz41rr47glmxid5"))))
+                "08qrgrc4hrximb2gqnl69g01s93rhf2842jfxdjljc1dbwj1qsmk"))))
     (build-system python-build-system)
     (arguments
      '(#:phases
-- 
cgit v1.2.3


From 4e028d7ad2f5119663bba80e7c258e6141f4cf27 Mon Sep 17 00:00:00 2001
From: Alex Vong <alexvong1995@gmail.com>
Date: Sun, 25 Feb 2018 06:48:47 +0800
Subject: gnu: Add perl-cairo.

* gnu/packages/gtk.scm (perl-cairo): New public variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
---
 gnu/packages/gtk.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm
index 2939e4f648..be8a9a0844 100644
--- a/gnu/packages/gtk.scm
+++ b/gnu/packages/gtk.scm
@@ -17,6 +17,7 @@
 ;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -40,6 +41,7 @@
   #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system perl)
   #:use-module (guix build-system python)
   #:use-module (guix build-system waf)
   #:use-module (gnu packages)
@@ -1238,6 +1240,31 @@ targeted at GTK 2.x, and can be used in conjunction with gnome-python to
 write GNOME applications.")
     (license license:lgpl2.1+)))
 
+(define-public perl-cairo
+  (package
+    (name "perl-cairo")
+    (version "1.106")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "mirror://cpan/authors/id/X/XA/XAOC/Cairo-"
+                    version ".tar.gz"))
+              (sha256
+               (base32
+                "1i25kks408c54k2zxskvg54l5k3qadzm8n72ffga9jy7ic0h6j76"))))
+    (build-system perl-build-system)
+    (native-inputs
+     `(("perl-extutils-depends" ,perl-extutils-depends)
+       ("perl-extutils-pkgconfig" ,perl-extutils-pkgconfig)))
+    (inputs
+     `(("cairo" ,cairo)))
+    (home-page "http://search.cpan.org/dist/Cairo/")
+    (synopsis "Perl interface to the cairo 2d vector graphics library")
+    (description "Cairo provides Perl bindings for the vector graphics library
+cairo.  It supports multiple output targets, including PNG, PDF and SVG.  Cairo
+produces identical output on all those targets.")
+    (license license:lgpl2.1+)))
+
 (define-public girara
   (package
     (name "girara")
-- 
cgit v1.2.3


From 451f6e30ebfc32a8679daa71f8ff438ca03c73d1 Mon Sep 17 00:00:00 2001
From: Alex Vong <alexvong1995@gmail.com>
Date: Sun, 25 Feb 2018 06:49:54 +0800
Subject: gnu: Add perl-glib.

* gnu/packages/glib.scm (perl-glib): New public variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
---
 gnu/packages/glib.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/glib.scm b/gnu/packages/glib.scm
index 45d0d891c4..a64407a36f 100644
--- a/gnu/packages/glib.scm
+++ b/gnu/packages/glib.scm
@@ -8,6 +8,7 @@
 ;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Petter <petter@mykolab.ch>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -622,6 +623,33 @@ useful for C++.")
        ("python-pycairo" ,python2-pycairo)
        ("gobject-introspection" ,gobject-introspection)))))
 
+(define-public perl-glib
+  (package
+    (name "perl-glib")
+    (version "1.326")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "mirror://cpan/authors/id/X/XA/XAOC/Glib-"
+                    version ".tar.gz"))
+              (sha256
+               (base32
+                "0prn9kkdpwjq9qmzqashbhk3pq4gvlrmvm3b10xf1dhc48406382"))))
+    (build-system perl-build-system)
+    (native-inputs
+     `(("perl-extutils-depends" ,perl-extutils-depends)
+       ("perl-extutils-pkgconfig" ,perl-extutils-pkgconfig)))
+    (inputs
+     `(("glib" ,glib)))
+    (home-page "http://search.cpan.org/dist/Glib/")
+    (synopsis "Perl wrappers for the GLib utility and Object libraries")
+    (description "This module provides perl access to GLib and GLib's GObject
+libraries.  GLib is a portability and utility library; GObject provides a
+generic type system with inheritance and a powerful signal system.  Together
+these libraries are used as the foundation for many of the libraries that make
+up the Gnome environment, and are used in many unrelated projects.")
+    (license license:lgpl2.1+)))
+
 (define telepathy-glib
   (package
     (name "telepathy-glib")
-- 
cgit v1.2.3


From ee6911c7c0b5ad6a85241c420c72678cc8ee582e Mon Sep 17 00:00:00 2001
From: Alex Vong <alexvong1995@gmail.com>
Date: Sun, 25 Feb 2018 06:51:43 +0800
Subject: gnu: Add perl-pango.

* gnu/packages/gtk.scm (perl-pango): New public variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
---
 gnu/packages/gtk.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm
index be8a9a0844..0e4f9c86c4 100644
--- a/gnu/packages/gtk.scm
+++ b/gnu/packages/gtk.scm
@@ -1265,6 +1265,43 @@ cairo.  It supports multiple output targets, including PNG, PDF and SVG.  Cairo
 produces identical output on all those targets.")
     (license license:lgpl2.1+)))
 
+(define-public perl-pango
+  (package
+    (name "perl-pango")
+    (version "1.227")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://cpan/authors/id/X/XA/XAOC/Pango-"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "0wdcidnfnb6nm79fzfs39ivawj3x8m98a147fmcxgv1zvwia9c1l"))))
+    (build-system perl-build-system)
+    (native-inputs
+     `(("perl-extutils-depends" ,perl-extutils-depends)
+       ("perl-extutils-pkgconfig" ,perl-extutils-pkgconfig)))
+    (inputs
+     `(("pango" ,pango)))
+    (propagated-inputs
+     `(("perl-cairo" ,perl-cairo)
+       ("perl-glib" ,perl-glib)))
+    (home-page "http://search.cpan.org/dist/Pango/")
+    (synopsis "Layout and render international text")
+    (description "Pango is a library for laying out and rendering text, with an
+emphasis on internationalization.  Pango can be used anywhere that text layout
+is needed, but using Pango in conjunction with Cairo and/or Gtk2 provides a
+complete solution with high quality text handling and graphics rendering.
+
+Dynamically loaded modules handle text layout for particular combinations of
+script and font backend.  Pango provides a wide selection of modules, including
+modules for Hebrew, Arabic, Hangul, Thai, and a number of Indic scripts.
+Virtually all of the world's major scripts are supported.
+
+In addition to the low level layout rendering routines, Pango includes
+@code{Pango::Layout}, a high level driver for laying out entire blocks of text,
+and routines to assist in editing internationalized text.")
+    (license license:lgpl2.1+)))
+
 (define-public girara
   (package
     (name "girara")
-- 
cgit v1.2.3


From b5bbcda3ee7d7fbbf74724afc41e55cc2a265d8b Mon Sep 17 00:00:00 2001
From: Alex Vong <alexvong1995@gmail.com>
Date: Sun, 25 Feb 2018 06:51:09 +0800
Subject: gnu: Add perl-gtk2.

* gnu/packages/gtk.scm (perl-gtk2): New public variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
---
 gnu/packages/gtk.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm
index 0e4f9c86c4..ceb3f4dc4e 100644
--- a/gnu/packages/gtk.scm
+++ b/gnu/packages/gtk.scm
@@ -1265,6 +1265,33 @@ cairo.  It supports multiple output targets, including PNG, PDF and SVG.  Cairo
 produces identical output on all those targets.")
     (license license:lgpl2.1+)))
 
+(define-public perl-gtk2
+  (package
+    (name "perl-gtk2")
+    (version "1.24992")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://cpan/authors/id/X/XA/XAOC/Gtk2-"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "1044rj3wbfmgaif2jb0k28m2aczli6ai2n5yvn6pr7zjyw16kvd2"))))
+    (build-system perl-build-system)
+    (native-inputs
+     `(("perl-extutils-depends" ,perl-extutils-depends)
+       ("perl-extutils-pkgconfig" ,perl-extutils-pkgconfig)))
+    (inputs
+     `(("gtk+" ,gtk+-2)))
+    (propagated-inputs
+     `(("perl-pango" ,perl-pango)))
+    (home-page "http://search.cpan.org/dist/Gtk2/")
+    (synopsis "Perl interface to the 2.x series of the Gimp Toolkit library")
+    (description "Perl bindings to the 2.x series of the Gtk+ widget set.
+This module allows you to write graphical user interfaces in a Perlish and
+object-oriented way, freeing you from the casting and memory management in C,
+yet remaining very close in spirit to original API.")
+    (license license:lgpl2.1+)))
+
 (define-public perl-pango
   (package
     (name "perl-pango")
-- 
cgit v1.2.3


From 6f45e45d4daf1d336b22ecef8b1d304fe46ba586 Mon Sep 17 00:00:00 2001
From: Alex Vong <alexvong1995@gmail.com>
Date: Sun, 25 Feb 2018 06:52:10 +0800
Subject: gnu: Add youtube-viewer.

* gnu/packages/video.scm (youtube-viewer): New public variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
---
 gnu/packages/video.scm | 54 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 54 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 0d939ab6d3..8190b0ffc1 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -53,6 +53,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system meson)
+  #:use-module (guix build-system perl)
   #:use-module (guix build-system python)
   #:use-module (guix build-system waf)
   #:use-module (gnu packages)
@@ -1311,6 +1312,59 @@ audio, images) from the Web.  It can use either mpv or vlc for playback.")
     (home-page "https://you-get.org/")
     (license license:expat)))
 
+(define-public youtube-viewer
+  (package
+    (name "youtube-viewer")
+    (version "3.3.3")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/trizen/youtube-viewer/archive/"
+                    version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1j572his6qmazlmyrbnfq62s9bqml875ay7wy26byy9hfc7m0vgk"))))
+    (build-system perl-build-system)
+    (native-inputs
+     `(("perl-module-build" ,perl-module-build)))
+    ;; FIXME: Add optional dependencies once available:
+    ;; perl-lwp-useragent-cached and perl-term-readline-gnu
+    (inputs
+     `(("perl-data-dump" ,perl-data-dump)
+       ("perl-file-sharedir" ,perl-file-sharedir)
+       ("perl-gtk2" ,perl-gtk2)
+       ("perl-json" ,perl-json)
+       ("perl-libwww" ,perl-libwww)
+       ("perl-lwp-protocol-https" ,perl-lwp-protocol-https)
+       ("perl-mozilla-ca" ,perl-mozilla-ca)
+       ("perl-unicode-linebreak" ,perl-unicode-linebreak)))
+    (arguments
+     `(#:modules ((guix build perl-build-system)
+                  (guix build utils)
+                  (srfi srfi-26))
+       #:module-build-flags '("--gtk")
+       #:phases (modify-phases %standard-phases
+                  (add-after 'install 'wrap-program
+                    (lambda* (#:key outputs #:allow-other-keys)
+                      (let ((bin-dir (string-append (assoc-ref outputs "out")
+                                                    "/bin/"))
+                            (perl-path (getenv "PERL5LIB")))
+                        (for-each (cut wrap-program <>
+                                       `("PERL5LIB" ":" prefix (,perl-path)))
+                                  (find-files bin-dir))
+                        #t))))))
+    (synopsis
+     "Lightweight application for searching and streaming videos from YouTube")
+    (description
+     "Youtube-viewer searches and plays YouTube videos in a native player.
+It comes with various search options; it can search for videos, playlists
+and/or channels.  The videos are streamed directly in a selected video player
+at the best resolution (customizable) and with closed-captions (if available).
+Both command-line and GTK2 interface are available.")
+    (home-page "https://github.com/trizen/youtube-viewer")
+    (license license:perl-license)))
+
 (define-public libbluray
   (package
     (name "libbluray")
-- 
cgit v1.2.3


From f03ec1e595b878a6cd2d4771aa14fe848bcdd1e4 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 20:01:03 +0100
Subject: gnu: feh: Update to 2.24.

* gnu/packages/image-viewers.scm (feh): Update to 2.24.
---
 gnu/packages/image-viewers.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/image-viewers.scm b/gnu/packages/image-viewers.scm
index ff34da9f4a..a3887ee22d 100644
--- a/gnu/packages/image-viewers.scm
+++ b/gnu/packages/image-viewers.scm
@@ -59,7 +59,7 @@
 (define-public feh
   (package
     (name "feh")
-    (version "2.23.2")
+    (version "2.24")
     (home-page "https://feh.finalrewind.org/")
     (source (origin
               (method url-fetch)
@@ -67,7 +67,7 @@
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "1hw9xhhmm404ircmd7aw9n51n23wzjxzmav272ldk1pxb2jk3hcn"))))
+                "148qbxkk5m7i3cxymnfwi7aikqjyfxr306dlqm9ndp6x932js5wq"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases (delete 'configure))
-- 
cgit v1.2.3


From 954b677195653ab2061f679fdfc1fcdfd575c72d Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 20:13:41 +0100
Subject: gnu: p11-kit: Update to 0.23.10.

* gnu/packages/tls.scm (p11-kit): Update to 0.23.10.
---
 gnu/packages/tls.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm
index 2233b5974c..45f5255665 100644
--- a/gnu/packages/tls.scm
+++ b/gnu/packages/tls.scm
@@ -125,7 +125,7 @@ in intelligent transportation networks.")
 (define-public p11-kit
   (package
     (name "p11-kit")
-    (version "0.23.9")
+    (version "0.23.10")
     (source
      (origin
       (method url-fetch)
@@ -133,7 +133,7 @@ in intelligent transportation networks.")
                           "download/" version "/p11-kit-" version ".tar.gz"))
       (sha256
        (base32
-        "0qyvnkb5hfi94wv3bn67y20hcbbvynvjwxpk7k9sh1si6ff69hg1"))))
+        "0hxfwnyb5yllvlsh0cj6favcph36gm94b6df7zhl7xay48zjl8gr"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
-- 
cgit v1.2.3


From 6b3ee23b7aaac3ee045d4282cb87f40ab25fc961 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 20:17:31 +0100
Subject: gnu: ldb: Update to 1.3.2.

* gnu/packages/samba.scm (ldb): Update to 1.3.2.
---
 gnu/packages/samba.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/samba.scm b/gnu/packages/samba.scm
index 5ea7858a89..10b26c0ce9 100644
--- a/gnu/packages/samba.scm
+++ b/gnu/packages/samba.scm
@@ -338,14 +338,14 @@ many event types, including timers, signals, and the classic file descriptor eve
 (define-public ldb
   (package
     (name "ldb")
-    (version "1.3.1")
+    (version "1.3.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.samba.org/ftp/ldb/ldb-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1lnbcazm1kqqcc7syy0xbq9srhbylkqhpsmsbsm4c3xfangjr7xi"))))
+                "1avn4fl393kc80krbc47phbp0argdkys62ycs8vm934a6nvz0gnf"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases
-- 
cgit v1.2.3


From 53453d7acc516fb806f81589e0fa3daf4a6349bf Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 20:29:46 +0100
Subject: gnu: wavpack: Fix CVE-2018-6767.

* gnu/packages/patches/wavpack-CVE-2018-6767.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/audio.scm (wavpack)[source](patches): Add it.
---
 gnu/local.mk                                     |   1 +
 gnu/packages/audio.scm                           |   3 +-
 gnu/packages/patches/wavpack-CVE-2018-6767.patch | 119 +++++++++++++++++++++++
 3 files changed, 122 insertions(+), 1 deletion(-)
 create mode 100644 gnu/packages/patches/wavpack-CVE-2018-6767.patch

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index 24368727f2..9cc00b844c 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1142,6 +1142,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/vsearch-unbundle-cityhash.patch		\
   %D%/packages/patches/vte-CVE-2012-2738-pt1.patch			\
   %D%/packages/patches/vte-CVE-2012-2738-pt2.patch			\
+  %D%/packages/patches/wavpack-CVE-2018-6767.patch		\
   %D%/packages/patches/wavpack-CVE-2018-7253.patch		\
   %D%/packages/patches/wavpack-CVE-2018-7254.patch		\
   %D%/packages/patches/weechat-python.patch			\
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 369af141fa..1cf6441df0 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -2378,7 +2378,8 @@ stretching and pitch scaling of audio.  This package contains the library.")
               (method url-fetch)
               (uri (string-append "http://www.wavpack.com/"
                                   name "-" version ".tar.bz2"))
-              (patches (search-patches "wavpack-CVE-2018-7253.patch"
+              (patches (search-patches "wavpack-CVE-2018-6767.patch"
+                                       "wavpack-CVE-2018-7253.patch"
                                        "wavpack-CVE-2018-7254.patch"))
               (sha256
                (base32
diff --git a/gnu/packages/patches/wavpack-CVE-2018-6767.patch b/gnu/packages/patches/wavpack-CVE-2018-6767.patch
new file mode 100644
index 0000000000..f49a8f0fd6
--- /dev/null
+++ b/gnu/packages/patches/wavpack-CVE-2018-6767.patch
@@ -0,0 +1,119 @@
+Fix CVE-2018-6767:
+https://nvd.nist.gov/vuln/detail/CVE-2018-6767
+https://security-tracker.debian.org/tracker/CVE-2018-6767
+
+Patch copied from upstream source repository:
+https://github.com/dbry/WavPack/commit/d5bf76b5a88d044a1be1d5656698e3ba737167e5
+
+From d5bf76b5a88d044a1be1d5656698e3ba737167e5 Mon Sep 17 00:00:00 2001
+From: David Bryant <david@wavpack.com>
+Date: Sun, 4 Feb 2018 11:28:15 -0800
+Subject: [PATCH] issue #27, do not overwrite stack on corrupt RF64 file
+
+---
+ cli/riff.c | 39 ++++++++++++++++++++++++++++++++-------
+ 1 file changed, 32 insertions(+), 7 deletions(-)
+
+diff --git a/cli/riff.c b/cli/riff.c
+index 8b1af45..de98c1e 100644
+--- a/cli/riff.c
++++ b/cli/riff.c
+@@ -42,6 +42,7 @@ typedef struct {
+ 
+ #pragma pack(pop)
+ 
++#define CS64ChunkFormat "4D"
+ #define DS64ChunkFormat "DDDL"
+ 
+ #define WAVPACK_NO_ERROR    0
+@@ -101,13 +102,13 @@ int ParseRiffHeaderConfig (FILE *infile, char *infilename, char *fourcc, Wavpack
+ 
+         if (!strncmp (chunk_header.ckID, "ds64", 4)) {
+             if (chunk_header.ckSize < sizeof (DS64Chunk) ||
+-                !DoReadFile (infile, &ds64_chunk, chunk_header.ckSize, &bcount) ||
+-                bcount != chunk_header.ckSize) {
++                !DoReadFile (infile, &ds64_chunk, sizeof (DS64Chunk), &bcount) ||
++                bcount != sizeof (DS64Chunk)) {
+                     error_line ("%s is not a valid .WAV file!", infilename);
+                     return WAVPACK_SOFT_ERROR;
+             }
+             else if (!(config->qmode & QMODE_NO_STORE_WRAPPER) &&
+-                !WavpackAddWrapper (wpc, &ds64_chunk, chunk_header.ckSize)) {
++                !WavpackAddWrapper (wpc, &ds64_chunk, sizeof (DS64Chunk))) {
+                     error_line ("%s", WavpackGetErrorMessage (wpc));
+                     return WAVPACK_SOFT_ERROR;
+             }
+@@ -315,10 +316,11 @@ int ParseRiffHeaderConfig (FILE *infile, char *infilename, char *fourcc, Wavpack
+ 
+ int WriteRiffHeader (FILE *outfile, WavpackContext *wpc, int64_t total_samples, int qmode)
+ {
+-    int do_rf64 = 0, write_junk = 1;
++    int do_rf64 = 0, write_junk = 1, table_length = 0;
+     ChunkHeader ds64hdr, datahdr, fmthdr;
+     RiffChunkHeader riffhdr;
+     DS64Chunk ds64_chunk;
++    CS64Chunk cs64_chunk;
+     JunkChunk junkchunk;
+     WaveHeader wavhdr;
+     uint32_t bcount;
+@@ -380,6 +382,7 @@ int WriteRiffHeader (FILE *outfile, WavpackContext *wpc, int64_t total_samples,
+     strncpy (riffhdr.formType, "WAVE", sizeof (riffhdr.formType));
+     total_riff_bytes = sizeof (riffhdr) + wavhdrsize + sizeof (datahdr) + ((total_data_bytes + 1) & ~(int64_t)1);
+     if (do_rf64) total_riff_bytes += sizeof (ds64hdr) + sizeof (ds64_chunk);
++    total_riff_bytes += table_length * sizeof (CS64Chunk);
+     if (write_junk) total_riff_bytes += sizeof (junkchunk);
+     strncpy (fmthdr.ckID, "fmt ", sizeof (fmthdr.ckID));
+     strncpy (datahdr.ckID, "data", sizeof (datahdr.ckID));
+@@ -394,11 +397,12 @@ int WriteRiffHeader (FILE *outfile, WavpackContext *wpc, int64_t total_samples,
+ 
+     if (do_rf64) {
+         strncpy (ds64hdr.ckID, "ds64", sizeof (ds64hdr.ckID));
+-        ds64hdr.ckSize = sizeof (ds64_chunk);
++        ds64hdr.ckSize = sizeof (ds64_chunk) + (table_length * sizeof (CS64Chunk));
+         CLEAR (ds64_chunk);
+         ds64_chunk.riffSize64 = total_riff_bytes;
+         ds64_chunk.dataSize64 = total_data_bytes;
+         ds64_chunk.sampleCount64 = total_samples;
++        ds64_chunk.tableLength = table_length;
+         riffhdr.ckSize = (uint32_t) -1;
+         datahdr.ckSize = (uint32_t) -1;
+         WavpackNativeToLittleEndian (&ds64hdr, ChunkHeaderFormat);
+@@ -409,6 +413,14 @@ int WriteRiffHeader (FILE *outfile, WavpackContext *wpc, int64_t total_samples,
+         datahdr.ckSize = (uint32_t) total_data_bytes;
+     }
+ 
++    // this "table" is just a dummy placeholder for testing (normally not written)
++
++    if (table_length) {
++        strncpy (cs64_chunk.ckID, "dmmy", sizeof (cs64_chunk.ckID));
++        cs64_chunk.chunkSize64 = 12345678;
++        WavpackNativeToLittleEndian (&cs64_chunk, CS64ChunkFormat);
++    }
++
+     // write the RIFF chunks up to just before the data starts
+ 
+     WavpackNativeToLittleEndian (&riffhdr, ChunkHeaderFormat);
+@@ -418,8 +430,21 @@ int WriteRiffHeader (FILE *outfile, WavpackContext *wpc, int64_t total_samples,
+ 
+     if (!DoWriteFile (outfile, &riffhdr, sizeof (riffhdr), &bcount) || bcount != sizeof (riffhdr) ||
+         (do_rf64 && (!DoWriteFile (outfile, &ds64hdr, sizeof (ds64hdr), &bcount) || bcount != sizeof (ds64hdr))) ||
+-        (do_rf64 && (!DoWriteFile (outfile, &ds64_chunk, sizeof (ds64_chunk), &bcount) || bcount != sizeof (ds64_chunk))) ||
+-        (write_junk && (!DoWriteFile (outfile, &junkchunk, sizeof (junkchunk), &bcount) || bcount != sizeof (junkchunk))) ||
++        (do_rf64 && (!DoWriteFile (outfile, &ds64_chunk, sizeof (ds64_chunk), &bcount) || bcount != sizeof (ds64_chunk)))) {
++            error_line ("can't write .WAV data, disk probably full!");
++            return FALSE;
++    }
++
++    // again, this is normally not written except for testing
++
++    while (table_length--)
++        if (!DoWriteFile (outfile, &cs64_chunk, sizeof (cs64_chunk), &bcount) || bcount != sizeof (cs64_chunk)) {
++            error_line ("can't write .WAV data, disk probably full!");
++            return FALSE;
++        }
++
++
++    if ((write_junk && (!DoWriteFile (outfile, &junkchunk, sizeof (junkchunk), &bcount) || bcount != sizeof (junkchunk))) ||
+         !DoWriteFile (outfile, &fmthdr, sizeof (fmthdr), &bcount) || bcount != sizeof (fmthdr) ||
+         !DoWriteFile (outfile, &wavhdr, wavhdrsize, &bcount) || bcount != wavhdrsize ||
+         !DoWriteFile (outfile, &datahdr, sizeof (datahdr), &bcount) || bcount != sizeof (datahdr)) {
-- 
cgit v1.2.3


From 3374dcc78c49f3a94da471e500bd13eab7723429 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Wed, 28 Feb 2018 21:30:11 +0200
Subject: gnu: keepassxc: Update to 2.3.0.

* gnu/packages/password-utils.scm (keepassxc): Update to 2.3.0.
---
 gnu/packages/password-utils.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm
index e8639c02e1..5a1d89b644 100644
--- a/gnu/packages/password-utils.scm
+++ b/gnu/packages/password-utils.scm
@@ -89,7 +89,7 @@ human.")
 (define-public keepassxc
   (package
     (name "keepassxc")
-    (version "2.2.4")
+    (version "2.3.0")
     (source
      (origin
        (method url-fetch)
@@ -98,10 +98,11 @@ human.")
                            version "-src.tar.xz"))
        (sha256
         (base32
-         "1pfkq1m5vb90kx67vyw70s1hc4ivjsvq2535vm6wdwwsncna6bz5"))))
+         "1v6v59fnbbsssbwy4is6hh2l4qqwy3ddb6dp2jk8clx0xbd5hn7c"))))
     (build-system cmake-build-system)
     (inputs
-     `(("libgcrypt" ,libgcrypt)
+     `(("argon2" ,argon2)
+       ("libgcrypt" ,libgcrypt)
        ("libxi" ,libxi)
        ("libxtst" ,libxtst)
        ("qtbase" ,qtbase)
-- 
cgit v1.2.3


From da1b30bd931563927545cd97fd47c07ca4d5f8c4 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Wed, 28 Feb 2018 21:44:23 +0200
Subject: gnu: keepassxc: Enable various plugins.

* gnu/packages/password-utils.scm (keepassxc)[arguments]: Add
configure-flags to enable favicons, browser integration and ssh-agent.
[inputs]: Add curl, libsodium.
---
 gnu/packages/password-utils.scm | 8 ++++++++
 1 file changed, 8 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm
index 5a1d89b644..955302dcb7 100644
--- a/gnu/packages/password-utils.scm
+++ b/gnu/packages/password-utils.scm
@@ -44,6 +44,8 @@
   #:use-module (gnu packages base)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages crypto)
+  #:use-module (gnu packages curl)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnupg)
@@ -100,9 +102,15 @@ human.")
         (base32
          "1v6v59fnbbsssbwy4is6hh2l4qqwy3ddb6dp2jk8clx0xbd5hn7c"))))
     (build-system cmake-build-system)
+    (arguments
+     '(#:configure-flags '("-DWITH_XC_NETWORKING=YES"
+                           "-DWITH_XC_BROWSER=YES"
+                           "-DWITH_XC_SSHAGENT=YES")))
     (inputs
      `(("argon2" ,argon2)
+       ("curl" ,curl) ; XC_NETWORKING
        ("libgcrypt" ,libgcrypt)
+       ("libsodium" ,libsodium) ; XC_BROWSER
        ("libxi" ,libxi)
        ("libxtst" ,libxtst)
        ("qtbase" ,qtbase)
-- 
cgit v1.2.3


From bcc65510839d1b1800e0fd93b7e4c4d8f79a754c Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Wed, 28 Feb 2018 22:10:47 +0200
Subject: gnu: ccl: Patch absolute file-name.

* gnu/packages/lisp.scm (ccl)[arguments]: In 'pre-build add substitution
for /bin/pwd.
---
 gnu/packages/lisp.scm | 2 ++
 1 file changed, 2 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index f05d7eec78..a506566a05 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -484,6 +484,8 @@ statistical profiler, a code coverage tool, and many other extensions.")
            ;; Enter the source directory for the current platform's lisp
            ;; kernel, and run 'make clean' to remove the precompiled one.
            (lambda _
+             (substitute* "lisp-kernel/m4macros.m4"
+               (("/bin/pwd") (which "pwd")))
              (chdir (string-append
                      "lisp-kernel/"
                      ,(match (or (%current-target-system) (%current-system))
-- 
cgit v1.2.3


From 63e48300d19b848dfe75880581338c2c73b7b0df Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Wed, 28 Feb 2018 16:43:59 +0100
Subject: gnu: guile-static-stripped: Remove dependency on bash-minimal.

Previously guile-static-stripped, which is embedded in the initrd, would
depend on 'bash-minimal' and 'glibc'; the closure size was 77 MiB.  Now
the closure size is down to 45.7 MiB.

Reported by Danny Milosavljevic <dannym@scratchpost.org> in
<https://lists.gnu.org/archive/html/guix-devel/2018-02/msg00505.html>.

* gnu/packages/make-bootstrap.scm (%guile-static): Remove the
'pre-configure' phase.
(%guile-static-stripped)[arguments]: Add #:allowed-references.
---
 gnu/packages/make-bootstrap.scm | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/make-bootstrap.scm b/gnu/packages/make-bootstrap.scm
index f1c4bf7bc5..779b7ef5aa 100644
--- a/gnu/packages/make-bootstrap.scm
+++ b/gnu/packages/make-bootstrap.scm
@@ -532,6 +532,13 @@ for `sh' in $PATH, and without nscd, and with static NSS modules."
                       ''("LDFLAGS=-ldl"))
                      ((#:phases phases '%standard-phases)
                       `(modify-phases ,phases
+
+                         ;; Do not record the absolute file name of 'sh' in
+                         ;; (ice-9 popen).  This makes 'open-pipe' unusable in
+                         ;; a build chroot ('open-pipe*' is fine) but avoids
+                         ;; keeping a reference to Bash.
+                         (delete 'pre-configure)
+
                          (add-before 'configure 'static-guile
                            (lambda _
                              (substitute* "libguile/Makefile.in"
@@ -557,7 +564,9 @@ for `sh' in $PATH, and without nscd, and with static NSS modules."
     (name "guile-static-stripped")
     (build-system trivial-build-system)
     (arguments
-     `(#:modules ((guix build utils))
+     ;; The end result should depend on nothing but itself.
+     `(#:allowed-references ("out")
+       #:modules ((guix build utils))
        #:builder
        (let ()
          (use-modules (guix build utils))
-- 
cgit v1.2.3


From 4c853b7c11e96eb68891c5e48fefa835913fb589 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Wed, 28 Feb 2018 22:01:16 +0100
Subject: gnu: guile-static-stripped: Add 'finit_module' wrapper.

* gnu/packages/patches/guile-linux-syscalls.patch: Add
'load-linux-module/fd' procedure.
---
 gnu/packages/patches/guile-linux-syscalls.patch | 50 +++++++++++++++++++++++--
 1 file changed, 46 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/patches/guile-linux-syscalls.patch b/gnu/packages/patches/guile-linux-syscalls.patch
index 69970a3e60..12cddff47b 100644
--- a/gnu/packages/patches/guile-linux-syscalls.patch
+++ b/gnu/packages/patches/guile-linux-syscalls.patch
@@ -3,17 +3,21 @@ This patch adds bindings to Linux syscalls for which glibc has symbols.
 Using the FFI would have been nice, but that's not an option when using
 a statically-linked Guile in an initrd that doesn't have libc.so around.
 
---- guile-2.0.11/libguile/posix.c.orig	2014-02-28 15:01:27.000000000 -0500
-+++ guile-2.0.11/libguile/posix.c	2015-06-21 14:28:23.624251038 -0400
-@@ -2245,6 +2245,295 @@
+diff --git a/libguile/posix.c b/libguile/posix.c
+index b0fcad5fd..1343186e3 100644
+--- a/libguile/posix.c
++++ b/libguile/posix.c
+@@ -2341,6 +2341,335 @@ scm_init_popen (void)
  }
- #endif
+ #endif /* HAVE_START_CHILD */
  
 +
 +/* Linux! */
 +#ifdef __linux__
 +
 +#include <sys/mount.h>
++#include <sys/syscall.h>
++
 +#include "libguile/foreign.h"
 +#include "libguile/bytevectors.h"
 +
@@ -91,6 +95,16 @@ a statically-linked Guile in an initrd that doesn't have libc.so around.
 +   ARGS, a space-separated list of options.  */
 +extern long init_module (void *module, unsigned long len, const char *args);
 +
++/* Load a kernel module from FD.  FLAGS must be a bitwise or of
++   MODULE_INIT_* constants.  The GNU libc doesn't provide a wrapper for
++   this one so we use 'syscall'.  */
++static int
++finit_module (int fd, const char *args, int flags)
++{
++  return syscall (SYS_finit_module, fd, args, flags);
++}
++
++
 +SCM_DEFINE (scm_load_linux_module, "load-linux-module", 1, 1, 0,
 +	    (SCM data, SCM options),
 +	    "Load the Linux kernel module whose contents are in bytevector "
@@ -121,6 +135,34 @@ a statically-linked Guile in an initrd that doesn't have libc.so around.
 +}
 +#undef FUNC_NAME
 +
++SCM_DEFINE (scm_load_linux_module_fd, "load-linux-module/fd", 1, 2, 0,
++	    (SCM fd, SCM options, SCM flags),
++	    "Load the Linux kernel module from the file at FD, "
++	    "with the arguments from the OPTIONS string, and "
++            "optionally the given FLAGS.")
++#define FUNC_NAME s_scm_load_linux_module_fd
++{
++  long err;
++  int c_fd, c_flags;
++  char *c_options;
++
++  c_fd = scm_to_int (fd);
++  c_options =
++    scm_to_locale_string (SCM_UNBNDP (options) ? scm_nullstr : options);
++  c_flags = SCM_UNBNDP (flags) ? 0 : scm_to_int (flags);
++
++  err = finit_module (c_fd, c_options, c_flags);
++
++  free (c_options);
++
++  if (err != 0)
++    SCM_SYSERROR;
++
++  return SCM_UNSPECIFIED;
++}
++#undef FUNC_NAME
++
++
 +/* Rebooting, halting, and all that.  */
 +
 +#include <sys/reboot.h>
-- 
cgit v1.2.3


From 649eb8b5674a92638c4cbb2562cfc45935c0f06e Mon Sep 17 00:00:00 2001
From: Konrad Hinsen <konrad.hinsen@fastmail.net>
Date: Wed, 28 Feb 2018 15:21:24 +0100
Subject: gnu: Add sala.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/password-utils.scm (sala): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/password-utils.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm
index 955302dcb7..96a51f0dd4 100644
--- a/gnu/packages/password-utils.scm
+++ b/gnu/packages/password-utils.scm
@@ -16,6 +16,7 @@
 ;;; Copyright © 2017 Manolis Fragkiskos Ragkousis <manolis837@gmail.com>
 ;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -612,3 +613,31 @@ password hash types most commonly found on various Unix systems, supported out
 of the box are Windows LM hashes, plus lots of other hashes and ciphers.  This
 is the community-enhanced, \"jumbo\" version of John the Ripper.")
       (license license:gpl2+))))
+
+(define-public sala
+  (package
+    (name "sala")
+    (version "1.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "sala" version))
+       (sha256
+        (base32
+         "13qgmc3i2a0cqp8jqrfl93lnphfagb32pgfikc1gza2a14asxzi8"))))
+    (build-system python-build-system)
+    (arguments
+     ;; Sala is supposed to work with Python 3.2 or higher,
+     ;; but it doesn't work with Python 3.6. Better stick
+     ;; to Python 2, which works fine.
+     `(#:python ,python-2))
+    (propagated-inputs
+     `(("gnupg" ,gnupg)
+       ("pwgen" ,pwgen)))
+    (home-page "http://www.digip.org/sala/")
+    (synopsis "Encrypted plaintext password store")
+    (description
+     "Store passwords and other bits of sensitive plain-text information
+to encrypted files on a directory hierarchy.  The information is protected
+by GnuPG's symmetrical encryption.")
+    (license license:expat)))
-- 
cgit v1.2.3


From aa08ab38cd1726abc396adabe823040c2968e884 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 12 Feb 2018 11:08:54 +0100
Subject: gnu: dropbear: Update to 2018.76.

* gnu/packages/ssh.scm (dropbear): Update to 2018.76.
---
 gnu/packages/ssh.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/ssh.scm b/gnu/packages/ssh.scm
index b439094c26..d7b1897051 100644
--- a/gnu/packages/ssh.scm
+++ b/gnu/packages/ssh.scm
@@ -6,7 +6,7 @@
 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2016 Christopher Allan Webber <cwebber@dustycloud.org>
-;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Stefan Reichör <stefan@xsteve.at>
 ;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 ng0 <ng0@n0.is>
@@ -408,7 +408,7 @@ TCP, not the SSH protocol.")
 (define-public dropbear
   (package
     (name "dropbear")
-    (version "2017.75")
+    (version "2018.76")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -416,9 +416,9 @@ TCP, not the SSH protocol.")
                     name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "1309cm2aw62n9m3h38prvgsqr8bj85hfasgnvwkd42cp3k5ivg3c"))))
+                "0rgavbzw7jrs5wslxm0dnwx2m409yzxd9hazd92r7kx8xikr3yzj"))))
     (build-system gnu-build-system)
-    (arguments  `(#:tests? #f)) ; There is no "make check" or anything similar
+    (arguments `(#:tests? #f)) ; there is no "make check" or anything similar
     (inputs `(("zlib" ,zlib)))
     (synopsis "Small SSH server and client")
     (description "Dropbear is a relatively small SSH server and
-- 
cgit v1.2.3


From 30bbb86ae3ffb591f9a9fe39d5f7efe33a72c31f Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 28 Feb 2018 16:51:28 +0100
Subject: gnu: git-remote-gcrypt: Update to 1.0.2.

* gnu/packages/version-control.scm (git-remote-gcrypt): Update to 1.0.2.
---
 gnu/packages/version-control.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index ef19382365..6c05ab59db 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -473,7 +473,7 @@ to lock down your entire repository.")
 (define-public git-remote-gcrypt
   (package
    (name "git-remote-gcrypt")
-   (version "1.0.1")
+   (version "1.0.2")
    (source (origin
              (method git-fetch)
              (uri (git-reference
@@ -482,7 +482,7 @@ to lock down your entire repository.")
              (file-name (string-append name "-" version "-checkout"))
              (sha256
               (base32
-               "0znrx77vpm4a8l7yiybsxk5vrawijqqfxmp1p2yhaaw8cbgrj7az"))))
+               "0kc6qi5gavziqlwnzpy7v4ah7yw860v3i8pyna6way0cfr0qnpr2"))))
    (build-system trivial-build-system)
    (arguments
     `(#:modules ((guix build utils))
-- 
cgit v1.2.3


From 0828bd82bd72bf198ee8374f45aca2e3db96daf9 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 28 Feb 2018 16:26:14 +0100
Subject: gnu: libftdi: Update to 1.4.

* gnu/packages/libftdi.scm (libftdi): Update to 1.4.
---
 gnu/packages/libftdi.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/libftdi.scm b/gnu/packages/libftdi.scm
index 208e13546e..78f849d02d 100644
--- a/gnu/packages/libftdi.scm
+++ b/gnu/packages/libftdi.scm
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 Manolis Fragkiskos Ragkousis <manolis837@gmail.com>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -27,7 +28,7 @@
 (define-public libftdi
   (package
     (name "libftdi")
-    (version "1.1")
+    (version "1.4")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -35,7 +36,7 @@
                     version ".tar.bz2"))
               (sha256
                (base32
-                "088yh8pxd6q53ssqndydcw1dkq51cjqyahc03lm6iip22cdazcf0"))))
+                "0x0vncf6i92slgrn0h7ghkskqbglbs534220qa84d0qg114zndpc"))))
     (build-system cmake-build-system)
     (propagated-inputs
      `(("libusb" ,libusb))) ; required by libftdi1.pc
-- 
cgit v1.2.3


From 4321aeb6d34904cb9401e769009315e9c86c1941 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 28 Feb 2018 22:53:47 +0100
Subject: gnu: html-xml-utils: Update to 7.6.

* gnu/packages/xml.scm (html-xml-utils): Update to 7.6.
---
 gnu/packages/xml.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm
index 67e1ca7427..add374c899 100644
--- a/gnu/packages/xml.scm
+++ b/gnu/packages/xml.scm
@@ -1109,7 +1109,7 @@ XSLT and EXSLT.")
 (define-public html-xml-utils
  (package
    (name "html-xml-utils")
-   (version "7.5")
+   (version "7.6")
    (source
     (origin
       (method url-fetch)
@@ -1118,7 +1118,7 @@ XSLT and EXSLT.")
             version ".tar.gz"))
       (sha256
        (base32
-        "0cbmqa9c4bc4ikk7vmgd65ixh2pl9mr336c4his3m8l7rgsjnh8n"))))
+        "0l97ps089byy62838wf2jwvvc465iw29z9r5kwmwcq7f3bn11y3m"))))
    (build-system gnu-build-system)
    (home-page "https://www.w3.org/Tools/HTML-XML-utils/")
    (synopsis "Command line utilities to manipulate HTML and XML files")
-- 
cgit v1.2.3


From 9d43579f2d7d517de3a67c41b2429b467c651514 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 28 Feb 2018 22:57:04 +0100
Subject: gnu: dovecot: Update to 2.3.0.1 [fixes CVE-2017-14461].

* gnu/packages/mail.scm (dovecot): Update to 2.3.0.1.
[source]: Remove upstreamed patch.
* gnu/packages/patches/dovecot-CVE-2017-15132.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/local.mk                                      |  1 -
 gnu/packages/mail.scm                             |  5 ++--
 gnu/packages/patches/dovecot-CVE-2017-15132.patch | 36 -----------------------
 3 files changed, 2 insertions(+), 40 deletions(-)
 delete mode 100644 gnu/packages/patches/dovecot-CVE-2017-15132.patch

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index 9cc00b844c..3d0bd38e50 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -618,7 +618,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/docbook-xsl-nonrecursive-string-subst.patch	\
   %D%/packages/patches/doc++-include-directives.patch		\
   %D%/packages/patches/doc++-segfault-fix.patch			\
-  %D%/packages/patches/dovecot-CVE-2017-15132.patch		\
   %D%/packages/patches/doxygen-test.patch			\
   %D%/packages/patches/dvd+rw-tools-add-include.patch 		\
   %D%/packages/patches/eigen-arm-neon-fixes.patch		\
diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index 9fbfddbec1..8d3544f908 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -1180,16 +1180,15 @@ facilities for checking incoming mail.")
 (define-public dovecot
   (package
     (name "dovecot")
-    (version "2.3.0")
+    (version "2.3.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://www.dovecot.org/releases/"
                            (version-major+minor version) "/"
                            name "-" version ".tar.gz"))
-       (patches (search-patches "dovecot-CVE-2017-15132.patch"))
        (sha256 (base32
-                "10c5myzgys866c3x6jdr1s9x9pqnjd5vpyz8z384sph21m3wnq6y"))))
+                "0lzisrdgrj5qqwjb7bv99mf2aljm568r6g108yisp0s644z2nxxb"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
diff --git a/gnu/packages/patches/dovecot-CVE-2017-15132.patch b/gnu/packages/patches/dovecot-CVE-2017-15132.patch
deleted file mode 100644
index 32666b8557..0000000000
--- a/gnu/packages/patches/dovecot-CVE-2017-15132.patch
+++ /dev/null
@@ -1,36 +0,0 @@
-Fix CVE-2017-15132:
-
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-15132
-
-Patch copied from upstream source repository:
-
-https://github.com/dovecot/core/commit/1a29ed2f96da1be22fa5a4d96c7583aa81b8b060
-
-From 1a29ed2f96da1be22fa5a4d96c7583aa81b8b060 Mon Sep 17 00:00:00 2001
-From: Timo Sirainen <timo.sirainen@dovecot.fi>
-Date: Mon, 18 Dec 2017 16:50:51 +0200
-Subject: [PATCH] lib-auth: Fix memory leak in auth_client_request_abort()
-
-This caused memory leaks when authentication was aborted. For example
-with IMAP:
-
-a AUTHENTICATE PLAIN
-*
-
-Broken by 9137c55411aa39d41c1e705ddc34d5bd26c65021
----
- src/lib-auth/auth-client-request.c | 1 +
- 1 file changed, 1 insertion(+)
-
-diff --git a/src/lib-auth/auth-client-request.c b/src/lib-auth/auth-client-request.c
-index 480fb42b30..046f7c307d 100644
---- a/src/lib-auth/auth-client-request.c
-+++ b/src/lib-auth/auth-client-request.c
-@@ -186,6 +186,7 @@ void auth_client_request_abort(struct auth_client_request **_request)
- 
- 	auth_client_send_cancel(request->conn->client, request->id);
- 	call_callback(request, AUTH_REQUEST_STATUS_ABORT, NULL, NULL);
-+	pool_unref(&request->pool);
- }
- 
- unsigned int auth_client_request_get_id(struct auth_client_request *request)
-- 
cgit v1.2.3


From c1cb8576453db450493726ab44f34910dfa10ed7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 28 Feb 2018 22:12:52 +0100
Subject: gnu: Add java-ecj-3.

* gnu/packages/java.scm (java-ecj-3): New variable.
---
 gnu/packages/java.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 2b7a76fda3..4ea6f4d8c3 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -2018,6 +2018,41 @@ debugging, etc.")
              (delete-file-recursively "lib") #t))
          (replace 'install (install-jars "bin/lib")))))))
 
+;; This is the last 3.x release of ECJ
+(define-public java-ecj-3
+  (package
+    (name "java-ecj")
+    (version "3.8.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://archive.eclipse.org/eclipse/"
+                                  "downloads/drops/R-" version
+                                  "-201301310800/ecjsrc-" version ".jar"))
+              (sha256
+               (base32
+                "01mdj14jw11g1jfnki4fi8229p0c6zzckd38zqy2w4m3cjcvsx04"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:tests? #f ; none included
+       #:jdk ,icedtea-7 ; doesn't build with JDK8+
+       #:make-flags (list "-f" "src/build.xml")
+       #:build-target "build"
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-manifest
+           (lambda _
+             ;; Record the main class to make ecj executable.
+             (with-atomic-file-replacement "src/META-INF/MANIFEST.MF"
+               (lambda (in out)
+                 (display "Manifest-Version: 1.0
+Main-Class: org.eclipse.jdt.internal.compiler.batch.Main\n"
+                          out)))))
+         (replace 'install (install-jars ".")))))
+    (home-page "https://eclipse.org")
+    (synopsis "Eclipse Java development tools core batch compiler")
+    (description "This package provides the Eclipse Java core batch compiler.")
+    (license license:epl1.0)))
+
 (define-public java-classpathx-servletapi
   (package
     (name "java-classpathx-servletapi")
-- 
cgit v1.2.3


From f201b18ed7d7f8ab640f2e571aad765cf3c572dd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 28 Feb 2018 22:13:12 +0100
Subject: gnu: Add java-ecj-3.5.

* gnu/packages/java.scm (java-ecj-3.5): New variable.
---
 gnu/packages/java.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 4ea6f4d8c3..7a90bfba00 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -2053,6 +2053,37 @@ Main-Class: org.eclipse.jdt.internal.compiler.batch.Main\n"
     (description "This package provides the Eclipse Java core batch compiler.")
     (license license:epl1.0)))
 
+;; This is needed for java-cisd-args4j
+(define-public java-ecj-3.5
+  (package (inherit java-ecj-3)
+    (version "3.5.1")
+    (source (origin
+              (method url-fetch/zipbomb)
+              (uri (string-append "http://archive.eclipse.org/eclipse/"
+                                  "downloads/drops/R-" version
+                                  "-200909170800/ecjsrc-" version ".zip"))
+              (sha256
+               (base32
+                "1vnl2mavisc567bip736xzsvvbjif5279wc4a7pbdik5wlir8qr7"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:tests? #f ; none included
+       #:jdk ,icedtea-7 ; doesn't build with JDK8+
+       #:build-target "build"
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-manifest
+           (lambda _
+             ;; Record the main class to make ecj executable.
+             (with-atomic-file-replacement "META-INF/MANIFEST.MF"
+               (lambda (in out)
+                 (dump-port in out)
+                 (display "Main-Class: org.eclipse.jdt.internal.compiler.batch.Main\n"
+                          out)))))
+         (replace 'install (install-jars ".")))))
+    (native-inputs
+     `(("unzip" ,unzip)))))
+
 (define-public java-classpathx-servletapi
   (package
     (name "java-classpathx-servletapi")
-- 
cgit v1.2.3


From 602f54f436d41634adaa56e4ff645a6bad202daf Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 27 Feb 2018 20:36:58 +0100
Subject: gnu: java-jnacl: Use invoke.

* gnu/packages/java.scm (java-jnacl)[arguments]: Use "invoke".
---
 gnu/packages/java.scm | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 7a90bfba00..bc2fb32eba 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -7538,18 +7538,18 @@ to use.")
              #t))
          (replace 'check
            (lambda _
-             (system* "ant" "compile-tests")
-             (and
-               (zero? (system* "java" "-cp" (string-append (getenv "CLASSPATH")
-                                                           ":build/classes"
-                                                           ":build/test-classes")
-                               "org.testng.TestNG" "-testclass"
-                               "build/test-classes/com/neilalexander/jnacl/NaclSecretBoxTest.class"))
-               (zero? (system* "java" "-cp" (string-append (getenv "CLASSPATH")
-                                                           ":build/classes"
-                                                           ":build/test-classes")
-                               "org.testng.TestNG" "-testclass"
-                               "build/test-classes/com/neilalexander/jnacl/NaClTest.class"))))))))
+             (invoke "ant" "compile-tests")
+             (invoke "java" "-cp" (string-append (getenv "CLASSPATH")
+                                                 ":build/classes"
+                                                 ":build/test-classes")
+                     "org.testng.TestNG" "-testclass"
+                     "build/test-classes/com/neilalexander/jnacl/NaclSecretBoxTest.class")
+             (invoke "java" "-cp" (string-append (getenv "CLASSPATH")
+                                                 ":build/classes"
+                                                 ":build/test-classes")
+                     "org.testng.TestNG" "-testclass"
+                     "build/test-classes/com/neilalexander/jnacl/NaClTest.class")
+             #t)))))
     (native-inputs
      `(("java-testng" ,java-testng)
        ("java-fest-util" ,java-fest-util)
-- 
cgit v1.2.3


From e15864281615d3bc72d772b9bea704accd9262c3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 27 Feb 2018 20:39:38 +0100
Subject: gnu: java-jnacl: Correct license.

* gnu/packages/java.scm (java-jnacl)[license]: Change to BSD-2.
---
 gnu/packages/java.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index bc2fb32eba..e7715b4b3c 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -7558,7 +7558,7 @@ to use.")
     (synopsis "Java implementation of NaCl")
     (description "Pure Java implementation of the NaCl: Networking and
 Cryptography library.")
-    (license license:mpl2.0)))
+    (license license:bsd-2)))
 
 (define-public java-mvel2
   (package
-- 
cgit v1.2.3


From 8333c206a90977c5080313b1cb85b0513bd8e12d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 27 Feb 2018 20:40:02 +0100
Subject: gnu: java-jnacl: Simplify build phase.

* gnu/packages/java.scm (java-jnacl)[arguments]: Simplify "fix-tests" phase.
---
 gnu/packages/java.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index e7715b4b3c..a197da819c 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -7531,9 +7531,8 @@ to use.")
        (modify-phases %standard-phases
          (add-before 'build 'fix-tests
            (lambda _
-             (substitute* "src/test/java/com/neilalexander/jnacl/NaClTest.java"
-               (("assertions.Assertions") "assertions.api.Assertions"))
-             (substitute* "src/test/java/com/neilalexander/jnacl/NaclSecretBoxTest.java"
+             (substitute* '("src/test/java/com/neilalexander/jnacl/NaClTest.java"
+                            "src/test/java/com/neilalexander/jnacl/NaclSecretBoxTest.java")
                (("assertions.Assertions") "assertions.api.Assertions"))
              #t))
          (replace 'check
-- 
cgit v1.2.3


From 3e87923a67bb1352651ee0877633934fa0457f72 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 27 Feb 2018 20:43:05 +0100
Subject: gnu: java-jnacl: Update to 0.1.0-2.094e819.

* gnu/packages/java.scm (java-jnacl): Update to 0.1.0-2.094e819.
---
 gnu/packages/java.scm | 94 ++++++++++++++++++++++++++-------------------------
 1 file changed, 48 insertions(+), 46 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index a197da819c..c527e6898b 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -7511,53 +7511,55 @@ to use.")
     (license license:asl2.0)))
 
 (define-public java-jnacl
-  (package
-    (name "java-jnacl")
-    (version "0.1.0")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                     (url "https://github.com/neilalexander/jnacl")
-                     (commit "40c322e0a42637ab17cdf941138eeaf2494055f8")))
-              (sha256
-               (base32
-                "1pspnmp44q61a2q4bpslpxw86rfn8s5l0xgvyrikqgdvg7ypx597"))))
-    (build-system ant-build-system)
-    (arguments
-     `(#:jar-name "java-jnacl.jar"
-       #:source-dir "src/main/java"
-       #:jdk ,icedtea-8
-       #:phases
-       (modify-phases %standard-phases
-         (add-before 'build 'fix-tests
-           (lambda _
-             (substitute* '("src/test/java/com/neilalexander/jnacl/NaClTest.java"
-                            "src/test/java/com/neilalexander/jnacl/NaclSecretBoxTest.java")
-               (("assertions.Assertions") "assertions.api.Assertions"))
-             #t))
-         (replace 'check
-           (lambda _
-             (invoke "ant" "compile-tests")
-             (invoke "java" "-cp" (string-append (getenv "CLASSPATH")
-                                                 ":build/classes"
-                                                 ":build/test-classes")
-                     "org.testng.TestNG" "-testclass"
-                     "build/test-classes/com/neilalexander/jnacl/NaclSecretBoxTest.class")
-             (invoke "java" "-cp" (string-append (getenv "CLASSPATH")
-                                                 ":build/classes"
-                                                 ":build/test-classes")
-                     "org.testng.TestNG" "-testclass"
-                     "build/test-classes/com/neilalexander/jnacl/NaClTest.class")
-             #t)))))
-    (native-inputs
-     `(("java-testng" ,java-testng)
-       ("java-fest-util" ,java-fest-util)
-       ("java-fest-assert" ,java-fest-assert)))
-    (home-page "https://github.com/neilalexander/jnacl")
-    (synopsis "Java implementation of NaCl")
-    (description "Pure Java implementation of the NaCl: Networking and
+  (let ((commit "094e819afdd63ea81a499b3bcb42a271006bebd9")
+        (revision "2"))
+    (package
+      (name "java-jnacl")
+      (version (string-append "0.1.0-" revision "." (string-take commit 7)))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/neilalexander/jnacl.git")
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "1d6g6xhn83byv5943n7935wwjsk0ibk0qdvqgr699qqgqqmwisbb"))))
+      (build-system ant-build-system)
+      (arguments
+       `(#:jar-name "java-jnacl.jar"
+         #:source-dir "src/main/java"
+         #:jdk ,icedtea-8
+         #:phases
+         (modify-phases %standard-phases
+           (add-before 'build 'fix-tests
+             (lambda _
+               (substitute* '("src/test/java/com/neilalexander/jnacl/NaClTest.java"
+                              "src/test/java/com/neilalexander/jnacl/NaclSecretBoxTest.java")
+                 (("assertions.Assertions") "assertions.api.Assertions"))
+               #t))
+           (replace 'check
+             (lambda _
+               (invoke "ant" "compile-tests")
+               (invoke "java" "-cp" (string-append (getenv "CLASSPATH")
+                                                   ":build/classes"
+                                                   ":build/test-classes")
+                       "org.testng.TestNG" "-testclass"
+                       "build/test-classes/com/neilalexander/jnacl/NaclSecretBoxTest.class")
+               (invoke "java" "-cp" (string-append (getenv "CLASSPATH")
+                                                   ":build/classes"
+                                                   ":build/test-classes")
+                       "org.testng.TestNG" "-testclass"
+                       "build/test-classes/com/neilalexander/jnacl/NaClTest.class")
+               #t)))))
+      (native-inputs
+       `(("java-testng" ,java-testng)
+         ("java-fest-util" ,java-fest-util)
+         ("java-fest-assert" ,java-fest-assert)))
+      (home-page "https://github.com/neilalexander/jnacl")
+      (synopsis "Java implementation of NaCl")
+      (description "Pure Java implementation of the NaCl: Networking and
 Cryptography library.")
-    (license license:bsd-2)))
+      (license license:bsd-2))))
 
 (define-public java-mvel2
   (package
-- 
cgit v1.2.3


From 8c7d32e07c39df8a0d95c142eb46ecf0f8b65e57 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 27 Feb 2018 20:43:56 +0100
Subject: gnu: java-jnacl: Do not prefix jar with "java-".

* gnu/packages/java.scm (java-jnacl)[arguments]: Rename jar to "jnacl.jar".
---
 gnu/packages/java.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index c527e6898b..6350b57a80 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -7526,7 +7526,7 @@ to use.")
                   "1d6g6xhn83byv5943n7935wwjsk0ibk0qdvqgr699qqgqqmwisbb"))))
       (build-system ant-build-system)
       (arguments
-       `(#:jar-name "java-jnacl.jar"
+       `(#:jar-name "jnacl.jar"
          #:source-dir "src/main/java"
          #:jdk ,icedtea-8
          #:phases
-- 
cgit v1.2.3


From 080d0b605aa7cb0dc433d98b24a0bfeea63a2798 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 27 Feb 2018 20:45:53 +0100
Subject: gnu: java-commons-jexl-2: Use invoke.

* gnu/packages/java.scm (java-commons-jexl-2)[arguments]: Use invoke.
---
 gnu/packages/java.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 6350b57a80..830ecaf2ff 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -7654,8 +7654,9 @@ configuration and string construction.")
          (add-before 'build 'run-javacc
            (lambda _
              (with-directory-excursion "src/main/java/org/apache/commons/jexl2/parser/"
-               (and (zero? (system* "java" "jjtree" "Parser.jjt"))
-                    (zero? (system* "java" "javacc" "Parser.jj")))))))))
+               (invoke "java" "jjtree" "Parser.jjt")
+               (invoke "java" "javacc" "Parser.jj"))
+             #t)))))
     (inputs
      `(("java-commons-logging-minimal" ,java-commons-logging-minimal)))
     (native-inputs
-- 
cgit v1.2.3


From 6338ea9a88cb651a9796bdb2a62786d61acd5ad1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 27 Feb 2018 20:48:49 +0100
Subject: gnu: java-hawtjni: Simplify build phases.

* gnu/packages/java.scm (java-hawtjni)[arguments]: Use "invoke" instead of
"system*"; use "install-file" instead of "mkdir-p" and "copy-file".
---
 gnu/packages/java.scm | 25 +++++++++++--------------
 1 file changed, 11 insertions(+), 14 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 830ecaf2ff..579ab9b41c 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -8384,26 +8384,23 @@ including pre-existing objects that you do not have source-code of.")
        (modify-phases %standard-phases
          (add-before 'build 'build-native
            (lambda* (#:key inputs #:allow-other-keys)
-             (with-directory-excursion "hawtjni-generator/src/main/resources/"
-               (and
-                 (system* "gcc" "-c" "hawtjni.c" "-o" "hawtjni.o"
-                          "-fPIC" "-O2"
-                          (string-append "-I" (assoc-ref inputs "jdk") "/include/linux"))
-                 (system* "gcc" "-c" "hawtjni-callback.c" "-o" "hawtjni-callback.o"
-                          "-fPIC" "-O2"
-                          (string-append "-I" (assoc-ref inputs "jdk") "/include/linux"))
-                 (system* "gcc" "-o" "libhawtjni.so" "-shared"
-                          "hawtjni.o" "hawtjni-callback.o")))))
+             (let ((include (string-append "-I" (assoc-ref inputs "jdk") "/include/linux")))
+               (with-directory-excursion "hawtjni-generator/src/main/resources/"
+                 (invoke "gcc" "-c" "hawtjni.c" "-o" "hawtjni.o"
+                         "-fPIC" "-O2" include)
+                 (invoke "gcc" "-c" "hawtjni-callback.c" "-o" "hawtjni-callback.o"
+                         "-fPIC" "-O2" include)
+                 (invoke "gcc" "-o" "libhawtjni.so" "-shared"
+                         "hawtjni.o" "hawtjni-callback.o")))
+             #t))
          (add-after 'install 'install-native
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
                     (lib (string-append out "/lib"))
                     (inc (string-append out "/include")))
-               (mkdir-p lib)
-               (mkdir-p inc)
                (with-directory-excursion "hawtjni-generator/src/main/resources/"
-                 (copy-file "libhawtjni.so" (string-append lib "/libhawtjni.so"))
-                 (copy-file "hawtjni.h" (string-append inc "/hawtjni.h"))))
+                 (install-file "libhawtjni.so" lib)
+                 (install-file "hawtjni.h" inc)))
              #t)))))
     (inputs
      `(("java-commons-cli" ,java-commons-cli)
-- 
cgit v1.2.3


From 3d6925ef51995cf4aab1c128cfcb6c322c0c5467 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 27 Feb 2018 20:52:00 +0100
Subject: gnu: java-jansi-native: Fix description.

* gnu/packages/java.scm (java-jansi-native)[description]: Replace placeholder
text with an actual description.
---
 gnu/packages/java.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 579ab9b41c..1c84358301 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -8465,8 +8465,9 @@ that is part of the SWT Tools project.")
      `(("java-hawtjni" ,java-hawtjni)))
     (home-page "https://fusesource.github.io/jansi/")
     (synopsis "Native library for jansi")
-    (description "Java-jansi-native contains the native library for the jansi
-frobnication library/framework.")
+    (description "This package provides the native library for jansi, a small
+Java library that allows you to use ANSI escape sequences to format your
+console output.")
     (license license:asl2.0)))
 
 (define-public java-jansi
-- 
cgit v1.2.3


From e85c1bf6cd72887eb20680ac8ebf578b5831e6f6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 27 Feb 2018 20:53:15 +0100
Subject: gnu: java-jansi-native: Simplify.

* gnu/packages/java.scm (java-jansi-native)[arguments]: Use "invoke"; remove
useless "mkdir-p".
---
 gnu/packages/java.scm | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 1c84358301..3c208ffe64 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -8437,14 +8437,14 @@ that is part of the SWT Tools project.")
              (with-directory-excursion "src/main/native-package/src"
                (substitute* "jansi_ttyname.c"
                  (("#include \"jansi_.*") ""))
-               (and
-                 (system* "gcc" "-c" "jansi_ttyname.c" "-o" "jansi_ttyname.o"
-                          (string-append "-I" (assoc-ref inputs "java-hawtjni")
-                                         "/include")
-                          (string-append "-I" (assoc-ref inputs "jdk")
-                                         "/include/linux")
-                          "-fPIC" "-O2")
-                 (system* "gcc" "-o" "libjansi.so" "-shared" "jansi_ttyname.o")))))
+               (invoke "gcc" "-c" "jansi_ttyname.c" "-o" "jansi_ttyname.o"
+                       (string-append "-I" (assoc-ref inputs "java-hawtjni")
+                                      "/include")
+                       (string-append "-I" (assoc-ref inputs "jdk")
+                                      "/include/linux")
+                       "-fPIC" "-O2")
+               (invoke "gcc" "-o" "libjansi.so" "-shared" "jansi_ttyname.o")
+               #t)))
          (add-before 'build 'install-native
            (lambda _
              (let ((dir (string-append "build/classes/META-INF/native/"
@@ -8457,7 +8457,6 @@ that is part of the SWT Tools project.")
              #t))
          (add-after 'install 'install-native
            (lambda* (#:key outputs #:allow-other-keys)
-             (mkdir-p (string-append (assoc-ref outputs "out") "/include"))
              (install-file "src/main/native-package/src/jansi.h"
                            (string-append (assoc-ref outputs "out") "/include"))
              #t)))))
-- 
cgit v1.2.3


From 13f38d31a4cf3d3dcc7935c21b3288c65f143f00 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 27 Feb 2018 20:56:02 +0100
Subject: gnu: antlr3-3.1: Use invoke.

* gnu/packages/java.scm (antlr3-3.1)[arguments]: Use invoke.
---
 gnu/packages/java.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 3c208ffe64..b3a0c89366 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -5709,12 +5709,13 @@ import org.antlr.grammar.v2.ANTLRTreePrinter;"))
                (for-each (lambda (file)
                            (display file)
                            (newline)
-                           (system* "antlr" "-o" dir (string-append dir file)))
+                           (invoke "antlr" "-o" dir (string-append dir file)))
                          '("antlr.g" "antlr.print.g" "assign.types.g"
                            "buildnfa.g" "define.g")))
              (format #t "codegen.g\n")
-             (system* "antlr" "-o" "src/org/antlr/codegen"
-                      "src/org/antlr/codegen/codegen.g")))
+             (invoke "antlr" "-o" "src/org/antlr/codegen"
+                     "src/org/antlr/codegen/codegen.g")
+             #t))
          (add-before 'build 'fix-build-xml
            (lambda _
              (substitute* "build.xml"
-- 
cgit v1.2.3


From ec32bc9860fc54b8a4f874f7c67465172b2e1ec2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 27 Feb 2018 20:56:32 +0100
Subject: gnu: antlr3-3.1: Remove version from package name.

* gnu/packages/java.scm (antlr3-3.1)[name]: Remove.
[arguments]: Adjust accordingly.
---
 gnu/packages/java.scm | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index b3a0c89366..9e9c10125c 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -5666,7 +5666,6 @@ import org.antlr.grammar.v2.ANTLRTreePrinter;"))
 (define antlr3-3.1
   (package
     (inherit antlr3)
-    (name "antlr3-3.1")
     (version "3.1")
     (source (origin
               (method url-fetch)
@@ -5677,7 +5676,7 @@ import org.antlr.grammar.v2.ANTLRTreePrinter;"))
                (base32
                 "0sfimc9cpbgrihz4giyygc8afgpma2c93yqpwb951giriri6x66z"))))
     (arguments
-     `(#:jar-name (string-append ,name "-" ,version ".jar")
+     `(#:jar-name (string-append "antlr3-" ,version ".jar")
        #:source-dir "src:runtime/Java/src"
        #:tests? #f
        #:phases
-- 
cgit v1.2.3


From 1b6bc5167519d5c87b87fd4d7e367fbbe54c9b2e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 27 Feb 2018 21:00:24 +0100
Subject: gnu: java-lz4: Use invoke.

* gnu/packages/java.scm (java-lz4)[arguments]: Use invoke.
---
 gnu/packages/java.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 9e9c10125c..8cc3b7201e 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -7696,7 +7696,8 @@ by technical operatives or consultants working with enterprise platforms.")
          (add-before 'configure 'generate-source
            (lambda _
              (with-directory-excursion "src/build/source_templates"
-               (zero? (system* "mvel2" "../gen_sources.mvel" "../../java"))))))))
+               (invoke "mvel2" "../gen_sources.mvel" "../../java"))
+             #t)))))
     (native-inputs
      `(("mvel" ,java-mvel2)))
     (home-page "https://jpountz.github.io/lz4-java")
-- 
cgit v1.2.3


From 9be4b9fa582090a74395e18883e9d97c1b1119e2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 27 Feb 2018 21:02:03 +0100
Subject: gnu: java-bouncycastle-bcprov: Use invoke.

* gnu/packages/java.scm (java-bouncycastle-bcprov)[arguments]: Use invoke.
---
 gnu/packages/java.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 8cc3b7201e..113c75603c 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -7727,7 +7727,8 @@ algorithms and xxHash hashing algorithm.")
            (lambda _
              (mkdir-p "src")
              (with-directory-excursion "src"
-               (zero? (system* "unzip" "../src.zip"))))))))
+               (invoke "unzip" "../src.zip"))
+             #t)))))
     (native-inputs
      `(("unzip" ,unzip)
        ("junit" ,java-junit)))
-- 
cgit v1.2.3


From 201084ac1ff9cace8350ff820f1b30b1720540fe Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 27 Feb 2018 21:03:37 +0100
Subject: gnu: java-bouncycastle-bcpkix: Use invoke.

* gnu/packages/java.scm (java-bouncycastle-bcpkix)[arguments]: Use invoke.
---
 gnu/packages/java.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 113c75603c..0f8c04e8ba 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -7759,7 +7759,8 @@ for the Java programming language.")
            (lambda _
              (mkdir-p "src")
              (with-directory-excursion "src"
-               (zero? (system* "unzip" "../src.zip"))))))))
+               (invoke "unzip" "../src.zip"))
+             #t)))))
     (native-inputs
      `(("unzip" ,unzip)
        ("junit" ,java-junit)))
-- 
cgit v1.2.3


From c1d22365691258500156f4b423f51bac6d9af3b4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 28 Feb 2018 23:01:23 +0100
Subject: gnu: Remove emacs-nov.

The package already exists with the name "emacs-nov-el".

* gnu/packages/emacs.scm (emacs-nov): Remove.
---
 gnu/packages/emacs.scm | 35 -----------------------------------
 1 file changed, 35 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index bb3bf1cf8a..99fe213219 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -3581,41 +3581,6 @@ form is esxml.  This is the form that is returned by such functions as
 xml-related libraries.")
     (license license:gpl3+)))
 
-(define-public emacs-nov
-  (package
-    (name "emacs-nov")
-    (version "0.2.2")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/wasamasa/nov.el/archive/"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
-              (sha256
-               (base32
-                "0pc07cr2qfa66pxyxhvgrxiwssykisj25yjxvx3qr4v7bp5qmms7"))))
-    (build-system emacs-build-system)
-    (propagated-inputs
-     `(("emacs-dash" ,emacs-dash)
-       ("emacs-esxml" ,emacs-esxml)))
-    (home-page "https://github.com/wasamasa/nov.el")
-    (synopsis "Major mode for reading EPUB files in Emacs")
-    (description
-     "This package provides a major mode for reading EPUB documents.
-Features:
-@itemize
-@item Basic navigation (jump to table of contents (TOC), previous/next chapter)
-@item Remembering and restoring the last read position
-@item Jump to next chapter when scrolling beyond end
-@item Renders EPUB2 (.ncx) and EPUB3 (<nav>) TOCs
-@item Hyperlinks to internal and external targets
-@item Supports textual and image documents
-@item View source of document files
-@item Metadata display
-@item Image rescaling
-@end itemize\n")
-    (license license:gpl3+)))
-
 (define-public emacs-queue
   (package
     (name "emacs-queue")
-- 
cgit v1.2.3


From 2adfe819f08ab19cfee7ae381b960de4c110441e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 28 Feb 2018 23:02:36 +0100
Subject: gnu: Remove duplicate definition of emacs-esxml.

* gnu/packages/emacs.scm (emacs-esxml): Remove.
---
 gnu/packages/emacs.scm | 22 ----------------------
 1 file changed, 22 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 99fe213219..67bbb153fb 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -3559,28 +3559,6 @@ The purpose of this library is to wrap all the quirks and hassle of
 @code{package.el} into a sane API.")
     (license license:gpl3+)))
 
-(define-public emacs-esxml
-  (package
-    (name "emacs-esxml")
-    (version "0.3.4")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/tali713/esxml/archive/"
-                    version ".tar.gz"))
-              (sha256
-               (base32
-                "01yk4ibbln3ykrin2124hfdi53fsp9gv7j49qw93s2ls52c9zb2f"))))
-    (build-system emacs-build-system)
-    (home-page "https://github.com/tali713/esxml")
-    (synopsis "Elisp library for working with XML, ESXML and SXML")
-    (description
-     "This library provides two formats for XML code generation.  The primary
-form is esxml.  This is the form that is returned by such functions as
-@code{libxml-parse-xml-region} and it is used internally by emacs in many
-xml-related libraries.")
-    (license license:gpl3+)))
-
 (define-public emacs-queue
   (package
     (name "emacs-queue")
-- 
cgit v1.2.3


From acb59d99dbb8779ecf41cdbba45d2ce8ba88f5ed Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Wed, 28 Feb 2018 23:20:02 -0500
Subject: gnu: Fix Borg crashes with Python msgpack > 0.5

The Python msgpack library changed its name, but borg (and possibly
other packages) still uses the old name.

Fixes <https://bugs.gnu.org/30662>.

* gnu/packages/python.scm (python-msgpack-transitional): New variable.
* gnu/packages/backup.scm (borg)[inputs]: Use it.
---
 gnu/packages/backup.scm |  5 ++++-
 gnu/packages/python.scm | 18 ++++++++++++++++++
 2 files changed, 22 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index 48d4b08af6..2fafa2c4a6 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -547,7 +547,10 @@ detection, and lossless compression.")
        ("lz4" ,lz4)
        ("openssl" ,openssl)
        ("python-llfuse" ,python-llfuse)
-       ("python-msgpack" ,python-msgpack)
+       ;; The Python msgpack library changed its name so Borg requires this
+       ;; transitional package for now:
+       ;; <https://bugs.gnu.org/30662>
+       ("python-msgpack" ,python-msgpack-transitional)
        ("zstd" ,zstd)))
     (synopsis "Deduplicated, encrypted, authenticated and compressed backups")
     (description "Borg is a deduplicating backup program.  Optionally, it
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 064d79002d..69101c78b9 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -5869,6 +5869,24 @@ reading and writing MessagePack data.")
     (home-page "https://pypi.python.org/pypi/msgpack/")
     (license license:asl2.0)))
 
+;; This msgpack library's name changed from "python-msgpack" to "msgpack" with
+;; release 0.5. Some packages like borg still call it by the old name for now.
+;; <https://bugs.gnu.org/30662>
+(define-public python-msgpack-transitional
+  (package
+    (inherit python-msgpack)
+    (arguments
+     (substitute-keyword-arguments (package-arguments python-msgpack)
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (add-after 'unpack 'configure-transitional
+             (lambda _
+               ;; Keep using the old name.
+               (substitute* "setup.py"
+                 (("TRANSITIONAL = False")
+                   "TRANSITIONAL = 1"))
+               #t))))))))
+
 (define-public python2-msgpack
   (package-with-python2 python-msgpack))
 
-- 
cgit v1.2.3


From 35e2d0cfaeb2d97965f385f859a5b5063cd4ac46 Mon Sep 17 00:00:00 2001
From: Rene <pacoon@protonmail.com>
Date: Wed, 28 Feb 2018 20:33:36 -0600
Subject: gnu: nautilus: Use meson-build-system, update to 3.26.2.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/gnome.scm (nautilus): Update to 3.26.2.
[build-system]: Use meson-build-system.
[native-inputs]: Add desktop-file-utils and gtk+:bin.
[inputs]: Add libselinux.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/gnome.scm | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index f52f3227d1..d6f7e9e281 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -12,7 +12,7 @@
 ;;; Copyright © 2015, 2016, 2017, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 David Thompson <davet@gnu.org>
 ;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2016, 2017 Rene Saavedra <rennes@openmailbox.org>
+;;; Copyright © 2016, 2017, 2018 Rene Saavedra <pacoon@protonmail.com>
 ;;; Copyright © 2016 Jochem Raat <jchmrt@riseup.net>
 ;;; Copyright © 2016, 2017 Kei Kebreau <kkebreau@posteo.net>
 ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org>
@@ -5727,7 +5727,7 @@ shared object databases, search tools and indexing.")
 (define-public nautilus
   (package
     (name "nautilus")
-    (version "3.24.2.1")
+    (version "3.26.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/" name "/"
@@ -5735,16 +5735,17 @@ shared object databases, search tools and indexing.")
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "1cv138z04qx0fh1a2z2hvxy4p1x15vdv5gmkx5f3hb6c3w2rsz9m"))))
-    (build-system glib-or-gtk-build-system)
+                "1d0l4vgcjqj4671hb6s2a56baqlasbxn3wl6vfrpdsk5qq299jbr"))))
+    (build-system meson-build-system)
     (arguments
-     '(#:configure-flags
-       '("--disable-selinux") ; XXX: not packaged
+     '(#:glib-or-gtk? #t
        ;; XXX: FAIL: check-nautilus
        ;;   Settings schema 'org.gnome.nautilus.preferences' is not installed
        #:tests? #f))
     (native-inputs
-     `(("glib:bin" ,glib "bin") ; for glib-mkenums, etc.
+     `(("desktop-file-utils" ,desktop-file-utils) ; for update-desktop-database
+       ("glib:bin" ,glib "bin")         ; for glib-mkenums, etc.
+       ("gtk+:bin" ,gtk+ "bin")         ; for gtk-update-icon-cache
        ("gobject-introspection" ,gobject-introspection)
        ("intltool" ,intltool)
        ("pkg-config" ,pkg-config)))
@@ -5754,7 +5755,8 @@ shared object databases, search tools and indexing.")
        ("exempi" ,exempi)
        ("gnome-desktop" ,gnome-desktop)
        ("gnome-autoar" ,gnome-autoar)
-       ("nettle" ,nettle)    ; XXX required by libarchive.pc via gnome-autoar
+       ("libselinux" ,libselinux)
+       ("nettle" ,nettle) ; XXX required by libarchive.pc via gnome-autoar
        ("tracker" ,tracker)
        ;; XXX: gtk+ is required by libnautilus-extension.pc
        ;;
-- 
cgit v1.2.3


From 21b5fc253e5da057a090c1f76734291aef88a0e2 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Thu, 1 Mar 2018 17:38:55 +0100
Subject: gnu: cuirass: Update to aa4c778.

* gnu/packages/ci.scm (cuirass): Update to aa4c778.
---
 gnu/packages/ci.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm
index b5cfa7f1ab..a559a4011d 100644
--- a/gnu/packages/ci.scm
+++ b/gnu/packages/ci.scm
@@ -187,8 +187,8 @@ their dependencies.")
       (license l:gpl3+))))
 
 (define-public cuirass
-  (let ((commit "4ab2f2c3f084ffd9d0f77134cc1af0f8cf0e13be")
-        (revision "12"))
+  (let ((commit "aa4c7784940581b5e271b9c7c4ac80b6ee1ee309")
+        (revision "13"))
     (package
       (name "cuirass")
       (version (string-append "0.0.1-" revision "." (string-take commit 7)))
@@ -200,7 +200,7 @@ their dependencies.")
                 (file-name (string-append name "-" version))
                 (sha256
                  (base32
-                  "1r97z5lkzg6vx014rfmv1pp3x3bl1shb6wkcgnlncwqf56a9bzi1"))))
+                  "1827vgk47rcgm2x0cxzvg79ni6vazjzr8hr9pljlvbd9awzr7hxp"))))
       (build-system gnu-build-system)
       (arguments
        '(#:modules ((guix build utils)
-- 
cgit v1.2.3


From 789445a10a23245cd81c556c28049a2b84fa7043 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 20:33:48 +0100
Subject: gnu: xorgproto: Update to 2018.4.

* gnu/packages/xorg.scm (xorgproto): Update to 2018.4.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index 78f99f334a..a7099b4516 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -4771,14 +4771,14 @@ common definitions and porting layer.")
 (define-public xorgproto
   (package
     (name "xorgproto")
-    (version "2018.3")
+    (version "2018.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://xorg/individual/proto/"
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "1rdhw28n1gp7yylwia41jhih66gfx75nxgrmi2ggglzvzqhwr0x8"))))
+                "180mqkp70i44rkmj430pmn9idssvffrgv4y5h19fm698a7h8bs7y"))))
     (build-system gnu-build-system)
     (propagated-inputs
      ;; To get util-macros in (almost?) all package inputs.
-- 
cgit v1.2.3


From 9ed31fca8100612491397da5060109f1b42d0c9a Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 20:38:37 +0100
Subject: gnu: libmspub: Update to 0.1.4.

* gnu/packages/libreoffice.scm (libmspub): Update to 0.1.4.
[source](uri): Use HTTPS.
---
 gnu/packages/libreoffice.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm
index b7c675d274..0f432b8684 100644
--- a/gnu/packages/libreoffice.scm
+++ b/gnu/packages/libreoffice.scm
@@ -468,14 +468,14 @@ Aldus/Macromedia/Adobe FreeHand documents.")
 (define-public libmspub
   (package
     (name "libmspub")
-    (version "0.1.2")
+    (version "0.1.4")
     (source
      (origin
       (method url-fetch)
-      (uri (string-append "http://dev-www.libreoffice.org/src/" name "/"
+      (uri (string-append "https://dev-www.libreoffice.org/src/" name "/"
                           name "-" version ".tar.xz"))
       (sha256 (base32
-               "03sn6lxpr49sdq6j8q7fw7yjybyfahhs03z80388mh105pwapfmh"))))
+               "1fhkn013gzg59f4z7rldpbi0nj7lgdqzxanspsqa6axvmahw2dpg"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("doxygen" ,doxygen)
-- 
cgit v1.2.3


From c7cc1fcbe09d6728921018475b18c5c63ef91ca9 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 20:39:17 +0100
Subject: gnu: libpagemaker: Update to 0.0.4.

* gnu/packages/libreoffice.scm (libpagemaker): Update to 0.0.4.
[source](uri): Use HTTPS.
---
 gnu/packages/libreoffice.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm
index 0f432b8684..29238ff21e 100644
--- a/gnu/packages/libreoffice.scm
+++ b/gnu/packages/libreoffice.scm
@@ -495,14 +495,14 @@ Microsoft Publisher documents of all versions.")
 (define-public libpagemaker
   (package
     (name "libpagemaker")
-    (version "0.0.3")
+    (version "0.0.4")
     (source
      (origin
       (method url-fetch)
-      (uri (string-append "http://dev-www.libreoffice.org/src/" name "/"
+      (uri (string-append "https://dev-www.libreoffice.org/src/" name "/"
                           name "-" version ".tar.xz"))
       (sha256 (base32
-               "1minj0q14d44qfas81a8lkpgj288h5xlkjp084sfx17xv9axr5nq"))))
+               "17ai8ajffr0ixxmmcv3k5vgjlcsix38ldb4fw2arild70pbsrbb6"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("doxygen" ,doxygen)
-- 
cgit v1.2.3


From 814bc35d55b53b55a252f74fe5e66ed8fec40105 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 20:40:44 +0100
Subject: gnu: libabw: Update to 0.1.2.

* gnu/packages/libreoffice.scm (libabw): Update to 0.1.2.
---
 gnu/packages/libreoffice.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm
index 29238ff21e..1ad3294cb6 100644
--- a/gnu/packages/libreoffice.scm
+++ b/gnu/packages/libreoffice.scm
@@ -295,14 +295,14 @@ as Alfresco or Nuxeo.")
 (define-public libabw
   (package
     (name "libabw")
-    (version "0.1.1")
+    (version "0.1.2")
     (source
      (origin
       (method url-fetch)
-      (uri (string-append "http://dev-www.libreoffice.org/src/" name "/"
+      (uri (string-append "https://dev-www.libreoffice.org/src/" name "/"
                           name "-" version ".tar.xz"))
       (sha256 (base32
-               "0zi1zj4fpxgpglbbb5n1kg3dmhqq5rpf46lli89r5daavp19iing"))))
+               "11949iscdb99f2jplxjd39282jxcrf2fw0sqbh5dl7gqb96r8whb"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("doxygen" ,doxygen)
-- 
cgit v1.2.3


From fe29681717e9abc5792ed52ede7469fa2bd986bb Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 20:42:54 +0100
Subject: gnu: libe-book: Update to 0.1.3.

* gnu/packages/libreoffice.scm (libe-book): Update to 0.1.3.
[propagated-inputs]: Add LIBLANGTAG.
---
 gnu/packages/libreoffice.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm
index 1ad3294cb6..316602adbc 100644
--- a/gnu/packages/libreoffice.scm
+++ b/gnu/packages/libreoffice.scm
@@ -190,7 +190,7 @@ into other word processors.")
 (define-public libe-book
   (package
     (name "libe-book")
-    (version "0.1.2")
+    (version "0.1.3")
     (source
       (origin
         (method url-fetch)
@@ -198,7 +198,7 @@ into other word processors.")
                             version "/libe-book-" version ".tar.xz"))
         (sha256
           (base32
-            "1v48pd32r2pfysr3a3igc4ivcf6vvb26jq4pdkcnq75p70alp2bz"))))
+            "1yg1vws1wggzhjw672bpgh2x541g5i9wryf67g51m0r79zrqz3by"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("cppunit" ,cppunit)
@@ -206,6 +206,7 @@ into other word processors.")
        ("pkg-config" ,pkg-config)))
     (propagated-inputs ; in Requires or Requires.private field of .pkg
      `(("icu4c" ,icu4c)
+       ("liblangtag" ,liblangtag)
        ("librevenge" ,librevenge)
        ("libxml2" ,libxml2)))
     (inputs
-- 
cgit v1.2.3


From 52fb59ef253d9550ca4cfa095c2c0c2360d79095 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 28 Feb 2018 20:59:15 +0100
Subject: gnu: imagemagick: Update to 6.9.9-36.

* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.9-36.
---
 gnu/packages/imagemagick.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/imagemagick.scm b/gnu/packages/imagemagick.scm
index 97b3225a77..cc03f8fc2d 100644
--- a/gnu/packages/imagemagick.scm
+++ b/gnu/packages/imagemagick.scm
@@ -47,14 +47,14 @@
     ;; The 7 release series has an incompatible API, while the 6 series is still
     ;; maintained. Don't update to 7 until we've made sure that the ImageMagick
     ;; users are ready for the 7-series API.
-    (version "6.9.9-35")
+    (version "6.9.9-36")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://imagemagick/ImageMagick-"
                                  version ".tar.xz"))
              (sha256
               (base32
-               "09c8298v7112y579mfp0bgsa3gsmcx2l5zbgfkwply4ihszprh0i"))))
+               "1nhv3cmg4npqibhchp3qgm9pld3n94xwwzv5hgn2s7lqz0zc0vd8"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags '("--with-frozenpaths" "--without-gcc-arch")
-- 
cgit v1.2.3


From 04e7b1e7f91a649dd6cf424c27d73d5d7aeae52b Mon Sep 17 00:00:00 2001
From: Christopher Lemmer Webber <cwebber@dustycloud.org>
Date: Thu, 1 Mar 2018 11:00:30 -0600
Subject: gnu: golly: Fix source url.

* gnu/packages/games.scm (golly): Fix source url.
---
 gnu/packages/games.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index 272e9bce96..5917bbd69c 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -370,7 +370,7 @@ effects and music to make a completely free game.")
     (version "3.1")
     (source (origin
               (method url-fetch)
-              (uri (string-append "mirror://sourceforge/golly/golly-"
+              (uri (string-append "mirror://sourceforge/golly/golly/golly-"
                                   version "/golly-" version
                                   "-src.tar.gz"))
               (sha256
-- 
cgit v1.2.3


From 1debc5b9d281660a73b6ed777546213b0d9b7b32 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 1 Mar 2018 21:11:43 +0100
Subject: gnu: ghc-uuid: Fix build.

* gnu/packages/haskell.scm (ghc-uuid)[arguments]: Allow building with a newer
version of QuickCheck.
---
 gnu/packages/haskell.scm | 2 ++
 1 file changed, 2 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index dbb9ebc808..5c6e07a671 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -8532,6 +8532,8 @@ functions.")
         (base32
          "09xhk42yhxvqmka0iqrv3338asncz8cap3j0ic0ps896f2581b6z"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:configure-flags (list "--allow-newer=QuickCheck")))
     (inputs `(("ghc-cryptohash-sha1" ,ghc-cryptohash-sha1)
               ("ghc-cryptohash-md5" ,ghc-cryptohash-md5)
               ("ghc-entropy" ,ghc-entropy)
-- 
cgit v1.2.3


From 643817e44534f58b28bb41bf75ebf7ad240e49f4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 19 Feb 2018 18:41:25 +0100
Subject: gnu: Add patchmatrix.

* gnu/packages/music.scm (patchmatrix): New variable.
---
 gnu/packages/music.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 63b82900c0..65dfa92896 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -3726,6 +3726,34 @@ notation and includes basic support for digital audio.")
     (home-page "http://www.rosegardenmusic.com/")
     (license license:gpl2)))
 
+(define-public patchmatrix
+  (package
+    (name "patchmatrix")
+    (version "0.12.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/OpenMusicKontrollers/patchmatrix.git")
+                    (commit version)))
+              (file-name (string-append "patchmatrix-" version "-checkout"))
+              (sha256
+               (base32
+                "19ivp7h5vq6r1qhmycjxzvrgg7fc4a3v5vb3n4c7afs4z3pj53zi"))))
+    (build-system cmake-build-system)
+    (arguments '(#:tests? #f))          ; no test target
+    (inputs
+     `(("jack" ,jack-1)
+       ("lv2" ,lv2)
+       ("mesa" ,mesa)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (home-page "https://github.com/OpenMusicKontrollers/patchmatrix")
+    (synopsis "Simple JACK patch bay")
+    (description "PatchMatrix is a patch bay for the JACK audio connection
+kit.  It provides a patch bay in flow matrix style for audio, MIDI, CV, and
+OSC connections.")
+    (license license:artistic2.0)))
+
 (define-public sorcer
   (package
     (name "sorcer")
-- 
cgit v1.2.3


From 40a7997e63c4035a4e897f3aa3945751cca8ef3e Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Thu, 1 Mar 2018 16:41:37 +0200
Subject: gnu: efl: Update to 1.20.7.

* gnu/packages/enlightenment.scm (efl): Update to 1.20.7.
---
 gnu/packages/enlightenment.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/enlightenment.scm b/gnu/packages/enlightenment.scm
index 413bc5f102..c96c19f9f9 100644
--- a/gnu/packages/enlightenment.scm
+++ b/gnu/packages/enlightenment.scm
@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015 Tomáš Čech <sleep_walker@suse.cz>
 ;;; Copyright © 2015 Daniel Pimentel <d4n1@member.fsf.org>
-;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 ng0 <ng0@infotropique.org>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -60,7 +60,7 @@
 (define-public efl
   (package
     (name "efl")
-    (version "1.20.6")
+    (version "1.20.7")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -68,7 +68,7 @@
                     version ".tar.xz"))
               (sha256
                (base32
-                "1h9jkb1pkp2g6ld7ra9mxgblx3x5id4162ja697klx9mfjkpxijn"))))
+                "1zkn5ix81xck3n84dxvkjh4alwc6zj8x989d0zqi5c6ppijvgadh"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
-- 
cgit v1.2.3


From 360ea2bbd5089f1d309bb18e0890896f3a21c428 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Thu, 1 Mar 2018 22:18:23 +0200
Subject: gnu: efl: Use separate "include" output.

* gnu/packages/enlightenment.scm (efl)[outputs]: Add 'include' output.
---
 gnu/packages/enlightenment.scm | 2 ++
 1 file changed, 2 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/enlightenment.scm b/gnu/packages/enlightenment.scm
index c96c19f9f9..8550a89640 100644
--- a/gnu/packages/enlightenment.scm
+++ b/gnu/packages/enlightenment.scm
@@ -69,6 +69,8 @@
               (sha256
                (base32
                 "1zkn5ix81xck3n84dxvkjh4alwc6zj8x989d0zqi5c6ppijvgadh"))))
+    (outputs '("out"       ; 49 MB
+               "include")) ; 17 MB
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
-- 
cgit v1.2.3


From b1808932890a7f2f0d61dcfd015a644e4e5bcc16 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 1 Mar 2018 21:15:40 +0100
Subject: gnu: r-dexseq: Update to 1.24.3.

* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.3.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c427a6d036..911a2ee762 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6017,14 +6017,14 @@ distribution.")
 (define-public r-dexseq
   (package
     (name "r-dexseq")
-    (version "1.24.2")
+    (version "1.24.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DEXSeq" version))
        (sha256
         (base32
-         "18nh8ynxirfwkmc4sawdxgl7w1sl9ny5zpv8zbhv9vi5vgb8pxmj"))))
+         "0xip73hlbr3zry9d7ly9vvvsbb3xjcmfa09lr9fdy528dwjrf084"))))
     (properties `((upstream-name . "DEXSeq")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 99e4b11d81292d6c2cdabe8018fd8da144f84d9c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 1 Mar 2018 21:15:50 +0100
Subject: gnu: r-shortread: Update to 1.36.1.

* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.36.1.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 911a2ee762..0b9ac7b0bf 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6200,14 +6200,14 @@ testing and other simple calculations.")
 (define-public r-shortread
   (package
     (name "r-shortread")
-    (version "1.36.0")
+    (version "1.36.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ShortRead" version))
        (sha256
         (base32
-         "06mknlsmd4hnaxzdjapgvp2kgdnf9w103y500dsac5jgsz4vwzcz"))))
+         "1cyv47632m9ljkxfsvnvmd19sb607ys5kz8fwh6v39dnw16g0a6m"))))
     (properties `((upstream-name . "ShortRead")))
     (build-system r-build-system)
     (inputs
-- 
cgit v1.2.3


From 22d96920d36ef87ba459dcf1db10641c5ba3ee25 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 1 Mar 2018 21:16:00 +0100
Subject: gnu: r-edger: Update to 3.20.9.

* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.9.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0b9ac7b0bf..0ce038ada7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6968,13 +6968,13 @@ names in their natural, rather than lexicographic, order.")
 (define-public r-edger
   (package
     (name "r-edger")
-    (version "3.20.8")
+    (version "3.20.9")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "edgeR" version))
               (sha256
                (base32
-                "0g7bj6w61blw3m22hw9rc01n554k9qkjizh7njr3j4shmhads58d"))))
+                "0y52snwbz37xzdd7gihdkqczbndlfzmmypv6hri3ymjyfmlx6qaw"))))
     (properties `((upstream-name . "edgeR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From eb8971b7421ccca75d540f0d7b3b4ed09f283e89 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 1 Mar 2018 21:16:12 +0100
Subject: gnu: r-limma: Update to 3.34.9.

* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.9.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0ce038ada7..e76d91c062 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7034,13 +7034,13 @@ coding changes and predict coding outcomes.")
 (define-public r-limma
   (package
     (name "r-limma")
-    (version "3.34.8")
+    (version "3.34.9")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "limma" version))
               (sha256
                (base32
-                "0bmxsgz2yll83sd3wbxsrsfd35468igb0d8lldym0d0lqfz906bw"))))
+                "1y2fm61g5i0fn0j3l31xvwh9zww9bpkc4nwzb1d0yv1cag20jkdc"))))
     (build-system r-build-system)
     (home-page "http://bioinf.wehi.edu.au/limma")
     (synopsis "Package for linear models for microarray and RNA-seq data")
-- 
cgit v1.2.3


From 535014ce605ea10b1642b065a9cf08c565ae43d7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 1 Mar 2018 21:16:23 +0100
Subject: gnu: r-genomicranges: Update to 1.30.3.

* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.3.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e76d91c062..97bbc6cf38 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7089,13 +7089,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
-    (version "1.30.2")
+    (version "1.30.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicRanges" version))
               (sha256
                (base32
-                "0c3r155603vb4zjs3adqa72770bh8karc11y8gl62l1m24jrkbnj"))))
+                "07cszc9ri94nzk4dffwnsj247ih6pchnrzrvnb0q4dkk33gwy8n1"))))
     (properties
      `((upstream-name . "GenomicRanges")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 61cbd49b305363e4965b3d14bf4b1935427138e2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 1 Mar 2018 21:16:35 +0100
Subject: gnu: r-topgo: Update to 2.30.1.

* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.30.1.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 97bbc6cf38..8985156e52 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7519,13 +7519,13 @@ information about the latest version of the Gene Ontologies.")
 (define-public r-topgo
   (package
     (name "r-topgo")
-    (version "2.30.0")
+    (version "2.30.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "topGO" version))
               (sha256
                (base32
-                "1hqffz5qp7glxdvjp37005g8qk5nam3f9wpf6d1wjnzpar04f3dz"))))
+                "1cgz4knxr328xfqlhl6ypxl6x86rfrlqz748kn94ainxjzz55i6x"))))
     (properties
      `((upstream-name . "topGO")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 6a0e13906b2832455ac6aacd02293a341c4e51fa Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 1 Mar 2018 21:16:45 +0100
Subject: gnu: r-wgcna: Update to 1.63.

* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.63.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8985156e52..0b189378b4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8365,14 +8365,14 @@ in SNV base substitution data.")
 (define-public r-wgcna
   (package
     (name "r-wgcna")
-    (version "1.62")
+    (version "1.63")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "WGCNA" version))
        (sha256
         (base32
-         "0c52rp09gqphz6g5x9jzkdcsyvfrknq0dkq9saslgy8q8ap974vx"))))
+         "1225dqm68bynkmklnsxdqdd3zqrpzbvqwyly8ibxmk75z33xz309"))))
     (properties `((upstream-name . "WGCNA")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 9aaf2813e2601a89c4dd3584f49f170f18b6279a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 1 Mar 2018 21:16:57 +0100
Subject: gnu: r-scran: Update to 1.6.8.

* gnu/packages/bioinformatics.scm (r-scran): Update to 1.6.8.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0b189378b4..e5e9192993 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10588,14 +10588,14 @@ quality control.")
 (define-public r-scran
   (package
     (name "r-scran")
-    (version "1.6.7")
+    (version "1.6.8")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scran" version))
        (sha256
         (base32
-         "0zfm5i8xrnzb3894xygqd6zkbwaa2x3z74wbxw39fcjhyhxv2hmb"))))
+         "07wniyrh2fhhkz28v0bfgpvpi1hkkn2cvhacrvvvck142j79944x"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-beachmat" ,r-beachmat)
-- 
cgit v1.2.3


From 9d6f39252907e58de5d39be4ec59fb324f549bfb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 1 Mar 2018 21:17:07 +0100
Subject: gnu: r-truncnorm: Update to 1.0-8.

* gnu/packages/cran.scm (r-truncnorm): Update to 1.0-8.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index e1fb1b6215..730ee8adb6 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1472,14 +1472,14 @@ imputations.")
 (define-public r-truncnorm
   (package
     (name "r-truncnorm")
-    (version "1.0-7")
+    (version "1.0-8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "truncnorm" version))
        (sha256
         (base32
-         "1qac05z50618y4bw1d7yznsli1bv82s0g8h37iacrjrdkv87bmy7"))))
+         "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/truncnorm/")
     (synopsis "Truncated normal distribution")
-- 
cgit v1.2.3


From 5e3867345588445776cc6e3e146bd35822706f8b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 1 Mar 2018 21:17:17 +0100
Subject: gnu: r-pillar: Update to 1.2.1.

* gnu/packages/cran.scm (r-pillar): Update to 1.2.1.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 730ee8adb6..9279d1da83 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2139,14 +2139,14 @@ display.")
 (define-public r-pillar
   (package
     (name "r-pillar")
-    (version "1.1.0")
+    (version "1.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pillar" version))
        (sha256
         (base32
-         "1gh3j2pbbf5y4d5nyqnlr0x27jjyvjjspcccmw61airs1n6rx8jq"))))
+         "1ryd7m570y6q3w71wd5dz042b3d0dv24g2rbkw1kdx0n6jj9gsbd"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cli" ,r-cli)
-- 
cgit v1.2.3


From 29c9c9c2c1dda48f51d43fc8a88d3213b5c01077 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 1 Mar 2018 21:17:26 +0100
Subject: gnu: r-rmysql: Update to 0.10.14.

* gnu/packages/databases.scm (r-rmysql): Update to 0.10.14.
---
 gnu/packages/databases.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 56984af6e2..b99cd3d3d5 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -2042,14 +2042,14 @@ and web services platform functionality.")
 (define-public r-rmysql
   (package
     (name "r-rmysql")
-    (version "0.10.13")
+    (version "0.10.14")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RMySQL" version))
        (sha256
         (base32
-         "1j0vr2l4s02cg2hzgr3pla96pjj4h85sxw28lidy58rg5awnsf82"))))
+         "01891kn263b02y6addgpy3gn5axg7m10bqbqv7dg9yx9k85am590"))))
     (properties `((upstream-name . "RMySQL")))
     (build-system r-build-system)
     (native-inputs
-- 
cgit v1.2.3


From 744e06e7170954d98bf0f990ba45318877aaae36 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 1 Mar 2018 21:17:40 +0100
Subject: gnu: r-mass: Update to 7.3-49.

* gnu/packages/statistics.scm (r-mass): Update to 7.3-49.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index c1012a635b..2c5308159a 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -318,14 +318,14 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
 (define-public r-mass
   (package
     (name "r-mass")
-    (version "7.3-48")
+    (version "7.3-49")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "MASS" version))
        (sha256
         (base32
-         "02q95ba909p2gxnzfp295ipxjnv14f7bm55nicxwn2kj8hizpzqd"))))
+         "1yjbnj1p4z0vw84wga8q5fyqiw4n6r7pc6rdwam7vsbiamyzfcqs"))))
     (properties `((upstream-name . "MASS")))
     (build-system r-build-system)
     (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
-- 
cgit v1.2.3


From e24ccf46f15b2a3fc0ba4cd9470aabd74b39559e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 1 Mar 2018 21:17:53 +0100
Subject: gnu: r-rpart: Update to 4.1-13.

* gnu/packages/statistics.scm (r-rpart): Update to 4.1-13.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 2c5308159a..090f532232 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -554,14 +554,14 @@ single hidden layer, and for multinomial log-linear models.")
 (define-public r-rpart
   (package
     (name "r-rpart")
-    (version "4.1-12")
+    (version "4.1-13")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rpart" version))
        (sha256
         (base32
-         "177p03w4m0qshb3sqkdyixim3f44g2an31v3vlbjmpzjvd5ff6yq"))))
+         "0k29qx3k3pj5sgrpg0p47yd8i811rmdakaw57bigpq1449asc4cf"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/rpart")
     (synopsis "Recursive partitioning and regression trees")
-- 
cgit v1.2.3


From e3ddb563297c9707a8fc0e5c64e55915a4e842a5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 1 Mar 2018 21:18:04 +0100
Subject: gnu: r-gdtools: Update to 0.1.7.

* gnu/packages/statistics.scm (r-gdtools): Update to 0.1.7.
[inputs]: Add zlib.
---
 gnu/packages/statistics.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 090f532232..084f1a2f2c 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1098,20 +1098,21 @@ agnes cluster diagrams.")
 (define-public r-gdtools
   (package
     (name "r-gdtools")
-    (version "0.1.6")
+    (version "0.1.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gdtools" version))
        (sha256
         (base32
-         "103wnc8sq0iwcnj4j14hd420d2dqdyf13s3f25icsznrlyzdkhf5"))))
+         "122k9spymawfnfyksxyapwq9cigydy5nrjwhrwrhy3qkax3aycf6"))))
     (build-system r-build-system)
     (native-inputs
      `(("r-rcpp" ,r-rcpp)
        ("pkg-config" ,pkg-config)))
     (inputs
-     `(("cairo" ,cairo)))
+     `(("cairo" ,cairo)
+       ("zlib" ,zlib)))
     (propagated-inputs
      `(("r-withr" ,r-withr)))
     (home-page "https://cran.r-project.org/web/packages/gdtools")
-- 
cgit v1.2.3


From 36e1202b2c47925f45317d1df99a35b0f1344627 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 1 Mar 2018 21:18:19 +0100
Subject: gnu: r-yaml: Update to 2.1.17.

* gnu/packages/statistics.scm (r-yaml): Update to 2.1.17.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 084f1a2f2c..6dc99c1b19 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1331,13 +1331,13 @@ syntax that can be converted to XHTML or other formats.")
 (define-public r-yaml
   (package
     (name "r-yaml")
-    (version "2.1.16")
+    (version "2.1.17")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "yaml" version))
               (sha256
                (base32
-                "1xlsmqal607w6c9rx86061y1fwpbyd5lqp9bad5n7cc9a0blpnkm"))))
+                "10y6wnv2v8k396far29haqv2s82p4zm04rrsxk183wg19gb51was"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/yaml/")
     (synopsis "Methods to convert R data to YAML and back")
-- 
cgit v1.2.3


From dafd13d5b2afa5b65fafae37088b7c023a91d767 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 1 Mar 2018 21:18:30 +0100
Subject: gnu: r-rcpparmadillo: Update to 0.8.400.0.0.

* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.8.400.0.0.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 6dc99c1b19..166cdde833 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2482,13 +2482,13 @@ well as additional utilities such as panel and axis annotation functions.")
 (define-public r-rcpparmadillo
   (package
     (name "r-rcpparmadillo")
-    (version "0.8.300.1.0")
+    (version "0.8.400.0.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RcppArmadillo" version))
               (sha256
                (base32
-                "0p6cbnwxgzigf7n5qhqvxdr3nd3pq3c2qq6pskqz7avzf813fy83"))))
+                "11y2ksf46zw6fcz0kk70szyfn7qqxwwd33xylrxvnyb7ldmbc5yr"))))
     (properties `((upstream-name . "RcppArmadillo")))
     (build-system r-build-system)
     (native-inputs
-- 
cgit v1.2.3


From 35d12b05f0d063f9968ba4c2629ca52cceee08ff Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 1 Mar 2018 21:18:47 +0100
Subject: gnu: r-rmarkdown: Update to 1.9.

* gnu/packages/statistics.scm (r-rmarkdown): Update to 1.9.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 166cdde833..d2bcf4aabd 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2576,14 +2576,14 @@ certain criterion, e.g., it contains a certain regular file.")
 (define-public r-rmarkdown
   (package
     (name "r-rmarkdown")
-    (version "1.8")
+    (version "1.9")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "rmarkdown" version))
         (sha256
           (base32
-            "0q1y1qx87xp6vf9h7mfl77rqhmd01xl53l9ap9qj99bfvpabb572"))))
+            "0wq6kbhrkv3fhcy4hg5yyv9gdvf8gr4nsjwdifs4ih8lnn0dmdyb"))))
     (properties `((upstream-name . "rmarkdown")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From eaf0905970378dd438f3f8f705ff8e6bc3e506c0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 1 Mar 2018 21:18:58 +0100
Subject: gnu: r-tidyselect: Update to 0.2.4.

* gnu/packages/statistics.scm (r-tidyselect): Update to 0.2.4.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index d2bcf4aabd..e5d448083c 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3578,14 +3578,14 @@ the 'lite' version of the more complete @code{viridis} package.")
 (define-public r-tidyselect
   (package
     (name "r-tidyselect")
-    (version "0.2.3")
+    (version "0.2.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tidyselect" version))
        (sha256
         (base32
-         "0b0w30yq30c7bwpaghp3hp0nncqwcmvrra9j58fhx9jihay3l68c"))))
+         "1592dbzawhd1hpsp9919l4sifyiaaj6xr7lnhsbwa6jwmmb0xcsw"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-glue" ,r-glue)
-- 
cgit v1.2.3


From bfae3f71217e867806276e0415b75ea655531461 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 1 Mar 2018 21:19:10 +0100
Subject: gnu: r-lubridate: Update to 1.7.3.

* gnu/packages/statistics.scm (r-lubridate): Update to 1.7.3.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index e5d448083c..1c180645d4 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -5357,14 +5357,14 @@ is supported.")
 (define-public r-lubridate
   (package
     (name "r-lubridate")
-    (version "1.7.2")
+    (version "1.7.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lubridate" version))
        (sha256
         (base32
-         "0k417a1xp5gxf77ycbnx5apzpc5d25sjm83ss7wmqpbnhnr5dcav"))))
+         "1pzkqfiahnsdm3zx46asgn8fw43vlxvbh7r4cn70c7ffmxabzzrc"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rcpp" ,r-rcpp)
-- 
cgit v1.2.3


From b79e1fbe962c0ba9134ffb7d1250170aaeafdecf Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 1 Mar 2018 21:19:21 +0100
Subject: gnu: r-httpuv: Update to 1.3.6.1.

* gnu/packages/web.scm (r-httpuv): Update to 1.3.6.1.
---
 gnu/packages/web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 4876918b53..e3412f60e2 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -3780,13 +3780,13 @@ CDF, Atom 0.3, and Atom 1.0 feeds.")
 (define-public r-httpuv
   (package
     (name "r-httpuv")
-    (version "1.3.6")
+    (version "1.3.6.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "httpuv" version))
               (sha256
                (base32
-                "1nzbcw1dm4l5qc9156kz95rdb8bwnpdr57wfc87w8arv7m0i40bc"))))
+                "11kffpki4pgh352dlwsm4lnf1dcd5vs51cnimbshadyk3jprwxdf"))))
     (build-system r-build-system)
     (native-inputs `(("r-rcpp" ,r-rcpp)))
     (home-page "https://github.com/rstudio/httpuv")
-- 
cgit v1.2.3


From b672a8160755bab07fb3c13dbc43dcc26525a7b7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 19 Feb 2018 20:04:06 +0100
Subject: gnu: Graft glibc to allow execution on Linux 2.6.32.

* gnu/packages/patches/glibc-allow-kernel-2.6.32.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/base.scm (glibc/linux)[replacement]: New field.
(glibc-2.26-patched): New variable.
---
 gnu/local.mk                                       |  3 +-
 gnu/packages/base.scm                              | 11 ++++++
 .../patches/glibc-allow-kernel-2.6.32.patch        | 39 ++++++++++++++++++++++
 3 files changed, 52 insertions(+), 1 deletion(-)
 create mode 100644 gnu/packages/patches/glibc-allow-kernel-2.6.32.patch

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index 3d0bd38e50..ee99882c5f 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -7,7 +7,7 @@
 # Copyright © 2016, 2017, 2018 Kei Kebreau <kkebreau@posteo.net>
 # Copyright © 2016, 2017 Rene Saavedra <rennes@openmailbox.org>
 # Copyright © 2016 Adonay "adfeno" Felipe Nogueira <https://libreplanet.org/wiki/User:Adfeno> <adfeno@openmailbox.org>
-# Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
+# Copyright © 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 # Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
 # Copyright © 2016, 2017, 2018 Alex Vong <alexvong1995@gmail.com>
 # Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
@@ -708,6 +708,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/glibc-CVE-2017-1000366-pt1.patch		\
   %D%/packages/patches/glibc-CVE-2017-1000366-pt2.patch		\
   %D%/packages/patches/glibc-CVE-2017-1000366-pt3.patch		\
+  %D%/packages/patches/glibc-allow-kernel-2.6.32.patch		\
   %D%/packages/patches/glibc-bootstrap-system.patch		\
   %D%/packages/patches/glibc-ldd-x86_64.patch			\
   %D%/packages/patches/glibc-locales.patch			\
diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm
index b2c1d232fb..23107a823e 100644
--- a/gnu/packages/base.scm
+++ b/gnu/packages/base.scm
@@ -12,6 +12,7 @@
 ;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -537,6 +538,7 @@ store.")
    ;; Note: Always use a dot after the minor version since various places rely
    ;; on "version-major+minor" to determine where locales are found.
    (version "2.26.105-g0890d5379c")
+   (replacement glibc-2.26-patched)
    (source (origin
             (method url-fetch)
             (uri (string-append "https://alpha.gnu.org/gnu/guix/mirror/"
@@ -839,6 +841,15 @@ GLIBC/HURD for a Hurd host"
 ;; Below are old libc versions, which we use mostly to build locale data in
 ;; the old format (which the new libc cannot cope with.)
 
+(define glibc-2.26-patched
+  (package
+    (inherit glibc)
+    (replacement #f)
+    (source (origin
+              (inherit (package-source glibc))
+              (patches (cons (search-patch "glibc-allow-kernel-2.6.32.patch")
+                             (origin-patches (package-source glibc))))))))
+
 (define-public glibc-2.25
   (package
     (inherit glibc)
diff --git a/gnu/packages/patches/glibc-allow-kernel-2.6.32.patch b/gnu/packages/patches/glibc-allow-kernel-2.6.32.patch
new file mode 100644
index 0000000000..ce18b874c4
--- /dev/null
+++ b/gnu/packages/patches/glibc-allow-kernel-2.6.32.patch
@@ -0,0 +1,39 @@
+diff --git a/sysdeps/unix/sysv/linux/configure b/sysdeps/unix/sysv/linux/configure
+index cace758c01..38fe7fe0b0 100644
+--- a/sysdeps/unix/sysv/linux/configure
++++ b/sysdeps/unix/sysv/linux/configure
+@@ -69,7 +69,7 @@ fi
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for kernel header at least $minimum_kernel" >&5
+ $as_echo_n "checking for kernel header at least $minimum_kernel... " >&6; }
+ decnum=`echo "$minimum_kernel.0.0.0" | sed 's/\([0-9]*\)\.\([0-9]*\)\.\([0-9]*\).*/(\1 * 65536 + \2 * 256 + \3)/'`;
+-abinum=`echo "$minimum_kernel.0.0.0" | sed 's/\([0-9]*\)\.\([0-9]*\)\.\([0-9]*\).*/\1,\2,\3/'`;
++abinum=`echo "2.6.32.0.0.0" | sed 's/\([0-9]*\)\.\([0-9]*\)\.\([0-9]*\).*/\1,\2,\3/'`;
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ /* end confdefs.h.  */
+ #include <linux/version.h>
+diff --git a/sysdeps/unix/sysv/linux/configure.ac b/sysdeps/unix/sysv/linux/configure.ac
+index 13abda0a51..6abc12eaed 100644
+--- a/sysdeps/unix/sysv/linux/configure.ac
++++ b/sysdeps/unix/sysv/linux/configure.ac
+@@ -50,7 +50,7 @@ fi
+ AC_MSG_CHECKING(for kernel header at least $minimum_kernel)
+ changequote(,)dnl
+ decnum=`echo "$minimum_kernel.0.0.0" | sed 's/\([0-9]*\)\.\([0-9]*\)\.\([0-9]*\).*/(\1 * 65536 + \2 * 256 + \3)/'`;
+-abinum=`echo "$minimum_kernel.0.0.0" | sed 's/\([0-9]*\)\.\([0-9]*\)\.\([0-9]*\).*/\1,\2,\3/'`;
++abinum=`echo "2.6.32.0.0.0" | sed 's/\([0-9]*\)\.\([0-9]*\)\.\([0-9]*\).*/\1,\2,\3/'`;
+ changequote([,])dnl
+ AC_TRY_COMPILE([#include <linux/version.h>
+ #if LINUX_VERSION_CODE < $decnum
+diff --git a/sysdeps/unix/sysv/linux/dl-osinfo.h b/sysdeps/unix/sysv/linux/dl-osinfo.h
+index 823cd8224d..482caaeeec 100644
+--- a/sysdeps/unix/sysv/linux/dl-osinfo.h
++++ b/sysdeps/unix/sysv/linux/dl-osinfo.h
+@@ -39,7 +39,7 @@
+ 	  GLRO(dl_osversion) = version;					      \
+ 									      \
+ 	/* Now we can test with the required version.  */		      \
+-	if (__LINUX_KERNEL_VERSION > 0 && version < __LINUX_KERNEL_VERSION)   \
++	if (__LINUX_KERNEL_VERSION > 0 && version < __LINUX_KERNEL_VERSION && version != 0x020620)   \
+ 	  /* Not sufficent.  */						      \
+ 	  FATAL ("FATAL: kernel too old\n");				      \
+       }									      \
-- 
cgit v1.2.3


From db317b38dc3fadf4759da8209740c616d1b599b7 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 28 Feb 2018 23:54:36 +0100
Subject: gnu: dbacl: Update phase style.

* gnu/packages/textutils.scm (dbacl)[arguments]: Substitute INVOKE for SYSTEM* and end phases with #t.
---
 gnu/packages/textutils.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm
index 1417bea4e5..c9714988d6 100644
--- a/gnu/packages/textutils.scm
+++ b/gnu/packages/textutils.scm
@@ -508,10 +508,12 @@ in a portable way.")
          (add-after 'unpack 'delete-test
            ;; See comments about the license.
            (lambda _
-             (delete-file "src/tests/dbacl-jap.shin")))
+             (delete-file "src/tests/dbacl-jap.shin")
+             #t))
          (add-after 'delete-sample6-and-japanese 'autoreconf
            (lambda _
-             (zero? (system* "autoreconf" "-vif"))))
+             (invoke "autoreconf" "-vif")
+             #t))
          (add-after 'unpack 'fix-test-files
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
-- 
cgit v1.2.3


From 7314a5475e8fe0fc7ffe17d2cc30b4ae8c5381b2 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 28 Feb 2018 23:55:49 +0100
Subject: gnu: dbacl: Use HTTPS home page.

* gnu/packages/textutils.scm (dbacl)[home-page]: Use HTTPS.
---
 gnu/packages/textutils.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm
index c9714988d6..d75ba7766e 100644
--- a/gnu/packages/textutils.scm
+++ b/gnu/packages/textutils.scm
@@ -534,7 +534,7 @@ in a portable way.")
        ("autoconf" ,autoconf)
        ("automake" ,automake)
        ("pkg-config" ,pkg-config)))
-    (home-page "http://www.lbreyer.com/dbacl.html")
+    (home-page "https://www.lbreyer.com/dbacl.html")
     (synopsis "Bayesian text and email classifier")
     (description
      "dbacl is a fast Bayesian text and email classifier.  It builds a variety
-- 
cgit v1.2.3


From 4f5452ab3aaccb17a6e4e3c9b3029cd1ed408102 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 1 Mar 2018 00:46:23 +0100
Subject: gnu: libftdi: Use HTTPS home page.

* gnu/packages/libftdi.scm (libftdi)[home-page]: Use HTTPS.
---
 gnu/packages/libftdi.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/libftdi.scm b/gnu/packages/libftdi.scm
index 78f849d02d..bbb98ff1f4 100644
--- a/gnu/packages/libftdi.scm
+++ b/gnu/packages/libftdi.scm
@@ -40,7 +40,7 @@
     (build-system cmake-build-system)
     (propagated-inputs
      `(("libusb" ,libusb))) ; required by libftdi1.pc
-    (home-page "http://www.intra2net.com/en/developer/libftdi/")
+    (home-page "https://www.intra2net.com/en/developer/libftdi/")
     (synopsis "FTDI USB driver with bitbang mode")
     (description
      "libFTDI is a library to talk to FTDI chips: FT232BM,
-- 
cgit v1.2.3


From 4972f9cc0a55e35e1c025190f57921f9ddcc5c36 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 1 Mar 2018 00:47:18 +0100
Subject: gnu: nagios: Update to 4.3.4.

* gnu/packages/monitoring.scm (nagios): Update to 4.3.4.
---
 gnu/packages/monitoring.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/monitoring.scm b/gnu/packages/monitoring.scm
index d7a1641ad8..c5a86d02c6 100644
--- a/gnu/packages/monitoring.scm
+++ b/gnu/packages/monitoring.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2016 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2018 Sou Bunnbu <iyzsong@member.fsf.org>
 ;;; Copyright © 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -40,7 +41,7 @@
 (define-public nagios
   (package
     (name "nagios")
-    (version "4.2.4")
+    (version "4.3.4")
     ;; XXX: Nagios 4.2.x and later bundle a copy of AngularJS.
     (source (origin
               (method url-fetch)
@@ -49,7 +50,7 @@
                     version "/nagios-" version ".tar.gz"))
               (sha256
                (base32
-                "0w0blbwiw0ps04b7gkyyk89qkgwsxh6gydhmggbm1kl3ar3mq1dh"))
+                "1wa4m952sb23dqi5w759adimsp21bkhp598rpq9dnhz3v497h2y9"))
               (modules '((guix build utils)))
               (snippet
                ;; Ensure reproducibility.
-- 
cgit v1.2.3


From 57c734a628091f45cea205acfceba34d2dda3ef9 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 1 Mar 2018 06:50:39 +0100
Subject: gnu: liblo: Update to 0.29.

* gnu/packages/audio.scm (liblo): Update to 0.29.
---
 gnu/packages/audio.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 1cf6441df0..a9d29345a6 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -1628,14 +1628,14 @@ essential distortions.")
 (define-public liblo
   (package
     (name "liblo")
-    (version "0.28")
+    (version "0.29")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://sourceforge/liblo/liblo/" version
                                  "/liblo-" version ".tar.gz"))
              (sha256
               (base32
-               "02drgnpirvl2ihvzgsmn02agr5sj3vipzzw9vma56qlkgfvak56s"))))
+               "0sn0ckc1d0845mhsaa62wf7f9v0c0ykiq796a30ja5096kib9qdc"))))
     (build-system gnu-build-system)
     (arguments
      `(;; liblo test FAILED
-- 
cgit v1.2.3


From 66b89ee28e1b15ff962b68e91fcd84562102fc2f Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 1 Mar 2018 16:29:31 +0100
Subject: gnu: python-stem: Update phase style.

* gnu/packages/python.scm (python-stem)[arguments]: Substitute INVOKE
for SYSTEM* and end phase with #t.
---
 gnu/packages/python.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 69101c78b9..0b7ff440f0 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -9366,7 +9366,8 @@ etc.")
        (modify-phases %standard-phases
          (replace 'check
            (lambda _
-             (zero? (system* "./run_tests.py" "--unit")))))))
+             (invoke "./run_tests.py" "--unit")
+             #t)))))
     (native-inputs
      `(("python-mock" ,python-mock)
        ("python-pep8" ,python-pep8)
-- 
cgit v1.2.3


From fbb0164a5f7087a81ef5f79a4134432969f926cf Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 1 Mar 2018 16:30:40 +0100
Subject: gnu: privoxy: Update phase style.

* gnu/packages/tor.scm (privoxy)[arguments]: Substitute INVOKE for
SYSTEM* and end phase with #t.
---
 gnu/packages/tor.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm
index 4a39100511..f598672d91 100644
--- a/gnu/packages/tor.scm
+++ b/gnu/packages/tor.scm
@@ -146,7 +146,8 @@ rejects UDP traffic from the application you're using.")
            (lambda _
              ;; Unfortunately, this is not a tarball produced by
              ;; "make dist".
-             (zero? (system* "autoreconf" "-vfi")))))
+             (invoke "autoreconf" "-vfi")
+             #t)))
        #:tests? #f))
     (inputs
      `(("w3m" ,w3m)
-- 
cgit v1.2.3


From 68e7632db052105b70704cd2c1cc42a568e9bf4a Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 1 Mar 2018 16:31:06 +0100
Subject: gnu: onionshare: Update phase style.

* gnu/packages/tor.scm (onionshare)[arguments]: Substitute INVOKE for
SYSTEM* and end phase with #t.
---
 gnu/packages/tor.scm | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm
index f598672d91..50295da5dc 100644
--- a/gnu/packages/tor.scm
+++ b/gnu/packages/tor.scm
@@ -231,7 +231,9 @@ networks.")
            ;; After all the patching we run the tests after installing.
            ;; This is also a known issue:
            ;; https://github.com/micahflee/onionshare/issues/284
-           (lambda _ (zero? (system* "nosetests" "test")))))))
+           (lambda _
+             (invoke "nosetests" "test")
+             #t)))))
     (native-inputs
      `(("python-nose" ,python-nose)))
     (inputs
-- 
cgit v1.2.3


From a9c0a133c045f82e1084e7485c6cc65ace131fa3 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 1 Mar 2018 16:34:38 +0100
Subject: gnu: python-stem: Update to 1.6.0.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/python.scm (python-stem): Update to 1.6.0.
[arguments]: Add ‘fix-test-environment’ phase.
---
 gnu/packages/python.scm | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 0b7ff440f0..126424183b 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -9352,18 +9352,25 @@ etc.")
 (define-public python-stem
   (package
     (name "python-stem")
-    (version "1.5.4")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "stem" version))
        (sha256
         (base32
-         "1j7pnblrn0yr6jmxvsq6y0ihmxmj5x50jl2n2606w67f6wq16j9n"))))
+         "1va9p3ij7lxg6ixfsvaql06dn11l3fgpxmss1dhlvafm7sqizznp"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
+         (add-before 'check 'fix-test-environment
+           (lambda _
+             ;; Fixes: FileNotFoundError: [Errno 2] No such file or directory:
+             ;; '/tmp/guix-build-python-stem-1.6.0.drv-0/stem-1.6.0/.gitignore'.
+             (with-output-to-file ".gitignore"
+               (lambda _ (format #t "%")))
+             #t))
          (replace 'check
            (lambda _
              (invoke "./run_tests.py" "--unit")
-- 
cgit v1.2.3


From bb47da4a6ad012eb32a3792a9bf7337996f1c41e Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 1 Mar 2018 18:21:25 +0100
Subject: gnu: php: Update to 7.2.3.

* gnu/packages/php.scm (php): Update to 7.2.3.
---
 gnu/packages/php.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/php.scm b/gnu/packages/php.scm
index b9a5eb4bf2..1ed3dc7ce0 100644
--- a/gnu/packages/php.scm
+++ b/gnu/packages/php.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -52,7 +53,7 @@
 (define-public php
   (package
     (name "php")
-    (version "7.2.1")
+    (version "7.2.3")
     (home-page "https://secure.php.net/")
     (source (origin
               (method url-fetch)
@@ -60,7 +61,7 @@
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "08l8zmp8wbavq6wlgx19irz59csb44jhbsr172bfsq36v8pzhv3c"))
+                "07v5bq5b97zdqwmig6sxqsdb50vdf04w6jzmjq5kqh9gaqdlzadk"))
               (modules '((guix build utils)))
               (snippet
                '(with-directory-excursion "ext"
-- 
cgit v1.2.3


From 1ff14bf2cdc698e1aa3418a3bbea023e80075e50 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 1 Mar 2018 20:34:50 +0100
Subject: gnu: sdcc: Update to 3.7.0.

* gnu/packages/sdcc.scm (sdcc): Update to 3.7.0.
---
 gnu/packages/sdcc.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/sdcc.scm b/gnu/packages/sdcc.scm
index 331425d98f..a3746537dc 100644
--- a/gnu/packages/sdcc.scm
+++ b/gnu/packages/sdcc.scm
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016 David Craven <david@craven.ch>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -30,7 +31,7 @@
 (define-public sdcc
   (package
     (name "sdcc")
-    (version "3.6.0")
+    (version "3.7.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -38,7 +39,7 @@
                     "/" version "/sdcc-src-" version ".tar.bz2"))
               (sha256
                (base32
-                "0x53gh5yrrfjvlnkk29mjn8hq4v52alrsf7c8nsyzzq13sqwwpg8"))))
+                "13llvx0j3v5qa7qd4fh7nix4j3alpd3ccprxvx163c4q8q4lfkc5"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("bison" ,bison)
-- 
cgit v1.2.3


From 738aa0ca1d1b86286cf8f57620a50c4b093031b8 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 1 Mar 2018 20:36:09 +0100
Subject: gnu: sdcc: Fix typo in description.

* gnu/packages/sdcc.scm (sdcc)[description]: Fix (upstream) typo.  Add
hyphens.
---
 gnu/packages/sdcc.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/sdcc.scm b/gnu/packages/sdcc.scm
index a3746537dc..6d05470101 100644
--- a/gnu/packages/sdcc.scm
+++ b/gnu/packages/sdcc.scm
@@ -60,10 +60,10 @@
              #t)))))
     (home-page "http://sdcc.sourceforge.net")
     (synopsis "Small devices C compiler")
-    (description "SDCC is a retargettable, optimizing Standard C compiler suite
-that targets the Intel MCS51 based microprocessors (8031, 8032, 8051, 8052, ...),
+    (description "SDCC is a retargetable, optimizing Standard C compiler suite
+that targets the Intel MCS51-based microprocessors (8031, 8032, 8051, 8052, ...),
 Maxim (formerly Dallas) DS80C390 variants, Freescale (formerly Motorola)
-HC08 based (hc08, s08), Zilog Z80 based MCUs (z80, z180, gbz80, Rabbit
+HC08-based (hc08, s08), Zilog Z80-based MCUs (z80, z180, gbz80, Rabbit
 2000/3000, Rabbit 3000A, TLCS-90) and STMicroelectronics STM8.
 Work is in progress on supporting the Microchip PIC16 and PIC18 targets.
 It can be retargeted for other microprocessors.")
-- 
cgit v1.2.3


From 8147d7c675e663c45d5e1ccbeebb72daeaba0b91 Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Thu, 1 Mar 2018 20:34:51 +0100
Subject: gnu: php: Fix test failure.

* gnu/packages/php.scm (php)[inputs]: Use gd-for-php.
(gd-for-php): New private variable.
* gnu/packages/patches/gd-CVE-2018-5711.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
---
 gnu/local.mk                                |  1 +
 gnu/packages/patches/gd-CVE-2018-5711.patch | 61 +++++++++++++++++++++++++++++
 gnu/packages/php.scm                        | 17 +++++---
 3 files changed, 73 insertions(+), 6 deletions(-)
 create mode 100644 gnu/packages/patches/gd-CVE-2018-5711.patch

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index ee99882c5f..ba5af56bd9 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -681,6 +681,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/gcc-6-source-date-epoch-2.patch		\
   %D%/packages/patches/gcr-disable-failing-tests.patch		\
   %D%/packages/patches/gcr-fix-collection-tests-to-work-with-gpg-21.patch	\
+  %D%/packages/patches/gd-CVE-2018-5711.patch			\
   %D%/packages/patches/gd-fix-tests-on-i686.patch		\
   %D%/packages/patches/gd-freetype-test-failure.patch		\
   %D%/packages/patches/gegl-CVE-2012-4433.patch			\
diff --git a/gnu/packages/patches/gd-CVE-2018-5711.patch b/gnu/packages/patches/gd-CVE-2018-5711.patch
new file mode 100644
index 0000000000..83b12cde63
--- /dev/null
+++ b/gnu/packages/patches/gd-CVE-2018-5711.patch
@@ -0,0 +1,61 @@
+This patch is adapted from commit a11f47475e6443b7f32d21f2271f28f417e2ac04 and
+fixes CVE-2018-5711.
+
+From a11f47475e6443b7f32d21f2271f28f417e2ac04 Mon Sep 17 00:00:00 2001
+From: "Christoph M. Becker" <cmbecker69@gmx.de>
+Date: Wed, 29 Nov 2017 19:37:38 +0100
+Subject: [PATCH] Fix #420: Potential infinite loop in gdImageCreateFromGifCtx
+
+Due to a signedness confusion in `GetCode_` a corrupt GIF file can
+trigger an infinite loop.  Furthermore we make sure that a GIF without
+any palette entries is treated as invalid *after* open palette entries
+have been removed.
+
+CVE-2018-5711
+
+See also https://bugs.php.net/bug.php?id=75571.
+---
+ src/gd_gif_in.c             |  12 ++++++------
+ 1 file changed, 38 insertions(+), 6 deletions(-)
+
+diff --git a/src/gd_gif_in.c b/src/gd_gif_in.c
+index daf26e7..0a8bd71 100644
+--- a/src/gd_gif_in.c
++++ b/src/gd_gif_in.c
+@@ -335,11 +335,6 @@ terminated:
+ 		return 0;
+ 	}
+ 
+-	if(!im->colorsTotal) {
+-		gdImageDestroy(im);
+-		return 0;
+-	}
+-
+ 	/* Check for open colors at the end, so
+ 	 * we can reduce colorsTotal and ultimately
+ 	 * BitsPerPixel */
+@@ -351,6 +346,11 @@ terminated:
+ 		}
+ 	}
+ 
++	if(!im->colorsTotal) {
++		gdImageDestroy(im);
++		return 0;
++	}
++
+ 	return im;
+ }
+ 
+@@ -447,7 +447,7 @@ static int
+ GetCode_(gdIOCtx *fd, CODE_STATIC_DATA *scd, int code_size, int flag, int *ZeroDataBlockP)
+ {
+ 	int i, j, ret;
+-	unsigned char count;
++	int count;
+ 
+ 	if(flag) {
+ 		scd->curbit = 0;
+
+-- 
+2.13.6
+
diff --git a/gnu/packages/php.scm b/gnu/packages/php.scm
index 1ed3dc7ce0..f3f279a533 100644
--- a/gnu/packages/php.scm
+++ b/gnu/packages/php.scm
@@ -50,6 +50,15 @@
   #:use-module (guix build-system gnu)
   #:use-module ((guix licenses) #:prefix license:))
 
+(define gd-for-php
+  (package
+    (inherit gd)
+    (source (origin
+             (inherit (package-source gd))
+             (patches (search-patches "gd-fix-tests-on-i686.patch"
+                                      "gd-freetype-test-failure.patch"
+                                      "gd-CVE-2018-5711.patch"))))))
+
 (define-public php
   (package
     (name "php")
@@ -278,11 +287,7 @@
                          "ext/mbstring/tests/mb_ereg_variation3.phpt"
                          "ext/mbstring/tests/mb_ereg_replace_variation1.phpt"
                          "ext/mbstring/tests/bug72994.phpt"
-                         "ext/ldap/tests/ldap_set_option_error.phpt"
-                         
-                         ;; XXX: This is CVE-2018-5711. There is no fix yet in libgd.
-                         ;; See https://github.com/libgd/libgd/issues/420
-                         "ext/gd/tests/bug75571.phpt"))
+                         "ext/ldap/tests/ldap_set_option_error.phpt"))
 
              ;; Skip tests requiring network access.
              (setenv "SKIP_ONLINE_TESTS" "1")
@@ -299,7 +304,7 @@
        ("curl" ,curl)
        ("cyrus-sasl" ,cyrus-sasl)
        ("freetype" ,freetype)
-       ("gd" ,gd)
+       ("gd" ,gd-for-php)
        ("gdbm" ,gdbm)
        ("glibc" ,glibc)
        ("gmp" ,gmp)
-- 
cgit v1.2.3


From 50266960339fb534ff65657d7718c4e853280961 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Thu, 1 Mar 2018 17:57:22 -0500
Subject: gnu: linux-libre@4.4: Update to 4.4.119.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.119.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 420bdf5a47..183d27e6ca 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -408,8 +408,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.4
-  (make-linux-libre "4.4.118"
-                    "0di91awl8ii1fxrfyqbpfpn134apcc98fas7yisjg87f16bn4azl"
+  (make-linux-libre "4.4.119"
+                    "1cicg1yxf6rvaz8jcz8mdvnkrba9hd16pkp9mm602bzgks6s1fy9"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
-- 
cgit v1.2.3


From 8b1f76c443ce45ca9564d5231f5ac9d31618c08a Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Thu, 1 Mar 2018 17:58:04 -0500
Subject: gnu: linux-libre@4.9: Update to 4.9.85.

* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.85.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 183d27e6ca..07c677f7ba 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -402,8 +402,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.84"
-                    "08bgdcysva2igz4rc55slyz7nbzwz5skakh5c2iahsklg343pwbw"
+  (make-linux-libre "4.9.85"
+                    "17anlawvbzw6m2lrbriy7kfncdllkl7n8vjzwl2dnrgxddavd3rf"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
-- 
cgit v1.2.3


From 433765e5994af166e986716eeccae1f7ddc961e7 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Thu, 1 Mar 2018 17:58:35 -0500
Subject: gnu: linux-libre@4.14: Update to 4.14.23.

* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.23.
(%linux-libre-4.14-hash): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 07c677f7ba..93c31da587 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -392,8 +392,8 @@ It has been modified to remove all non-free binary blobs.")
                     %linux-compatible-systems
                     #:configuration-file kernel-config))
 
-(define %linux-libre-4.14-version "4.14.22")
-(define %linux-libre-4.14-hash "1lhswcvgl077kzsln3nxmrdbnlc3b8mphjjmkqz0f2663wa6rhcv")
+(define %linux-libre-4.14-version "4.14.23")
+(define %linux-libre-4.14-hash "0mz8v67zj3wn3kdjb2a781vx7nc1imi7kmlvf1h1m0f37hw0s47y")
 
 (define-public linux-libre-4.14
   (make-linux-libre %linux-libre-4.14-version
-- 
cgit v1.2.3


From da525e714a96213a3258d8e8b0f7a6090c53e90e Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Thu, 1 Mar 2018 17:59:21 -0500
Subject: gnu: linux-libre: Update to 4.15.7.

* gnu/packages/linux.scm (%linux-libre-version): Update to 4.15.7.
(%linux-libre-hash): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 93c31da587..b922989018 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -383,8 +383,8 @@ It has been modified to remove all non-free binary blobs.")
 ;; supports qemu "virt" machine and possibly a large number of ARM boards.
 ;; See : https://wiki.debian.org/DebianKernel/ARMMP.
 
-(define %linux-libre-version "4.15.6")
-(define %linux-libre-hash "13mv6wrhwjw2wll918c1r9l872wzzanvyi8rk6gv0k6cg0f56jal")
+(define %linux-libre-version "4.15.7")
+(define %linux-libre-hash "1h17wc12lvva5vcm2z06cf57ywxb6i2snm9vxixw1lwibnksrb6l")
 
 (define-public linux-libre
   (make-linux-libre %linux-libre-version
-- 
cgit v1.2.3


From e9802319f7df328e8deb13d576ba31732183f693 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Thu, 1 Mar 2018 19:59:55 -0500
Subject: gnu: memcached: Update to 1.5.6.

* gnu/packages/databases.scm (memcached): Update to 1.5.6.
---
 gnu/packages/databases.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index b99cd3d3d5..19c8efc9d4 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -396,14 +396,15 @@ mapping from string keys to string values.")
 (define-public memcached
   (package
     (name "memcached")
-    (version "1.5.0")
+    (version "1.5.6")
     (source
      (origin
        (method url-fetch)
        (uri (string-append
              "https://memcached.org/files/memcached-" version ".tar.gz"))
        (sha256
-        (base32 "0chwc0g7wfvcad36z8pf2jbgygdnm9nm1l6pwjsn3d2b089gh0f0"))))
+        (base32
+         "00szy9d4szaixi260dcd4846zci04y0sd47ia2lzg0bxkn2ywxcn"))))
     (build-system gnu-build-system)
     (inputs
      `(("libevent" ,libevent)
-- 
cgit v1.2.3


From bb17b2be49fbe50cfc44b5987f7c32fc0db1ccc5 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Thu, 1 Mar 2018 18:04:43 -0500
Subject: gnu: postgresql: Update to 10.3 [fixes CVE-2018-1058].

* gnu/packages/databases.scm (postgresql): Update to 10.3.
---
 gnu/packages/databases.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 19c8efc9d4..1793089003 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -700,14 +700,14 @@ as a drop-in replacement of MySQL.")
 (define-public postgresql
   (package
     (name "postgresql")
-    (version "10.2")
+    (version "10.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://ftp.postgresql.org/pub/source/v"
                                   version "/postgresql-" version ".tar.bz2"))
               (sha256
                (base32
-                "1bav2iyi93h866skrrlqlvsp4sfv1sfww1s305zpzffxcadh0cpy"))))
+                "06lkcwsf851z49zqcws5yc77s2yrbaazf2nvbk38hpp31rw6i8kf"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags '("--with-uuid=e2fs")
-- 
cgit v1.2.3


From 703a8b7dc5ff0f7150c3eec18298b53e05d2da6b Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Thu, 1 Mar 2018 18:05:20 -0500
Subject: gnu: postgresql@9.6: Update to 9.6.8 [fixes CVE-2018-1058].

* gnu/packages/databases.scm (postgresql-9.6): Update to 9.6.8.
---
 gnu/packages/databases.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 1793089003..ba4ad9f9b9 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -745,14 +745,14 @@ pictures, sounds, or video.")
   (package
     (inherit postgresql)
     (name "postgresql")
-    (version "9.6.6")
+    (version "9.6.8")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://ftp.postgresql.org/pub/source/v"
                                   version "/postgresql-" version ".tar.bz2"))
               (sha256
                (base32
-                "0m417h30s18rwa7yzkqqcdb22ifpcda2fpg2cyx8bxvjp3ydz71r"))))))
+                "0w7bwf19wbdd3jjbjv03cnx56qka4801srcbsayk9v792awv7zga"))))))
 
 (define-public qdbm
   (package
-- 
cgit v1.2.3


From 8863f2f05106c225566df1c040560f5d97af78ca Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Thu, 1 Mar 2018 22:45:25 -0500
Subject: gnu: icecat: Update to 52.6.0-gnu1.

* gnu/packages/gnuzilla.scm (icecat): Update to 52.6.0-gnu1.
[source]: Remove patches that are no longer needed.
* gnu/packages/patches/icecat-bug-1348660-pt5.patch,
gnu/packages/patches/icecat-bug-1414945.patch,
gnu/packages/patches/icecat-bug-1415133.patch,
gnu/packages/patches/icecat-bug-1424373-pt2.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.
---
 gnu/local.mk                                      |   4 -
 gnu/packages/gnuzilla.scm                         | 117 +---
 gnu/packages/patches/icecat-bug-1348660-pt5.patch | 727 ----------------------
 gnu/packages/patches/icecat-bug-1414945.patch     |  73 ---
 gnu/packages/patches/icecat-bug-1415133.patch     |  40 --
 gnu/packages/patches/icecat-bug-1424373-pt2.patch | 183 ------
 6 files changed, 2 insertions(+), 1142 deletions(-)
 delete mode 100644 gnu/packages/patches/icecat-bug-1348660-pt5.patch
 delete mode 100644 gnu/packages/patches/icecat-bug-1414945.patch
 delete mode 100644 gnu/packages/patches/icecat-bug-1415133.patch
 delete mode 100644 gnu/packages/patches/icecat-bug-1424373-pt2.patch

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index ba5af56bd9..dfe3ff5fc3 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -774,10 +774,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/hwloc-tests-without-sysfs.patch		\
   %D%/packages/patches/hydra-disable-darcs-test.patch		\
   %D%/packages/patches/icecat-avoid-bundled-libraries.patch	\
-  %D%/packages/patches/icecat-bug-1348660-pt5.patch		\
-  %D%/packages/patches/icecat-bug-1415133.patch			\
-  %D%/packages/patches/icecat-bug-1414945.patch			\
-  %D%/packages/patches/icecat-bug-1424373-pt2.patch		\
   %D%/packages/patches/icecat-use-system-graphite2.patch	\
   %D%/packages/patches/icecat-use-system-harfbuzz.patch		\
   %D%/packages/patches/id3lib-CVE-2007-4460.patch			\
diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm
index 8d9573fb81..e3f1bfe8c0 100644
--- a/gnu/packages/gnuzilla.scm
+++ b/gnu/packages/gnuzilla.scm
@@ -401,7 +401,7 @@ security standards.")
 (define-public icecat
   (package
     (name "icecat")
-    (version "52.3.0-gnu1")
+    (version "52.6.0-gnu1")
     (source
      (origin
       (method url-fetch)
@@ -410,7 +410,7 @@ security standards.")
                           "/" name "-" version ".tar.bz2"))
       (sha256
        (base32
-        "00jki754d6310fxj1b7dbhqj69y5igck6gqg6rgfya243nsb56k9"))
+        "09fn54glqg1aa93hnz5zdcy07cps09dbni2b4200azh6nang630a"))
       (patches
        (list
         (search-patch "icecat-avoid-bundled-libraries.patch")
@@ -418,120 +418,7 @@ security standards.")
         (search-patch "icecat-use-system-graphite2.patch")
         (mozilla-patch "icecat-bug-546387.patch"         "d13e3fefb76e" "1b760r0bg2ydbl585wlmajljh1nlisrwxvjws5b28a3sgjy01i6k")
         (mozilla-patch "icecat-bug-1350152.patch"        "f822bda79c28" "1wf56169ca874shr6r7qx40s17h2gwj7ngmpyylrpmd1c6hipvsj")
-        (mozilla-patch "icecat-bug-1388166.patch"        "fbb0bdb191d5" "1y8wpj38vw1dd6f375s9i0mrk9bd8z8gz5g70p4qynfllpkn072d")
-        (mozilla-patch "icecat-CVE-2017-7810-pt1.patch"  "fbddb5cdd3c7" "0k5nyl2z1y2rx9fwqyfj64678yv6v3pnmshgk552pbzqmaf8i1hq")
-        (mozilla-patch "icecat-CVE-2017-7810-pt2.patch"  "76c25987a275" "095b9vwsiza9ikbnnppfcld16h75x5bxjfxc73913y04n0i42ifh")
-        (mozilla-patch "icecat-CVE-2017-7810-pt3.patch"  "32eec29a85a5" "057simakqg56jvas1wkskg5kszn96m74nca26x08d5w7rzmbv1q2")
-        (mozilla-patch "icecat-bug-1373222.patch"        "ecef71fa933f" "0vsymgy5j702lamvh2riahni7rdj9ba3bd6i4a2m22d638rwp1i2")
-        (mozilla-patch "icecat-CVE-2017-7814.patch"      "68a444daf85b" "1faaadaajidzb9i00710zxdyv370hlrdg1l5rw2ymfmzbjj4jqyd")
-        (mozilla-patch "icecat-bug-1376825.patch"        "eeeec9cafc4e" "188qf6zi9kyxb33330yia6wmrd5mdyqn5hr1cl38zy7m3akv8srh")
-        (mozilla-patch "icecat-bug-1385272.patch"        "d68fa12fbffc" "13gh97vz9n2b7303jcvr1072iy8bghy9chvbmxzvw82prvkscavw")
-        (mozilla-patch "icecat-bug-1390002.patch"        "c24e6fc9f689" "0aswhy5fz2f6wzd5j5gg3nqvz707ip344089h2z2chcp146vxmf4")
-        (mozilla-patch "icecat-CVE-2017-7810-pt4.patch"  "ae110cf77596" "0gdrkfq9wy9cfcdgbj14ci86xgh2prkbz69pfy97r9igd8059syw")
-        (mozilla-patch "icecat-CVE-2017-7810-pt5.patch"  "b8417112486d" "1hya6lccz7vm51v4f6ww072794cwzmfn9xhxmvrnqbiyspxx5fz4")
-        (mozilla-patch "icecat-bug-1386905.patch"        "badbf4308211" "0fj1pyjqfdsbrlfykwmkzav2nvdj1f4grwq3cal9f7ay6wjnfs9b")
-        (mozilla-patch "icecat-CVE-2017-7810-pt6.patch"  "d78675515c78" "03w5hqy40xkckbaf5bm9kdbdqvp9ffvpk9mlrc9lja6b7qa4pjhg")
-        (mozilla-patch "icecat-bug-1382303.patch"        "f01155fe4d54" "0hnz1kvmvspg6453kydsklbvrjgzn8x3djvrym3f2xl2yinaf90d")
-        (mozilla-patch "icecat-bug-1393467.patch"        "4eec2a60622c" "1h006mwcsagq7mz7haymwgr7fn4zj14n5lxbjcmhdqrxdvma2hjj")
-        (mozilla-patch "icecat-bug-1384801.patch"        "9556e792f905" "0i74r807189s8i78483caiifw68cn7fs543i4cys6k3gn12dhhjy")
-        (mozilla-patch "icecat-CVE-2017-7823.patch"      "bd284765b5bc" "1c4hss87kc4qwx30magbqczm9h7zmwirjfc8zimqbrnwv9bbsfh3")
-        (mozilla-patch "icecat-CVE-2017-7805.patch"      "113da8d46aa4" "1vy0lw659mwixmb57mgybga152rdwqd5zj1g7nfw1zgp15pfwr75")
-        (mozilla-patch "icecat-bug-1376399.patch"        "58a574502ca9" "1zmg91pg0s5nwngc32a4fywidvxyaayvx1h052fsv0i4cfm16l9v")
-        (mozilla-patch "icecat-bug-1396570.patch"        "24db61862c54" "0af1jjfma042xvn0xhgims1yvb2b51nhn4m0pcfwg3fn0llmka03")
-        (mozilla-patch "icecat-CVE-2017-7819.patch"      "1a02f11c6efe" "18a9qvdvrqw34qw3lljg6gkn358jl23lyimhmbc964023rhs36sz")
-        (mozilla-patch "icecat-CVE-2017-7810-pt7.patch"  "002686d9536f" "065g0d759wfiaj69b1sqg7l08p2knc0q9m9hvkgwwsf0r78xcbjj")
-        (mozilla-patch "icecat-CVE-2017-7810-pt8.patch"  "eaadb31758d8" "0b3k3la6ykac5mbp9gyqqgjbmj19vx9sl1b0wp387qar0p12nyaz")
-        (mozilla-patch "icecat-bug-1368269.patch"        "0cff5e66e0f4" "0jb0wqi7c0ih4441s1908j6gv18v4inh7k2w47h3c9nhz4rgyrw7")
-        (mozilla-patch "icecat-CVE-2017-7793.patch"      "6ff3c82962f0" "0bw82034kdmrpznigbavzzsiybzrw8giyf8v0z2cxf6mwl72bf9k")
-        (mozilla-patch "icecat-bug-1400399.patch"        "d6f78b1349b7" "0i3gwr2al3xl65yfa3nimvy8dp0jzpx21f6bjw18xwn7zkkh9j54")
-        (mozilla-patch "icecat-bug-1400721.patch"        "285cde398833" "0a1i32zl30wfyw7zkqj595s94n6wdlg5c495m0910pd05pjg3qam")
-        (mozilla-patch "icecat-CVE-2017-7826-pt01.patch" "98b3988592a6" "03wy173lj6mvmh5q92brf596h8676h0zasgqfnndpvsmsiaih120")
-        (mozilla-patch "icecat-CVE-2017-7826-pt02.patch" "47590f0c274b" "0zsys6dcyhfb4a8k2dhsls7425jg6r1ijlrsn1lc5smwyf62zx5v")
-        (mozilla-patch "icecat-CVE-2017-7826-pt03.patch" "55b435cbbb55" "1gcasaqrxa13a55v05bkxl3d1md829kpfhqiaws83wn08x28l0my")
-        (mozilla-patch "icecat-CVE-2017-7826-pt04.patch" "8549cf2dab3e" "168gs32ncavaj9xn4gwhh9i01cbpnhgx9yn333apsrc1gwknpvsr")
-        (mozilla-patch "icecat-CVE-2017-7826-pt05.patch" "349acf56ff49" "1vwn87rdryfjsn809pl50xmr82q98gz3vz9h6clkd905vbd9rwz7")
-        (mozilla-patch "icecat-CVE-2017-7826-pt06.patch" "3af5bf8bdea0" "07az28dnpxr36j7i3llxkrlkrmg0bwk4f3sm75x1f0r1v5575p3p")
-        (mozilla-patch "icecat-CVE-2017-7826-pt07.patch" "592df6088926" "1gy27idik4b6wcg4szww08cmpcljssja8wql6w1d807h7ni65lr7")
-        (mozilla-patch "icecat-CVE-2017-7826-pt08.patch" "77a2d4610275" "13ysbwflnysj4rs45ibckd621s0vyg1s8dvannlvanvrz1g72zcz")
-        (mozilla-patch "icecat-CVE-2017-7826-pt09.patch" "2b30335d0b95" "0hs5cwickvfw7r5dn7y148jgr2b21hl613qp83k56634d0y64qwp")
-        (mozilla-patch "icecat-CVE-2017-7826-pt10.patch" "d6f008f95598" "0xclxrbg7pv8pa2j15p0gy9c8sigy2i9j0kvazl5fbyg6jsg3xgd")
-        (mozilla-patch "icecat-CVE-2017-7826-pt11.patch" "ab9b51cd75ac" "08jy3rbkyh934aw261ls0s87947d2mhss7xqk1xfdir9crij2g27")
-        (mozilla-patch "icecat-bug-1343147-pt1.patch"    "971d6345bc3a" "13791cvc51i991i5qyz6gp94vwzwkx479bnr8fsf8dw7z72wrsch")
-        (mozilla-patch "icecat-bug-1343147-pt2.patch"    "60df7db06669" "0r372g1zksvkzyz0qpq0mp30frilgsfxxx2xida8xc08wgxp5lh9")
-        (mozilla-patch "icecat-CVE-2017-7826-pt12.patch" "df49c25e6e4c" "0j77xbkxpflqf4jlccrv61vq0jgp4lfn8kb0zw1lswp3cyd6ml4i")
-        (mozilla-patch "icecat-CVE-2017-7826-pt13.patch" "3b899f872623" "01zjcpm8yp4s8yf4mj1bzq01aylmi69kd8qv0rrcl9hmj4g3pzr2")
-        (mozilla-patch "icecat-CVE-2017-7826-pt14.patch" "3d6d558ae6a6" "17wynknvs5wi7m9g5vn43rjmivbg1l6pnv8jymz1ccidy27qgdqi")
-        (mozilla-patch "icecat-CVE-2017-7826-pt15.patch" "8426754b7130" "0bbm2294bkvld55rdbpsc8b82ljqdcxpbg6cwdzvwfhqayl2pnqm")
-        (mozilla-patch "icecat-CVE-2017-7828-pt1.patch"  "5ddd5d2aa769" "12z5i8h6qwjb1h1fvp2426bgsnsxx539d8k2is9x1q4133356niy")
-        (mozilla-patch "icecat-CVE-2017-7826-pt16.patch" "dd068f4e132a" "17qy9c1vfkz3pj6y8qmqbic73wrangsbdlylk2s54nbzhhp9cj1g")
-        (mozilla-patch "icecat-CVE-2017-7826-pt17.patch" "e6bd533b57e9" "1mmqav9yhxd0j47yffcdykaqjibfwjsk0jn0f44099s87y8qn9zy")
-        (mozilla-patch "icecat-CVE-2017-7826-pt18.patch" "2a87fb6b9c07" "0z0scw4y1vqhqkbw1ag14g8xrif14l95x7fd50q2sw425lli29lc")
-        (mozilla-patch "icecat-bug-1404910.patch"        "5007f2472f64" "0ns1l4yipwbb52sps2xzg30qd1rkpwykxq4chjg3wllhmcxbvvpw")
-        (mozilla-patch "icecat-CVE-2017-7830.patch"      "04e3b5c1f0b2" "0nmv3jnx94ykxg64xkiwc8kx4df8zw7y5yzjnxz1sll2v88b9hmf")
-        (mozilla-patch "icecat-CVE-2017-7828-pt2.patch"  "2f48c03d9b3f" "16qdy3rahmkhsjnzqjcgzg1a4k7czd40m04gs9i75cd88kbripri")
-        (mozilla-patch "icecat-bug-1348660-pt1.patch"    "a352bfcbaf55" "1j3kxnhci9fh3lj8rizbcfv8xzn5kikxwpfy8a091d51sdn20873")
-        (mozilla-patch "icecat-bug-1348660-pt2.patch"    "57f43e2ab9b5" "1jva4y79zb85npak3mddrx5rsf4mxczb314kcr8yhlkwqv0nx5sp")
-        (mozilla-patch "icecat-bug-1348660-pt3.patch"    "917d65bb8896" "0k29y8i96lanqjjm6vybg0s6gjbk1mz5bfnga6aj1g0hnb7c3s8d")
-        (mozilla-patch "icecat-bug-1348660-pt4.patch"    "28934912eede" "1mhxw26050l3d09n8w912a86df87afcshvsk9k1k375anfk0927x")
-        (search-patch  "icecat-bug-1348660-pt5.patch")
-        (mozilla-patch "icecat-bug-1348660-pt6.patch"    "556ff3bfb9fc" "0kckjc8jp885xfaiwx2b9qnk1plqjhi0mwhjjcmfajvh3l3mrl8h")
-        (mozilla-patch "icecat-bug-1350564.patch"        "2abf26abb2a2" "0axdzp9g9k74wpkwrsdx263h01sv9bd3rarhhl68xnvc7n6i45lx")
-        (mozilla-patch "icecat-bug-1404787.patch"        "8335e1d7b140" "17d7kb8ginzflhdkrbi60vh2b907spbzmvwih7a595gqpihmnqqn")
-        (mozilla-patch "icecat-CVE-2017-7826-pt19.patch" "de336078d36b" "0gyzbap8hr1iywk0x2x0h7z7zp7q89hi56h8c03vvc7771dkvjkf")
-        (mozilla-patch "icecat-bug-1047098-pt1.patch"    "088577f0c46e" "0y3sz6kx07ls7jsvhqhhrl6v69a94wqvv3lz7hnplah23y06h17z")
-        (mozilla-patch "icecat-bug-1047098-pt2.patch"    "c7e3abf74023" "11dcjzx56v4yb2dvm23j2g86q8yva2hc69lmb7s5w18l6ygwwhzr")
-        (mozilla-patch "icecat-bug-1047098-pt3.patch"    "36bd15d14c5a" "0cb3l3hpsgk674f08kfamxhqfga3ah5v904gpxq9ag006vzd2cxz")
-        (mozilla-patch "icecat-bug-1404105.patch"        "2909ba991f31" "126vssj57dc800347f075wlnjzcwamnxxmgxl9w78jpb0hj9gf16")
-        (search-patch  "icecat-bug-1415133.patch")
-        (mozilla-patch "icecat-bug-1355576.patch"        "cf34a0574e58" "1z7sa1d12hypgivm5xxn32s58afpjcij97jvnafcgnfvxywrgr1m")
-        (mozilla-patch "icecat-CVE-2017-7843.patch"      "f6216ea8b8fc" "0jnhdkj0ch9mj01mzlvhjgf8zsxlbg6m7yvpq99qr7xmg0pzbgwl")
-        (mozilla-patch "icecat-bug-1413741.patch"        "4e00ce2897c4" "0k95vi31glia2i03djidkc0gkwp9qldy34fz1rxcj56a1iphbq7w")
-        (mozilla-patch "icecat-CVE-2018-5089-pt01.patch" "92d450811409" "0xsvggnr0y65nd52nkbjvpcbs5nd84pvbayk5vinbx1mnk2wh2vy")
-        (mozilla-patch "icecat-CVE-2018-5089-pt02.patch" "7eba7d14704a" "1vi17qmjzh3kji14iz370kvs4425asgp93ns2chf5ldlq5b9196g")
-        (mozilla-patch "icecat-CVE-2018-5089-pt03.patch" "457d023c167e" "11g8hg8yp20lsn52dx1ym8r4yjsnsmx0h182d6nbl6ab9wp7d1m9")
-        (mozilla-patch "icecat-CVE-2018-5089-pt04.patch" "5e7b16213198" "14c4x6c3mygf8p77n9bia5rndjpngbvik1r1ylk97k3ggy4fj6zh")
-        (mozilla-patch "icecat-CVE-2018-5102.patch"      "0712b6cbbdc8" "0rllsq6ckpms7g9k6qky1gr5rz1gav4widrha6w1s9f88cbrqgk5")
-        (mozilla-patch "icecat-CVE-2018-5089-pt05.patch" "084c427ccf99" "0sjdy2iang09a9g6liavpjgry04dp6smjgj0y7lp5lfqijdr8q2d")
-        (mozilla-patch "icecat-CVE-2018-5089-pt06.patch" "1bfb3d8d4510" "0c2dcxj74ijs6qf9sqcbj8w998hblic66vy41818z7xnw46j5j1j")
-        (mozilla-patch "icecat-bug-1414425.patch"        "5623e01e63a8" "08dn3v96bsb61hy3wfxz43fhn1mk9vlm5ydvdjgi3wiqadvacgzs")
-        (mozilla-patch "icecat-CVE-2018-5089-pt07.patch" "14a389d40329" "0f4gbak5bd2walxrxs3myig28v9lhvplf3a1nws1a4ajx80slzq1")
-        (mozilla-patch "icecat-bug-1415441.patch"        "7339297cddb7" "017lbw0mn5rwzb2abfw6qrk07m3r96vwbj81cmqvdfnmprcjni5j")
-        (mozilla-patch "icecat-CVE-2018-5096.patch"      "aa55d4cdaee5" "1l3qwjfx0jsbbw2dg8bsnx7k47zibamgswndq0d1bchnmary62aw")
-        (mozilla-patch "icecat-bug-1382358.patch"        "762f4e53889a" "0n61zrb6rz9bhhdsqs5ziwaiy81pq52c76p9qmi9hrxbn24ism1k")
-        (mozilla-patch "icecat-CVE-2018-5089-pt08.patch" "0152d097672f" "16ybg718calvciv00kil8s97lhh11hj6gx0acf73r44xfkvm8nfg")
-        (search-patch  "icecat-bug-1414945.patch")
-        (mozilla-patch "icecat-CVE-2018-5089-pt09.patch" "079356ed5317" "107c0b93g2k743wvhwz2ps3j6p09qld7d0raljijv5y5n8q4wp92")
-        (mozilla-patch "icecat-CVE-2018-5089-pt10.patch" "93e4994a892c" "00r2qxw3619529vy9d04dl9kcziqy3fv3iawgy9svzygyx1kj5wx")
-        (mozilla-patch "icecat-CVE-2018-5089-pt11.patch" "f8a6e1864832" "1wbxn0v50637yjg8b8675k01x9cyx95jpjxpyqfaa97762qkznba")
-        (mozilla-patch "icecat-CVE-2018-5089-pt12.patch" "0cc1c9068714" "1qmqpi14zs7c95k3c7396gpp6apb622k0mgv553kw4rr81nj1yac")
-        (mozilla-patch "icecat-CVE-2018-5095.patch"      "ce6f3fb2bf58" "1b1msb5d5jsgrqa2hkbsrm0n54qdmx1b2bf65v44v17appa03lra")
-        (mozilla-patch "icecat-CVE-2018-5103.patch"      "6b4d3c5d5e51" "074p93dhwr1ckhypkjpblnmg9hg44a9030g1glqffi9dyn3iq3k4")
-        (mozilla-patch "icecat-bug-1411745.patch"        "1a510ee578a0" "1imb7glh2m1zwvvpvr4k4iddms5byqzr35j7kv3y5is77aiwl4z5")
         (mozilla-patch "icecat-bug-1411708.patch"        "34c968767eb7" "0l2jy201ikj3m3h66mvlsj4y0ki7cpm7x7nnfygbwnfxg42s1sip")
-        (mozilla-patch "icecat-CVE-2018-5091.patch"      "bc166be85bb4" "0w1lrjzfrfflaw4l6sfi3ir81iyi9gyfck5g41dwp0jc1b59jzvg")
-        (mozilla-patch "icecat-CVE-2018-5089-pt13.patch" "66cfc3c4047d" "05j8ic4lv2d2ygr6d62rkdlfyg2rpljalwrkkhllinw2dfi3n15b")
-        (mozilla-patch "icecat-CVE-2018-5098.patch"      "3236ffdf0ced" "1kvk4qyslaj1ldgs1wpxnf79zajcihzcd1zvbrg990i3hgyn3gk3")
-        (mozilla-patch "icecat-bug-1424373-pt1.patch"    "320032aaa068" "1ch282qibprz1q0f2imvynh4sg7gads6sf3ayhjcd62zjncpgyz7")
-        (search-patch  "icecat-bug-1424373-pt2.patch")
-        (mozilla-patch "icecat-CVE-2018-5089-pt14.patch" "c2945f1249eb" "18p0344w6grpyfiz8dczfw977p0qy37iqv95whgnrjli2ab51kji")
-        (mozilla-patch "icecat-CVE-2018-5117-pt1.patch"  "263165eacc54" "0518xnd9f4qkn7l0z73kldm9dr33y6hf054ril4f8r2j8s9fy33i")
-        (mozilla-patch "icecat-CVE-2018-5117-pt2.patch"  "58e87d9cc44e" "0j9qwjm25bmhw0sj426yl4fqaa6zknf5cjk0yisdd3895652n5i4")
-        (mozilla-patch "icecat-CVE-2018-5089-pt15.patch" "aa4b11615431" "0whfvwaj3dmk89ah2kbv7zz7a8ckqa0xajf5fl12bgl7q8c8ndnm")
-        (mozilla-patch "icecat-CVE-2018-5104.patch"      "66761c5bfbe1" "076128pxc7ik1zq2v0d5m6vd7nls2030jzdc4w0ggy8hd5yyb8g9")
-        (mozilla-patch "icecat-bug-1408631.patch"        "6f5c8df1925d" "1hgr18p5dwhlsan6jxlj3ay7cbfyywk40bpbnjc8gqmq6y25cn48")
-        (mozilla-patch "icecat-bug-1422735.patch"        "b88ef76f5687" "0rzpxfrhddc0238rq3r1b02j95g0rdplk1fjmk85m51xvggh9086")
-        (mozilla-patch "icecat-bug-1261963.patch"        "d0c98f5b6c12" "1z9jn19hnwjand9c0ifc39gq71nz17jjqy2s5fqr2z06y8qys62h")
-        (mozilla-patch "icecat-CVE-2018-5089-pt16.patch" "f7865afb1fe6" "0i7ydmcr1g0ih3myyxaxjq6wfg3rvq5j4893kjqksqihfqrkzs4j")
-        (mozilla-patch "icecat-CVE-2018-5097.patch"      "9fb7614319df" "1xirahk06w8pyw4pdh64f4pg3qcb7c8x8frrmad2895fagy14g4k")
-        (mozilla-patch "icecat-mitigate-spectre.patch"   "81d6465bd7c2" "1za5l249pb5x7f283vrimy0ankjzvwa99hfql3v4fm5a4grjkj9n")
-        (mozilla-patch "icecat-CVE-2018-5089-pt17.patch" "5f753161df25" "1k2mpwagz08wzxfzwy2b4a0pz0hkhdqby6n11i7pasx3ary670km")
-        (mozilla-patch "icecat-CVE-2018-5099.patch"      "b95d654de120" "1cv7nz2gsyjjigw6wv4xagh8q6bcg0971md8b6xjvz5m26aynlaw")
-        (mozilla-patch "icecat-bug-1408631.patch"        "3b1faddc0e5f" "0817x5mrdyjj0gc9yi19m6d78d18ypc9nbld64d2axhc8v9bz3xf")
-        (mozilla-patch "icecat-glibc-2.26.patch"         "57d4fae4dffe" "1sv7kp7m4i7n31ny8k7cpjsrqpxh5y5jm27sh2cgpj7fhi5kqsj2")
-        (mozilla-patch "icecat-CVE-2018-5089-pt18.patch" "fe271a2b9503" "11wr8mdxw01dlmzkq55hf0qd52cwmx4vk96cff66d4kkl1dbj6qn")
-        (mozilla-patch "icecat-CVE-2018-5089-pt19.patch" "410da936a1e8" "14dvaysz0svlh50kdabjhd2s5avz6p93sbyqhwik5rlvcg5ax5zp")
-        (mozilla-patch "icecat-CVE-2018-5089-pt20.patch" "8368a9a379e3" "0fqq01ms7m4kb9b10n8gy5n9n4x43crz2gn1r6c4ny52wzgm3j6f")
-        (mozilla-patch "icecat-CVE-2018-5089-pt21.patch" "a7c8e85285e2" "1caa2w5r8rqb1qrk4mgf2vw1k592idvqmgs8qfz2dp2744kk6z98")
         (mozilla-patch "icecat-bug-1375217.patch"        "00fc630c9a46" "17pcprp452nslk6sac6sili0p74zh8w3g0v1wsdn0ikm9xmnphhv")
         (mozilla-patch "icecat-bug-1261175.patch"        "f0ec180993d2" "0jiazxcwki83wr00fyh2g518ynsd33p7nk65zk4d1682gn22lc8v")
         (mozilla-patch "icecat-bug-1433005.patch"        "a6a9e26688c1" "0cvizvilb4k422j2gzqcbakznvsffmk6n6xn1ayj5rgxfaizkkqk")
diff --git a/gnu/packages/patches/icecat-bug-1348660-pt5.patch b/gnu/packages/patches/icecat-bug-1348660-pt5.patch
deleted file mode 100644
index b0bede3b38..0000000000
--- a/gnu/packages/patches/icecat-bug-1348660-pt5.patch
+++ /dev/null
@@ -1,727 +0,0 @@
-This is a subset of the following changeset from upstream:
-  https://hg.mozilla.org/releases/mozilla-esr52/raw-rev/5e07bd37ac61
-
-This excludes all test code from that changeset, including a GIT binary patch
-that is not supported by Guix's patch-and-repack mechanism.
-
-# HG changeset patch
-# User Jan Varga <jan.varga@gmail.com>
-# Date 1490181244 -3600
-# Node ID 5e07bd37ac6162f218dfe03ed83b5dcca9653b68
-# Parent  28934912eede9e14895baf4af7575ca9639f59ee
-Bug 1348660 - Part 5: Implement a method to retrieve usage data for all origins at once. r=btseng, a=lizzard
-
-diff --git a/dom/quota/ActorsChild.cpp b/dom/quota/ActorsChild.cpp
---- a/dom/quota/ActorsChild.cpp
-+++ b/dom/quota/ActorsChild.cpp
-@@ -137,16 +137,52 @@ QuotaUsageRequestChild::HandleResponse(n
-   AssertIsOnOwningThread();
-   MOZ_ASSERT(NS_FAILED(aResponse));
-   MOZ_ASSERT(mRequest);
- 
-   mRequest->SetError(aResponse);
- }
- 
- void
-+QuotaUsageRequestChild::HandleResponse(const nsTArray<OriginUsage>& aResponse)
-+{
-+  AssertIsOnOwningThread();
-+  MOZ_ASSERT(mRequest);
-+
-+  RefPtr<nsVariant> variant = new nsVariant();
-+
-+  if (aResponse.IsEmpty()) {
-+    variant->SetAsEmptyArray();
-+  } else {
-+    nsTArray<RefPtr<UsageResult>> usageResults;
-+
-+    const uint32_t count = aResponse.Length();
-+
-+    usageResults.SetCapacity(count);
-+
-+    for (uint32_t index = 0; index < count; index++) {
-+      auto& originUsage = aResponse[index];
-+
-+      RefPtr<UsageResult> usageResult = new UsageResult(originUsage.origin(),
-+                                                        originUsage.persisted(),
-+                                                        originUsage.usage());
-+
-+      usageResults.AppendElement(usageResult.forget());
-+    }
-+
-+    variant->SetAsArray(nsIDataType::VTYPE_INTERFACE_IS,
-+                        &NS_GET_IID(nsIQuotaUsageResult),
-+                        usageResults.Length(),
-+                        static_cast<void*>(usageResults.Elements()));
-+  }
-+
-+  mRequest->SetResult(variant);
-+}
-+
-+void
- QuotaUsageRequestChild::HandleResponse(const OriginUsageResponse& aResponse)
- {
-   AssertIsOnOwningThread();
-   MOZ_ASSERT(mRequest);
- 
-   RefPtr<OriginUsageResult> result =
-     new OriginUsageResult(aResponse.usage(),
-                           aResponse.fileUsage(),
-@@ -177,16 +213,20 @@ QuotaUsageRequestChild::Recv__delete__(c
-   AssertIsOnOwningThread();
-   MOZ_ASSERT(mRequest);
- 
-   switch (aResponse.type()) {
-     case UsageRequestResponse::Tnsresult:
-       HandleResponse(aResponse.get_nsresult());
-       break;
- 
-+    case UsageRequestResponse::TAllUsageResponse:
-+      HandleResponse(aResponse.get_AllUsageResponse().originUsages());
-+      break;
-+
-     case UsageRequestResponse::TOriginUsageResponse:
-       HandleResponse(aResponse.get_OriginUsageResponse());
-       break;
- 
-     default:
-       MOZ_CRASH("Unknown response type!");
-   }
- 
-diff --git a/dom/quota/ActorsChild.h b/dom/quota/ActorsChild.h
---- a/dom/quota/ActorsChild.h
-+++ b/dom/quota/ActorsChild.h
-@@ -93,16 +93,19 @@ private:
- 
-   // Only destroyed by QuotaChild.
-   ~QuotaUsageRequestChild();
- 
-   void
-   HandleResponse(nsresult aResponse);
- 
-   void
-+  HandleResponse(const nsTArray<OriginUsage>& aResponse);
-+
-+  void
-   HandleResponse(const OriginUsageResponse& aResponse);
- 
-   // IPDL methods are only called by IPDL.
-   virtual void
-   ActorDestroy(ActorDestroyReason aWhy) override;
- 
-   virtual bool
-   Recv__delete__(const UsageRequestResponse& aResponse) override;
-diff --git a/dom/quota/ActorsParent.cpp b/dom/quota/ActorsParent.cpp
---- a/dom/quota/ActorsParent.cpp
-+++ b/dom/quota/ActorsParent.cpp
-@@ -1039,16 +1039,42 @@ private:
-   // IPDL methods.
-   void
-   ActorDestroy(ActorDestroyReason aWhy) override;
- 
-   bool
-   RecvCancel() override;
- };
- 
-+class GetUsageOp final
-+  : public QuotaUsageRequestBase
-+{
-+  nsTArray<OriginUsage> mOriginUsages;
-+  nsDataHashtable<nsCStringHashKey, uint32_t> mOriginUsagesIndex;
-+
-+  bool mGetAll;
-+
-+public:
-+  explicit GetUsageOp(const UsageRequestParams& aParams);
-+
-+private:
-+  ~GetUsageOp()
-+  { }
-+
-+  nsresult
-+  TraverseRepository(QuotaManager* aQuotaManager,
-+                     PersistenceType aPersistenceType);
-+
-+  nsresult
-+  DoDirectoryWork(QuotaManager* aQuotaManager) override;
-+
-+  void
-+  GetResponse(UsageRequestResponse& aResponse) override;
-+};
-+
- class GetOriginUsageOp final
-   : public QuotaUsageRequestBase
- {
-   // If mGetGroupUsage is false, we use mUsageInfo to record the origin usage
-   // and the file usage. Otherwise, we use it to record the group usage and the
-   // limit.
-   UsageInfo mUsageInfo;
- 
-@@ -5693,16 +5719,20 @@ PQuotaUsageRequestParent*
- Quota::AllocPQuotaUsageRequestParent(const UsageRequestParams& aParams)
- {
-   AssertIsOnBackgroundThread();
-   MOZ_ASSERT(aParams.type() != UsageRequestParams::T__None);
- 
-   RefPtr<QuotaUsageRequestBase> actor;
- 
-   switch (aParams.type()) {
-+    case UsageRequestParams::TAllUsageParams:
-+      actor = new GetUsageOp(aParams);
-+      break;
-+
-     case UsageRequestParams::TOriginUsageParams:
-       actor = new GetOriginUsageOp(aParams);
-       break;
- 
-     default:
-       MOZ_CRASH("Should never get here!");
-   }
- 
-@@ -6033,16 +6063,189 @@ QuotaUsageRequestBase::RecvCancel()
-   if (mCanceled.exchange(true)) {
-     NS_WARNING("Canceled more than once?!");
-     return false;
-   }
- 
-   return true;
- }
- 
-+GetUsageOp::GetUsageOp(const UsageRequestParams& aParams)
-+  : mGetAll(aParams.get_AllUsageParams().getAll())
-+{
-+  AssertIsOnOwningThread();
-+  MOZ_ASSERT(aParams.type() == UsageRequestParams::TAllUsageParams);
-+}
-+
-+nsresult
-+GetUsageOp::TraverseRepository(QuotaManager* aQuotaManager,
-+                               PersistenceType aPersistenceType)
-+{
-+  AssertIsOnIOThread();
-+  MOZ_ASSERT(aQuotaManager);
-+
-+  nsresult rv;
-+
-+  nsCOMPtr<nsIFile> directory =
-+    do_CreateInstance(NS_LOCAL_FILE_CONTRACTID, &rv);
-+  if (NS_WARN_IF(NS_FAILED(rv))) {
-+    return rv;
-+  }
-+
-+  rv = directory->InitWithPath(aQuotaManager->GetStoragePath(aPersistenceType));
-+  if (NS_WARN_IF(NS_FAILED(rv))) {
-+    return rv;
-+  }
-+
-+  bool exists;
-+  rv = directory->Exists(&exists);
-+  if (NS_WARN_IF(NS_FAILED(rv))) {
-+    return rv;
-+  }
-+
-+  if (!exists) {
-+    return NS_OK;
-+  }
-+
-+  nsCOMPtr<nsISimpleEnumerator> entries;
-+  rv = directory->GetDirectoryEntries(getter_AddRefs(entries));
-+  if (NS_WARN_IF(NS_FAILED(rv))) {
-+    return rv;
-+  }
-+
-+  bool persistent = aPersistenceType == PERSISTENCE_TYPE_PERSISTENT;
-+
-+  bool hasMore;
-+  while (NS_SUCCEEDED((rv = entries->HasMoreElements(&hasMore))) &&
-+         hasMore && !mCanceled) {
-+    nsCOMPtr<nsISupports> entry;
-+    rv = entries->GetNext(getter_AddRefs(entry));
-+    if (NS_WARN_IF(NS_FAILED(rv))) {
-+      return rv;
-+    }
-+
-+    nsCOMPtr<nsIFile> originDir = do_QueryInterface(entry);
-+    MOZ_ASSERT(originDir);
-+
-+    bool isDirectory;
-+    rv = originDir->IsDirectory(&isDirectory);
-+    if (NS_WARN_IF(NS_FAILED(rv))) {
-+      return rv;
-+    }
-+
-+    if (!isDirectory) {
-+      nsString leafName;
-+      rv = originDir->GetLeafName(leafName);
-+      if (NS_WARN_IF(NS_FAILED(rv))) {
-+        return rv;
-+      }
-+
-+      if (!leafName.EqualsLiteral(DSSTORE_FILE_NAME)) {
-+        QM_WARNING("Something (%s) in the repository that doesn't belong!",
-+                   NS_ConvertUTF16toUTF8(leafName).get());
-+      }
-+      continue;
-+    }
-+
-+    int64_t timestamp;
-+    nsCString suffix;
-+    nsCString group;
-+    nsCString origin;
-+    bool isApp;
-+    rv = aQuotaManager->GetDirectoryMetadata2WithRestore(originDir,
-+                                                         persistent,
-+                                                         &timestamp,
-+                                                         suffix,
-+                                                         group,
-+                                                         origin,
-+                                                         &isApp);
-+    if (NS_WARN_IF(NS_FAILED(rv))) {
-+      return rv;
-+    }
-+
-+    if (!mGetAll &&
-+        aQuotaManager->IsOriginWhitelistedForPersistentStorage(origin)) {
-+      continue;
-+    }
-+
-+    OriginUsage* originUsage;
-+
-+    // We can't store pointers to OriginUsage objects in the hashtable
-+    // since AppendElement() reallocates its internal array buffer as number
-+    // of elements grows.
-+    uint32_t index;
-+    if (mOriginUsagesIndex.Get(origin, &index)) {
-+      originUsage = &mOriginUsages[index];
-+    } else {
-+      index = mOriginUsages.Length();
-+
-+      originUsage = mOriginUsages.AppendElement();
-+
-+      originUsage->origin() = origin;
-+      originUsage->persisted() = false;
-+      originUsage->usage() = 0;
-+
-+      mOriginUsagesIndex.Put(origin, index);
-+    }
-+
-+    UsageInfo usageInfo;
-+    rv = GetUsageForOrigin(aQuotaManager,
-+                           aPersistenceType,
-+                           group,
-+                           origin,
-+                           isApp,
-+                           &usageInfo);
-+    if (NS_WARN_IF(NS_FAILED(rv))) {
-+      return rv;
-+    }
-+
-+    originUsage->usage() = originUsage->usage() + usageInfo.TotalUsage();
-+  }
-+  if (NS_WARN_IF(NS_FAILED(rv))) {
-+    return rv;
-+  }
-+
-+  return NS_OK;
-+}
-+
-+nsresult
-+GetUsageOp::DoDirectoryWork(QuotaManager* aQuotaManager)
-+{
-+  AssertIsOnIOThread();
-+
-+  PROFILER_LABEL("Quota", "GetUsageOp::DoDirectoryWork",
-+                 js::ProfileEntry::Category::OTHER);
-+
-+  nsresult rv;
-+
-+  for (const PersistenceType type : kAllPersistenceTypes) {
-+    rv = TraverseRepository(aQuotaManager, type);
-+    if (NS_WARN_IF(NS_FAILED(rv))) {
-+      return rv;
-+    }
-+  }
-+
-+  return NS_OK;
-+}
-+
-+void
-+GetUsageOp::GetResponse(UsageRequestResponse& aResponse)
-+{
-+  AssertIsOnOwningThread();
-+
-+  aResponse = AllUsageResponse();
-+
-+  if (!mOriginUsages.IsEmpty()) {
-+    nsTArray<OriginUsage>& originUsages =
-+      aResponse.get_AllUsageResponse().originUsages();
-+
-+    mOriginUsages.SwapElements(originUsages);
-+  }
-+}
-+
- GetOriginUsageOp::GetOriginUsageOp(const UsageRequestParams& aParams)
-   : mParams(aParams.get_OriginUsageParams())
-   , mGetGroupUsage(aParams.get_OriginUsageParams().getGroupUsage())
- {
-   AssertIsOnOwningThread();
-   MOZ_ASSERT(aParams.type() == UsageRequestParams::TOriginUsageParams);
- }
- 
-diff --git a/dom/quota/PQuota.ipdl b/dom/quota/PQuota.ipdl
---- a/dom/quota/PQuota.ipdl
-+++ b/dom/quota/PQuota.ipdl
-@@ -12,24 +12,30 @@ include "mozilla/dom/quota/Serialization
- 
- using mozilla::dom::quota::PersistenceType
-   from "mozilla/dom/quota/PersistenceType.h";
- 
- namespace mozilla {
- namespace dom {
- namespace quota {
- 
-+struct AllUsageParams
-+{
-+  bool getAll;
-+};
-+
- struct OriginUsageParams
- {
-   PrincipalInfo principalInfo;
-   bool getGroupUsage;
- };
- 
- union UsageRequestParams
- {
-+  AllUsageParams;
-   OriginUsageParams;
- };
- 
- struct ClearOriginParams
- {
-   PrincipalInfo principalInfo;
-   PersistenceType persistenceType;
-   bool persistenceTypeIsExplicit;
-diff --git a/dom/quota/PQuotaUsageRequest.ipdl b/dom/quota/PQuotaUsageRequest.ipdl
---- a/dom/quota/PQuotaUsageRequest.ipdl
-+++ b/dom/quota/PQuotaUsageRequest.ipdl
-@@ -3,26 +3,39 @@
-  * You can obtain one at http://mozilla.org/MPL/2.0/. */
- 
- include protocol PQuota;
- 
- namespace mozilla {
- namespace dom {
- namespace quota {
- 
-+struct OriginUsage
-+{
-+  nsCString origin;
-+  bool persisted;
-+  uint64_t usage;
-+};
-+
-+struct AllUsageResponse
-+{
-+  OriginUsage[] originUsages;
-+};
-+
- struct OriginUsageResponse
- {
-   uint64_t usage;
-   uint64_t fileUsage;
-   uint64_t limit;
- };
- 
- union UsageRequestResponse
- {
-   nsresult;
-+  AllUsageResponse;
-   OriginUsageResponse;
- };
- 
- protocol PQuotaUsageRequest
- {
-   manager PQuota;
- 
- parent:
-diff --git a/dom/quota/QuotaManagerService.cpp b/dom/quota/QuotaManagerService.cpp
---- a/dom/quota/QuotaManagerService.cpp
-+++ b/dom/quota/QuotaManagerService.cpp
-@@ -490,16 +490,41 @@ QuotaManagerService::RemoveIdleObserver(
- 
- NS_IMPL_ADDREF(QuotaManagerService)
- NS_IMPL_RELEASE_WITH_DESTROY(QuotaManagerService, Destroy())
- NS_IMPL_QUERY_INTERFACE(QuotaManagerService,
-                         nsIQuotaManagerService,
-                         nsIObserver)
- 
- NS_IMETHODIMP
-+QuotaManagerService::GetUsage(nsIQuotaUsageCallback* aCallback,
-+                              bool aGetAll,
-+                              nsIQuotaUsageRequest** _retval)
-+{
-+  MOZ_ASSERT(NS_IsMainThread());
-+  MOZ_ASSERT(aCallback);
-+
-+  RefPtr<UsageRequest> request = new UsageRequest(aCallback);
-+
-+  AllUsageParams params;
-+
-+  params.getAll() = aGetAll;
-+
-+  nsAutoPtr<PendingRequestInfo> info(new UsageRequestInfo(request, params));
-+
-+  nsresult rv = InitiateRequest(info);
-+  if (NS_WARN_IF(NS_FAILED(rv))) {
-+    return rv;
-+  }
-+
-+  request.forget(_retval);
-+  return NS_OK;
-+}
-+
-+NS_IMETHODIMP
- QuotaManagerService::GetUsageForPrincipal(nsIPrincipal* aPrincipal,
-                                           nsIQuotaUsageCallback* aCallback,
-                                           bool aGetGroupUsage,
-                                           nsIQuotaUsageRequest** _retval)
- {
-   MOZ_ASSERT(NS_IsMainThread());
-   MOZ_ASSERT(aPrincipal);
-   MOZ_ASSERT(aCallback);
-diff --git a/dom/quota/QuotaRequests.cpp b/dom/quota/QuotaRequests.cpp
---- a/dom/quota/QuotaRequests.cpp
-+++ b/dom/quota/QuotaRequests.cpp
-@@ -86,16 +86,25 @@ RequestBase::GetResultCode(nsresult* aRe
-   if (!mHaveResultOrErrorCode) {
-     return NS_ERROR_FAILURE;
-   }
- 
-   *aResultCode = mResultCode;
-   return NS_OK;
- }
- 
-+UsageRequest::UsageRequest(nsIQuotaUsageCallback* aCallback)
-+  : mCallback(aCallback)
-+  , mBackgroundActor(nullptr)
-+  , mCanceled(false)
-+{
-+  AssertIsOnOwningThread();
-+  MOZ_ASSERT(aCallback);
-+}
-+
- UsageRequest::UsageRequest(nsIPrincipal* aPrincipal,
-                            nsIQuotaUsageCallback* aCallback)
-   : RequestBase(aPrincipal)
-   , mCallback(aCallback)
-   , mBackgroundActor(nullptr)
-   , mCanceled(false)
- {
-   AssertIsOnOwningThread();
-diff --git a/dom/quota/QuotaRequests.h b/dom/quota/QuotaRequests.h
---- a/dom/quota/QuotaRequests.h
-+++ b/dom/quota/QuotaRequests.h
-@@ -73,16 +73,18 @@ class UsageRequest final
- 
-   nsCOMPtr<nsIVariant> mResult;
- 
-   QuotaUsageRequestChild* mBackgroundActor;
- 
-   bool mCanceled;
- 
- public:
-+  explicit UsageRequest(nsIQuotaUsageCallback* aCallback);
-+
-   UsageRequest(nsIPrincipal* aPrincipal,
-                nsIQuotaUsageCallback* aCallback);
- 
-   void
-   SetBackgroundActor(QuotaUsageRequestChild* aBackgroundActor);
- 
-   void
-   ClearBackgroundActor()
-diff --git a/dom/quota/QuotaResults.cpp b/dom/quota/QuotaResults.cpp
---- a/dom/quota/QuotaResults.cpp
-+++ b/dom/quota/QuotaResults.cpp
-@@ -5,16 +5,53 @@
-  * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
- 
- #include "QuotaResults.h"
- 
- namespace mozilla {
- namespace dom {
- namespace quota {
- 
-+UsageResult::UsageResult(const nsACString& aOrigin,
-+                         bool aPersisted,
-+                         uint64_t aUsage)
-+  : mOrigin(aOrigin)
-+  , mUsage(aUsage)
-+  , mPersisted(aPersisted)
-+{
-+}
-+
-+NS_IMPL_ISUPPORTS(UsageResult,
-+                  nsIQuotaUsageResult)
-+
-+NS_IMETHODIMP
-+UsageResult::GetOrigin(nsACString& aOrigin)
-+{
-+  aOrigin = mOrigin;
-+  return NS_OK;
-+}
-+
-+NS_IMETHODIMP
-+UsageResult::GetPersisted(bool* aPersisted)
-+{
-+  MOZ_ASSERT(aPersisted);
-+
-+  *aPersisted = mPersisted;
-+  return NS_OK;
-+}
-+
-+NS_IMETHODIMP
-+UsageResult::GetUsage(uint64_t* aUsage)
-+{
-+  MOZ_ASSERT(aUsage);
-+
-+  *aUsage = mUsage;
-+  return NS_OK;
-+}
-+
- OriginUsageResult::OriginUsageResult(uint64_t aUsage,
-                                      uint64_t aFileUsage,
-                                      uint64_t aLimit)
-   : mUsage(aUsage)
-   , mFileUsage(aFileUsage)
-   , mLimit(aLimit)
- {
- }
-diff --git a/dom/quota/QuotaResults.h b/dom/quota/QuotaResults.h
---- a/dom/quota/QuotaResults.h
-+++ b/dom/quota/QuotaResults.h
-@@ -8,16 +8,36 @@
- #define mozilla_dom_quota_QuotaResults_h
- 
- #include "nsIQuotaResults.h"
- 
- namespace mozilla {
- namespace dom {
- namespace quota {
- 
-+class UsageResult
-+  : public nsIQuotaUsageResult
-+{
-+  nsCString mOrigin;
-+  uint64_t mUsage;
-+  bool mPersisted;
-+
-+public:
-+  UsageResult(const nsACString& aOrigin,
-+              bool aPersisted,
-+              uint64_t aUsage);
-+
-+private:
-+  virtual ~UsageResult()
-+  { }
-+
-+  NS_DECL_ISUPPORTS
-+  NS_DECL_NSIQUOTAUSAGERESULT
-+};
-+
- class OriginUsageResult
-   : public nsIQuotaOriginUsageResult
- {
-   uint64_t mUsage;
-   uint64_t mFileUsage;
-   uint64_t mLimit;
- 
- public:
-diff --git a/dom/quota/nsIQuotaManagerService.idl b/dom/quota/nsIQuotaManagerService.idl
---- a/dom/quota/nsIQuotaManagerService.idl
-+++ b/dom/quota/nsIQuotaManagerService.idl
-@@ -10,16 +10,31 @@ interface nsIPrincipal;
- interface nsIQuotaRequest;
- interface nsIQuotaUsageCallback;
- interface nsIQuotaUsageRequest;
- 
- [scriptable, builtinclass, uuid(1b3d0a38-8151-4cf9-89fa-4f92c2ef0e7e)]
- interface nsIQuotaManagerService : nsISupports
- {
-   /**
-+   * Schedules an asynchronous callback that will inspect all origins and
-+   * return the total amount of disk space being used by storages for each
-+   * origin separately.
-+   *
-+   * @param aCallback
-+   *        The callback that will be called when the usage is available.
-+   * @param aGetAll
-+   *        An optional boolean to indicate inspection of all origins,
-+   *        including internal ones.
-+   */
-+  [must_use] nsIQuotaUsageRequest
-+  getUsage(in nsIQuotaUsageCallback aCallback,
-+           [optional] in boolean aGetAll);
-+
-+  /**
-    * Schedules an asynchronous callback that will return the total amount of
-    * disk space being used by storages for the given origin.
-    *
-    * @param aPrincipal
-    *        A principal for the origin whose usage is being queried.
-    * @param aCallback
-    *        The callback that will be called when the usage is available.
-    * @param aGetGroupUsage
-diff --git a/dom/quota/nsIQuotaRequests.idl b/dom/quota/nsIQuotaRequests.idl
---- a/dom/quota/nsIQuotaRequests.idl
-+++ b/dom/quota/nsIQuotaRequests.idl
-@@ -18,16 +18,17 @@ interface nsIQuotaRequestBase : nsISuppo
- 
-   [must_use] readonly attribute nsresult resultCode;
- };
- 
- [scriptable, uuid(166e28e6-cf6d-4927-a6d7-b51bca9d3469)]
- interface nsIQuotaUsageRequest : nsIQuotaRequestBase
- {
-   // The result can contain one of these types:
-+  //   array of nsIQuotaUsageResult
-   //   nsIQuotaOriginUsageResult
-   [must_use] readonly attribute nsIVariant result;
- 
-   attribute nsIQuotaUsageCallback callback;
- 
-   [must_use] void
-   cancel();
- };
-diff --git a/dom/quota/nsIQuotaResults.idl b/dom/quota/nsIQuotaResults.idl
---- a/dom/quota/nsIQuotaResults.idl
-+++ b/dom/quota/nsIQuotaResults.idl
-@@ -1,16 +1,26 @@
- /* -*- Mode: C++; tab-width: 8; indent-tabs-mode: nil; c-basic-offset: 2 -*- */
- /* vim: set ts=2 et sw=2 tw=80: */
- /* This Source Code Form is subject to the terms of the Mozilla Public
-  * License, v. 2.0. If a copy of the MPL was not distributed with this
-  * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
- 
- #include "nsISupports.idl"
- 
-+[scriptable, function, uuid(d8c9328b-9aa8-4f5d-90e6-482de4a6d5b8)]
-+interface nsIQuotaUsageResult : nsISupports
-+{
-+  readonly attribute ACString origin;
-+
-+  readonly attribute boolean persisted;
-+
-+  readonly attribute unsigned long long usage;
-+};
-+
- [scriptable, function, uuid(96df03d2-116a-493f-bb0b-118c212a6b32)]
- interface nsIQuotaOriginUsageResult : nsISupports
- {
-   readonly attribute unsigned long long usage;
- 
-   readonly attribute unsigned long long fileUsage;
- 
-   readonly attribute unsigned long long limit;
-
diff --git a/gnu/packages/patches/icecat-bug-1414945.patch b/gnu/packages/patches/icecat-bug-1414945.patch
deleted file mode 100644
index 3638ace1c4..0000000000
--- a/gnu/packages/patches/icecat-bug-1414945.patch
+++ /dev/null
@@ -1,73 +0,0 @@
-Based on:
-  https://hg.mozilla.org/releases/mozilla-esr52/raw-rev/d303b3bb88c3
-
-Adapted to apply cleanly to IceCat.
-
-# HG changeset patch
-# User Philip Chimento <philip.chimento@gmail.com>
-# Date 1510012155 28800
-# Node ID d303b3bb88c3345d3a089901e2b6fe883d148e44
-# Parent  0152d097672f7e99504815cf7b06d9f303419fba
-Bug 1414945 - Don't use TimeDuration in static initializer. r=jandem, a=ritu
-
-On Darwin this would cause a race between two static initializers.
-
-diff --git a/js/src/shell/js.cpp b/js/src/shell/js.cpp
---- a/js/src/shell/js.cpp
-+++ b/js/src/shell/js.cpp
-@@ -138,17 +138,17 @@ static const size_t gMaxStackSize = 2 * 
- #else
- static const size_t gMaxStackSize = 128 * sizeof(size_t) * 1024;
- #endif
- 
- /*
-  * Limit the timeout to 30 minutes to prevent an overflow on platfoms
-  * that represent the time internally in microseconds using 32-bit int.
-  */
--static const TimeDuration MAX_TIMEOUT_INTERVAL = TimeDuration::FromSeconds(1800.0);
-+static const double MAX_TIMEOUT_SECONDS = 1800.0;
- 
- // SharedArrayBuffer and Atomics settings track IceCat.  Choose a custom setting
- // with --shared-memory={on,off}.
- #ifndef RELEASE_OR_BETA
- # define SHARED_MEMORY_DEFAULT 1
- #else
- # define SHARED_MEMORY_DEFAULT 0
- #endif
-@@ -3518,16 +3518,17 @@ Sleep_fn(JSContext* cx, unsigned argc, V
-         if (!ToNumber(cx, args[0], &t_secs))
-             return false;
-         if (mozilla::IsNaN(t_secs)) {
-             JS_ReportErrorASCII(cx, "sleep interval is not a number");
-             return false;
-         }
- 
-         duration = TimeDuration::FromSeconds(Max(0.0, t_secs));
-+        const TimeDuration MAX_TIMEOUT_INTERVAL = TimeDuration::FromSeconds(MAX_TIMEOUT_SECONDS);
-         if (duration > MAX_TIMEOUT_INTERVAL) {
-             JS_ReportErrorASCII(cx, "Excessive sleep interval");
-             return false;
-         }
-     }
-     {
-         LockGuard<Mutex> guard(sc->watchdogLock);
-         TimeStamp toWakeup = TimeStamp::Now() + duration;
-@@ -3675,16 +3676,17 @@ CancelExecution(JSContext* cx)
- 
- static bool
- SetTimeoutValue(JSContext* cx, double t)
- {
-     if (mozilla::IsNaN(t)) {
-         JS_ReportErrorASCII(cx, "timeout is not a number");
-         return false;
-     }
-+    const TimeDuration MAX_TIMEOUT_INTERVAL = TimeDuration::FromSeconds(MAX_TIMEOUT_SECONDS);
-     if (TimeDuration::FromSeconds(t) > MAX_TIMEOUT_INTERVAL) {
-         JS_ReportErrorASCII(cx, "Excessive timeout value");
-         return false;
-     }
-     GetShellContext(cx)->timeoutInterval = t;
-     if (!ScheduleWatchdog(cx, t)) {
-         JS_ReportErrorASCII(cx, "Failed to create the watchdog");
-         return false;
-
diff --git a/gnu/packages/patches/icecat-bug-1415133.patch b/gnu/packages/patches/icecat-bug-1415133.patch
deleted file mode 100644
index 4e322d21fb..0000000000
--- a/gnu/packages/patches/icecat-bug-1415133.patch
+++ /dev/null
@@ -1,40 +0,0 @@
-Based on:
-  https://hg.mozilla.org/releases/mozilla-esr52/raw-rev/22fe3ff3f923
-
-Adapted to apply cleanly to IceCat.
-
-# HG changeset patch
-# User Marco Bonardo <mbonardo@mozilla.com>
-# Date 1510052455 -3600
-# Node ID 22fe3ff3f92358596521f7155ddc512006022207
-# Parent  2909ba991f3134f9fbf4859cf08582f1c9845594
-Bug 1415133 - Downgrades from 55+ to ESR lose bookmarks. r=past a=lizzard
-
-MozReview-Commit-ID: 44Rw7m1FP4h
-
-diff --git a/toolkit/components/places/Database.cpp b/toolkit/components/places/Database.cpp
---- a/toolkit/components/places/Database.cpp
-+++ b/toolkit/components/places/Database.cpp
-@@ -761,16 +761,21 @@ Database::InitSchema(bool* aDatabaseMigr
-     // 2. implement a method that performs upgrade to your version from the
-     //    previous one.
-     //
-     // NOTE: The downgrade process is pretty much complicated by the fact old
-     //       versions cannot know what a new version is going to implement.
-     //       The only thing we will do for downgrades is setting back the schema
-     //       version, so that next upgrades will run again the migration step.
- 
-+    if (currentSchemaVersion > 36) {
-+      // These versions are not downgradable.
-+      return NS_ERROR_FILE_CORRUPTED;
-+    }
-+
-     if (currentSchemaVersion < DATABASE_SCHEMA_VERSION) {
-       *aDatabaseMigrated = true;
- 
-       if (currentSchemaVersion < 11) {
-         // These are versions older than IceCat 4 that are not supported
-         // anymore.  In this case it's safer to just replace the database.
-         return NS_ERROR_FILE_CORRUPTED;
-       }
-
diff --git a/gnu/packages/patches/icecat-bug-1424373-pt2.patch b/gnu/packages/patches/icecat-bug-1424373-pt2.patch
deleted file mode 100644
index cdc7226bd3..0000000000
--- a/gnu/packages/patches/icecat-bug-1424373-pt2.patch
+++ /dev/null
@@ -1,183 +0,0 @@
-Based on:
-  https://hg.mozilla.org/releases/mozilla-esr52/raw-rev/19ea736e7e3d
-
-Adapted to apply cleanly to IceCat.
-
-# HG changeset patch
-# User Mike Conley <mconley@mozilla.com>
-# Date 1513892173 18000
-# Node ID 19ea736e7e3d20555ee6633b9d7803c1225979e1
-# Parent  320032aaa06899f5585dcd0288059e5342118714
-Bug 1424373 - Rename crash report submission pref. r=Mossop a=jcristau
-
-diff --git a/browser/app/profile/icecat.js b/browser/app/profile/icecat.js
---- a/browser/app/profile/icecat.js
-+++ b/browser/app/profile/icecat.js
-@@ -1557,15 +1557,15 @@ pref("browser.crashReports.unsubmittedCh
- pref("browser.crashReports.unsubmittedCheck.enabled", false);
- #endif
- 
- // chancesUntilSuppress is how many times we'll show the unsubmitted
- // crash report notification across different days and shutdown
- // without a user choice before we suppress the notification for
- // some number of days.
- pref("browser.crashReports.unsubmittedCheck.chancesUntilSuppress", 4);
--pref("browser.crashReports.unsubmittedCheck.autoSubmit", false);
-+pref("browser.crashReports.unsubmittedCheck.autoSubmit2", false);
- 
- #ifdef NIGHTLY_BUILD
- // Enable the (fairly costly) client/server validation on nightly only. The other prefs
- // controlling validation are located in /services/sync/services-sync.js
- pref("services.sync.validation.enabled", true);
- #endif
-diff --git a/browser/base/content/test/tabcrashed/browser_autoSubmitRequest.js b/browser/base/content/test/tabcrashed/browser_autoSubmitRequest.js
---- a/browser/base/content/test/tabcrashed/browser_autoSubmitRequest.js
-+++ b/browser/base/content/test/tabcrashed/browser_autoSubmitRequest.js
-@@ -1,12 +1,12 @@
- "use strict";
- 
- const PAGE = "data:text/html,<html><body>A%20regular,%20everyday,%20normal%20page.";
--const AUTOSUBMIT_PREF = "browser.crashReports.unsubmittedCheck.autoSubmit";
-+const AUTOSUBMIT_PREF = "browser.crashReports.unsubmittedCheck.autoSubmit2";
- 
- const {TabStateFlusher} =
-   Cu.import("resource:///modules/sessionstore/TabStateFlusher.jsm", {});
- 
- // On debug builds, crashing tabs results in much thinking, which
- // slows down the test and results in intermittent test timeouts,
- // so we'll pump up the expected timeout for this test.
- requestLongerTimeout(2);
-diff --git a/browser/components/preferences/in-content/advanced.xul b/browser/components/preferences/in-content/advanced.xul
---- a/browser/components/preferences/in-content/advanced.xul
-+++ b/browser/components/preferences/in-content/advanced.xul
-@@ -51,18 +51,18 @@
- #ifdef MOZ_TELEMETRY_REPORTING
-   <preference id="toolkit.telemetry.enabled"
-               name="toolkit.telemetry.enabled"
-               type="bool"/>
- #endif
- 
-   <!-- Data Choices tab -->
- #ifdef MOZ_CRASHREPORTER
--  <preference id="browser.crashReports.unsubmittedCheck.autoSubmit"
--              name="browser.crashReports.unsubmittedCheck.autoSubmit"
-+  <preference id="browser.crashReports.unsubmittedCheck.autoSubmit2"
-+              name="browser.crashReports.unsubmittedCheck.autoSubmit2"
-               type="bool"/>
- #endif
- 
-   <!-- Network tab -->
-   <preference id="browser.cache.disk.capacity"
-               name="browser.cache.disk.capacity"
-               type="int"/>
-   <preference id="browser.offline-apps.notify"
-@@ -232,17 +232,17 @@
-           </hbox>
-         </vbox>
-       </groupbox>
- #endif
- #ifdef MOZ_CRASHREPORTER
-       <groupbox>
-         <caption>
-           <checkbox id="automaticallySubmitCrashesBox"
--                    preference="browser.crashReports.unsubmittedCheck.autoSubmit"
-+                    preference="browser.crashReports.unsubmittedCheck.autoSubmit2"
-                     label="&alwaysSubmitCrashReports.label;"
-                     accesskey="&alwaysSubmitCrashReports.accesskey;"/>
-         </caption>
-         <hbox class="indent">
-           <label flex="1">&crashReporterDesc2.label;</label>
-           <spacer flex="10"/>
-           <label id="crashReporterLearnMore"
-                  class="text-link">&crashReporterLearnMore.label;</label>
-diff --git a/browser/components/sessionstore/test/browser_background_tab_crash.js b/browser/components/sessionstore/test/browser_background_tab_crash.js
---- a/browser/components/sessionstore/test/browser_background_tab_crash.js
-+++ b/browser/components/sessionstore/test/browser_background_tab_crash.js
-@@ -142,17 +142,17 @@ add_task(function* test_background_crash
- /**
-  * Tests that if a content process crashes taking down only
-  * background tabs, and the user is configured to send backlogged
-  * crash reports automatically, that the tab crashed page is not
-  * shown.
-  */
- add_task(function* test_background_crash_autosubmit_backlogged() {
-   yield SpecialPowers.pushPrefEnv({
--    set: [["browser.crashReports.unsubmittedCheck.autoSubmit", true]],
-+    set: [["browser.crashReports.unsubmittedCheck.autoSubmit2", true]],
-   });
- 
-   yield setupBackgroundTabs(function*([tab1, tab2]) {
-     // Let's crash one of those background tabs now...
-     yield crashBackgroundTabs([tab1, tab2]);
- 
-     // Selecting the first tab should restore it.
-     let tabRestored = promiseTabRestored(tab1);
-diff --git a/browser/modules/ContentCrashHandlers.jsm b/browser/modules/ContentCrashHandlers.jsm
---- a/browser/modules/ContentCrashHandlers.jsm
-+++ b/browser/modules/ContentCrashHandlers.jsm
-@@ -865,21 +865,21 @@ this.UnsubmittedCrashHandler = {
-     return nb.appendNotification(message, notificationID,
-                                  "chrome://browser/skin/tab-crashed.svg",
-                                  nb.PRIORITY_INFO_HIGH, buttons,
-                                  eventCallback);
-   },
- 
-   get autoSubmit() {
-     return Services.prefs
--                   .getBoolPref("browser.crashReports.unsubmittedCheck.autoSubmit");
-+                   .getBoolPref("browser.crashReports.unsubmittedCheck.autoSubmit2");
-   },
- 
-   set autoSubmit(val) {
--    Services.prefs.setBoolPref("browser.crashReports.unsubmittedCheck.autoSubmit",
-+    Services.prefs.setBoolPref("browser.crashReports.unsubmittedCheck.autoSubmit2",
-                                val);
-   },
- 
-   /**
-    * Attempt to submit reports to the crash report server. Each
-    * report will have the "SubmittedFromInfobar" extra key set
-    * to true.
-    *
-diff --git a/browser/modules/test/browser_UnsubmittedCrashHandler.js b/browser/modules/test/browser_UnsubmittedCrashHandler.js
---- a/browser/modules/test/browser_UnsubmittedCrashHandler.js
-+++ b/browser/modules/test/browser_UnsubmittedCrashHandler.js
-@@ -344,17 +344,17 @@ add_task(function* test_can_submit_sever
-   clearPendingCrashReports();
- });
- 
- /**
-  * Tests that choosing "Send Always" flips the autoSubmit pref
-  * and sends the pending crash reports.
-  */
- add_task(function* test_can_submit_always() {
--  let pref = "browser.crashReports.unsubmittedCheck.autoSubmit";
-+  let pref = "browser.crashReports.unsubmittedCheck.autoSubmit2";
-   Assert.equal(Services.prefs.getBoolPref(pref), false,
-                "We should not be auto-submitting by default");
- 
-   let reportIDs = yield createPendingCrashReports(1);
-   let notification =
-     yield UnsubmittedCrashHandler.checkForUnsubmittedCrashReports();
-   Assert.ok(notification, "There should be a notification");
- 
-@@ -388,17 +388,17 @@ add_task(function* test_can_submit_alway
- 
- /**
-  * Tests that if the user has chosen to automatically send
-  * crash reports that no notification is displayed to the
-  * user.
-  */
- add_task(function* test_can_auto_submit() {
-   yield SpecialPowers.pushPrefEnv({ set: [
--    ["browser.crashReports.unsubmittedCheck.autoSubmit", true],
-+    ["browser.crashReports.unsubmittedCheck.autoSubmit2", true],
-   ]});
- 
-   let reportIDs = yield createPendingCrashReports(3);
-   let promiseReports = waitForSubmittedReports(reportIDs);
-   let notification =
-     yield UnsubmittedCrashHandler.checkForUnsubmittedCrashReports();
-   Assert.equal(notification, null, "There should be no notification");
-   info("Waiting on reports to be received.");
-
-- 
cgit v1.2.3


From 99654a1685005ef757b33bb7be2fbb8021c2a481 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Fri, 2 Mar 2018 00:04:24 -0500
Subject: gnu: icecat: Add more fixes from upstream mozilla-esr52.

* gnu/packages/gnuzilla.scm (icecat)[source]: Add selected fixes from the
upstream mozilla-esr52 repository.
---
 gnu/packages/gnuzilla.scm | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm
index e3f1bfe8c0..457a8fbcdc 100644
--- a/gnu/packages/gnuzilla.scm
+++ b/gnu/packages/gnuzilla.scm
@@ -423,7 +423,21 @@ security standards.")
         (mozilla-patch "icecat-bug-1261175.patch"        "f0ec180993d2" "0jiazxcwki83wr00fyh2g518ynsd33p7nk65zk4d1682gn22lc8v")
         (mozilla-patch "icecat-bug-1433005.patch"        "a6a9e26688c1" "0cvizvilb4k422j2gzqcbakznvsffmk6n6xn1ayj5rgxfaizkkqk")
         (mozilla-patch "icecat-bug-1434580.patch"        "198ad052621e" "1721zx8hifdlflrhvw6hmkdgjbvsmxl9n84iji5qywhlp2krdk9r")
-        (mozilla-patch "icecat-bug-1426087.patch"        "391ea77ebfdb" "1fhkvd0z6mvdkj7m0d3jlj42rsdw5r4x122c1wb1i428228ifw6n")))
+        (mozilla-patch "icecat-bug-1426087.patch"        "391ea77ebfdb" "1fhkvd0z6mvdkj7m0d3jlj42rsdw5r4x122c1wb1i428228ifw6n")
+        (mozilla-patch "icecat-bug-1416307.patch"        "54f2f7f93b30" "1ncjir16mqya37wgf6fy2rqki3vl433c4grjr3fypmlig6xfgg1l")
+        (mozilla-patch "icecat-bug-1430557.patch"        "2c4d7a59041b" "178c6gid89cvw52yqs43i6x6s5w0hslj0rfa2r8b4762ij3civ92")
+        (mozilla-patch "icecat-bug-1416529.patch"        "f87ef3774d5e" "0payf3az2w93nzl5qknqx290jbxk8v39rwhdgq7wyd5f245dywxk")
+        (mozilla-patch "icecat-bug-1324042.patch"        "ac743923f81d" "0msyr45xr1j5q4x6ah4r907pwjngyi0k6pp9y8ixk21cnwbzrdwx")
+        (mozilla-patch "icecat-bug-1428947.patch"        "456913d7e8b5" "0fx0s06kxxj7g4hllinaskgh41z3k48zml6yqqzxx485qk3hdh9x")
+        (mozilla-patch "icecat-bug-1334465-pt1.patch"    "f95c5b881442" "0iaddhf65jd9cycj4bw0b207n2jiqkr4q84jifzyqn4ygs75wdqd")
+        (mozilla-patch "icecat-bug-1334465-pt2.patch"    "8a4265c8fb41" "1d9zfdbrlw9wzr84b7pj7lxgy487lsx0kfd89287hjk0al8m6vrw")
+        (mozilla-patch "icecat-bug-1398021.patch"        "28855df568d8" "1kmq836gniplxpjnvq8lhbcc1aqi56al628r1mzdy94b5yb0lis3")
+        (mozilla-patch "icecat-bug-1388020.patch"        "e8ab2736499b" "0n28vcd65rxsyq3z22rfcfksryfndhm1i3g6ah3akg11jnagqf5v")
+        (mozilla-patch "icecat-bug-1437087.patch"        "014877bf17ea" "0hk90pnf7h7kvidji6ydvva1zpyraipn03pjhvprdqr7k2fqzmsz")
+        (mozilla-patch "icecat-bug-1437507.patch"        "5b3a5de48912" "1ifya05rcd34ryp9zawdacihhkkf2m0xn2q8m8c6v78bvxj0mgig")
+        (mozilla-patch "icecat-bug-1440926.patch"        "1df9b4404acd" "1sd59vsarfsbh3vlrzrqv6n1ni7vxdzm83j6s6g0fygl1h8kwijg")
+        (mozilla-patch "icecat-bug-1430173-pt1.patch"    "9124c3972e2b" "13ns5yy39yzfx7lrkv4rgwdz6s6q0z4i09wkbxdvnkfsz17cd17i")
+        (mozilla-patch "icecat-bug-1430173-pt2.patch"    "9f6dc031be51" "0bv2p98z5ahp3x9wxnhwxn87g21djvzzp7jy55ik90hqixsbhwdl")))
       (modules '((guix build utils)))
       (snippet
        '(begin
-- 
cgit v1.2.3


From 1a6fb8dac1a9d7ae6d1a9b07bb0df6e4b606cb87 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 2 Mar 2018 00:54:26 +0100
Subject: gnu: python-flask-babel: Update to 0.11.2.

* gnu/packages/python-web.scm (python-flask-babel): Update to 0.11.2.
---
 gnu/packages/python-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 47fc5cd63a..18022ecd5e 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -138,14 +138,14 @@ between a web browser and web server.")
 (define-public python-flask-babel
   (package
     (name "python-flask-babel")
-    (version "0.11.1")
+    (version "0.11.2")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "Flask-Babel" version))
         (sha256
           (base32
-            "16b80cipdba9xj3jlaiaq6wgrgpjb70w3j01jjy9hbp4k71kd6yj"))))
+            "0ff9n165vhf1nhv6807ckhpp224jw7k7sd7jz5kfh3sbpl85gmy0"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-flask" ,python-flask)
-- 
cgit v1.2.3


From 3c5658c596d570b4f2381de9ee9abd87a292a35b Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 2 Mar 2018 00:55:45 +0100
Subject: gnu: python-cssutils: Update to 1.0.2.

* gnu/packages/python-web.scm (python-cssutils): Update to 1.0.2.
---
 gnu/packages/python-web.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 18022ecd5e..dd14446b09 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -332,19 +332,19 @@ for clients and servers.")
 (define-public python-cssutils
   (package
     (name "python-cssutils")
-    (version "1.0.1")
+    (version "1.0.2")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "cssutils" version))
         (sha256
          (base32
-          "0qwha9x1wml2qmipbcz03gndnlwhzrjdvw9i09si247a90l8p8fq"))))
+          "1bxchrbqzapwijap0yhlxdil1w9bmwvgx77aizlkhc2mcxjg1z52"))))
     (build-system python-build-system)
     (native-inputs
-      `(("unzip" ,unzip))) ; for unpacking the source
+     `(("unzip" ,unzip)))               ; for unpacking the source
     (arguments
-     `(#:tests? #f))                    ;tests require python-pbr < 1.7.0
+     `(#:tests? #f))                    ; tests require python-pbr < 1.7.0
     (home-page "http://cthedot.de/cssutils/")
     (synopsis
       "CSS Cascading Style Sheets library for Python")
-- 
cgit v1.2.3


From 6f21aca728cdfd32fb8f64b4805425d297b31429 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 2 Mar 2018 00:58:49 +0100
Subject: gnu: python-ndg-httpsclient: Update to 0.4.4.

* gnu/packages/python-web.scm (python-ndg-httpsclient): Update to 0.4.4.
---
 gnu/packages/python-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index dd14446b09..513a455967 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -956,13 +956,13 @@ facilities for defining, registering and looking up components.")
 (define-public python-ndg-httpsclient
   (package
     (name "python-ndg-httpsclient")
-    (version "0.4.2")
+    (version "0.4.4")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "ndg_httpsclient" version))
               (sha256
                 (base32
-                  "1b5qirv46v4dpnmfqviwq42mdwfcby4dxmz0i41wad2337pqf2aq"))))
+                  "0sl5ak1r1xil9ms0a9fh9fm6ncml65kgnjpjfic9dhnaimwx997v"))))
     (build-system python-build-system)
     (arguments
      '(;; The tests appear to require networking.
-- 
cgit v1.2.3


From e46dd02d99fccabecd59bf8bd3664a67e24053c0 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 2 Mar 2018 01:00:52 +0100
Subject: gnu: python-webtest: Update to 2.0.29.

* gnu/packages/python-web.scm (python-webtest): Update to 2.0.29.
---
 gnu/packages/python-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 513a455967..8f5827cd2c 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1306,14 +1306,14 @@ file.")
 (define-public python-webtest
   (package
     (name "python-webtest")
-    (version "2.0.20")
+    (version "2.0.29")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "WebTest" version))
        (sha256
         (base32
-         "0bv0qhdjakdsdgj4sk21gnpp8xp8bga4x03p6gjb83ihrsb7n4xv"))))
+         "0bcj1ica5lnmj5zbvk46x28kgphcsgh7sfnwjmn0cr94mhawrg6v"))))
     (build-system python-build-system)
     (arguments
      `(;; Unfortunately we have to disable tests!
-- 
cgit v1.2.3


From bda82eff18c97c773b4f503932c1df0f04086c2c Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 2 Mar 2018 01:04:35 +0100
Subject: gnu: python-s3transfer: Update to 0.1.13.

* gnu/packages/python-web.scm (python-s3transfer): Update to 0.1.13.
---
 gnu/packages/python-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 8f5827cd2c..769b3dea51 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1700,13 +1700,13 @@ Betamax.")
 (define-public python-s3transfer
   (package
     (name "python-s3transfer")
-    (version "0.1.11")
+    (version "0.1.13")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "s3transfer" version))
               (sha256
                (base32
-                "0yfrfnf404cxzn3iswibqjxklsl0b1lwgqiml6pwiqj79a7zbwbn"))))
+                "1harvyn1s8v54n1w5h7c0lg4bgjh68aylhg28s8n174q53h1ip4h"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
-- 
cgit v1.2.3


From 05075433a2b8661200a6f40fc1319414a9e44b7d Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 2 Mar 2018 01:09:24 +0100
Subject: gnu: python-htmlmin: Update to 0.1.12.

* gnu/packages/python-web.scm (python-htmlmin): Update to 0.1.12.
---
 gnu/packages/python-web.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 769b3dea51..ed3d2ec57b 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1877,16 +1877,16 @@ specs from your Flask-Restful projects.")
 (define-public python-htmlmin
   (package
     (name "python-htmlmin")
-    (version "0.1.10")
+    (version "0.1.12")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "htmlmin" version))
        (sha256
         (base32
-         "0qxa93j3p1ak32qh8d9kshqv8v3z0hkc13dwbhp5cn7sn3xmsp6a"))))
+         "0y51xhabw6x8jk8k93xl8vznshpz3jb6l28075r5sjip613fzhah"))))
     (arguments
-     `(#:tests? #f)) ;htmlmin has no tests
+     `(#:tests? #f))                    ; no tests
     (build-system python-build-system)
     (home-page "https://htmlmin.readthedocs.org/en/latest/")
     (synopsis "HTML minifier")
-- 
cgit v1.2.3


From 6a192184ecd0b1e99d59cfd115475ff9cb6de866 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 2 Mar 2018 01:09:50 +0100
Subject: gnu: python-flask-script: Update to 2.0.6.

* gnu/packages/python-web.scm (python-flask-script): Update to 2.0.6.
---
 gnu/packages/python-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index ed3d2ec57b..9dc0650230 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -2081,14 +2081,14 @@ this it tries to be opinion-free and very extendable.")
 (define-public python-flask-script
   (package
   (name "python-flask-script")
-  (version "2.0.5")
+  (version "2.0.6")
   (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "Flask-Script" version))
       (sha256
         (base32
-          "0zqh2yq8zk7m9b4xw1ryqmrljkdigfb3hk5155a3b5hkfnn6xxyf"))))
+          "0r8w2v89nj6b9p91p495cga5m72a673l2wc0hp0zqk05j4yrc9b4"))))
   (build-system python-build-system)
   (propagated-inputs
    `(("python-flask" ,python-flask)
-- 
cgit v1.2.3


From 12adfdf0b6fe84346f2a578a341ae8537ac0606f Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 2 Mar 2018 04:39:51 +0100
Subject: gnu: Update (gnu packages python-web) phase styles.

* gnu/packages/python-web.scm (python-openid, python-terminado)
(python-geventhttpclient, python-cachecontrol, python-webencodings)
(python-s3transfer)[arguments]: Substitute INVOKE for SYSTEM* and end
phases with #t.
---
 gnu/packages/python-web.scm | 24 ++++++++++++++++--------
 1 file changed, 16 insertions(+), 8 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 9dc0650230..3ab7dafa42 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -254,7 +254,8 @@ C, yielding parse times that can be a thirtieth of the html5lib parse times.")
        (modify-phases %standard-phases
          (replace 'check
            (lambda _
-             (zero? (system* "py.test" "-v" "webencodings/tests.py")))))))
+             (invoke "py.test" "-v" "webencodings/tests.py")
+             #t)))))
     (native-inputs
      `(("python-pytest" ,python-pytest)))
     (home-page "https://github.com/SimonSapin/python-webencodings")
@@ -295,7 +296,8 @@ is Python’s.")
        (modify-phases %standard-phases
         (replace 'check
           (lambda _
-            (zero? (system* "./admin/runtests")))))))
+            (invoke "./admin/runtests")
+            #t)))))
     (properties `((python2-variant . ,(delay python2-openid))))
     (propagated-inputs
      `(("python-defusedxml" ,python-defusedxml)))
@@ -451,7 +453,8 @@ teams extension for python-openid.")
        ;;     (lambda _
        ;;       ;; 'setup.py test' hits an AssertionError on BSD-specific
        ;;       ;; "tornado/platform/kqueue.py". This is the supported method:
-       ;;       (zero? (system* "python" "-m" "tornado.test")))))
+       ;;       (invoke- "python" "-m" "tornado.test")
+       ;;       #t)))
        #:tests? #f))
     (native-inputs
      `(("python-certifi" ,python-certifi)))
@@ -522,7 +525,8 @@ web framework, either via the basic or digest authentication schemes.")
        (modify-phases %standard-phases
          (replace 'check
                   (lambda _
-                    (zero? (system* "nosetests")))))))
+                    (invoke "nosetests")
+                    #t)))))
     (home-page "https://github.com/takluyver/terminado")
     (synopsis "Terminals served to term.js using Tornado websockets")
     (description "This package provides a Tornado websocket backend for the
@@ -1519,7 +1523,8 @@ library.")
          (add-after 'install 'check
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (add-installed-pythonpath inputs outputs)
-             (zero? (system* "py.test" "src/geventhttpclient/tests" "-v")))))))
+             (invoke "py.test" "src/geventhttpclient/tests" "-v")
+             #t)))))
     (native-inputs
      `(("python-pytest" ,python-pytest)))
     (propagated-inputs
@@ -1629,7 +1634,8 @@ provide an easy-to-use Python interface for building OAuth1 and OAuth2 clients."
              (setenv "PYTHONPATH"
                      (string-append (getcwd) "/build/lib:"
                                     (getenv "PYTHONPATH")))
-             (zero? (system* "py.test" "-vv")))))))
+             (invoke "py.test" "-vv")
+             #t)))))
     (native-inputs
      `(("python-pytest" ,python-pytest)
        ("python-redis" ,python-redis)
@@ -1715,7 +1721,8 @@ Betamax.")
            (lambda _
              ;; 7 of the 'integration' tests require network access or login
              ;; credentials.
-             (zero? (system* "nosetests" "--exclude=integration")))))))
+             (invoke "nosetests" "--exclude=integration")
+             #t)))))
     (native-inputs
      `(("python-docutils" ,python-docutils)
        ("python-mock" ,python-mock)
@@ -1831,7 +1838,8 @@ transfers.")
        ;; (modify-phases %standard-phases
        ;;   (replace 'check
        ;;     (lambda _
-       ;;       (zero? (system* "nosetests")))))))
+       ;;       (invoke "nosetests")
+       ;;       #t)))))
     (propagated-inputs
       `(("python-aniso8601" ,python-aniso8601)
         ("python-flask" ,python-flask)
-- 
cgit v1.2.3


From bb5c35820448ef9b83b59a49e94b73ae2d8f7052 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 1 Mar 2018 23:18:52 +0100
Subject: gnu: b43-tools: Update to 0.0.0-1.27892ef.

* gnu/packages/firmware.scm (b43-tools): Update to 0.0.0-1.27892ef.
[version]: Use our standard versioning scheme.
---
 gnu/packages/firmware.scm | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm
index 12595dc31c..5f82f7c31a 100644
--- a/gnu/packages/firmware.scm
+++ b/gnu/packages/firmware.scm
@@ -3,6 +3,7 @@
 ;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2017 David Craven <david@craven.ch>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -94,11 +95,11 @@ Linux-libre.")
     (license (license:non-copyleft "http://directory.fsf.org/wiki/License:ClearBSD"))))
 
 (define-public b43-tools
-  (let ((commit "8dce53297966b31b6c70a7a03c2433978dd9f288")
-        (rev "1"))
+  (let ((commit "27892ef741e7f1d08cb939744f8b8f5dac7b04ae")
+        (revision "1"))
     (package
       (name "b43-tools")
-      (version (string-append "20140625-" rev "." (string-take commit 7)))
+      (version (git-version "0.0.0" revision commit))
       (source
        (origin
          (method git-fetch)
@@ -108,7 +109,7 @@ Linux-libre.")
          (file-name (string-append name "-" version "-checkout"))
          (sha256
           (base32
-           "08k7sdr9jagm43r2zv4h03j86klhkblpk73p12444a3vzg1gy1lv"))))
+           "1wgmj4d65izbhprwb5bcwimc2ryv19b9066lqzy4sa5m6wncm9cn"))))
       (build-system gnu-build-system)
       (native-inputs
        `(("flex" ,flex)
@@ -117,11 +118,11 @@ Linux-libre.")
        `(#:modules ((srfi srfi-1)
                     (guix build gnu-build-system)
                     (guix build utils))
-         #:tests? #f                    ;no tests
+         #:tests? #f                    ; no tests
          #:phases
          (let ((subdirs '("assembler" "disassembler")))
            (modify-phases %standard-phases
-             (delete 'configure)
+             (delete 'configure)        ; no configure script
              (add-before 'build 'patch-/bin/true
                (lambda _
                  (substitute* (find-files "." "Makefile")
-- 
cgit v1.2.3


From 315c89f5ba89e18bd365846a62944820a8760b83 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 1 Mar 2018 23:19:27 +0100
Subject: gnu: b43-tools: Update phase style.

* gnu/packages/firmware.scm (b43-tools)[arguments]: Substitute INVOKE
for SYSTEM* and FOR-EACH for EVERY, and end phases with #t.
---
 gnu/packages/firmware.scm | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm
index 5f82f7c31a..d9d0c2910c 100644
--- a/gnu/packages/firmware.scm
+++ b/gnu/packages/firmware.scm
@@ -130,19 +130,20 @@ Linux-libre.")
                  #t))
              (replace 'build
                (lambda _
-                 (every (lambda (dir)
-                          (zero? (system* "make" "-C" dir "CC=gcc")))
-                        subdirs)))
+                 (for-each (lambda (dir)
+                             (invoke "make" "-C" dir "CC=gcc"))
+                           subdirs)
+                 #t))
              (replace 'install
                (lambda* (#:key outputs #:allow-other-keys)
                  (let ((out (assoc-ref outputs "out")))
                    (mkdir-p (string-append out "/bin"))
-                   (every (lambda (dir)
-                            (zero?
-                             (system* "make" "-C" dir
-                                      (string-append "PREFIX=" out)
-                                      "install")))
-                          subdirs))))))))
+                   (for-each (lambda (dir)
+                               (invoke "make" "-C" dir
+                                       (string-append "PREFIX=" out)
+                                       "install"))
+                             subdirs)
+                   #t)))))))
       (home-page
        "http://bues.ch/cms/hacking/misc.html#linux_b43_driver_firmware_tools")
       (synopsis "Collection of tools for the b43 wireless driver")
-- 
cgit v1.2.3


From 3ebf12ea0e380e3619618701b58564cf9423517c Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 1 Mar 2018 23:24:33 +0100
Subject: gnu: b43-tools: Use HTTPS home page.

* gnu/packages/firmware.scm (b43-tools)[home-page]: Use HTTPS.
---
 gnu/packages/firmware.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm
index d9d0c2910c..6a96f7a1f5 100644
--- a/gnu/packages/firmware.scm
+++ b/gnu/packages/firmware.scm
@@ -145,7 +145,7 @@ Linux-libre.")
                              subdirs)
                    #t)))))))
       (home-page
-       "http://bues.ch/cms/hacking/misc.html#linux_b43_driver_firmware_tools")
+       "https://bues.ch/cms/hacking/misc.html#linux_b43_driver_firmware_tools")
       (synopsis "Collection of tools for the b43 wireless driver")
       (description
        "The b43 firmware tools is a collection of firmware extractor,
-- 
cgit v1.2.3


From 0dae492195a0d6e54ed76e43902541bab4ead2e3 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 1 Mar 2018 22:51:19 +0100
Subject: gnu: ovmf: Use HTTPS home page.

* gnu/packages/firmware.scm (ovmf)[home-page]: Use HTTPS.
---
 gnu/packages/firmware.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm
index 6a96f7a1f5..1579ba472f 100644
--- a/gnu/packages/firmware.scm
+++ b/gnu/packages/firmware.scm
@@ -301,7 +301,7 @@ coreboot.")
                    '()))
              #t)))))
     (supported-systems '("x86_64-linux" "i686-linux"))
-    (home-page "http://www.tianocore.org")
+    (home-page "https://www.tianocore.org")
     (synopsis "UEFI firmware for QEMU")
     (description "OVMF is an EDK II based project to enable UEFI support for
 Virtual Machines.  OVMF contains a sample UEFI firmware for QEMU and KVM.")
-- 
cgit v1.2.3


From f563d1990466e067e7c73eab553fe1ee20a44ffe Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 1 Mar 2018 23:06:41 +0100
Subject: gnu: ovmf: Update phase style.

* gnu/packages/firmware.scm (ovmf): Substitute INVOKE for SYSTEM* and
end phases with #t.
---
 gnu/packages/firmware.scm | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm
index 1579ba472f..0e1539cf66 100644
--- a/gnu/packages/firmware.scm
+++ b/gnu/packages/firmware.scm
@@ -261,7 +261,7 @@ coreboot.")
                (setenv "WORKSPACE" cwd)
                (setenv "EDK_TOOLS_PATH" tools)
                (setenv "PATH" (string-append (getenv "PATH") ":" bin))
-               (system* "bash" "edksetup.sh" "BaseTools")
+               (invoke "bash" "edksetup.sh" "BaseTools")
                (substitute* "Conf/target.txt"
                  (("^TARGET[ ]*=.*$") "TARGET = RELEASE\n")
                  (("^TOOL_CHAIN_TAG[ ]*=.*$") "TOOL_CHAIN_TAG = GCC49\n")
@@ -270,14 +270,16 @@ coreboot.")
                           (number->string (parallel-job-count)))))
                ;; Build build support.
                (setenv "BUILD_CC" "gcc")
-               (zero? (system* "make" "-C" (string-append tools "/Source/C"))))))
+               (invoke "make" "-C" (string-append tools "/Source/C"))
+               #t)))
          (add-after 'build 'build-ia32
            (lambda _
              (substitute* "Conf/target.txt"
                (("^TARGET_ARCH[ ]*=.*$") "TARGET_ARCH = IA32\n")
                (("^ACTIVE_PLATFORM[ ]*=.*$")
                 "ACTIVE_PLATFORM = OvmfPkg/OvmfPkgIa32.dsc\n"))
-             (zero? (system* "build"))))
+             (invoke "build")
+             #t))
          ,@(if (string=? "x86_64-linux" (%current-system))
              '((add-after 'build 'build-x64
                 (lambda _
@@ -285,7 +287,8 @@ coreboot.")
                     (("^TARGET_ARCH[ ]*=.*$") "TARGET_ARCH = X64\n")
                     (("^ACTIVE_PLATFORM[ ]*=.*$")
                      "ACTIVE_PLATFORM = OvmfPkg/OvmfPkgX64.dsc\n"))
-                  (zero? (system* "build")))))
+                  (invoke "build")
+                  #t)))
              '())
          (delete 'build)
          (replace 'install
-- 
cgit v1.2.3


From 65a3c342b0e53a23509ad479cb5140f09dd008bd Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 1 Mar 2018 23:48:09 +0100
Subject: gnu: ath9k-htc-firmware: Use INSTALL-FILE.

* gnu/packages/firmware.scm (ath9k-htc-firmware)[arguments]: Substitute
INSTALL-FILE for COPY-FILE with MKDIR-P.
---
 gnu/packages/firmware.scm | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm
index 0e1539cf66..da7430b063 100644
--- a/gnu/packages/firmware.scm
+++ b/gnu/packages/firmware.scm
@@ -71,11 +71,8 @@
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out    (assoc-ref outputs "out"))
                     (fw-dir (string-append out "/lib/firmware")))
-               (mkdir-p fw-dir)
                (for-each (lambda (file)
-                           (copy-file file
-                                      (string-append fw-dir "/"
-                                                     (basename file))))
+                           (install-file file fw-dir))
                          (find-files "." "\\.fw$"))
               #t))))
        #:tests? #f))
-- 
cgit v1.2.3


From f136c8f23d6dc0b52540456d50187f3417afb5e3 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 1 Mar 2018 23:50:57 +0100
Subject: gnu: gnome-mpv: Update to 0.14.

* gnu/packages/video.scm (gnome-mpv): Update to 0.14.
---
 gnu/packages/video.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 8190b0ffc1..e4e71e9dcc 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -1091,7 +1091,7 @@ projects while introducing many more.")
 (define-public gnome-mpv
   (package
     (name "gnome-mpv")
-    (version "0.13")
+    (version "0.14")
     (source
      (origin
        (method url-fetch)
@@ -1100,7 +1100,7 @@ projects while introducing many more.")
                            ".tar.xz"))
        (sha256
         (base32
-         "1w944ymyssgfcjiczrq4saig90crw9b9hhdsnchfbjsw173qi8n5"))))
+         "03kjwd5jq0i5ajnvhjwf5019bjjaa16xkdrhdkiz1k58ipjvvj93"))))
     (native-inputs
      `(("intltool" ,intltool)
        ("pkg-config" ,pkg-config)))
-- 
cgit v1.2.3


From 5c0f68e84491b03332e0f070f43c54effac3c64f Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 2 Mar 2018 00:22:09 +0100
Subject: gnu: fossil: Update phase style.

* gnu/packages/version-control.scm (fossil)[arguments]: Substitute
INVOKE for SYSTEM* and end phases with #t.
---
 gnu/packages/version-control.scm | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index 6c05ab59db..05f50869a3 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -1643,14 +1643,15 @@ repository\" with git-annex.")
        #:phases (modify-phases %standard-phases
                   (replace 'configure
                     (lambda* (#:key outputs (configure-flags '())
-                                    #:allow-other-keys)
+                              #:allow-other-keys)
                       ;; The 'configure' script is not an autoconf script and
                       ;; chokes on unrecognized options.
-                      (zero? (apply system*
-                                    "./configure"
-                                    (string-append "--prefix="
-                                                   (assoc-ref outputs "out"))
-                                    configure-flags))))
+                      (apply invoke
+                             "./configure"
+                             (string-append "--prefix="
+                                            (assoc-ref outputs "out"))
+                             configure-flags)
+                      #t))
                   (add-before 'check 'test-setup
                     (lambda _
                       (setenv "USER" "guix")
-- 
cgit v1.2.3


From 2c1cc27f8fffa3fbce8cf75cd45ea3ec2f8f4ee5 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 2 Mar 2018 00:28:48 +0100
Subject: gnu: fortify-headers: Update to 0.9.

* gnu/packages/suckless.scm (fortify-headers): Update to 0.9.
---
 gnu/packages/suckless.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/suckless.scm b/gnu/packages/suckless.scm
index 8a5f158878..c343b42274 100644
--- a/gnu/packages/suckless.scm
+++ b/gnu/packages/suckless.scm
@@ -564,7 +564,7 @@ environment variable.")
 (define-public fortify-headers
   (package
     (name "fortify-headers")
-    (version "0.8")
+    (version "0.9")
     (source
      (origin
        (method url-fetch)
@@ -572,7 +572,7 @@ environment variable.")
                            name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1cacdczpjb49c4i1168g541wnl3i3gbpv2m2wbnmw5wddlyhgkdg"))))
+         "1z517ajy34l2k5lz2gvhbmia9xjgagffi4s22azqxnlmgb1g2xfg"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; No tests
-- 
cgit v1.2.3


From d338321ddbd8545ff711254abc5d80c5b8cb3698 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 2 Mar 2018 00:33:37 +0100
Subject: gnu: qscintilla: Use HTTPS home page.

* gnu/packages/qt.scm (qscintilla)[home-page]: Use HTTPS.
---
 gnu/packages/qt.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm
index 4c4249bb90..a8c2729ee8 100644
--- a/gnu/packages/qt.scm
+++ b/gnu/packages/qt.scm
@@ -1735,7 +1735,7 @@ contain over 620 classes.")
                  (string-append out "/lib/qt$${QT_MAJOR_VERSION}")))
                (invoke "qmake")))))))
     (native-inputs `(("qtbase" ,qtbase)))
-    (home-page "http://www.riverbankcomputing.co.uk/software/qscintilla/intro")
+    (home-page "https://www.riverbankcomputing.co.uk/software/qscintilla/intro")
     (synopsis "Qt port of the Scintilla C++ editor control")
     (description "QScintilla is a port to Qt of Neil Hodgson's Scintilla C++
 editor control.  QScintilla includes features especially useful when editing
-- 
cgit v1.2.3


From 467834d5505473dc853677be4ca7d151e28fd669 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 2 Mar 2018 01:14:53 +0100
Subject: gnu: ghc-abstract-deque: Fix typos in description.

* gnu/packages/haskell.scm (ghc-abstract-deque)[description]: Fix typos.
---
 gnu/packages/haskell.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 5c6e07a671..3ff78047db 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -8181,12 +8181,12 @@ Background: There exists a feature space for queues that extends between:
 @itemize
 @item Simple, single-ended, non-concurrent, bounded queues
 
-@item Double-ended, threadsafe, growable queues with important points
-inbetween (such as the queues used for work-stealing).
+@item Double-ended, thread-safe, growable queues with important points
+in between (such as the queues used for work stealing).
 @end itemize
 
 This package includes an interface for Deques that allows the programmer
-to use a single API for all of the above, while using the type-system to
+to use a single API for all of the above, while using the type system to
 select an efficient implementation given the requirements (using type families).
 
 This package also includes a simple reference implementation based on
-- 
cgit v1.2.3


From 3a5c02777d6a51620d8cb8afa01602bc669bbfea Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 2 Mar 2018 01:40:20 +0100
Subject: gnu: highlight: Update to 3.42.

* gnu/packages/pretty-print.scm (highlight): Update to 3.42.
---
 gnu/packages/pretty-print.scm | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/pretty-print.scm b/gnu/packages/pretty-print.scm
index 2f61de8994..e8baefa1d4 100644
--- a/gnu/packages/pretty-print.scm
+++ b/gnu/packages/pretty-print.scm
@@ -4,7 +4,7 @@
 ;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -242,7 +242,7 @@ seen in a terminal.")
 (define-public highlight
   (package
     (name "highlight")
-    (version "3.33")
+    (version "3.42")
     (source
      (origin
        (method url-fetch)
@@ -250,10 +250,10 @@ seen in a terminal.")
                            version ".tar.bz2"))
        (sha256
         (base32
-         "0g2whi6pxl640795vymikm82a1my841jmh7fiqzbrjpc9wsk1db4"))))
+         "07iihzy8ckzdrxqd6bzbij4hy4mmlixibjnjviqfihd0hh1q30m5"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:tests? #f ; no tests
+     `(#:tests? #f                      ; no tests
        #:make-flags
        (let ((confdir (string-append %output "/share/highlight/config/")))
          (list (string-append "PREFIX=" %output)
@@ -261,7 +261,7 @@ seen in a terminal.")
                (string-append "conf_dir=" confdir)))
        #:phases
        (modify-phases %standard-phases
-         (delete 'configure)
+         (delete 'configure)            ; no configure script
          (add-after 'unpack 'fix-search-for-lua
            (lambda _
              (substitute* "src/makefile"
-- 
cgit v1.2.3


From 6e48fbb19a420ea0be1d922ebdce36d7beb0240f Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 2 Mar 2018 01:41:40 +0100
Subject: gnu: highlight: Don't hard-code Lua version.

* gnu/packages/pretty-print.scm (highlight)[arguments]: Construct the
Lua prefix programatically instead of hard-coding it.
---
 gnu/packages/pretty-print.scm | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/pretty-print.scm b/gnu/packages/pretty-print.scm
index e8baefa1d4..6edfba95cc 100644
--- a/gnu/packages/pretty-print.scm
+++ b/gnu/packages/pretty-print.scm
@@ -27,6 +27,7 @@
   #:use-module (guix download)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
+  #:use-module (guix utils)
   #:use-module (gnu packages)
   #:use-module (gnu packages ghostscript)
   #:use-module (gnu packages groff)
@@ -266,7 +267,8 @@ seen in a terminal.")
            (lambda _
              (substitute* "src/makefile"
                (("(pkg-config.*)lua" _ prefix)
-                (string-append prefix "lua-5.3")))
+                (string-append prefix "lua-" ,(version-major+minor
+                                               (package-version lua)))))
              #t)))))
     (inputs
      `(("lua" ,lua)
-- 
cgit v1.2.3


From dc8584d2b17f75bdf653b977e29821fb5692d7b2 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 2 Mar 2018 02:24:23 +0100
Subject: gnu: perl-test-harness: Update to 3.41.

* gnu/packages/perl-check.scm (perl-test-harness): Update to 3.41.
---
 gnu/packages/perl-check.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl-check.scm b/gnu/packages/perl-check.scm
index 110ba45d3d..6464385327 100644
--- a/gnu/packages/perl-check.scm
+++ b/gnu/packages/perl-check.scm
@@ -529,7 +529,7 @@ contents of a file is equal to a particular string.")
 (define-public perl-test-harness
   (package
     (name "perl-test-harness")
-    (version "3.39")
+    (version "3.41")
     (source
      (origin
        (method url-fetch)
@@ -537,7 +537,7 @@ contents of a file is equal to a particular string.")
                            "Test-Harness-" version ".tar.gz"))
        (sha256
         (base32
-         "0chiqnzmna2mglm37nzxvn9qhq2j31iwz3i9isqjs7bf3k449gb9"))))
+         "0cgdgzywvscbvb9i0dmd2ls5jwqlnf2z6hx4f4lljpvdjd59v3m8"))))
     (build-system perl-build-system)
     (arguments
      `(#:phases
-- 
cgit v1.2.3


From defe0282c29cbc9bdb774ebdf8095a02c4aaea98 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 2 Mar 2018 02:30:53 +0100
Subject: gnu: perl-mozilla-ca: Update to 20180117.

* gnu/packages/perl.scm (perl-mozilla-ca): Update to 20180117.
---
 gnu/packages/perl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 556d8d31b4..e44d5c3f0f 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -6008,7 +6008,7 @@ of data.")
 (define-public perl-mozilla-ca
   (package
     (name "perl-mozilla-ca")
-    (version "20160104")
+    (version "20180117")
     (source
      (origin
        (method url-fetch)
@@ -6016,7 +6016,7 @@ of data.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "0aizn08lrdrgjz9vagkjmw2c7sxn46fzz521v9dbcqii4jd0d9r7"))))
+         "01p4ykyilk1639dxgjaa2n7rz1f0zbqxkq11yc9n6xcz26z9zk7j"))))
     (build-system perl-build-system)
     (home-page "http://search.cpan.org/dist/Mozilla-CA/")
     (synopsis "Mozilla's CA cert bundle in PEM format")
-- 
cgit v1.2.3


From 139ecdee8e592c515eea8cff4b918f0655196b4c Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 2 Mar 2018 02:43:54 +0100
Subject: gnu: delta: Remove redundant code.

* gnu/packages/debug.scm (delta)[arguments]: Remove unneeded MKDIR-P
calls.
---
 gnu/packages/debug.scm | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/debug.scm b/gnu/packages/debug.scm
index 2354f0fbb9..6b566b0097 100644
--- a/gnu/packages/debug.scm
+++ b/gnu/packages/debug.scm
@@ -66,8 +66,6 @@
                     (bin (string-append out "/bin"))
                     (doc (string-append out "/share/doc/delta-" ,version)))
                (begin
-                 (mkdir-p bin)
-                 (mkdir-p doc)
                  (for-each (lambda (h)
                              (install-file h doc))
                            `("License.txt" ,@(find-files "www" ".*\\.html")))
@@ -75,7 +73,7 @@
                              (install-file b bin))
                            `("delta" "multidelta" "topformflat"))))
              #t))
-         (delete 'configure))))
+         (delete 'configure))))         ; no configure script
     (home-page "http://delta.tigris.org/")
     (synopsis "Heuristical file minimizer")
     (description
-- 
cgit v1.2.3


From a40f732bb6a8fc2f22d5931efad428a7cbdbe609 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 2 Mar 2018 04:35:08 +0100
Subject: gnu: python-webencodings: Fix typo in description.

* gnu/packages/python-web.scm (python-webencodings)[description]: Fix typo.
---
 gnu/packages/python-web.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 3ab7dafa42..d9721f1375 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -265,7 +265,7 @@ C, yielding parse times that can be a thirtieth of the html5lib parse times.")
 something like @code{Content-Type: text/html; charset=latin1}, tools need
 to use a particular set of aliases for encoding labels as well as some
 overriding rules.  For example, @code{US-ASCII} and @code{iso-8859-1} on
-the web are actually aliases for @code{windows-1252}, and an @code{UTF-8}
+the web are actually aliases for @code{windows-1252}, and a @code{UTF-8}
 or @code{UTF-16} BOM takes precedence over any other encoding declaration.
 The WHATWG @url{https://encoding.spec.whatwg.org/,Encoding} standard
 defines all such details so that implementations do not have to
-- 
cgit v1.2.3


From 5658b4ce693637123375ccf594c3b4557b643224 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 2 Mar 2018 05:01:16 +0100
Subject: gnu: zerofree: Update to 1.1.1.

* gnu/packages/linux.scm (zerofree): Update to 1.1.1.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index b922989018..b4d81943e1 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -873,7 +873,7 @@ ext3 or ext4 partition.")
 (define-public zerofree
   (package
     (name "zerofree")
-    (version "1.1.0")
+    (version "1.1.1")
     (home-page "https://frippery.org/uml/")
     (source (origin
               (method url-fetch)
@@ -881,7 +881,7 @@ ext3 or ext4 partition.")
                                   ".tgz"))
               (sha256
                (base32
-                "059g29x5r1xj6wcj4xj85l8w6qrxyl86yqbybjqqz6nxz4falxzf"))))
+                "0rrqfa5z103ws89vi8kfvbks1cfs74ix6n1wb6vs582vnmhwhswm"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases
-- 
cgit v1.2.3


From 6fda93e6c8aa25c2b482a0502be9d39335ed2172 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 2 Mar 2018 05:16:00 +0100
Subject: gnu: libpsl: Update to 0.20.1.

* gnu/packages/web.scm (libpsl): Update to 0.20.1.
---
 gnu/packages/web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index e3412f60e2..f9b7e3f70f 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -799,7 +799,7 @@ for efficient socket-like bidirectional reliable communication channels.")
 (define-public libpsl
   (package
     (name "libpsl")
-    (version "0.20.0")
+    (version "0.20.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/rockdaboot/libpsl/"
@@ -807,7 +807,7 @@ for efficient socket-like bidirectional reliable communication channels.")
                                   "/libpsl-" version ".tar.gz"))
               (sha256
                (base32
-                "0rsjm6mb71nnj6ikr2dq5qmny314v3j7m07zz1i7m6v8hxxm98i7"))))
+                "17r18y25ka2ck2ykfidbg4a7jpyzmkqwrzplgqjp7mwd2l9rc6cm"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
-- 
cgit v1.2.3


From b01a1b34f2345e66e2ba4b647fca75e7951567d6 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 2 Mar 2018 05:16:27 +0100
Subject: gnu: nghttp2: Update to 1.31.0.

* gnu/packages/web.scm (nghttp2): Update to 1.31.0.
---
 gnu/packages/web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index f9b7e3f70f..760f4ef2ab 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -6350,7 +6350,7 @@ derivation by David Revoy from the original MonsterID by Andreas Gohr.")
 (define-public nghttp2
   (package
     (name "nghttp2")
-    (version "1.30.0")
+    (version "1.31.0")
     (source
      (origin
        (method url-fetch)
@@ -6359,7 +6359,7 @@ derivation by David Revoy from the original MonsterID by Andreas Gohr.")
                            name "-" version ".tar.xz"))
        (sha256
         (base32
-         "1b2j7il0wp8hi4jl3cah7fkshmg29cchdski9cw74gx5496gp6h8"))))
+         "1ivs74v9sa2sds3dq0s7vn9bkmhr2hgwyg1an1rah3agqwnkqmrn"))))
     (build-system gnu-build-system)
     (outputs (list "out"
                    "lib"))              ; only libnghttp2
-- 
cgit v1.2.3


From 5f4565b18fa0bdb0388265c9e97e284826327c3a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 2 Mar 2018 22:21:00 +0100
Subject: gnu: Add r-network.

* gnu/packages/cran.scm (r-network): New variable.
---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 9279d1da83..211d292397 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2225,3 +2225,23 @@ meta-analysis of significance values including the methods of Edgington,
 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
 published results; and a routine for graphical display.")
     (license license:gpl2)))
+
+(define-public r-network
+  (package
+    (name "r-network")
+    (version "1.13.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "network" version))
+       (sha256
+        (base32
+         "11sg330xb7gcnl3f6lwhhjdabz6mk43828i2np635pqw4s4yl13s"))))
+    (build-system r-build-system)
+    (home-page "http://statnet.org/")
+    (synopsis "Classes for relational data")
+    (description
+     "This package provides tools to create and modify network objects.  The
+@code{network} class can represent a range of relational data types, and
+supports arbitrary vertex/edge/graph attributes.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 07a2f34d5c8342b88530f8cb968090eccd0da91c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 2 Mar 2018 22:22:20 +0100
Subject: gnu: Add r-statnet-common.

* gnu/packages/cran.scm (r-statnet-common): New variable.
---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 211d292397..e06eb60e94 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2245,3 +2245,23 @@ published results; and a routine for graphical display.")
 @code{network} class can represent a range of relational data types, and
 supports arbitrary vertex/edge/graph attributes.")
     (license license:gpl2+)))
+
+(define-public r-statnet-common
+  (package
+    (name "r-statnet-common")
+    (version "4.0.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "statnet.common" version))
+        (sha256
+          (base32
+            "0yw6l5b4qv0jqlg4zyczas7m12a5pyqghs6ydxy2f6v6vxkijvi0"))))
+    (properties
+      `((upstream-name . "statnet.common")))
+    (build-system r-build-system)
+    (home-page "http://www.statnet.org")
+    (synopsis "R scripts and utilities used by the Statnet software")
+    (description "This package provides non-statistical utilities used by the
+software developed by the Statnet Project.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From 1088744d8748a4ed81accdacab95eb397de0f23b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 2 Mar 2018 22:22:32 +0100
Subject: gnu: Add r-sna.

* gnu/packages/cran.scm (r-sna): New variable.
---
 gnu/packages/cran.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index e06eb60e94..2e229e9e0f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2265,3 +2265,27 @@ supports arbitrary vertex/edge/graph attributes.")
     (description "This package provides non-statistical utilities used by the
 software developed by the Statnet Project.")
     (license license:gpl3)))
+
+(define-public r-sna
+  (package
+    (name "r-sna")
+    (version "2.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "sna" version))
+       (sha256
+        (base32
+         "1ks8819qvpdfansfqj9p32s1rhvl26frvbi78m4rx1wd1qcv74i2"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-network" ,r-network)
+       ("r-statnet-common" ,r-statnet-common)))
+    (home-page "http://www.statnet.org")
+    (synopsis "Tools for social network analysis")
+    (description
+     "This package provides a range of tools for social network analysis,
+including node and graph-level indices, structural distance and covariance
+methods, structural equivalence detection, network regression, random graph
+generation, and 2D/3D network visualization.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 4e35c4290ef64e8fba376f9c3d9754757ebf89da Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 2 Mar 2018 22:22:54 +0100
Subject: gnu: Add r-rbiofabric.

* gnu/packages/graph.scm (r-rbiofabric): New variable.
---
 gnu/packages/graph.scm | 29 ++++++++++++++++++++++++++++-
 1 file changed, 28 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 70df77b5d2..19c9b2269b 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -18,6 +18,7 @@
 
 (define-module (gnu packages graph)
   #:use-module (guix download)
+  #:use-module (guix git-download)
   #:use-module (guix packages)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system python)
@@ -172,3 +173,29 @@ model.")
      "This package interfaces R with the graphviz library for plotting R graph
 objects from the @code{graph} package.")
     (license license:epl1.0)))
+
+(define-public r-rbiofabric
+  (let ((commit "666c2ae8b0a537c006592d067fac6285f71890ac")
+        (revision "1"))
+    (package
+      (name "r-rbiofabric")
+      (version (string-append "0.3-" revision "." (string-take commit 7)))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/wjrl/RBioFabric.git")
+                      (commit commit)))
+                (file-name (string-append name "-" version "-checkout"))
+                (sha256
+                 (base32
+                  "1yahqrcrqpbcywv73y9rlmyz8apdnp08afialibrr93ch0p06f8z"))))
+      (build-system r-build-system)
+      (propagated-inputs
+       `(("r-igraph" ,r-igraph)))
+      (home-page "http://www.biofabric.org/")
+      (synopsis "BioFabric network visualization")
+      (description "This package provides an implementation of the function
+@code{bioFabric} for creating scalable network digrams where nodes are
+represented by horizontal lines, and edges are represented by vertical
+lines.")
+      (license license:expat))))
-- 
cgit v1.2.3


From 93c21ddc8620ec1e6930b85161cdbc89fc459f02 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 2 Mar 2018 22:55:10 +0100
Subject: gnu: Add r-ttr.

* gnu/packages/cran.scm (r-ttr): New variable.
---
 gnu/packages/cran.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 2e229e9e0f..63f1405472 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2289,3 +2289,28 @@ including node and graph-level indices, structural distance and covariance
 methods, structural equivalence detection, network regression, random graph
 generation, and 2D/3D network visualization.")
     (license license:gpl2+)))
+
+(define-public r-ttr
+  (package
+    (name "r-ttr")
+    (version "0.23-3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "TTR" version))
+       (sha256
+        (base32
+         "07r62ngyzjl4aszdxnr3n6bnbcgcap32yhd430jsilicg8n06di1"))))
+    (properties `((upstream-name . "TTR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-curl" ,r-curl)
+       ("r-xts" ,r-xts)
+       ("r-zoo" ,r-zoo)))
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "https://github.com/joshuaulrich/TTR")
+    (synopsis "Technical trading rules")
+    (description
+     "This package provides functions and data to construct technical trading
+rules with R.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From 0b64332c74fa09d768349c05b0db6bd309962781 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 2 Mar 2018 23:03:10 +0100
Subject: gnu: Add r-leaps.

* gnu/packages/cran.scm (r-leaps): New variable.
---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 63f1405472..4f54b40149 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2314,3 +2314,23 @@ generation, and 2D/3D network visualization.")
      "This package provides functions and data to construct technical trading
 rules with R.")
     (license license:gpl2)))
+
+(define-public r-leaps
+  (package
+    (name "r-leaps")
+    (version "3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "leaps" version))
+       (sha256
+        (base32
+         "11gjmn1azrjw5xlvdb4gknj9985kck9x8zb9np1rnk2smp6pka2m"))))
+    (build-system r-build-system)
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "http://cran.r-project.org/web/packages/leaps/")
+    (synopsis "Regression subset selection")
+    (description
+     "This package provides tools for regression subset selection, including
+exhaustive search.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From d3cb62e58d99a23a9154a9b03fdffa496c36d337 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 2 Mar 2018 23:05:02 +0100
Subject: gnu: Add r-splus2r.

* gnu/packages/cran.scm (r-splus2r): New variable.
---
 gnu/packages/cran.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 4f54b40149..b0dcaccbdd 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2334,3 +2334,25 @@ rules with R.")
      "This package provides tools for regression subset selection, including
 exhaustive search.")
     (license license:gpl2+)))
+
+(define-public r-splus2r
+  (package
+    (name "r-splus2r")
+    (version "1.2-2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "splus2R" version))
+       (sha256
+        (base32
+         "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
+    (properties `((upstream-name . "splus2R")))
+    (build-system r-build-system)
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "http://cran.r-project.org/web/packages/splus2R/")
+    (synopsis "Supplemental S-PLUS functionality in R")
+    (description
+     "Currently there are many functions in S-PLUS that are missing in R.  To
+facilitate the conversion of S-PLUS packages to R packages, this package
+provides some missing S-PLUS functionality in R.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From 034ac9d67a3cbb4cf0976ff1c796a35f6a73cb2f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 2 Mar 2018 23:05:14 +0100
Subject: gnu: Add r-ifultools.

* gnu/packages/cran.scm (r-ifultools): New variable.
---
 gnu/packages/cran.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b0dcaccbdd..613ed130d3 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2356,3 +2356,24 @@ exhaustive search.")
 facilitate the conversion of S-PLUS packages to R packages, this package
 provides some missing S-PLUS functionality in R.")
     (license license:gpl2)))
+
+(define-public r-ifultools
+  (package
+    (name "r-ifultools")
+    (version "2.0-4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ifultools" version))
+       (sha256
+        (base32
+         "0pv2msaa1rmj8csxdclzi2jwg9pfdvh87blj9j3xa3myisglq092"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mass" ,r-mass)
+       ("r-splus2r" ,r-splus2r)))
+    (home-page "http://cran.r-project.org/web/packages/ifultools/")
+    (synopsis "Insightful research tools")
+    (description "This package provides C code used by the wmtsa, fractal, and
+sapa R packages.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From 0be7effefa4aaa39a2312b9b57d8bed5811e4069 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 2 Mar 2018 23:05:35 +0100
Subject: gnu: Add r-sapa.

* gnu/packages/cran.scm (r-sapa): New variable.
---
 gnu/packages/cran.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 613ed130d3..1f76dac57c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2377,3 +2377,25 @@ provides some missing S-PLUS functionality in R.")
     (description "This package provides C code used by the wmtsa, fractal, and
 sapa R packages.")
     (license license:gpl2)))
+
+(define-public r-sapa
+  (package
+    (name "r-sapa")
+    (version "2.0-2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "sapa" version))
+       (sha256
+        (base32
+         "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ifultools" ,r-ifultools)
+       ("r-splus2r" ,r-splus2r)))
+    (home-page "http://cran.r-project.org/web/packages/sapa/")
+    (synopsis "Spectral analysis for physical applications")
+    (description "This package provides software for the book Spectral
+Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
+Cambridge University Press, 1993.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From dceb159206e8336f855d768a83c2da6b9dd95982 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 2 Mar 2018 23:05:43 +0100
Subject: gnu: Add r-quantmod.

* gnu/packages/cran.scm (r-quantmod): New variable.
---
 gnu/packages/cran.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 1f76dac57c..8c811269f3 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2399,3 +2399,27 @@ sapa R packages.")
 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
 Cambridge University Press, 1993.")
     (license license:gpl2)))
+
+(define-public r-quantmod
+  (package
+    (name "r-quantmod")
+    (version "0.4-12")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "quantmod" version))
+       (sha256
+        (base32
+         "0y7gh0k1s10vdsfch8777avbhf99mc9crikvx7ahqrw0j631vmhq"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-curl" ,r-curl)
+       ("r-ttr" ,r-ttr)
+       ("r-xts" ,r-xts)
+       ("r-zoo" ,r-zoo)))
+    (home-page "http://cran.r-project.org/web/packages/quantmod/")
+    (synopsis "Quantitative financial modelling framework")
+    (description "This package provides a quantitative financial modelling
+framework to allow users to specify, build, trade, and analyse quantitative
+financial trading strategies.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From b6dc3255386a61de6abe5fa26afd760a3e8573a0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 2 Mar 2018 23:05:52 +0100
Subject: gnu: Add r-tseries.

* gnu/packages/cran.scm (r-tseries): New variable.
---
 gnu/packages/cran.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 8c811269f3..e9d243d992 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2423,3 +2423,28 @@ Cambridge University Press, 1993.")
 framework to allow users to specify, build, trade, and analyse quantitative
 financial trading strategies.")
     (license license:gpl3)))
+
+(define-public r-tseries
+  (package
+    (name "r-tseries")
+    (version "0.10-43")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "tseries" version))
+       (sha256
+        (base32
+         "1yjxhj7l1p2przczl6frggfcr5iwda9lbcsmh0y75gbbbps14yf2"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-quadprog" ,r-quadprog)
+       ("r-quantmod" ,r-quantmod)
+       ("r-zoo" ,r-zoo)))
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "http://cran.r-project.org/web/packages/tseries/")
+    (synopsis "Time series analysis and computational finance")
+    (description
+     "This package provides functions relating to time series analysis and
+computational finance.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From a2c079a780b8a8c552577eb43f6d855e7fede2c6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 2 Mar 2018 23:06:00 +0100
Subject: gnu: Add r-wmtsa.

* gnu/packages/cran.scm (r-wmtsa): New variable.
---
 gnu/packages/cran.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index e9d243d992..b6610cb93f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2448,3 +2448,27 @@ financial trading strategies.")
      "This package provides functions relating to time series analysis and
 computational finance.")
     (license license:gpl2)))
+
+(define-public r-wmtsa
+  (package
+    (name "r-wmtsa")
+    (version "2.0-3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "wmtsa" version))
+       (sha256
+        (base32
+         "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ifultools" ,r-ifultools)
+       ("r-mass" ,r-mass)
+       ("r-splus2r" ,r-splus2r)))
+    (home-page "http://cran.r-project.org/web/packages/wmtsa/")
+    (synopsis "Wavelet methods for time series analysis")
+    (description
+     "This package provides software to accompany the book \"Wavelet Methods
+for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
+University Press, 2000.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From 4993a02ad70b3fb152bfb2b9f91ab9fc590220f4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 2 Mar 2018 23:06:10 +0100
Subject: gnu: Add r-tsa.

* gnu/packages/cran.scm (r-tsa): New variable.
---
 gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b6610cb93f..750e82ad60 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2472,3 +2472,29 @@ computational finance.")
 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
 University Press, 2000.")
     (license license:gpl2)))
+
+(define-public r-tsa
+  (package
+    (name "r-tsa")
+    (version "1.01")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "TSA" version))
+       (sha256
+        (base32
+         "0cm97hwxm6vfgy9mc3kgwq6dnmn86p8a4avnfjbai048qnwrn6hx"))))
+    (properties `((upstream-name . "TSA")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-leaps" ,r-leaps)
+       ("r-locfit" ,r-locfit)
+       ("r-mgcv" ,r-mgcv)
+       ("r-tseries" ,r-tseries)))
+    (home-page "http://www.stat.uiowa.edu/~kchan/TSA.htm")
+    (synopsis "Time series analysis")
+    (description
+     "This package contains R functions and datasets detailed in the book
+\"Time Series Analysis with Applications in R (second edition)\" by Jonathan
+Cryer and Kung-Sik Chan.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 19da7fe314629e894ef201fdf8ca10ca4555b6b0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 2 Mar 2018 23:06:17 +0100
Subject: gnu: Add r-extradistr.

* gnu/packages/cran.scm (r-extradistr): New variable.
---
 gnu/packages/cran.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 750e82ad60..5d1f24aa08 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2498,3 +2498,26 @@ University Press, 2000.")
 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
 Cryer and Kung-Sik Chan.")
     (license license:gpl2+)))
+
+(define-public r-extradistr
+  (package
+    (name "r-extradistr")
+    (version "1.8.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "extraDistr" version))
+       (sha256
+        (base32
+         "0ywn4qwnamv36l1hw27l9y5kh3v6ha5781wsv2bz6szqjgg7kdb3"))))
+    (properties `((upstream-name . "extraDistr")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)))
+    (home-page "https://github.com/twolodzko/extraDistr")
+    (synopsis "Additional univariate and multivariate distributions")
+    (description
+     "This package implements density, distribution functions, quantile
+functions and random generation functions for a large number of univariate and
+multivariate distributions.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From 5b25bc55dc6e23936719e2748b5d9445ce9eea97 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 2 Mar 2018 23:06:26 +0100
Subject: gnu: Add r-fractal.

* gnu/packages/cran.scm (r-fractal): New variable.
---
 gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 5d1f24aa08..d4aeb26171 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2521,3 +2521,29 @@ Cryer and Kung-Sik Chan.")
 functions and random generation functions for a large number of univariate and
 multivariate distributions.")
     (license license:gpl2)))
+
+(define-public r-fractal
+  (package
+    (name "r-fractal")
+    (version "2.0-4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "fractal" version))
+       (sha256
+        (base32
+         "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ifultools" ,r-ifultools)
+       ("r-mass" ,r-mass)
+       ("r-sapa" ,r-sapa)
+       ("r-scatterplot3d" ,r-scatterplot3d)
+       ("r-splus2r" ,r-splus2r)
+       ("r-wmtsa" ,r-wmtsa)))
+    (home-page "http://cran.r-project.org/web/packages/fractal/")
+    (synopsis "Fractal time series modeling and analysis")
+    (description
+     "This package provides tools for stochastic fractal and deterministic
+chaotic time series analysis.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From 6615a364212ac7e731ecf0e9357317257f7114de Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 2 Mar 2018 23:06:33 +0100
Subject: gnu: Add r-urca.

* gnu/packages/cran.scm (r-urca): New variable.
---
 gnu/packages/cran.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index d4aeb26171..1c8b9ba521 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2547,3 +2547,24 @@ multivariate distributions.")
      "This package provides tools for stochastic fractal and deterministic
 chaotic time series analysis.")
     (license license:gpl2)))
+
+(define-public r-urca
+  (package
+    (name "r-urca")
+    (version "1.3-0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "urca" version))
+       (sha256
+        (base32
+         "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-nlme" ,r-nlme)))
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "http://cran.r-project.org/web/packages/urca/")
+    (synopsis "Unit root and cointegration tests for time series data")
+    (description
+     "This package provides unit root and cointegration tests encountered in
+applied econometric analysis.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From d32e57248954d20ef892ee9fbc3bae9afa1299d1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 2 Mar 2018 23:06:41 +0100
Subject: gnu: Add r-cubature.

* gnu/packages/cran.scm (r-cubature): New variable.
---
 gnu/packages/cran.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 1c8b9ba521..f7b657bc3a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2568,3 +2568,28 @@ chaotic time series analysis.")
      "This package provides unit root and cointegration tests encountered in
 applied econometric analysis.")
     (license license:gpl2+)))
+
+(define-public r-cubature
+  (package
+    (name "r-cubature")
+    (version "1.3-11")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "cubature" version))
+       (sha256
+        (base32
+         "06f6gsvbb732p80r6hxvzh4ik546icxfvx21dyh65ypmw3kgm64k"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)))
+    (home-page "https://github.com/bnaras/cubature")
+    (synopsis "Adaptive multivariate integration over hypercubes")
+    (description
+     "This package is an R wrapper around the cubature C library for adaptive
+multivariate integration over hypercubes.  This version provides both
+@code{hcubature} and @code{pcubature} routines in addition to a vector
+interface.")
+    ;; The included cubature C library is released under GPLv2+, but the
+    ;; wrapper declares the license to be GPLv3+.
+    (license (list license:gpl2+ license:gpl3+))))
-- 
cgit v1.2.3


From 7531ee842c19c481b3e4785b36cf6558b054e6b2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 2 Mar 2018 23:06:50 +0100
Subject: gnu: Add r-trend.

* gnu/packages/cran.scm (r-trend): New variable.
---
 gnu/packages/cran.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index f7b657bc3a..ce676334c6 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2593,3 +2593,34 @@ interface.")
     ;; The included cubature C library is released under GPLv2+, but the
     ;; wrapper declares the license to be GPLv3+.
     (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-trend
+  (package
+    (name "r-trend")
+    (version "1.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "trend" version))
+       (sha256
+        (base32
+         "06yifqbsvxbmk5gld4z2nnyhf59v8ks5xjwacmb25mv9r6bn388b"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-extradistr" ,r-extradistr)))
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "http://cran.r-project.org/web/packages/trend/")
+    (synopsis "Non-parametric trend tests and change-point detection")
+    (description
+     "The analysis of environmental data often requires the detection of
+trends and change-points.  This package includes tests for trend
+detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
+Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
+Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
+correlation trend test), change-point detection (Lanzante's test procedures,
+Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
+Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
+Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
+sample Robust Rank-Order Distributional Test.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From f96eda90d5b015057dfd28d4ef7466dbae4bc3f5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 2 Mar 2018 23:06:57 +0100
Subject: gnu: Add r-expm.

* gnu/packages/cran.scm (r-expm): New variable.
---
 gnu/packages/cran.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ce676334c6..e7efab78ec 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2624,3 +2624,24 @@ Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
 sample Robust Rank-Order Distributional Test.")
     (license license:gpl3)))
+
+(define-public r-expm
+  (package
+    (name "r-expm")
+    (version "0.999-2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "expm" version))
+       (sha256
+        (base32
+         "1mihl67kvv1xv0figp25jkmwfn4iwkcx15cng2348y8gm6zybw9q"))))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-matrix" ,r-matrix)))
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "http://r-forge.r-project.org/projects/expm/")
+    (synopsis "Tools for matrix exponentials and related quantities")
+    (description
+     "This package provides tools for the computation of the matrix
+exponential, logarithm, square root, and related quantities.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 68b6a67e94a2c4e57444b0aa3714910d0ad0190b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 2 Mar 2018 23:07:04 +0100
Subject: gnu: Add r-complexplus.

* gnu/packages/cran.scm (r-complexplus): New variable.
---
 gnu/packages/cran.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index e7efab78ec..a82700fb38 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2645,3 +2645,25 @@ sample Robust Rank-Order Distributional Test.")
      "This package provides tools for the computation of the matrix
 exponential, logarithm, square root, and related quantities.")
     (license license:gpl2+)))
+
+(define-public r-complexplus
+  (package
+    (name "r-complexplus")
+    (version "2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "complexplus" version))
+       (sha256
+        (base32
+         "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-expm" ,r-expm)
+       ("r-matrix" ,r-matrix)))
+    (home-page "http://cran.r-project.org/web/packages/complexplus/")
+    (synopsis "Functions of complex or real variables")
+    (description
+     "This package extends several functions to the complex domain, including
+the matrix exponential and logarithm, and the determinant.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From 7b81a7eabf71ccf989d2b3e33ff7d1801b848558 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 2 Mar 2018 23:07:12 +0100
Subject: gnu: Add r-phontools.

* gnu/packages/cran.scm (r-phontools): New variable.
---
 gnu/packages/cran.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index a82700fb38..d20635b91b 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2667,3 +2667,25 @@ exponential, logarithm, square root, and related quantities.")
      "This package extends several functions to the complex domain, including
 the matrix exponential and logarithm, and the determinant.")
     (license license:gpl2)))
+
+(define-public r-phontools
+  (package
+    (name "r-phontools")
+    (version "0.2-2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "phonTools" version))
+       (sha256
+        (base32
+         "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
+    (properties `((upstream-name . "phonTools")))
+    (build-system r-build-system)
+    (home-page "http://www.santiagobarreda.com/rscripts.html")
+    (synopsis "Tools for phonetic and acoustic analyses")
+    (description
+     "This package contains tools for the organization, display, and analysis
+of the sorts of data frequently encountered in phonetics research and
+experimentation, including the easy creation of IPA vowel plots, and the
+creation and manipulation of WAVE audio files.")
+    (license license:bsd-2)))
-- 
cgit v1.2.3


From d976454c6b65264eb1be6b69852a69fe5f6cf6e1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 2 Mar 2018 23:07:20 +0100
Subject: gnu: Add r-np.

* gnu/packages/cran.scm (r-np): New variable.
---
 gnu/packages/cran.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index d20635b91b..14351e6ae0 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2689,3 +2689,27 @@ of the sorts of data frequently encountered in phonetics research and
 experimentation, including the easy creation of IPA vowel plots, and the
 creation and manipulation of WAVE audio files.")
     (license license:bsd-2)))
+
+(define-public r-np
+  (package
+    (name "r-np")
+    (version "0.60-6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "np" version))
+       (sha256
+        (base32
+         "1y72x5j9j9mcgcy2xizk31gl843hfkngxdn8s4qw7yhw2qj79hsr"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-boot" ,r-boot)
+       ("r-cubature" ,r-cubature)
+       ("r-quantreg" ,r-quantreg)))
+    (home-page "https://github.com/JeffreyRacine/R-Package-np")
+    (synopsis "Non-parametric kernel smoothing methods for mixed data types")
+    (description "This package provides non-parametric (and semi-parametric)
+kernel methods that seamlessly handle a mix of continuous, unordered, and
+ordered factor data types.")
+    ;; Any version of the GPL.
+    (license license:gpl3+)))
-- 
cgit v1.2.3


From 2a112be09aebb3da15958e58fb677e3fa76e2bd8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 2 Mar 2018 23:07:26 +0100
Subject: gnu: Add r-powerplus.

* gnu/packages/cran.scm (r-powerplus): New variable.
---
 gnu/packages/cran.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 14351e6ae0..7433a561ad 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2713,3 +2713,28 @@ kernel methods that seamlessly handle a mix of continuous, unordered, and
 ordered factor data types.")
     ;; Any version of the GPL.
     (license license:gpl3+)))
+
+(define-public r-powerplus
+  (package
+    (name "r-powerplus")
+    (version "3.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "powerplus" version))
+       (sha256
+        (base32
+         "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-complexplus" ,r-complexplus)
+       ("r-expm" ,r-expm)
+       ("r-mass" ,r-mass)
+       ("r-matrix" ,r-matrix)
+       ("r-phontools" ,r-phontools)))
+    (home-page "http://cran.r-project.org/web/packages/powerplus/")
+    (synopsis "Exponentiation operations")
+    (description
+     "This package provides tools for the computation of matrix and scalar
+exponentiation.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From fa5965990d583cd9d87f7abc07d1874616cd262b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 2 Mar 2018 23:24:57 +0100
Subject: gnu: Add r-hpar.

* gnu/packages/bioconductor.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
---
 gnu/local.mk                  |  1 +
 gnu/packages/bioconductor.scm | 42 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 43 insertions(+)
 create mode 100644 gnu/packages/bioconductor.scm

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index dfe3ff5fc3..9684d949f6 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -76,6 +76,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/bash.scm				\
   %D%/packages/bdw-gc.scm			\
   %D%/packages/benchmark.scm			\
+  %D%/packages/bioconductor.scm			\
   %D%/packages/bioinformatics.scm		\
   %D%/packages/bittorrent.scm			\
   %D%/packages/bison.scm			\
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
new file mode 100644
index 0000000000..f557dce8e5
--- /dev/null
+++ b/gnu/packages/bioconductor.scm
@@ -0,0 +1,42 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages bioconductor)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix build-system r)
+  #:use-module (gnu packages))
+
+(define-public r-hpar
+  (package
+    (name "r-hpar")
+    (version "1.20.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "hpar" version))
+       (sha256
+        (base32
+         "0s5v79mgxdx862v1jrdf5pdap81nz5vjx25ni8s3sl97ldckf6j8"))))
+    (build-system r-build-system)
+    (home-page "https://bioconductor.org/packages/hpar/")
+    (synopsis "Human Protein Atlas in R")
+    (description "This package provides a simple interface to and data from
+the Human Protein Atlas project.")
+    (license license:artistic2.0)))
-- 
cgit v1.2.3


From 62a4b952c041d5643f1a1ef05450dd8fb59e9bbf Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 2 Mar 2018 23:43:55 +0100
Subject: gnu: python-xopen: Update to 0.3.2.

* gnu/packages/python.scm (python-xopen): Update to 0.3.2.
---
 gnu/packages/python.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 126424183b..5f701701a4 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -7,7 +7,7 @@
 ;;; Copyright © 2014, 2015 Federico Beffa <beffa@fbengineering.ch>
 ;;; Copyright © 2015 Omar Radwan <toxemicsquire4@gmail.com>
 ;;; Copyright © 2015 Pierre-Antoine Rault <par@rigelk.eu>
-;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015, 2016 Christopher Allan Webber <cwebber@dustycloud.org>
 ;;; Copyright © 2015 Eric Dvorsak <eric@dvorsak.fr>
 ;;; Copyright © 2015, 2016 David Thompson <davet@gnu.org>
@@ -10173,14 +10173,14 @@ network.")
 (define-public python-xopen
   (package
     (name "python-xopen")
-    (version "0.1.1")
+    (version "0.3.2")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "xopen" version))
         (sha256
           (base32
-           "1wx6mylzcsyhjl19ycb83qq6iqpmr927lz62njfsar6ldsj0qcni"))
+           "0bzjmn3rl1cd3d2q39cjwnkhaspk2b0hfj3rl64pclm44ihg5fb6"))
         (file-name (string-append name "-" version ".tar.gz"))))
     (build-system python-build-system)
     (home-page "https://github.com/marcelm/xopen/")
-- 
cgit v1.2.3


From 3ede1550e8310a8a544c1fb0f7f372c60c00bbe0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 2 Mar 2018 23:44:16 +0100
Subject: gnu: cutadapt: Update to 1.16.

* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.16.
[source]: Fetch via git.
[arguments]: Remove.
[native-inputs]: Replace python-nose with python-pytest.
---
 gnu/packages/bioinformatics.scm | 32 ++++++++------------------------
 1 file changed, 8 insertions(+), 24 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e5e9192993..e13f1b369f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1854,38 +1854,22 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
 (define-public cutadapt
   (package
     (name "cutadapt")
-    (version "1.14")
+    (version "1.16")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/marcelm/cutadapt/archive/v"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/marcelm/cutadapt.git")
+                    (commit (string-append "v" version))))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "16gbpiwy4m48vq2h5wqar3i8vr6vcj9gcl2qvqim19x6ya9dp8kd"))))
+                "09pr02067jiks19nc0aby4xp70hhgvb554i2y1c04rv1m401w7q8"))))
     (build-system python-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         ;; The tests must be run after installation.
-         (delete 'check)
-         (add-after 'install 'check
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (setenv "PYTHONPATH"
-                     (string-append
-                      (getenv "PYTHONPATH")
-                      ":" (assoc-ref outputs "out")
-                      "/lib/python"
-                      (string-take (string-take-right
-                                    (assoc-ref inputs "python") 5) 3)
-                      "/site-packages"))
-             (zero? (system* "nosetests" "-P" "tests")))))))
     (inputs
      `(("python-xopen" ,python-xopen)))
     (native-inputs
      `(("python-cython" ,python-cython)
-       ("python-nose" ,python-nose)))
+       ("python-pytest" ,python-pytest)))
     (home-page "https://cutadapt.readthedocs.io/en/stable/")
     (synopsis "Remove adapter sequences from nucleotide sequencing reads")
     (description
-- 
cgit v1.2.3


From 081d143d3b20c6d06039d31454ac16b5108ec22a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 3 Mar 2018 10:39:17 +0100
Subject: gnu: r-performanceanalytics: Update to 1.5.2.

* gnu/packages/cran.scm (r-performanceanalytics): Update to 1.5.2.
[propagated-inputs]: Add r-quadprog.
[native-inputs]: Remove gfortran.
---
 gnu/packages/cran.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 7433a561ad..f8d17e1ad2 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1637,21 +1637,21 @@ simplifying cross-class interoperability.")
 (define-public r-performanceanalytics
   (package
     (name "r-performanceanalytics")
-    (version "1.4.3541")
+    (version "1.5.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "PerformanceAnalytics" version))
        (sha256
         (base32
-         "1czchsccsbdfjw743j6rm101q2q01pggyl8zmlva213pwm86zb3v"))))
+         "01bgm57z079g6r505w3bj293zkbd49fwa8sg55z87vizwavipml6"))))
     (properties
      `((upstream-name . "PerformanceAnalytics")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-xts" ,r-xts)
+     `(("r-quadprog" ,r-quadprog)
+       ("r-xts" ,r-xts)
        ("r-zoo" ,r-zoo)))
-    (native-inputs `(("gfortran" ,gfortran)))
     (home-page "http://r-forge.r-project.org/projects/returnanalytics/")
     (synopsis "Econometric tools for performance and risk analysis")
     (description "This is a collection of econometric functions for
-- 
cgit v1.2.3


From fac40f38fed5e219d28a1b41135ec5961a28993f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 3 Mar 2018 10:39:55 +0100
Subject: gnu: r-dbi: Update to 0.8.

* gnu/packages/statistics.scm (r-dbi): Update to 0.8.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 1c180645d4..620edfa9fb 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1188,13 +1188,13 @@ evaluation (NSE) in R.")
 (define-public r-dbi
   (package
     (name "r-dbi")
-    (version "0.7")
+    (version "0.8")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "DBI" version))
               (sha256
                (base32
-                "04fyrxdpqcygg5wviy637y6lgk64xqjjq31lvv4hwqj5kbaxamr5"))))
+                "16nf8flxr5vdz8yrpprfbzydy3ajixkp9hc8ibd9n7r9nc29waym"))))
     (build-system r-build-system)
     (home-page "https://github.com/rstats-db/DBI")
     (synopsis "R database interface")
-- 
cgit v1.2.3


From ec8b3d48ff7f73f772e4e254c58f118935070189 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 3 Mar 2018 10:40:05 +0100
Subject: gnu: r-httpuv: Update to 1.3.6.2.

* gnu/packages/web.scm (r-httpuv): Update to 1.3.6.2.
---
 gnu/packages/web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 760f4ef2ab..23bcc5fb1c 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -3780,13 +3780,13 @@ CDF, Atom 0.3, and Atom 1.0 feeds.")
 (define-public r-httpuv
   (package
     (name "r-httpuv")
-    (version "1.3.6.1")
+    (version "1.3.6.2")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "httpuv" version))
               (sha256
                (base32
-                "11kffpki4pgh352dlwsm4lnf1dcd5vs51cnimbshadyk3jprwxdf"))))
+                "0h3hkw575b211bxma23inbq1565wkhiapgasd539h219apqs534f"))))
     (build-system r-build-system)
     (native-inputs `(("r-rcpp" ,r-rcpp)))
     (home-page "https://github.com/rstudio/httpuv")
-- 
cgit v1.2.3


From f4009ade25b5e7b72db10df089894928b75fde7d Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 2 Mar 2018 22:19:08 +0100
Subject: gnu: sdl2: Update to 2.0.8.

* gnu/packages/sdl.scm (sdl2): Update to 2.0.8.
---
 gnu/packages/sdl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/sdl.scm b/gnu/packages/sdl.scm
index c56e5d94c8..222fd5b6f1 100644
--- a/gnu/packages/sdl.scm
+++ b/gnu/packages/sdl.scm
@@ -99,7 +99,7 @@ joystick, and graphics hardware.")
 (define-public sdl2
   (package (inherit sdl)
     (name "sdl2")
-    (version "2.0.7")
+    (version "2.0.8")
     (source (origin
              (method url-fetch)
              (uri
@@ -107,7 +107,7 @@ joystick, and graphics hardware.")
                              version ".tar.gz"))
              (sha256
               (base32
-               "0pjdpxla5kh1w1b0shxrx97a116vyy31njxi0jhyvqhk8d6cfdgf"))))
+               "1v4js1gkr75hzbxzhwzzif0sf9g07234sd23x1vdaqc661bprizd"))))
     (arguments
      (substitute-keyword-arguments (package-arguments sdl)
        ((#:configure-flags flags)
-- 
cgit v1.2.3


From 74a2f8ff1fc61e759afd71f2503dd9a9365c9226 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 2 Mar 2018 22:36:23 +0100
Subject: gnu: hdparm: Update to 9.54.

* gnu/packages/linux.scm (hdparm): Update to 9.54.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index b4d81943e1..0b544dd61f 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -2530,14 +2530,14 @@ thanks to the use of namespaces.")
 (define-public hdparm
   (package
     (name "hdparm")
-    (version "9.53")
+    (version "9.54")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/" name "/" name "/"
                                   name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1rb5086gp4l1h1fn2nk10ziqxjxigsd0c1zczahwc5k9vy8zawr6"))))
+                "0ghnhdj7wfw6acfyhdawpfa5n9kvkvzgi1fw6i7sghgbjx5nhyjd"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags (let ((out (assoc-ref %outputs "out")))
-- 
cgit v1.2.3


From 83a9003c5d6560d3a7873f1be43f5e2d57b2b0a1 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 2 Mar 2018 22:40:45 +0100
Subject: gnu: libseccomp: Update to 2.3.3.

* gnu/packages/linux.scm (libseccomp): Update to 2.3.3.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 0b544dd61f..1f9e084e85 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -3717,7 +3717,7 @@ of flash storage.")
 (define-public libseccomp
   (package
     (name "libseccomp")
-    (version "2.3.2")
+    (version "2.3.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/seccomp/libseccomp/"
@@ -3725,7 +3725,7 @@ of flash storage.")
                                   "/libseccomp-" version ".tar.gz"))
               (sha256
                (base32
-                "18dwfxzsw3agiy2dxbflrkhmjgvlji0wwkk636nabh2ng41qrp1x"))))
+                "0mdiyfljrkfl50q1m3ws8yfcyfjwf1zgkvcva8ffcwncji18zhkz"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("which" ,which)))
-- 
cgit v1.2.3


From dbefd3ff72debf27e59abaecbbf0dd94a879f829 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 9 Feb 2018 00:02:45 +0100
Subject: gnu: wv: Edit description.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Wv is still unmaintained – this just makes it more obvious.

* gnu/packages/wv.scm (wv)[description]: Mention the product versions in
addition to internal file format ones.  Align more closely with the
upstream description.
---
 gnu/packages/wv.scm | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/wv.scm b/gnu/packages/wv.scm
index 12201faa3a..866cfee222 100644
--- a/gnu/packages/wv.scm
+++ b/gnu/packages/wv.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 Marek Benc <merkur32@gmail.com>
 ;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -52,11 +53,12 @@
         ("pkg-config" ,pkg-config)))
     (synopsis "Microsoft Word conversion library and utilities")
     (description
-      "wv converts Word 2,6,7,8,9 files to HTML and LaTeX.  The Word 2
-conversion is still incomplete (no formatting), but it will do a passable job
-extracting the text, which is what you probably want anyway.
+     "wv converts files written by Word 2000, 97, 95, and 6 (known internally as
+Word 9, 8, 7, and 6) to HTML or LaTeX.  Word 2 documents can still be converted
+to plain text but will lack formatting.
 
-libwv can be used as a library by third party programs, AbiWord uses it as its
-word importer, and KWord may use it in the future.")
+Othe programs can use wv as a library to convert Word documents to other
+formats.  AbiWord uses it as its Word importer, and KWord uses concepts and
+code from wv in theirs.")
     (home-page "http://wvware.sourceforge.net/")
     (license license:gpl2+)))
-- 
cgit v1.2.3


From 9d13f82da88c5832444534270801da0ee813a397 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 2 Mar 2018 22:39:35 +0100
Subject: gnu: sslh: Update to 1.19c.

* gnu/packages/networking.scm (sslh): Update to 1.19c.
---
 gnu/packages/networking.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm
index cd3f4f124b..5816474370 100644
--- a/gnu/packages/networking.scm
+++ b/gnu/packages/networking.scm
@@ -1031,7 +1031,7 @@ library remains flexible, portable, and easily embeddable.")
 (define-public sslh
   (package
     (name "sslh")
-    (version "1.19b")
+    (version "1.19c")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/yrutschle/sslh/archive/v"
@@ -1039,7 +1039,7 @@ library remains flexible, portable, and easily embeddable.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0p0zfy5ifzj7508zqidgkf8g43frm7l5xcs5s6v7132lypcsbd4k"))))
+                "0pd8hifa9h0rm7vms3k6ic1k29xigrlv2idc5wgcafmb1v1243di"))))
     (build-system gnu-build-system)
     (native-inputs
      `(;; Test dependencies.
-- 
cgit v1.2.3


From e6d30cf7552502b59c2996b5b1d530c38b88c4f7 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 2 Mar 2018 17:38:28 +0100
Subject: gnu: conky: Remove redundant MKDIR-P.

* gnu/packages/conky.scm (conky)[arguments]: Remove redundant MKDIR-P.
---
 gnu/packages/conky.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/conky.scm b/gnu/packages/conky.scm
index 22a0427b9a..0da9f8438b 100644
--- a/gnu/packages/conky.scm
+++ b/gnu/packages/conky.scm
@@ -60,8 +60,8 @@
              #t))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
-             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
-               (mkdir-p bin)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin")))
                (install-file "src/conky" bin))
              #t)))))
     (inputs
-- 
cgit v1.2.3


From 75377c6c485f5dc93d42f59fe39eb7c12fe75da6 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 3 Mar 2018 02:50:09 +0100
Subject: gnu: quagga: Update to 1.2.4.

* gnu/packages/networking.scm (quagga): Update to 1.2.4.
---
 gnu/packages/networking.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm
index 5816474370..d4c9d40d7a 100644
--- a/gnu/packages/networking.scm
+++ b/gnu/packages/networking.scm
@@ -1403,14 +1403,14 @@ does not use SSH and requires a pre-shared symmetric key.")
 (define-public quagga
   (package
     (name "quagga")
-    (version "1.2.3")
+    (version "1.2.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://savannah/quagga/quagga-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0cddxip9gd579parx64n6d7iq937ikrb8qxgvjxjm406l43hjb7f"))
+                "1lsksqxij5f1llqn86pkygrf5672kvrqn1kvxghi169hqf1c0r73"))
               (patches
                (search-patches "quagga-reproducible-build.patch"))))
     (build-system gnu-build-system)
-- 
cgit v1.2.3


From add928d35fb7a182662ecfdf261cc6a4c98b3c67 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 3 Mar 2018 11:56:23 +0100
Subject: gnu: ghc-refact: Fix typo in description.

* gnu/packages/haskell.scm (ghc-refact)[description]: Fix typo.
---
 gnu/packages/haskell.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 3ff78047db..e7401e5cf4 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1072,7 +1072,7 @@ patterns as per the HaRP extension as well as HSX-style embedded XML syntax.")
     (synopsis "Specify refactorings to perform with apply-refact")
     (description
      "This library provides a datatype which can be interpreted by
-@code{apply-refact}.  It exists as a seperate library so that applications can
+@code{apply-refact}.  It exists as a separate library so that applications can
 specify refactorings without depending on GHC.")
     (license license:bsd-3)))
 
-- 
cgit v1.2.3


From 433dc74611b0338ae15c7a7dc344a802c5667a34 Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Mon, 9 Oct 2017 06:57:26 +0100
Subject: gnu: networking: Add czmq.

* gnu/packages/networking.scm (czmq): New variable.
---
 gnu/packages/networking.scm | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm
index d4c9d40d7a..3c18620bd2 100644
--- a/gnu/packages/networking.scm
+++ b/gnu/packages/networking.scm
@@ -267,6 +267,42 @@ filtering (subscriptions), seamless access to multiple transport protocols and
 more.")
     (license license:lgpl3+)))
 
+(define-public czmq
+  (package
+    (name "czmq")
+    (version "4.1.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/zeromq/" name
+                    "/releases/download/v" version
+                    "/" name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "04gwf61rijwm6b2wblwv8gky1gdrbfmg1d19hf72kdc691ds7vrv"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(;; TODO Tests fail for some reason:
+       ;;  * zauth: OK
+       ;;  * zbeacon: OK (skipping test, no UDP broadcasting)
+       ;; E: (czmq_selftest) 18-02-24 16:25:52 No broadcast interface found, (ZSYS_INTERFACE=lo)
+       ;; make[2]: *** [Makefile:2245: check-local] Segmentation fault
+       ;; make[2]: Leaving directory '/tmp/guix-build-czmq-4.1.0.drv-0/czmq-4.1.0'
+       ;; make[1]: *** [Makefile:2032: check-am] Error 2
+       ;; make[1]: Leaving directory '/tmp/guix-build-czmq-4.1.0.drv-0/czmq-4.1.0'
+       ;; make: *** [Makefile:1588: check-recursive] Error 1
+       ;; phase `check' failed after 19.4 seconds
+       #:tests? #f
+       #:configure-flags '("--enable-drafts")))
+    (inputs
+     `(("zeromq" ,zeromq)))
+    (home-page "http://zeromq.org")
+    (synopsis "High-level C bindings for ØMQ")
+    (description
+     "czmq provides bindings for the ØMQ core API that hides the differences
+between different versions of ØMQ.")
+    (license license:mpl2.0)))
+
 (define-public librdkafka
   (package
     (name "librdkafka")
-- 
cgit v1.2.3


From cf646acf96d0567bea124dc8ea2a0782ad3f4e8d Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Tue, 10 Oct 2017 20:00:49 +0100
Subject: gnu: Add ruby-mocha-on-bacon.

* gnu/packages/ruby.scm (ruby-mocha-on-bacon): New variable.
---
 gnu/packages/ruby.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index b15e1a2717..5ba140e01d 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -1502,6 +1502,30 @@ allows mocking and stubbing of methods on real (non-mock) classes.")
     (home-page "http://gofreerange.com/mocha/docs")
     (license license:expat)))
 
+(define-public ruby-mocha-on-bacon
+  (package
+    (name "ruby-mocha-on-bacon")
+    (version "0.2.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "mocha-on-bacon" version))
+       (sha256
+        (base32
+         "1h49b33rq889hn8x3wp9byczl91va16jh1w4d2wyy4yj23icdrcp"))))
+    (build-system ruby-build-system)
+    (arguments
+     ;; rubygems.org release missing tests
+     '(#:tests? #f))
+    (propagated-inputs `(("ruby-mocha" ,ruby-mocha)))
+    (synopsis "Mocha adapter for Bacon")
+    (description
+     "This package provides a Mocha adapter for Bacon, allowing you to use the
+Mocha stubbing and mocking library with Bacon, a small RSpec clone.")
+    (home-page
+     "https://github.com/alloy/mocha-on-bacon")
+    (license license:expat)))
+
 (define-public ruby-net-ssh
   (package
     (name "ruby-net-ssh")
-- 
cgit v1.2.3


From a8d2bf3cab8ba5472620c1fb8d68c02836a04f1b Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Tue, 10 Oct 2017 20:00:21 +0100
Subject: gnu: Add ruby-bacon-bits.

* gnu/packages/ruby.scm (ruby-bacon-bits): New variable.
---
 gnu/packages/ruby.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 5ba140e01d..31a97f0b74 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -1094,6 +1094,30 @@ features.")
     (home-page "https://github.com/chneukirchen/bacon")
     (license license:expat)))
 
+(define-public ruby-bacon-bits
+  (package
+    (name "ruby-bacon-bits")
+    (version "0.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "bacon-bits" version))
+       (sha256
+        (base32
+         "1ghpj8ja94lhi8rgi872hqk4fd2amz2k7g9znd64z5dj7v6l0dmx"))))
+    (build-system ruby-build-system)
+    (arguments
+     ;; No tests
+     '(#:tests? #f))
+    (propagated-inputs `(("ruby-bacon" ,ruby-bacon)))
+    (synopsis "Extensions to Bacon, for disabling tests, before and after
+blocks and more")
+    (description
+     "This extends the bacon testing framework with useful extensions to
+disable tests, have before and after blocks that run once and more.")
+    (home-page "https://github.com/cldwalker/bacon-bits")
+    (license license:expat)))
+
 (define-public ruby-connection-pool
   (package
     (name "ruby-connection-pool")
-- 
cgit v1.2.3


From afdb437c82ddc0d8c6cb64b934129bcab8169a48 Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Tue, 10 Oct 2017 20:02:19 +0100
Subject: gnu: Add ruby-bond.

* gnu/packages/ruby.scm (ruby-bond): New variable.
---
 gnu/packages/ruby.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 31a97f0b74..456afb3f54 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -1361,6 +1361,34 @@ as a base class when writing classes that depend upon
     (home-page "https://github.com/masover/blankslate")
     (license license:expat)))
 
+(define-public ruby-bond
+  (package
+    (name "ruby-bond")
+    (version "0.5.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "bond" version))
+       (sha256
+        (base32
+         "1r19ifc4skyl2gxnifrxa5jvbbay9fb2in79ppgv02b6n4bhsw90"))))
+    (build-system ruby-build-system)
+    (native-inputs
+     `(("ruby-bacon" ,ruby-bacon)
+       ("ruby-bacon-bits" ,ruby-bacon-bits)
+       ("ruby-mocha-on-bacon" ,ruby-mocha-on-bacon)))
+    (synopsis "Bond can provide custom autocompletion for arguments, methods
+and more")
+    (description
+     "Bond can autocomplete argument(s) to methods, uniquely completing per
+module, per method and per argument.  Bond provides a configuration system and
+a DSL for creating custom completions and completion rules.  Bond can also
+load completions that ship with gems.  Bond is able to offer more than irb's
+completion since it uses the full line of input when completing as opposed to
+irb's last-word approach.")
+    (home-page "http://tagaholic.me/bond/")
+    (license license:expat)))
+
 (define-public ruby-instantiator
   (package
     (name "ruby-instantiator")
-- 
cgit v1.2.3


From fe5dd5f44659139b7327a3cf887dbb03741e4e42 Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Tue, 10 Oct 2017 20:07:45 +0100
Subject: gnu: Add ruby-czmq-ffi-gen.

* gnu/packages/ruby.scm (ruby-czmq-ffi-gen): New variable.
---
 gnu/packages/ruby.scm | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 456afb3f54..a9725af81e 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -36,6 +36,7 @@
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages java)
   #:use-module (gnu packages libffi)
+  #:use-module (gnu packages networking)
   #:use-module (gnu packages python)
   #:use-module (gnu packages ragel)
   #:use-module (gnu packages tls)
@@ -635,6 +636,46 @@ format.")
     (home-page "https://github.com/nicksieger/ci_reporter")
     (license license:expat)))
 
+(define-public ruby-czmq-ffi-gen
+  (package
+    (name "ruby-czmq-ffi-gen")
+    (version "0.13.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "czmq-ffi-gen" version))
+       (sha256
+        (base32
+         "1yf719dmf4mwks1hqdsy6i5kzfvlsha69sfnhb2fr2cgk2snbys3"))))
+    (build-system ruby-build-system)
+    (arguments
+     '(#:tests? #f ;; Tests are not included in the release on rubygems.org
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-lib_dirs
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "lib/czmq-ffi-gen/czmq/ffi.rb"
+               (("lib\\_dirs = \\[.*\\]")
+                (string-append "lib_dirs = ['"
+                               (assoc-ref inputs "czmq") "/lib"
+                               "']")))
+             (substitute* "lib/czmq-ffi-gen/libzmq.rb"
+               (("lib\\_dirs = \\[.*\\]")
+                (string-append "lib_dirs = ['"
+                               (assoc-ref inputs "zeromq") "/lib"
+                               "']"))))))))
+    (inputs
+     `(("zeromq" ,zeromq)
+       ("czmq" ,czmq)))
+    (propagated-inputs `(("ruby-ffi" ,ruby-ffi)))
+    (synopsis "Low-level Ruby bindings for CZMQ (generated using zproject)")
+    (description
+     "These Ruby bindings are not intended to be directly used, but rather
+used by higher level bindings like those provided by CZTop.")
+    (home-page
+     "https://github.com/paddor/czmq-ffi-gen")
+    (license license:isc)))
+
 (define-public ruby-saikuro-treemap
   (package
     (name "ruby-saikuro-treemap")
-- 
cgit v1.2.3


From d0afff263c546fa7ef132b09ef04af7d178cd2ae Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Tue, 10 Oct 2017 20:08:09 +0100
Subject: gnu: Add ruby-cztop.

* gnu/packages/ruby.scm (ruby-cztop): New variable.
---
 gnu/packages/ruby.scm | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index a9725af81e..f94ac54001 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -676,6 +676,44 @@ used by higher level bindings like those provided by CZTop.")
      "https://github.com/paddor/czmq-ffi-gen")
     (license license:isc)))
 
+(define-public ruby-cztop
+  (package
+    (name "ruby-cztop")
+    (version "0.12.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "cztop" version))
+       (sha256
+        (base32
+         "0yqbpaiw5d7f271d73lyrsh8xpx6n4zi6xqwfgi00dacxrq3s3fa"))))
+    (build-system ruby-build-system)
+    (arguments
+     '(#:test-target "spec"
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-lib_paths
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "lib/cztop/poller/zmq.rb"
+               (("lib\\_paths = \\[.*\\]")
+                (string-append "lib_paths = ['"
+                               (assoc-ref inputs "zeromq") "/lib"
+                               "']"))))))))
+    (native-inputs
+     `(("bundler" ,bundler)
+       ("ruby-rspec" ,ruby-rspec)))
+    (inputs
+     `(("zeromq" ,zeromq)))
+    (propagated-inputs
+     `(("ruby-czmq-ffi-gen" ,ruby-czmq-ffi-gen)))
+    (synopsis "CZMQ Ruby bindings")
+    (description
+     "CZMQ Ruby bindings, based on the generated low-level FFI bindings of
+CZMQ.  The focus of of CZTop is on being easy to use and providing first class
+support for security mechanisms.")
+    (home-page "https://github.com/paddor/cztop")
+    (license license:isc)))
+
 (define-public ruby-saikuro-treemap
   (package
     (name "ruby-saikuro-treemap")
-- 
cgit v1.2.3


From b03eb6acb45cf6c0672e309204f5a92ce5fd88ce Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Tue, 10 Oct 2017 20:09:18 +0100
Subject: gnu: Add ruby-data_uri.

* gnu/packages/ruby.scm (ruby-data_uri): New variable.
---
 gnu/packages/ruby.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index f94ac54001..47cb8eea8c 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -1965,6 +1965,26 @@ run as a daemon and to be controlled by simple start/stop/restart commands.")
     (home-page "https://github.com/thuehlinger/daemons")
     (license license:expat)))
 
+(define-public ruby-data_uri
+  (package
+    (name "ruby-data_uri")
+    (version "0.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "data_uri" version))
+       (sha256
+        (base32
+         "0fzkxgdxrlbfl4537y3n9mjxbm28kir639gcw3x47ffchwsgdcky"))))
+    (build-system ruby-build-system)
+    (synopsis "URI class for parsing data URIs")
+    (description
+     "Data @acronym{URI, universal resource idenfitier}s allow resources to be
+embedded inside a URI.  The URI::Data class provides support for parsing these
+URIs using the normal URI.parse method.")
+    (home-page "https://github.com/dball/data_uri")
+    (license license:expat)))
+
 (define-public ruby-git
   (package
     (name "ruby-git")
-- 
cgit v1.2.3


From 8279b1d3b11ac3e0ad3d94b515695e6d7f2c3511 Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Tue, 10 Oct 2017 20:09:45 +0100
Subject: gnu: Add ruby-mimemagic.

* gnu/packages/ruby.scm (ruby-mimemagic): New variable.
---
 gnu/packages/ruby.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 47cb8eea8c..3d914d1c46 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3503,6 +3503,33 @@ that TURN is no longer being maintained.")
     (home-page "http://rubygems.org/gems/turn")
     (license license:expat)))
 
+(define-public ruby-mimemagic
+  (package
+    (name "ruby-mimemagic")
+    (version "0.3.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "mimemagic" version))
+       (sha256
+        (base32
+         "00ibc1mhvdfyfyl103xwb45621nwyqxf124cni5hyfhag0fn1c3q"))))
+    (build-system ruby-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         ;; This phase breaks the tests, as it patches some of the test data.
+         (delete 'patch-source-shebangs))))
+    (native-inputs
+     `(("ruby-bacon" ,ruby-bacon)))
+    (synopsis "Ruby library for MIME detection by extension or content")
+    (description
+     "@acronym{MIME, Multipurpose Internet Mail Extensions} detection by
+extension or content, using the freedesktop.org.xml shared-mime-info
+database.")
+    (home-page "https://github.com/minad/mimemagic")
+    (license license:expat)))
+
 (define-public ruby-mime-types-data
   (package
     (name "ruby-mime-types-data")
-- 
cgit v1.2.3


From 62b138caf55f8090e0ad8e04296dc0f98a4fd212 Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Tue, 10 Oct 2017 20:07:20 +0100
Subject: gnu: Add ruby-iruby.

* gnu/packages/ruby.scm (ruby-iruby): New variable.
---
 gnu/packages/ruby.scm | 56 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 56 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 3d914d1c46..ee5d20955c 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -281,6 +281,62 @@ an extensible architecture with a swappable backend.")
     (home-page "https://github.com/svenfuchs/i18n")
     (license license:expat)))
 
+(define-public ruby-iruby
+  (package
+    (name "ruby-iruby")
+    (version "0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "iruby" version))
+       (sha256
+        (base32
+         "1wdf2c0x8y6cya0n3y0p3p7b1sxkb2fdavdn2k58rf4rs37s7rzn"))))
+    (build-system ruby-build-system)
+    (arguments
+     ;; TODO: Tests currently fail.
+     ;;
+     ;; Finished in 1.764405s, 1.1335 runs/s, 5.1009 assertions/s.
+     ;;
+     ;;   1) Failure:
+     ;; IntegrationTest#test_interaction [/tmp/guix-build-ruby-iruby-0.3.drv-0/gem/test/integration_test.rb:25]:
+     ;; In [ expected
+     ;;
+     ;; 2 runs, 9 assertions, 1 failures, 0 errors, 0 skips
+     '(#:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-ipython
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "lib/iruby/command.rb"
+               (("version = `")
+                (string-append
+                 "version = `"
+                 (assoc-ref inputs "python-ipython")
+                 "/bin/"))
+               (("Kernel\\.exec\\('")
+                (string-append
+                 "Kernel.exec('"
+                 (assoc-ref inputs "python-ipython")
+                 "/bin/")))
+             #t)))))
+    (inputs
+     `(("python-ipython" ,python-ipython)))
+    (propagated-inputs
+     `(("ruby-bond" ,ruby-bond)
+       ("ruby-data_uri" ,ruby-data_uri)
+       ("ruby-mimemagic" ,ruby-mimemagic)
+       ("ruby-multi-json" ,ruby-multi-json)
+       ("ruby-cztop" ,ruby-cztop)
+       ;; Optional inputs
+       ("ruby-pry" ,ruby-pry)))
+    (synopsis "Ruby kernel for Jupyter/IPython")
+    (description
+     "This package provides a Ruby kernel for Jupyter/IPython frontends (e.g.
+notebook).")
+    (home-page "https://github.com/SciRuby/iruby")
+    (license license:expat)))
+
 ;; RSpec is the dominant testing library for Ruby projects.  Even RSpec's
 ;; dependencies use RSpec for their test suites!  To avoid these circular
 ;; dependencies, we disable tests for all of the RSpec-related packages.
-- 
cgit v1.2.3


From 0645da3fe3112a3568e646babf524bd9439ffb8e Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Sat, 3 Mar 2018 14:06:43 +0100
Subject: gnu: grammalecte: Update to 0.6.2.

* gnu/packages/dictionaries.scm (grammalecte): Update to 0.6.2.
[arguments]: Remove.
---
 gnu/packages/dictionaries.scm | 16 ++--------------
 1 file changed, 2 insertions(+), 14 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/dictionaries.scm b/gnu/packages/dictionaries.scm
index 25e4613170..1c1d6247a7 100644
--- a/gnu/packages/dictionaries.scm
+++ b/gnu/packages/dictionaries.scm
@@ -211,7 +211,7 @@ It comes with a German-English dictionary with approximately 270,000 entries.")
 (define-public grammalecte
   (package
     (name "grammalecte")
-    (version "0.6.1")
+    (version "0.6.2")
     (source
      (origin
        (method url-fetch/zipbomb)
@@ -219,20 +219,8 @@ It comes with a German-English dictionary with approximately 270,000 entries.")
                            "Grammalecte-fr-v" version ".zip"))
        (sha256
         (base32
-         "0bl342i7nqbg8swk3fxashg9liyp3jdnix59pndhy41cpm1xln4i"))))
+         "0pvblclvbxbfgmq0cvmpmzpf6bi6r41arndwprl7ab9kci9hi8j2"))))
     (build-system python-build-system)
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'fix-setup.py
-           ;; FIXME: "setup.py" contains a typo in 0.6.1 release. The
-           ;; issue was reported and fixed upstream
-           ;; (https://dicollecte.org/thread.php?prj=fr&t=674). This
-           ;; phase can be removed in next release.
-           (lambda _
-             (substitute* "setup.py"
-               (("server_options\\.") "grammalecte-server-options."))
-             #t)))))
     (home-page "https://www.dicollecte.org")
     (synopsis  "French spelling and grammar checker")
     (description "Grammalecte is a grammar checker dedicated to the French
-- 
cgit v1.2.3


From 5e332c57d1dd7f0326a25763634d90b272b8d821 Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Sat, 3 Mar 2018 14:21:20 +0100
Subject: gnu: wireshark: Update to 2.4.5.

* gnu/packages/networking.scm (wireshark): Update to 2.4.5.
---
 gnu/packages/networking.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm
index 3c18620bd2..bf4bee2f87 100644
--- a/gnu/packages/networking.scm
+++ b/gnu/packages/networking.scm
@@ -6,7 +6,7 @@
 ;;; Copyright © 2016 Raimon Grau <raimonster@gmail.com>
 ;;; Copyright © 2016, 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2016 John Darrington <jmd@gnu.org>
-;;; Copyright © 2016, 2017 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2016, 2017, 2018 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2016, 2017 ng0 <ng0@infotropique.org>
 ;;; Copyright © 2016, 2017 Arun Isaac <arunisaac@systemreboot.net>
@@ -534,7 +534,7 @@ of the same name.")
 (define-public wireshark
   (package
     (name "wireshark")
-    (version "2.4.4")
+    (version "2.4.5")
     (source
      (origin
        (method url-fetch)
@@ -542,7 +542,7 @@ of the same name.")
                            version ".tar.xz"))
        (sha256
         (base32
-         "0n3g28hrhifnchlz4av0blq4ykm4zaxwwxbzdm9wsba27677b6h4"))))
+         "1mvgy67rvnwj2kbc43s4il81jvz5ai0bx2j3j2js7x50zclyrcmk"))))
     (build-system gnu-build-system)
     (inputs `(("c-ares" ,c-ares)
               ("glib" ,glib)
-- 
cgit v1.2.3


From fb547c3429c32081d68f6f78d7fdfc95a4851348 Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Sat, 3 Mar 2018 14:23:17 +0100
Subject: gnu: dictionaries: Add copyright line.

* gnu/packages/dictionaries.scm: Add copyright line.
---
 gnu/packages/dictionaries.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/dictionaries.scm b/gnu/packages/dictionaries.scm
index 1c1d6247a7..3f50070ef7 100644
--- a/gnu/packages/dictionaries.scm
+++ b/gnu/packages/dictionaries.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Sou Bunnbu <iyzsong@gmail.com>
+;;; Copyright © 2017, 2018 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
-- 
cgit v1.2.3


From f9e0fcb28f90a95048cad989ab405222c7eb4904 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 10 Dec 2017 22:26:47 +0100
Subject: gnu: Add texlive-fonts-iwona.

* gnu/packages/tex.scm (texlive-fonts-iwona): New variable.
---
 gnu/packages/tex.scm | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index 4e8efc8faf..764f4fff15 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -3424,6 +3424,47 @@ TeX metrics (VF and TFM files) and macros for use with LaTeX.")
     ;; Any version of the GPL with font exception.
     (license license:gpl3+)))
 
+(define-public texlive-fonts-iwona
+  (package
+    (name "texlive-fonts-iwona")
+    (version "0.995b")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://jmn.pl/pliki/Iwona-tex-"
+                                  (string-map (lambda (c)
+                                                (if (char=? c #\.)
+                                                    #\_ c))
+                                              version)
+                                  ".zip"))
+              (sha256
+               (base32
+                "13684iqx5granpc5rfvqnmyvdpgpbr1x9y7i7y7bcaq0qxv7ph1x"))))
+    (build-system trivial-build-system)
+    (arguments
+     `(#:modules ((guix build utils))
+       #:builder
+       (begin
+         (use-modules (guix build utils))
+         (let ((target (string-append (assoc-ref %outputs "out")
+                                      "/share/texmf-dist/"))
+               (unzip  (string-append (assoc-ref %build-inputs "unzip")
+                                      "/bin/unzip")))
+           (system* unzip (assoc-ref %build-inputs "source"))
+           (mkdir-p target)
+           (copy-recursively "iwona" target)))))
+    (native-inputs
+     `(("unzip" ,unzip)))
+    (home-page "http://jmn.pl/en/kurier-i-iwona/")
+    (synopsis "Sans-serif typeface for TeX")
+    (description "Iwona is a two-element sans-serif typeface. It was created
+as an alternative version of the Kurier typeface, which was designed in 1975
+for a diploma in typeface design at the Warsaw Academy of Fine Arts under the
+supervision of Roman Tomaszewski.  Kurier was designed for linotype
+typesetting of newspapers and similar periodicals. The Iwona fonts are an
+alternative version of the Kurier fonts.  The difference lies in the absence
+of ink traps which typify the Kurier font.")
+    (license license:gfl1.0)))
+
 (define-public texlive-latex-titlesec
   (package
     (name "texlive-latex-titlesec")
-- 
cgit v1.2.3


From 30d554732a449c9d5dea630a07f687f1c9328393 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 22 Nov 2017 19:25:34 +0100
Subject: gnu: Add java-cisd-base.

* gnu/packages/java.scm (java-cisd-base): New variable.
---
 gnu/packages/java.scm | 149 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 149 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 0f8c04e8ba..1e2b30d8d9 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -2084,6 +2084,155 @@ Main-Class: org.eclipse.jdt.internal.compiler.batch.Main\n"
     (native-inputs
      `(("unzip" ,unzip)))))
 
+(define-public java-cisd-base
+  (let ((revision 38938)
+        (base-version "14.12.0"))
+    (package
+      (name "java-cisd-base")
+      (version (string-append base-version "-" (number->string revision)))
+      (source (origin
+                (method svn-fetch)
+                (uri (svn-reference
+                      (url (string-append "http://svnsis.ethz.ch/repos/cisd/"
+                                          "base/tags/release/"
+                                          (version-major+minor base-version)
+                                          ".x/" base-version "/base/"))
+                      (revision revision)))
+                (file-name (string-append "java-cisd-base-" version "-checkout"))
+                (sha256
+                 (base32
+                  "1i5adyf7nzclb0wydgwa1az04qliid8035vpahaandmkmigbnxiy"))
+                (modules '((guix build utils)))
+                (snippet
+                 '(begin
+                    ;; Delete included gradle jar
+                    (delete-file-recursively "gradle/wrapper")
+                    ;; Delete pre-built native libraries
+                    (delete-file-recursively "libs")
+                    #t))))
+      (build-system ant-build-system)
+      (arguments
+       `(#:make-flags '("-file" "build/build.xml")
+         #:test-target "jar-test"
+         #:jdk ,icedtea-8
+         #:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'unpack-build-resources
+             (lambda* (#:key inputs #:allow-other-keys)
+               (copy-recursively (assoc-ref inputs "build-resources")
+                                 "../build_resources")
+               #t))
+           (add-after 'unpack-build-resources 'fix-dependencies
+             (lambda* (#:key inputs #:allow-other-keys)
+               (substitute* "build/build.xml"
+                 (("\\$\\{lib\\}/testng/testng-jdk15.jar")
+                  (string-append (assoc-ref inputs "java-testng")
+                                 "/share/java/java-testng.jar"))
+                 (("\\$\\{lib\\}/commons-lang/commons-lang.jar")
+                  (string-append (assoc-ref inputs "java-commons-lang")
+                                 "/share/java/commons-lang-"
+                                 ,(package-version java-commons-lang) ".jar"))
+                 (("\\$\\{lib\\}/commons-io/commons-io.jar")
+                  (string-append (assoc-ref inputs "java-commons-io")
+                                 "/share/java/commons-io-"
+                                 ,(package-version java-commons-io)
+                                 "-SNAPSHOT.jar"))
+                 ;; Remove dependency on svn
+                 (("<build-info.*") "")
+                 (("\\$\\{revision.number\\}")
+                  ,(number->string revision))
+                 (("\\$\\{version.number\\}") ,base-version))
+               ;; Remove dependency on classycle
+               (substitute* "../build_resources/ant/build-common.xml"
+                 (("<taskdef name=\"dependency-checker.*") "")
+                 (("classname=\"classycle.*") "")
+                 (("classpath=\"\\$\\{lib\\}/classycle.*") ""))
+               #t))
+           ;; A few tests fail because of the lack of a proper /etc/groups and
+           ;; /etc/passwd file in the build container.
+           (add-after 'unpack 'disable-broken-tests
+             (lambda _
+               (substitute* "sourceTest/java/ch/systemsx/cisd/base/AllTests.java"
+                 (("Unix.isOperational\\(\\)") "false"))
+               #t))
+           ;; These decorators are almost useless and pull in an unpackaged
+           ;; dependency.
+           (add-after 'unpack 'remove-useless-decorators
+             (lambda _
+               (substitute* "source/java/ch/systemsx/cisd/base/unix/Unix.java"
+                 (("@Private") "")
+                 (("import ch.rinn.restrictions.Private;") ""))
+               (substitute* "sourceTest/java/ch/systemsx/cisd/base/unix/UnixTests.java"
+                 (("@Friend.*") "")
+                 (("import ch.rinn.restrictions.Friend;") ""))
+               #t))
+           (add-before 'configure 'build-native-code
+             (lambda* (#:key inputs #:allow-other-keys)
+               (let ((jdk (assoc-ref inputs "jdk"))
+                     (dir ,(match (%current-system)
+                             ("i686-linux"
+                              "i386-Linux")
+                             ((or "armhf-linux" "aarch64-linux")
+                              "arm-Linux")
+                             ((or "x86_64-linux")
+                              "amd64-Linux")
+                             (_ "unknown-Linux"))))
+                 (with-directory-excursion "source/c"
+                   (invoke "gcc" "-shared" "-O3" "-fPIC" "unix.c"
+                           (string-append "-I" jdk "/include")
+                           (string-append "-I" jdk "/include/linux")
+                           "-o" "libunix.so")
+                   (invoke "gcc" "-shared" "-O3" "-fPIC"
+                           "-DMACHINE_BYTE_ORDER=1"
+                           "copyCommon.c"
+                           "copyByteChar.c"
+                           "copyByteDouble.c"
+                           "copyByteFloat.c"
+                           "copyByteInt.c"
+                           "copyByteLong.c"
+                           "copyByteShort.c"
+                           (string-append "-I" jdk "/include")
+                           (string-append "-I" jdk "/include/linux")
+                           "-o" "libnativedata.so"))
+                 (install-file "source/c/libunix.so"
+                               (string-append "libs/native/unix/" dir))
+                 (install-file "source/c/libnativedata.so"
+                               (string-append "libs/native/nativedata/" dir))
+                 #t)))
+           ;; In the "check" phase we only build the test executable.
+           (add-after 'check 'run-tests
+             (lambda _
+               (invoke "java" "-jar" "targets/dist/sis-base-test.jar")
+               (delete-file "targets/dist/sis-base-test.jar")
+               #t))
+           (replace 'install (install-jars "targets/dist")))))
+      (native-inputs
+       `(("jdk" ,icedtea-8)
+         ("java-commons-lang" ,java-commons-lang)
+         ("java-commons-io" ,java-commons-io)
+         ("java-testng" ,java-testng)
+         ("build-resources"
+          ,(origin
+             (method svn-fetch)
+             (uri (svn-reference
+                   (url (string-append "http://svnsis.ethz.ch/repos/cisd/"
+                                       "base/tags/release/"
+                                       (version-major+minor base-version)
+                                       ".x/" base-version
+                                       "/build_resources/"))
+                   (revision revision)))
+             (sha256
+              (base32
+               "0b6335gkm4x895rac6kfg9d3rpq0sy19ph4zpg2gyw6asfsisjhk"))))))
+      (home-page "http://svnsis.ethz.ch")
+      (synopsis "Utility classes for libraries from ETH Zurich")
+      (description "This library supplies some utility classes needed for
+libraries from the SIS division at ETH Zurich like jHDF5.")
+      ;; The C sources are under a non-copyleft license, which looks like a
+      ;; variant of the BSD licenses.  The whole package is under the ASL2.0.
+      (license (list license:asl2.0
+                     (license:non-copyleft "file://source/c/COPYING"))))))
+
 (define-public java-classpathx-servletapi
   (package
     (name "java-classpathx-servletapi")
-- 
cgit v1.2.3


From 04ddca26e68af423c2bb3801803e8b476ac48315 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 23 Feb 2018 10:09:50 +0100
Subject: gnu: Add java-cisd-args4j.

* gnu/packages/java.scm (java-cisd-args4j): New variable.
---
 gnu/packages/java.scm | 114 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 114 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 1e2b30d8d9..7ad0c41268 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -2233,6 +2233,120 @@ libraries from the SIS division at ETH Zurich like jHDF5.")
       (license (list license:asl2.0
                      (license:non-copyleft "file://source/c/COPYING"))))))
 
+(define-public java-cisd-args4j
+  (let ((revision 39162)
+        (base-version "9.11.2"))
+    (package
+      (name "java-cisd-args4j")
+      (version (string-append base-version "-" (number->string revision)))
+      (source (origin
+                (method svn-fetch)
+                (uri (svn-reference
+                      (url (string-append "http://svnsis.ethz.ch/repos/cisd/"
+                                          "args4j/tags/release/"
+                                          (version-major+minor base-version)
+                                          ".x/" base-version "/args4j/"))
+                      (revision revision)))
+                (file-name (string-append "java-cisd-args4j-" version "-checkout"))
+                (sha256
+                 (base32
+                  "0hhqznjaivq7ips7mkwas78z42s6djsm20rrs7g1zd59rcsakxn2"))))
+      (build-system ant-build-system)
+      (arguments
+       `(#:make-flags '("-file" "build/build.xml")
+         #:tests? #f ; there are no tests
+         ;; There are weird build failures with JDK8, such as: "The type
+         ;; java.io.ObjectInputStream cannot be resolved. It is indirectly
+         ;; referenced from required .class files"
+         #:jdk ,icedtea-7
+         #:modules ((guix build ant-build-system)
+                    (guix build utils)
+                    (guix build java-utils)
+                    (sxml simple)
+                    (sxml transform)
+                    (sxml xpath))
+         #:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'unpack-build-resources
+             (lambda* (#:key inputs #:allow-other-keys)
+               (mkdir-p "../build_resources")
+               (invoke "tar" "xf" (assoc-ref inputs "build-resources")
+                       "-C" "../build_resources"
+                       "--strip-components=1")
+               (mkdir-p "../build_resources/lib")
+               #t))
+           (add-after 'unpack-build-resources 'fix-dependencies
+             (lambda* (#:key inputs #:allow-other-keys)
+               ;; FIXME: There should be a more convenient abstraction for
+               ;; editing XML files.
+               (with-directory-excursion "../build_resources/ant/"
+                 (chmod "build-common.xml" #o664)
+                 (call-with-output-file "build-common.xml.new"
+                   (lambda (port)
+                     (sxml->xml
+                      (pre-post-order
+                       (with-input-from-file "build-common.xml"
+                         (lambda _ (xml->sxml #:trim-whitespace? #t)))
+                       `(;; Remove dependency on classycle and custom ant tasks
+                         (taskdef   . ,(lambda (tag . kids)
+                                         (let ((name ((sxpath '(name *text*)) kids)))
+                                           (if (or (member "build-info" name)
+                                                   (member "dependency-checker" name)
+                                                   (member "build-java-subprojects" name)
+                                                   (member "project-classpath" name))
+                                               '() ; skip
+                                               `(,tag ,@kids)))))
+                         (typedef   . ,(lambda (tag . kids)
+                                         (let ((name ((sxpath '(name *text*)) kids)))
+                                           (if (member "recursive-jar" name)
+                                               '() ; skip
+                                               `(,tag ,@kids)))))
+                         (build-java-subprojects . ,(lambda _ '()))
+                         ;; Ignore everything else
+                         (*default* . ,(lambda (tag . kids) `(,tag ,@kids)))
+                         (*text*    . ,(lambda (_ txt) txt))))
+                      port)))
+                 (rename-file "build-common.xml.new" "build-common.xml"))
+               (substitute* "build/build.xml"
+                 (("\\$\\{lib\\}/cisd-base/cisd-base.jar")
+                  (string-append (assoc-ref inputs "java-cisd-base")
+                                 "/share/java/sis-base.jar"))
+                 ;; Remove dependency on svn
+                 (("<build-info.*") "")
+                 (("\\$\\{revision.number\\}")
+                  ,(number->string revision))
+                 (("\\$\\{version.number\\}") ,base-version)
+                 ;; Don't use custom ant tasks.
+                 (("recursive-jar") "jar")
+                 (("<project-classpath.*") ""))
+               #t))
+           (replace 'install (install-jars "targets/dist")))))
+      (inputs
+       `(("java-cisd-base" ,java-cisd-base)))
+      (native-inputs
+       `(("ecj" ,java-ecj-3.5)
+         ("build-resources"
+          ,(origin
+             (method svn-fetch)
+             (uri (svn-reference
+                   (url (string-append "http://svnsis.ethz.ch/repos/cisd/"
+                                       "args4j/tags/release/"
+                                       (version-major+minor base-version)
+                                       ".x/" base-version
+                                       "/build_resources/"))
+                   (revision revision)))
+             (sha256
+              (base32
+               "056cam4k8pll7ass31sy6gwn8g8719njc41yf4l02b0342nilkyf"))
+             (modules '((guix build utils)))
+             ;; Delete bundled pre-built jars.
+             (snippet
+              '(begin (delete-file-recursively "lib/") #t))))))
+      (home-page "http://svnsis.ethz.ch")
+      (synopsis "Command line parser library")
+      (description "This package provides a parser for command line arguments.")
+      (license license:asl2.0))))
+
 (define-public java-classpathx-servletapi
   (package
     (name "java-classpathx-servletapi")
-- 
cgit v1.2.3


From 2f0d041816b9bfe06b6b59815e497b9eac987fd3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 23 Feb 2018 10:10:12 +0100
Subject: gnu: Add java-cisd-jhdf5.

* gnu/packages/java.scm (java-cisd-jhdf5): New variable.
---
 gnu/packages/java.scm | 176 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 176 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 7ad0c41268..298874f757 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -59,6 +59,7 @@
   #:use-module (gnu packages image)
   #:use-module (gnu packages libffi)
   #:use-module (gnu packages linux) ;alsa
+  #:use-module (gnu packages maths)
   #:use-module (gnu packages web)
   #:use-module (gnu packages wget)
   #:use-module (gnu packages pkg-config)
@@ -2347,6 +2348,181 @@ libraries from the SIS division at ETH Zurich like jHDF5.")
       (description "This package provides a parser for command line arguments.")
       (license license:asl2.0))))
 
+(define-public java-cisd-jhdf5
+  (let ((revision 39162)
+        (base-version "14.12.6"))
+    (package
+      (name "java-cisd-jhdf5")
+      (version (string-append base-version "-" (number->string revision)))
+      (source (origin
+                (method svn-fetch)
+                (uri (svn-reference
+                      (url (string-append "http://svnsis.ethz.ch/repos/cisd/"
+                                          "jhdf5/tags/release/"
+                                          (version-major+minor base-version)
+                                          ".x/" base-version "/jhdf5/"))
+                      (revision revision)))
+                (file-name (string-append "java-cisd-jhdf5-" version "-checkout"))
+                (sha256
+                 (base32
+                  "13i17s2hn0q9drdqvp8csy7770p3hdbh9rp30ihln2ldkfawdmz0"))
+                (modules '((guix build utils)))
+                (snippet
+                 '(begin
+                    ;; Delete included gradle jar
+                    (delete-file-recursively "gradle/wrapper")
+                    ;; Delete pre-built native libraries
+                    (delete-file-recursively "libs")
+                    #t))))
+      (build-system ant-build-system)
+      (arguments
+       `(#:make-flags '("-file" "build/build.xml")
+         #:build-target "jar-all"
+         #:test-target "jar-test"
+         #:jdk ,icedtea-8
+         #:phases
+         (modify-phases %standard-phases
+           ;; Don't erase results from the build phase when building tests.
+           (add-after 'unpack 'separate-test-target-from-clean
+             (lambda _
+               (substitute* "build/build.xml"
+                 (("\"jar-test\" depends=\"clean, ")
+                  "\"jar-test\" depends=\""))
+               #t))
+           (add-after 'unpack 'unpack-build-resources
+             (lambda* (#:key inputs #:allow-other-keys)
+               (copy-recursively (assoc-ref inputs "build-resources")
+                                 "../build_resources")
+               (delete-file-recursively "../build_resources/lib/")
+               (mkdir-p "../build_resources/lib")
+               ;; Remove dependency on classycle
+               (substitute* "../build_resources/ant/build-common.xml"
+                 (("<taskdef name=\"dependency-checker.*") "")
+                 (("classname=\"classycle.*") "")
+                 (("classpath=\"\\$\\{lib\\}/classycle.*") ""))
+               ;; Remove dependency on svn
+               (substitute* "build/build.xml"
+                 (("<build-info.*") "")
+                 (("\\$\\{revision.number\\}")
+                  ,(number->string revision))
+                 (("\\$\\{version.number\\}") ,base-version))
+               #t))
+           (add-after 'unpack-build-resources 'fix-dependencies
+             (lambda* (#:key inputs #:allow-other-keys)
+               (substitute* "../build_resources/ant/build-common.xml"
+                 (("../libraries/testng/testng-jdk15.jar")
+                  (string-append (assoc-ref inputs "java-testng")
+                                 "/share/java/java-testng.jar")))
+               (substitute* "build/build.xml"
+                 (("\\$\\{lib\\}/sis-base/sis-base.jar")
+                  (string-append (assoc-ref inputs "java-cisd-base")
+                                 "/share/java/sis-base.jar"))
+                 (("\\$\\{lib\\}/cisd-args4j/cisd-args4j.jar")
+                  (string-append (assoc-ref inputs "java-cisd-args4j")
+                                 "/share/java/cisd-args4j.jar"))
+                 (("\\$\\{lib\\}/commons-lang/commons-lang.jar")
+                  (string-append (assoc-ref inputs "java-commons-lang")
+                                 "/share/java/commons-lang-"
+                                 ,(package-version java-commons-lang) ".jar"))
+                 (("\\$\\{lib\\}/commons-io/commons-io.jar")
+                  (string-append (assoc-ref inputs "java-commons-io")
+                                 "/share/java/commons-io-"
+                                 ,(package-version java-commons-io)
+                                 "-SNAPSHOT.jar"))
+                 (("\\$\\{lib\\}/testng/testng-jdk15.jar")
+                  (string-append (assoc-ref inputs "java-testng")
+                                 "/share/java/java-testng.jar"))
+                 (("\\$\\{lib\\}/junit4/junit.jar")
+                  (string-append (assoc-ref inputs "java-junit")
+                                 "/share/java/junit.jar"))
+                 (("\\$\\{lib\\}/jmock/hamcrest/hamcrest-core.jar")
+                  (string-append (assoc-ref inputs "java-hamcrest-core")
+                                 "/share/java/hamcrest-core.jar")))
+               ;; Remove dependency on ch.rinn.restrictions
+               (with-directory-excursion "source/java/ch/systemsx/cisd/hdf5/"
+                 (substitute* '("BitSetConversionUtils.java"
+                                "HDF5Utils.java")
+                   (("import ch.rinn.restrictions.Private;") "")
+                   (("@Private") "")))
+               (with-directory-excursion "sourceTest/java/ch/systemsx/cisd/hdf5/"
+                 (substitute* '("BitSetConversionTest.java"
+                                "h5ar/HDF5ArchiverTest.java")
+                   (("import ch.rinn.restrictions.Friend;") "")
+                   (("@Friend.*") ""))
+                 ;; Remove leftovers from removing @Friend
+                 (substitute* "h5ar/HDF5ArchiverTest.java"
+                   (("\\{ HDF5Archiver.class, IdCache.class, LinkRecord.class \\}\\)")
+                    "")))
+               #t))
+           (add-before 'configure 'build-native-library
+             (lambda* (#:key inputs #:allow-other-keys)
+               (let ((jdk  (assoc-ref inputs "jdk"))
+                     (hdf5 (assoc-ref inputs "hdf5"))
+                     (dir  ,(match (%current-system)
+                              ("i686-linux"
+                               "i386-Linux")
+                              ((or "armhf-linux" "aarch64-linux")
+                               "arm-Linux")
+                              ((or "x86_64-linux")
+                               "amd64-Linux")
+                              (_ "unknown-Linux"))))
+                 (with-directory-excursion "source/c"
+                   (apply invoke `("gcc" "-shared" "-O3"
+                                   "-fPIC"
+                                   "-Wl,--exclude-libs,ALL"
+                                   ,@(find-files "jhdf5" "\\.c$")
+                                   ,@(find-files "hdf-java" "\\.c$")
+                                   ,(string-append "-I" hdf5 "/include")
+                                   ,(string-append "-I" jdk "/include")
+                                   ,(string-append "-I" jdk "/include/linux")
+                                   ,(string-append hdf5 "/lib/libhdf5.a")
+                                   "-o" "libjhdf5.so" "-lz")))
+                 (install-file "source/c/libjhdf5.so"
+                               (string-append "libs/native/jhdf5/" dir))
+                 #t)))
+           ;; In the "check" phase we only build the test executable.
+           (add-after 'check 'run-tests
+             (lambda _
+               (invoke "java" "-jar" "targets/dist/sis-jhdf5-test.jar")
+               (delete-file "targets/dist/sis-jhdf5-test.jar")
+               #t))
+           (replace 'install
+             (install-jars "targets/dist")))))
+      (inputs
+       `(("java-cisd-base" ,java-cisd-base)
+         ("java-cisd-args4j" ,java-cisd-args4j)
+         ("java-commons-lang" ,java-commons-lang)
+         ("java-commons-io" ,java-commons-io)
+         ("hdf5" ,hdf5)
+         ("zlib" ,zlib)))
+      (native-inputs
+       `(("jdk" ,icedtea-8)
+         ("java-testng" ,java-testng)
+         ("java-junit" ,java-junit)
+         ("java-jmock" ,java-jmock)
+         ("java-hamcrest-core" ,java-hamcrest-core)
+         ("build-resources"
+          ,(origin
+             (method svn-fetch)
+             (uri (svn-reference
+                   (url (string-append "http://svnsis.ethz.ch/repos/cisd/"
+                                       "jhdf5/tags/release/"
+                                       (version-major+minor base-version)
+                                       ".x/" base-version
+                                       "/build_resources/"))
+                   (revision revision)))
+             (sha256
+              (base32
+               "0b6335gkm4x895rac6kfg9d3rpq0sy19ph4zpg2gyw6asfsisjhk"))))))
+      (home-page "https://wiki-bsse.ethz.ch/display/JHDF5/")
+      (synopsis "Java binding for HDF5")
+      (description "JHDF5 is a high-level API in Java for reading and writing
+HDF5 files, building on the libraries provided by the HDF Group.")
+      ;; The C sources are under a non-copyleft license, which looks like a
+      ;; variant of the BSD licenses.  The whole package is under the ASL2.0.
+      (license (list license:asl2.0
+                     (license:non-copyleft "file://source/c/COPYING"))))))
+
 (define-public java-classpathx-servletapi
   (package
     (name "java-classpathx-servletapi")
-- 
cgit v1.2.3


From bd975831c67af75c4603555195ac618765c06ccc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 23 Feb 2018 10:56:49 +0100
Subject: gnu: Add fastqc.

* gnu/packages/bioinformatics.scm (fastqc): New variable.
---
 gnu/packages/bioinformatics.scm | 79 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 79 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e13f1b369f..065dc477d8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3195,6 +3195,85 @@ VCF.")
        ("jdk" ,icedtea-8 "jdk")
        ("jdk-src" ,(car (assoc-ref (package-native-inputs icedtea-8) "jdk-drop")))))))
 
+(define-public fastqc
+  (package
+    (name "fastqc")
+    (version "0.11.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://www.bioinformatics.babraham.ac.uk/"
+                           "projects/fastqc/fastqc_v"
+                           version "_source.zip"))
+       (sha256
+        (base32
+         "18rrlkhcrxvvvlapch4dpj6xc6mpayzys8qfppybi8jrpgx5cc5f"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:tests? #f                      ; there are no tests
+       #:build-target "build"
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-dependencies
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "build.xml"
+               (("jbzip2-0.9.jar")
+                (string-append (assoc-ref inputs "java-jbzip2")
+                               "/share/java/jbzip2.jar"))
+               (("sam-1.103.jar")
+                (string-append (assoc-ref inputs "java-picard-1.113")
+                               "/share/java/sam-1.112.jar"))
+               (("cisd-jhdf5.jar")
+                (string-append (assoc-ref inputs "java-cisd-jhdf5")
+                               "/share/java/sis-jhdf5.jar")))
+             #t))
+         ;; There is no installation target
+         (replace 'install
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let* ((out   (assoc-ref outputs "out"))
+                    (bin   (string-append out "/bin"))
+                    (share (string-append out "/share/fastqc/"))
+                    (exe   (string-append share "/fastqc")))
+               (for-each mkdir-p (list bin share))
+               (copy-recursively "bin" share)
+               (substitute* exe
+                 (("my \\$java_bin = 'java';")
+                  (string-append "my $java_bin = '"
+                                 (assoc-ref inputs "java")
+                                 "/bin/java';")))
+               (chmod exe #o555)
+               (symlink exe (string-append bin "/fastqc"))
+               #t))))))
+    (inputs
+     `(("java" ,icedtea)
+       ("perl" ,perl)                   ; needed for the wrapper script
+       ("java-cisd-jhdf5" ,java-cisd-jhdf5)
+       ("java-picard-1.113" ,java-picard-1.113)
+       ("java-jbzip2" ,java-jbzip2)))
+    (native-inputs
+     `(("unzip" ,unzip)))
+    (home-page "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/")
+    (synopsis "Quality control tool for high throughput sequence data")
+    (description
+     "FastQC aims to provide a simple way to do some quality control
+checks on raw sequence data coming from high throughput sequencing
+pipelines.  It provides a modular set of analyses which you can use to
+give a quick impression of whether your data has any problems of which
+you should be aware before doing any further analysis.
+
+The main functions of FastQC are:
+
+@itemize
+@item Import of data from BAM, SAM or FastQ files (any variant);
+@item Providing a quick overview to tell you in which areas there may
+  be problems;
+@item Summary graphs and tables to quickly assess your data;
+@item Export of results to an HTML based permanent report;
+@item Offline operation to allow automated generation of reports
+  without running the interactive application.
+@end itemize\n")
+    (license license:gpl3+)))
+
 (define-public htslib
   (package
     (name "htslib")
-- 
cgit v1.2.3


From c8d996080ee7aefddad89ec155fae370d5ae2726 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 1 Mar 2018 19:41:33 +0100
Subject: gnu: Add java-la4j.

* gnu/packages/algebra.scm (java-la4j): New variable.
---
 gnu/packages/algebra.scm | 48 +++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 47 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 2bc8431033..a59346bd56 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -3,7 +3,7 @@
 ;;; Copyright © 2013, 2015, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016, 2017, 2018 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
@@ -35,6 +35,7 @@
   #:use-module (gnu packages gl)
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages image)
+  #:use-module (gnu packages java)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages mpi)
   #:use-module (gnu packages multiprecision)
@@ -46,9 +47,11 @@
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages xiph)
   #:use-module (gnu packages xorg)
+  #:use-module (guix build-system ant)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system cmake)
   #:use-module (guix download)
+  #:use-module (guix git-download)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix utils))
@@ -612,6 +615,49 @@ cosine/ sine transforms or DCT/DST).")
     (synopsis "Computing the discrete Fourier transform (AVX2-optimized)")
     (supported-systems '("x86_64-linux"))))
 
+(define-public java-la4j
+  (package
+    (name "java-la4j")
+    (version "0.6.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/vkostyukov/la4j.git")
+                    (commit version)))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "1qir8dr978cfvz9k12m2kbdwpyf6cqdf1d0ilb7lnkhbgq5i53w3"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "la4j.jar"
+       #:jdk ,icedtea-8
+       #:test-exclude (list "**/Abstract*.java"
+                            "**/MatrixTest.java"
+                            "**/DenseMatrixTest.java"
+                            "**/SparseMatrixTest.java"
+                            "**/VectorTest.java"
+                            "**/SparseVectorTest.java"
+                            "**/DenseVectorTest.java")))
+    (native-inputs
+     `(("java-junit" ,java-junit)
+       ("java-hamcrest-core" ,java-hamcrest-core)))
+    (home-page "http://la4j.org/")
+    (synopsis "Java library that provides Linear Algebra primitives and algorithms")
+    (description "The la4j library is a Java library that provides Linear
+Algebra primitives (matrices and vectors) and algorithms.  The key features of
+the la4j library are:
+
+@itemize
+@item No dependencies and tiny size
+@item Fluent object-oriented/functional API
+@item Sparse (CRS, CCS) and dense (1D/2D arrays) matrices
+@item Linear systems solving (Gaussian, Jacobi, Zeidel, Square Root, Sweep and other)
+@item Matrices decomposition (Eigenvalues/Eigenvectors, SVD, QR, LU, Cholesky and other)
+@item MatrixMarket/CSV IO formats support for matrices and vectors
+@end itemize\n")
+    (license license:asl2.0)))
+
 (define-public eigen
   (package
     (name "eigen")
-- 
cgit v1.2.3


From 24074b0bddb6af9386239b4bbf0132b30b4358f9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 1 Mar 2018 19:41:34 +0100
Subject: gnu: Add java-jlargearrays.

* gnu/packages/algebra.scm (java-jlargearrays): New variable.
---
 gnu/packages/algebra.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index a59346bd56..ebd75a7d36 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -658,6 +658,33 @@ the la4j library are:
 @end itemize\n")
     (license license:asl2.0)))
 
+(define-public java-jlargearrays
+  (package
+    (name "java-jlargearrays")
+    (version "1.6")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://search.maven.org/remotecontent?"
+                                  "filepath=pl/edu/icm/JLargeArrays/"
+                                  version "/JLargeArrays-" version
+                                  "-sources.jar"))
+              (file-name (string-append name "-" version ".jar"))
+              (sha256
+               (base32
+                "0v05iphpxbjnd7f4jf1rlqq3m8hslhcm0imdbsgxr20pi3xkaf2a"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "jlargearrays.jar"
+       #:tests? #f ; tests are not included in the release archive
+       #:jdk ,icedtea-8))
+    (propagated-inputs
+     `(("java-commons-math3" ,java-commons-math3)))
+    (home-page "https://gitlab.com/ICM-VisLab/JLargeArrays")
+    (synopsis "Library of one-dimensional arrays that can store up to 263 elements")
+    (description "JLargeArrays is a Java library of one-dimensional arrays
+that can store up to 263 elements.")
+    (license license:bsd-2)))
+
 (define-public eigen
   (package
     (name "eigen")
-- 
cgit v1.2.3


From 4e92911c828fda34636f90b653ec7046fd97602e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 1 Mar 2018 19:41:35 +0100
Subject: gnu: Add java-jtransforms.

* gnu/packages/algebra.scm (java-jtransforms): New variable.
---
 gnu/packages/algebra.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index ebd75a7d36..2aa1777db3 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -685,6 +685,34 @@ the la4j library are:
 that can store up to 263 elements.")
     (license license:bsd-2)))
 
+(define-public java-jtransforms
+  (package
+    (name "java-jtransforms")
+    (version "3.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://search.maven.org/remotecontent?"
+                                  "filepath=com/github/wendykierp/JTransforms/"
+                                  version "/JTransforms-" version "-sources.jar"))
+              (sha256
+               (base32
+                "1haw5m8shv5srgcpwkl853dz8bv6h90bzlhcps6mdpb4cixjirsg"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "jtransforms.jar"
+       #:tests? #f ; tests are not included in the release archive
+       #:jdk ,icedtea-8))
+    (propagated-inputs
+     `(("java-commons-math3" ,java-commons-math3)
+       ("java-jlargearrays" ,java-jlargearrays)))
+    (home-page "https://github.com/wendykierp/JTransforms")
+    (synopsis "Multithreaded FFT library written in pure Java")
+    (description "JTransforms is a multithreaded FFT library written in pure
+Java.  Currently, four types of transforms are available: @dfn{Discrete
+Fourier Transform} (DFT), @dfn{Discrete Cosine Transform} (DCT), @dfn{Discrete
+Sine Transform} (DST) and @dfn{Discrete Hartley Transform} (DHT).")
+    (license license:bsd-2)))
+
 (define-public eigen
   (package
     (name "eigen")
-- 
cgit v1.2.3


From dbb35813838bd4bcfbc1ea94207494bcfa2b5627 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 1 Mar 2018 19:41:36 +0100
Subject: gnu: Add java-jdistlib.

* gnu/packages/statistics.scm (java-jdistlib): New variable.
---
 gnu/packages/statistics.scm | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 620edfa9fb..baec1c47d2 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -32,11 +32,13 @@
   #:use-module (guix hg-download)
   #:use-module (guix git-download)
   #:use-module (guix utils)
+  #:use-module (guix build-system ant)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system r)
   #:use-module (guix build-system python)
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages)
+  #:use-module (gnu packages algebra)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cran)
@@ -5540,3 +5542,40 @@ inferring an appropriate positioning method.")
       (description "Did you ever wish you could make scatter plots with cat
 shaped points?  Now you can!")
       (license license:asl2.0))))
+
+(define-public java-jdistlib
+  (package
+    (name "java-jdistlib")
+    (version "0.4.5")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/jdistlib/jdistlib-"
+                                  version "-src.jar"))
+              (sha256
+               (base32
+                "1pkj8aahw9ydr1isbaqrkd05nvq98ik5jwwhf3yf3rky3z869v11"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "jdistlib.jar"
+       #:jdk ,icedtea-8
+       #:tests? #f ; no dedicated test directory
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-broken-encoding
+           (lambda _
+             (with-fluids ((%default-port-encoding "ISO-8859-1"))
+               (substitute* "src/jdistlib/Beta.java"
+                 (("Scheff.+-Tukey") "Scheffe-Tukey")))
+             #t)))))
+    (propagated-inputs
+     `(("java-jtransforms" ,java-jtransforms)))
+    (native-inputs
+     `(("java-junit" ,java-junit)))
+    (home-page "http://jdistlib.sourceforge.net/")
+    (synopsis "Java library of statistical distributions")
+    (description "JDistlib is the Java Statistical Distribution Library, a
+Java package that provides routines for various statistical distributions.")
+    ;; The files that were translated from R code are under GPLv2+; some files
+    ;; are under the GPLv3, which is a mistake.  The author confirmed in an
+    ;; email that this whole project should be under GPLv2+.
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 5fef15e50679a4e18df4fafede913c26d0029126 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 1 Mar 2018 19:41:37 +0100
Subject: gnu: Add java-biojava-core.

* gnu/packages/bioinformatics.scm (java-biojava-core): New variable.
---
 gnu/packages/bioinformatics.scm | 56 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 56 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 065dc477d8..4a90f30128 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11949,3 +11949,59 @@ variable number of row and column annotations.  Loom also supports sparse
 graphs.  This library makes it easy to work with @file{.loom} files for
 single-cell RNA-seq data.")
     (license license:bsd-3)))
+
+(define-public java-biojava-core
+  (package
+    (name "java-biojava-core")
+    (version "4.2.11")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/biojava/biojava")
+                    (commit (string-append "biojava-" version))))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "1bvryh2bpsvash8ln79cmc9sqm8qw72hz4xzwqxcrjm8ssxszhqk"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jdk ,icedtea-8
+       #:jar-name "biojava-core.jar"
+       #:source-dir "biojava-core/src/main/java/"
+       #:test-dir "biojava-core/src/test"
+       ;; These tests seem to require internet access.
+       #:test-exclude (list "**/SearchIOTest.java"
+                            "**/BlastXMLParserTest.java"
+                            "**/GenbankCookbookTest.java"
+                            "**/GenbankProxySequenceReaderTest.java")
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'copy-resources
+           (lambda _
+             (copy-recursively "biojava-core/src/main/resources"
+                               "build/classes")
+             #t))
+         (add-before 'check 'copy-test-resources
+           (lambda _
+             (copy-recursively "biojava-core/src/test/resources"
+                               "build/test-classes")
+             #t)))))
+    (propagated-inputs
+     `(("java-log4j-api" ,java-log4j-api)
+       ("java-log4j-core" ,java-log4j-core)
+       ("java-slf4j-api" ,java-slf4j-api)
+       ("java-slf4j-simple" ,java-slf4j-simple)))
+    (native-inputs
+     `(("java-junit" ,java-junit)
+       ("java-hamcrest-core" ,java-hamcrest-core)))
+    (home-page "http://biojava.org")
+    (synopsis "Core libraries of Java framework for processing biological data")
+    (description "BioJava is a project dedicated to providing a Java framework
+for processing biological data.  It provides analytical and statistical
+routines, parsers for common file formats, reference implementations of
+popular algorithms, and allows the manipulation of sequences and 3D
+structures.  The goal of the biojava project is to facilitate rapid
+application development for bioinformatics.
+
+This package provides the core libraries.")
+    (license license:lgpl2.1+)))
-- 
cgit v1.2.3


From 93abc975feca4d877b0a14a0dd8f3613dcbd7c9b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 1 Mar 2018 19:41:38 +0100
Subject: gnu: Add java-openchart2.

* gnu/packages/java.scm (java-openchart2): New variable.
---
 gnu/packages/java.scm | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 298874f757..1e671b90bb 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -9292,3 +9292,44 @@ against expected outcomes.")
        ("java-junit" ,java-junit)))
     (native-inputs
      `(("java-mockito-1" ,java-mockito-1)))))
+
+(define-public java-openchart2
+  (package
+    (name "java-openchart2")
+    (version "1.4.3")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://download.approximatrix.com/openchart2/"
+                                  "openchart2-" version ".source.zip"))
+              (sha256
+               (base32
+                "1xq96zm5r02n1blja0072jmmsifmxc40lbyfbnmcnr6mw42frh4g"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:test-target "test"
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-junit-errors
+           (lambda _
+             (with-directory-excursion "unittest/src/com/approximatrix/charting/"
+               (substitute* '("coordsystem/ticklocator/NumericXTickLocatorTest.java"
+                              "coordsystem/ticklocator/NumericYTickLocatorTest.java"
+                              "coordsystem/ticklocator/ObjectXTickLocatorTest.java"
+                              "model/DefaultChartDataModelConstraintsTest.java"
+                              "model/MultiScatterDataModelConstraintsTest.java"
+                              "model/threedimensional/DotPlotDataModelConstraintsTest.java")
+                 (("(assertEquals[^;]+);" before _)
+                  (string-append (string-drop-right before 2) ", 1E-6);"))))
+             #t))
+         (replace 'install (install-jars ".")))))
+    (native-inputs
+     `(("unzip" ,unzip)
+       ("java-junit" ,java-junit)
+       ("java-hamcrest-core" ,java-hamcrest-core)))
+    (home-page "http://approximatrix.com/products/openchart2/")
+    (synopsis "Simple plotting for Java")
+    (description "Openchart2 provides a simple, yet powerful, interface for
+Java programmers to create two-dimensional charts and plots.  The library
+features an assortment of graph styles, including advanced scatter plots, bar
+graphs, and pie charts.")
+    (license license:lgpl2.1+)))
-- 
cgit v1.2.3


From f09d16e5949b5d84529be9022034e217fbaad54d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 1 Mar 2018 19:41:39 +0100
Subject: gnu: Add java-forester.

* gnu/packages/bioinformatics.scm (java-forester): New variable.
---
 gnu/packages/bioinformatics.scm | 76 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 76 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4a90f30128..ef1e8606a9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11950,6 +11950,82 @@ graphs.  This library makes it easy to work with @file{.loom} files for
 single-cell RNA-seq data.")
     (license license:bsd-3)))
 
+;; We cannot use the latest commit because it requires Java 9.
+(define-public java-forester
+  (let ((commit "86b07efe302d5094b42deed9260f719a4c4ac2e6")
+        (revision "1"))
+    (package
+      (name "java-forester")
+      (version (string-append "0-" revision "." (string-take commit 7)))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/cmzmasek/forester.git")
+                      (commit commit)))
+                (file-name (string-append name "-" version "-checkout"))
+                (sha256
+                 (base32
+                  "0vxavc1yrf84yrnf20dq26hi0lglidk8d382xrxsy4qmlbjd276z"))
+                (modules '((guix build utils)))
+                (snippet
+                 '(begin
+                    ;; Delete bundled jars and pre-built classes
+                    (delete-file-recursively "forester/java/resources")
+                    (delete-file-recursively "forester/java/classes")
+                    (for-each delete-file (find-files "forester/java/" "\\.jar$"))
+                    ;; Delete bundled applications
+                    (delete-file-recursively "forester_applications")
+                    #t))))
+      (build-system ant-build-system)
+      (arguments
+       `(#:tests? #f ; there are none
+         #:jdk ,icedtea-8
+         #:modules ((guix build ant-build-system)
+                    (guix build utils)
+                    (guix build java-utils)
+                    (sxml simple)
+                    (sxml transform))
+         #:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'chdir
+             (lambda _ (chdir "forester/java") #t))
+           (add-after 'chdir 'fix-dependencies
+             (lambda _
+               (chmod "build.xml" #o664)
+               (call-with-output-file "build.xml.new"
+                 (lambda (port)
+                   (sxml->xml
+                    (pre-post-order
+                     (with-input-from-file "build.xml"
+                       (lambda _ (xml->sxml #:trim-whitespace? #t)))
+                     `(;; Remove all unjar tags to avoid repacking classes.
+                       (unjar     . ,(lambda _ '()))
+                       (*default* . ,(lambda (tag . kids) `(,tag ,@kids)))
+                       (*text*    . ,(lambda (_ txt) txt))))
+                    port)))
+               (rename-file "build.xml.new" "build.xml")
+               #t))
+           ;; FIXME: itext is difficult to package as it depends on a few
+           ;; unpackaged libraries.
+           (add-after 'chdir 'remove-dependency-on-unpackaged-itext
+             (lambda _
+               (delete-file "src/org/forester/archaeopteryx/PdfExporter.java")
+               (substitute* "src/org/forester/archaeopteryx/MainFrame.java"
+                 (("pdf_written_to = PdfExporter.*")
+                  "throw new IOException(\"PDF export is not available.\");"))
+               #t))
+           ;; There is no install target
+           (replace 'install (install-jars ".")))))
+      (propagated-inputs
+       `(("java-commons-codec" ,java-commons-codec)
+         ("java-openchart2" ,java-openchart2)))
+      (home-page "https://sites.google.com/site/cmzmasek/home/software/forester")
+      (synopsis "Phylogenomics libraries for Java")
+      (description "Forester is a collection of Java libraries for
+phylogenomics and evolutionary biology research.  It includes support for
+reading, writing, and exporting phylogenetic trees.")
+      (license license:lgpl2.1+))))
+
 (define-public java-biojava-core
   (package
     (name "java-biojava-core")
-- 
cgit v1.2.3


From 10645b9212d5eff74132edf60c90c3eb099a139f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 1 Mar 2018 19:41:40 +0100
Subject: gnu: Add java-forester-1.005.

* gnu/packages/bioinformatics.scm (java-forester-1.005): New variable.
---
 gnu/packages/bioinformatics.scm | 95 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 95 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ef1e8606a9..d64cda2340 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12026,6 +12026,101 @@ phylogenomics and evolutionary biology research.  It includes support for
 reading, writing, and exporting phylogenetic trees.")
       (license license:lgpl2.1+))))
 
+(define-public java-forester-1.005
+  (package
+    (name "java-forester")
+    (version "1.005")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://search.maven.org/remotecontent?"
+                                  "filepath=org/biojava/thirdparty/forester/"
+                                  version "/forester-" version "-sources.jar"))
+              (file-name (string-append name "-" version ".jar"))
+              (sha256
+               (base32
+                "04r8qv4rk3p71z4ajrvp11py1z46qrx0047j3zzs79s6lnsm3lcv"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:tests? #f ; there are none
+       #:jdk ,icedtea-8
+       #:modules ((guix build ant-build-system)
+                  (guix build utils)
+                  (guix build java-utils)
+                  (sxml simple)
+                  (sxml transform))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-dependencies
+           (lambda* (#:key inputs #:allow-other-keys)
+             (call-with-output-file "build.xml"
+               (lambda (port)
+                 (sxml->xml
+                  (pre-post-order
+                   (with-input-from-file "src/build.xml"
+                     (lambda _ (xml->sxml #:trim-whitespace? #t)))
+                   `(;; Remove all unjar tags to avoid repacking classes.
+                     (unjar     . ,(lambda _ '()))
+                     (*default* . ,(lambda (tag . kids) `(,tag ,@kids)))
+                     (*text*    . ,(lambda (_ txt) txt))))
+                  port)))
+             (copy-file (assoc-ref inputs "synth_look_and_feel_1.xml")
+                        "synth_look_and_feel_1.xml")
+             (copy-file (assoc-ref inputs "phyloxml.xsd")
+                        "phyloxml.xsd")
+             (substitute* "build.xml"
+               (("../resources/synth_laf/synth_look_and_feel_1.xml")
+                "synth_look_and_feel_1.xml")
+               (("../resources/phyloxml_schema/1.10/phyloxml.xsd")
+                "phyloxml.xsd"))
+             #t))
+         ;; FIXME: itext is difficult to package as it depends on a few
+         ;; unpackaged libraries.
+         (add-after 'unpack 'remove-dependency-on-unpackaged-itext
+           (lambda _
+             (delete-file "src/org/forester/archaeopteryx/PdfExporter.java")
+             (substitute* '("src/org/forester/archaeopteryx/MainFrame.java"
+                            "src/org/forester/archaeopteryx/MainFrameApplication.java")
+               (("pdf_written_to = PdfExporter.*")
+                "throw new IOException(\"PDF export is not available.\"); /*")
+               ((".getPrintSizeX\\(\\), getOptions\\(\\).getPrintSizeY\\(\\) \\);") "*/")
+               (("getCurrentTreePanel\\(\\).getHeight\\(\\) \\);") "*/"))
+             #t))
+         (add-after 'unpack 'delete-pre-built-classes
+           (lambda _ (delete-file-recursively "src/classes") #t))
+         ;; There is no install target
+         (replace 'install (install-jars ".")))))
+    (propagated-inputs
+     `(("java-commons-codec" ,java-commons-codec)
+       ("java-openchart2" ,java-openchart2)))
+    ;; The source archive does not contain the resources.
+    (native-inputs
+     `(("phyloxml.xsd"
+        ,(origin
+           (method url-fetch)
+           (uri (string-append "https://raw.githubusercontent.com/cmzmasek/forester/"
+                               "b61cc2dcede0bede317db362472333115756b8c6/"
+                               "forester/resources/phyloxml_schema/1.10/phyloxml.xsd"))
+           (file-name (string-append name "-phyloxml-" version ".xsd"))
+           (sha256
+            (base32
+             "1zxc4m8sn4n389nqdnpxa8d0k17qnr3pm2y5y6g6vh4k0zm52npv"))))
+       ("synth_look_and_feel_1.xml"
+        ,(origin
+           (method url-fetch)
+           (uri (string-append "https://raw.githubusercontent.com/cmzmasek/forester/"
+                               "29e04321615da6b35c1e15c60e52caf3f21d8e6a/"
+                               "forester/java/classes/resources/synth_look_and_feel_1.xml"))
+           (file-name (string-append name "-synth-look-and-feel-" version ".xml"))
+           (sha256
+            (base32
+             "1gv5602gv4k7y7713y75a4jvj7i9s7nildsbdl7n9q10sc2ikg8h"))))))
+    (home-page "https://sites.google.com/site/cmzmasek/home/software/forester")
+    (synopsis "Phylogenomics libraries for Java")
+    (description "Forester is a collection of Java libraries for
+phylogenomics and evolutionary biology research.  It includes support for
+reading, writing, and exporting phylogenetic trees.")
+    (license license:lgpl2.1+)))
+
 (define-public java-biojava-core
   (package
     (name "java-biojava-core")
-- 
cgit v1.2.3


From b28c803708d41c4a5323e31e01f7b6044fcc6dda Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 1 Mar 2018 19:41:41 +0100
Subject: gnu: Add java-biojava-phylo.

* gnu/packages/bioinformatics.scm (java-biojava-phylo): New variable.
---
 gnu/packages/bioinformatics.scm | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d64cda2340..fbb3264ef5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12176,3 +12176,39 @@ application development for bioinformatics.
 
 This package provides the core libraries.")
     (license license:lgpl2.1+)))
+
+(define-public java-biojava-phylo
+  (package (inherit java-biojava-core)
+    (name "java-biojava-phylo")
+    (build-system ant-build-system)
+    (arguments
+     `(#:jdk ,icedtea-8
+       #:jar-name "biojava-phylo.jar"
+       #:source-dir "biojava-phylo/src/main/java/"
+       #:test-dir "biojava-phylo/src/test"
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'copy-resources
+           (lambda _
+             (copy-recursively "biojava-phylo/src/main/resources"
+                               "build/classes")
+             #t))
+         (add-before 'check 'copy-test-resources
+           (lambda _
+             (copy-recursively "biojava-phylo/src/test/resources"
+                               "build/test-classes")
+             #t)))))
+    (propagated-inputs
+     `(("java-log4j-api" ,java-log4j-api)
+       ("java-log4j-core" ,java-log4j-core)
+       ("java-slf4j-api" ,java-slf4j-api)
+       ("java-slf4j-simple" ,java-slf4j-simple)
+       ("java-biojava-core" ,java-biojava-core)
+       ("java-forester" ,java-forester)))
+    (native-inputs
+     `(("java-junit" ,java-junit)
+       ("java-hamcrest-core" ,java-hamcrest-core)))
+    (home-page "http://biojava.org")
+    (synopsis "Biojava interface to the forester phylogenomics library")
+    (description "The phylo module provides a biojava interface layer to the
+forester phylogenomics library for constructing phylogenetic trees.")))
-- 
cgit v1.2.3


From 22c09c335beff3caa2b434165f09d88267269794 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 1 Mar 2018 19:41:42 +0100
Subject: gnu: Add java-biojava-alignment.

* gnu/packages/bioinformatics.scm (java-biojava-alignment): New variable.
---
 gnu/packages/bioinformatics.scm | 44 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fbb3264ef5..08d9be4bd7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12212,3 +12212,47 @@ This package provides the core libraries.")
     (synopsis "Biojava interface to the forester phylogenomics library")
     (description "The phylo module provides a biojava interface layer to the
 forester phylogenomics library for constructing phylogenetic trees.")))
+
+(define-public java-biojava-alignment
+  (package (inherit java-biojava-core)
+    (name "java-biojava-alignment")
+    (build-system ant-build-system)
+    (arguments
+     `(#:jdk ,icedtea-8
+       #:jar-name "biojava-alignment.jar"
+       #:source-dir "biojava-alignment/src/main/java/"
+       #:test-dir "biojava-alignment/src/test"
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'copy-resources
+           (lambda _
+             (copy-recursively "biojava-alignment/src/main/resources"
+                               "build/classes")
+             #t))
+         (add-before 'check 'copy-test-resources
+           (lambda _
+             (copy-recursively "biojava-alignment/src/test/resources"
+                               "build/test-classes")
+             #t)))))
+    (propagated-inputs
+     `(("java-log4j-api" ,java-log4j-api)
+       ("java-log4j-core" ,java-log4j-core)
+       ("java-slf4j-api" ,java-slf4j-api)
+       ("java-slf4j-simple" ,java-slf4j-simple)
+       ("java-biojava-core" ,java-biojava-core)
+       ("java-biojava-phylo" ,java-biojava-phylo)
+       ("java-forester" ,java-forester)))
+    (native-inputs
+     `(("java-junit" ,java-junit)
+       ("java-hamcrest-core" ,java-hamcrest-core)))
+    (home-page "http://biojava.org")
+    (synopsis "Biojava API for genetic sequence alignment")
+    (description "The alignment module of BioJava provides an API that
+contains
+
+@itemize
+@item implementations of dynamic programming algorithms for sequence
+  alignment;
+@item reading and writing of popular alignment file formats;
+@item a single-, or multi- threaded multiple sequence alignment algorithm.
+@end itemize\n")))
-- 
cgit v1.2.3


From e44da58c16f8c0dd8d9fb80f38f3e86a08fa22f9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 1 Mar 2018 19:41:43 +0100
Subject: gnu: Add java-biojava-core-4.0.

* gnu/packages/bioinformatics.scm (java-biojava-core-4.0): New variable.
---
 gnu/packages/bioinformatics.scm | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 08d9be4bd7..2f5413b35e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12256,3 +12256,17 @@ contains
 @item reading and writing of popular alignment file formats;
 @item a single-, or multi- threaded multiple sequence alignment algorithm.
 @end itemize\n")))
+
+(define-public java-biojava-core-4.0
+  (package (inherit java-biojava-core)
+    (name "java-biojava-core")
+    (version "4.0.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/biojava/biojava")
+                    (commit (string-append "biojava-" version))))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "13675f6y9aqi7bi2lk3s1z7a22ynccjiqwa8izh7p97xi9wsfmd8"))))))
-- 
cgit v1.2.3


From 5528f9e8f09f4a63b40647d61ec100c4c5326b3b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 1 Mar 2018 19:41:44 +0100
Subject: gnu: Add java-biojava-phylo-4.0.

* gnu/packages/bioinformatics.scm (java-biojava-phylo-4.0): New variable.
---
 gnu/packages/bioinformatics.scm | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2f5413b35e..37647a9b9b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12270,3 +12270,39 @@ contains
               (sha256
                (base32
                 "13675f6y9aqi7bi2lk3s1z7a22ynccjiqwa8izh7p97xi9wsfmd8"))))))
+
+(define-public java-biojava-phylo-4.0
+  (package (inherit java-biojava-core-4.0)
+    (name "java-biojava-phylo")
+    (build-system ant-build-system)
+    (arguments
+     `(#:jdk ,icedtea-8
+       #:jar-name "biojava-phylo.jar"
+       #:source-dir "biojava-phylo/src/main/java/"
+       #:test-dir "biojava-phylo/src/test"
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'copy-resources
+           (lambda _
+             (copy-recursively "biojava-phylo/src/main/resources"
+                               "build/classes")
+             #t))
+         (add-before 'check 'copy-test-resources
+           (lambda _
+             (copy-recursively "biojava-phylo/src/test/resources"
+                               "build/test-classes")
+             #t)))))
+    (propagated-inputs
+     `(("java-log4j-api" ,java-log4j-api)
+       ("java-log4j-core" ,java-log4j-core)
+       ("java-slf4j-api" ,java-slf4j-api)
+       ("java-slf4j-simple" ,java-slf4j-simple)
+       ("java-biojava-core" ,java-biojava-core-4.0)
+       ("java-forester" ,java-forester-1.005)))
+    (native-inputs
+     `(("java-junit" ,java-junit)
+       ("java-hamcrest-core" ,java-hamcrest-core)))
+    (home-page "http://biojava.org")
+    (synopsis "Biojava interface to the forester phylogenomics library")
+    (description "The phylo module provides a biojava interface layer to the
+forester phylogenomics library for constructing phylogenetic trees.")))
-- 
cgit v1.2.3


From 9ac7db1830a1b324524aa7d383c5f1b5e348237f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 1 Mar 2018 19:41:45 +0100
Subject: gnu: Add java-biojava-alignment-4.0.

* gnu/packages/bioinformatics.scm (java-biojava-alignment-4.0): New variable.
---
 gnu/packages/bioinformatics.scm | 44 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 37647a9b9b..f44dc32aa7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12306,3 +12306,47 @@ contains
     (synopsis "Biojava interface to the forester phylogenomics library")
     (description "The phylo module provides a biojava interface layer to the
 forester phylogenomics library for constructing phylogenetic trees.")))
+
+(define-public java-biojava-alignment-4.0
+  (package (inherit java-biojava-core-4.0)
+    (name "java-biojava-alignment")
+    (build-system ant-build-system)
+    (arguments
+     `(#:jdk ,icedtea-8
+       #:jar-name "biojava-alignment.jar"
+       #:source-dir "biojava-alignment/src/main/java/"
+       #:test-dir "biojava-alignment/src/test"
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'copy-resources
+           (lambda _
+             (copy-recursively "biojava-alignment/src/main/resources"
+                               "build/classes")
+             #t))
+         (add-before 'check 'copy-test-resources
+           (lambda _
+             (copy-recursively "biojava-alignment/src/test/resources"
+                               "build/test-classes")
+             #t)))))
+    (propagated-inputs
+     `(("java-log4j-api" ,java-log4j-api)
+       ("java-log4j-core" ,java-log4j-core)
+       ("java-slf4j-api" ,java-slf4j-api)
+       ("java-slf4j-simple" ,java-slf4j-simple)
+       ("java-biojava-core" ,java-biojava-core-4.0)
+       ("java-biojava-phylo" ,java-biojava-phylo-4.0)
+       ("java-forester" ,java-forester-1.005)))
+    (native-inputs
+     `(("java-junit" ,java-junit)
+       ("java-hamcrest-core" ,java-hamcrest-core)))
+    (home-page "http://biojava.org")
+    (synopsis "Biojava API for genetic sequence alignment")
+    (description "The alignment module of BioJava provides an API that
+contains
+
+@itemize
+@item implementations of dynamic programming algorithms for sequence
+  alignment;
+@item reading and writing of popular alignment file formats;
+@item a single-, or multi- threaded multiple sequence alignment algorithm.
+@end itemize\n")))
-- 
cgit v1.2.3


From 9a599c17b7dfca56ff8290902057ee6da933aed2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 1 Mar 2018 19:41:46 +0100
Subject: gnu: Add java-htsjdk-latest.

* gnu/packages/bioinformatics.scm (java-htsjdk-latest): New variable.
---
 gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f44dc32aa7..505672624d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3003,6 +3003,49 @@ sequencing (HTS) data.  There are also an number of useful utilities for
 manipulating HTS data.")
     (license license:expat)))
 
+(define-public java-htsjdk-latest
+  (package
+    (name "java-htsjdk")
+    (version "2.14.3")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/samtools/htsjdk.git")
+                    (commit version)))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "1lmya1fdjy03mz6zmdmd86j9v9vfhqb3952mqq075navx1i6g4bc"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:tests? #f                      ; test require Scala
+       #:jdk ,icedtea-8
+       #:jar-name "htsjdk.jar"
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'remove-useless-build.xml
+           (lambda _ (delete-file "build.xml") #t))
+         ;; The tests require the scalatest package.
+         (add-after 'unpack 'remove-tests
+           (lambda _ (delete-file-recursively "src/test") #t)))))
+    (inputs
+     `(("java-ngs" ,java-ngs)
+       ("java-snappy-1" ,java-snappy-1)
+       ("java-commons-compress" ,java-commons-compress)
+       ("java-commons-logging-minimal" ,java-commons-logging-minimal)
+       ("java-commons-jexl-2" ,java-commons-jexl-2)
+       ("java-xz" ,java-xz)))
+    (native-inputs
+     `(("java-junit" ,java-junit)))
+    (home-page "http://samtools.github.io/htsjdk/")
+    (synopsis "Java API for high-throughput sequencing data (HTS) formats")
+    (description
+     "HTSJDK is an implementation of a unified Java library for accessing
+common file formats, such as SAM and VCF, used for high-throughput
+sequencing (HTS) data.  There are also an number of useful utilities for
+manipulating HTS data.")
+    (license license:expat)))
+
 ;; This version matches java-htsjdk 2.3.0.  Later versions also require a more
 ;; recent version of java-htsjdk, which depends on gradle.
 (define-public java-picard
-- 
cgit v1.2.3


From 719fa958f395a44c87377eb61a6f81a7a57603fe Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 1 Mar 2018 19:41:47 +0100
Subject: gnu: Add java-htsjdk-2.10.1.

* gnu/packages/bioinformatics.scm (java-htsjdk-2.10.1): New variable.
---
 gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 505672624d..09a64a8d4d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3046,6 +3046,33 @@ sequencing (HTS) data.  There are also an number of useful utilities for
 manipulating HTS data.")
     (license license:expat)))
 
+;; This is needed for picard 2.10.3
+(define-public java-htsjdk-2.10.1
+  (package (inherit java-htsjdk-latest)
+    (name "java-htsjdk")
+    (version "2.10.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/samtools/htsjdk.git")
+                    (commit version)))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "1kxh7slm2pm3x9p6jxa1wqsq9a31dhiiflhxnxqcisan4k3rwia2"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:tests? #f                      ; tests require Scala
+       #:jdk ,icedtea-8
+       #:jar-name "htsjdk.jar"
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'remove-useless-build.xml
+           (lambda _ (delete-file "build.xml") #t))
+         ;; The tests require the scalatest package.
+         (add-after 'unpack 'remove-tests
+           (lambda _ (delete-file-recursively "src/test") #t)))))))
+
 ;; This version matches java-htsjdk 2.3.0.  Later versions also require a more
 ;; recent version of java-htsjdk, which depends on gradle.
 (define-public java-picard
-- 
cgit v1.2.3


From 72299db9feb6d9e1e0b5cc3262ec7c9cbf7fe729 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 1 Mar 2018 19:41:48 +0100
Subject: gnu: Add java-picard-2.10.3.

* gnu/packages/bioinformatics.scm (java-picard-2.10.3): New variable.
---
 gnu/packages/bioinformatics.scm | 84 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 84 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 09a64a8d4d..719f3e5f23 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3151,6 +3151,90 @@ commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and
 VCF.")
     (license license:expat)))
 
+;; This is needed for dropseq-tools
+(define-public java-picard-2.10.3
+  (package
+    (name "java-picard")
+    (version "2.10.3")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/broadinstitute/picard.git")
+                    (commit version)))
+              (file-name (string-append "java-picard-" version "-checkout"))
+              (sha256
+               (base32
+                "1ajlx31l6i1k3y2rhnmgq07sz99g2czqfqgkr9mihmdjp3gwjhvi"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "picard.jar"
+       ;; Tests require jacoco:coverage.
+       #:tests? #f
+       #:jdk ,icedtea-8
+       #:main-class "picard.cmdline.PicardCommandLine"
+       #:modules ((guix build ant-build-system)
+                  (guix build utils)
+                  (guix build java-utils)
+                  (sxml simple)
+                  (sxml transform)
+                  (sxml xpath))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'remove-useless-build.xml
+           (lambda _ (delete-file "build.xml") #t))
+         ;; This is necessary to ensure that htsjdk is found when using
+         ;; picard.jar as an executable.
+         (add-before 'build 'edit-classpath-in-manifest
+           (lambda* (#:key inputs #:allow-other-keys)
+             (chmod "build.xml" #o664)
+             (call-with-output-file "build.xml.new"
+               (lambda (port)
+                 (sxml->xml
+                  (pre-post-order
+                   (with-input-from-file "build.xml"
+                     (lambda _ (xml->sxml #:trim-whitespace? #t)))
+                   `((target    . ,(lambda (tag . kids)
+                                     (let ((name ((sxpath '(name *text*))
+                                                  (car kids)))
+                                           ;; FIXME: We're breaking the line
+                                           ;; early with a dummy path to
+                                           ;; ensure that the store reference
+                                           ;; isn't broken apart and can still
+                                           ;; be found by the reference
+                                           ;; scanner.
+                                           (msg (format #f
+                                                        "\
+Class-Path: /~a \
+ ~a/share/java/htsjdk.jar${line.separator}"
+                                                        ;; maximum line length is 70
+                                                        (string-tabulate (const #\b) 57)
+                                                        (assoc-ref inputs "java-htsjdk"))))
+                                       (if (member "manifest" name)
+                                           `(,tag ,@kids
+                                                  (echo
+                                                   (@ (message ,msg)
+                                                      (file "${manifest.file}")
+                                                      (append "true"))))
+                                           `(,tag ,@kids)))))
+                     (*default* . ,(lambda (tag . kids) `(,tag ,@kids)))
+                     (*text*    . ,(lambda (_ txt) txt))))
+                  port)))
+             (rename-file "build.xml.new" "build.xml")
+             #t)))))
+    (propagated-inputs
+     `(("java-htsjdk" ,java-htsjdk-2.10.1)))
+    (native-inputs
+     `(("java-testng" ,java-testng)
+       ("java-guava" ,java-guava)))
+    (home-page "http://broadinstitute.github.io/picard/")
+    (synopsis "Tools for manipulating high-throughput sequencing data and formats")
+    (description "Picard is a set of Java command line tools for manipulating
+high-throughput sequencing (HTS) data and formats.  Picard is implemented
+using the HTSJDK Java library to support accessing file formats that are
+commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and
+VCF.")
+    (license license:expat)))
+
 ;; This is the last version of Picard to provide net.sf.samtools
 (define-public java-picard-1.113
   (package (inherit java-picard)
-- 
cgit v1.2.3


From 1adeef3194dd7c8da6e78b17fb33e71bb0c9e24f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 1 Mar 2018 19:41:49 +0100
Subject: gnu: Add dropseq-tools.

* gnu/packages/bioinformatics.scm (dropseq-tools): New variable.
---
 gnu/packages/bioinformatics.scm | 137 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 137 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 719f3e5f23..75468aa967 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12504,3 +12504,140 @@ contains
 @item reading and writing of popular alignment file formats;
 @item a single-, or multi- threaded multiple sequence alignment algorithm.
 @end itemize\n")))
+
+(define-public dropseq-tools
+  (package
+    (name "dropseq-tools")
+    (version "1.13")
+    (source
+     (origin
+       (method url-fetch)
+       (uri "http://mccarrolllab.com/download/1276/")
+       (file-name (string-append "dropseq-tools-" version ".zip"))
+       (sha256
+        (base32
+         "0yrffckxqk5l8b5xb6z4laq157zd9mdypr2p4b4vq2bhjzi1sj0s"))
+       ;; Delete bundled libraries
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           (for-each delete-file (find-files "jar/lib" "\\.jar$"))
+           (delete-file-recursively "3rdParty")))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:tests? #f                      ; test data are not included
+       #:test-target "test"
+       #:build-target "all"
+       #:source-dir "public/src/"
+       #:jdk ,icedtea-8
+       #:make-flags
+       (list (string-append "-Dpicard.executable.dir="
+                            (assoc-ref %build-inputs "java-picard")
+                            "/share/java/"))
+       #:modules ((ice-9 match)
+                  (srfi srfi-1)
+                  (guix build utils)
+                  (guix build java-utils)
+                  (guix build ant-build-system))
+       #:phases
+       (modify-phases %standard-phases
+         ;; All dependencies must be linked to "lib", because that's where
+         ;; they will be searched for when the Class-Path property of the
+         ;; manifest is computed.
+         (add-after 'unpack 'record-references
+	   (lambda* (#:key inputs #:allow-other-keys)
+             (mkdir-p "jar/lib")
+             (let ((dirs (filter-map (match-lambda
+                                       ((name . dir)
+                                        (if (and (string-prefix? "java-" name)
+                                                 (not (string=? name "java-testng")))
+                                            dir #f)))
+                                     inputs)))
+               (for-each (lambda (jar)
+                           (symlink jar (string-append "jar/lib/" (basename jar))))
+                         (append-map (lambda (dir) (find-files dir "\\.jar$"))
+                                     dirs)))
+	     #t))
+         ;; There is no installation target
+         (replace 'install
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let* ((out     (assoc-ref outputs "out"))
+                    (bin     (string-append out "/bin"))
+                    (share   (string-append out "/share/java/"))
+                    (lib     (string-append share "/lib/"))
+                    (scripts (list "BAMTagHistogram"
+                                   "BAMTagofTagCounts"
+                                   "BaseDistributionAtReadPosition"
+                                   "CollapseBarcodesInPlace"
+                                   "CollapseTagWithContext"
+                                   "ConvertToRefFlat"
+                                   "CreateIntervalsFiles"
+                                   "DetectBeadSynthesisErrors"
+                                   "DigitalExpression"
+                                   "Drop-seq_alignment.sh"
+                                   "FilterBAM"
+                                   "FilterBAMByTag"
+                                   "GatherGeneGCLength"
+                                   "GatherMolecularBarcodeDistributionByGene"
+                                   "GatherReadQualityMetrics"
+                                   "PolyATrimmer"
+                                   "ReduceGTF"
+                                   "SelectCellsByNumTranscripts"
+                                   "SingleCellRnaSeqMetricsCollector"
+                                   "TagBamWithReadSequenceExtended"
+                                   "TagReadWithGeneExon"
+                                   "TagReadWithInterval"
+                                   "TrimStartingSequence"
+                                   "ValidateReference")))
+               (for-each mkdir-p (list bin share lib))
+               (install-file "dist/dropseq.jar" share)
+               (for-each (lambda (script)
+                           (chmod script #o555)
+                           (install-file script bin))
+                         scripts)
+               (substitute* (map (lambda (script)
+                                   (string-append bin "/" script))
+                                 scripts)
+                 (("^java") (which "java"))
+                 (("jar_deploy_dir=.*")
+                  (string-append "jar_deploy_dir=" share "\n"))))
+             #t))
+         ;; FIXME: We do this after stripping jars because we don't want it to
+         ;; copy all these jars and strip them.  We only want to install
+         ;; links.  Arguably, this is a problem with the ant-build-system.
+         (add-after 'strip-jar-timestamps 'install-links
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out     (assoc-ref outputs "out"))
+                    (share   (string-append out "/share/java/"))
+                    (lib     (string-append share "/lib/")))
+               (for-each (lambda (jar)
+                           (symlink (readlink jar)
+                                    (string-append lib (basename jar))))
+                         (find-files "jar/lib" "\\.jar$")))
+             #t)))))
+    (inputs
+     `(("jdk" ,icedtea-8)
+       ("java-picard" ,java-picard-2.10.3)
+       ("java-log4j-1.2-api" ,java-log4j-1.2-api)
+       ("java-commons-math3" ,java-commons-math3)
+       ("java-commons-jexl2" ,java-commons-jexl-2)
+       ("java-commons-collections4" ,java-commons-collections4)
+       ("java-commons-lang2" ,java-commons-lang)
+       ("java-commons-io" ,java-commons-io)
+       ("java-snappy-1.0.3-rc3" ,java-snappy-1)
+       ("java-guava" ,java-guava)
+       ("java-la4j" ,java-la4j)
+       ("java-biojava-core" ,java-biojava-core-4.0)
+       ("java-biojava-alignment" ,java-biojava-alignment-4.0)
+       ("java-jdistlib" ,java-jdistlib)
+       ("java-simple-xml" ,java-simple-xml)
+       ("java-snakeyaml" ,java-snakeyaml)))
+    (native-inputs
+     `(("unzip" ,unzip)
+       ("java-testng" ,java-testng)))
+    (home-page "http://mccarrolllab.com/dropseq/")
+    (synopsis "Tools for Drop-seq analyses")
+    (description "Drop-seq is a technology to enable biologists to
+analyze RNA expression genome-wide in thousands of individual cells at
+once.  This package provides tools to perform Drop-seq analyses.")
+    (license license:expat)))
-- 
cgit v1.2.3


From c94752ad22da4f90e16bc2402751bcc6bb6fd79a Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 3 Mar 2018 21:01:20 +0100
Subject: gnu: tor: Update to 0.3.2.10 [security fixes].

This release fixes TROVE-2018-001 (also tracked as CVE-2018-0490),
TROVE-2018-002 (CVE-2018-049), and TROVEs-2018-00{3,4} as well.

* gnu/packages/tor.scm (tor): Update to 0.3.2.10.
---
 gnu/packages/tor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm
index 50295da5dc..2d685fc7d5 100644
--- a/gnu/packages/tor.scm
+++ b/gnu/packages/tor.scm
@@ -47,14 +47,14 @@
 (define-public tor
   (package
     (name "tor")
-    (version "0.3.2.9")
+    (version "0.3.2.10")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://dist.torproject.org/tor-"
                                  version ".tar.gz"))
              (sha256
               (base32
-               "03qn55c969zynnx71r82iaqnadpzq0qclq0zmjhb3n4qma8pnnj3"))))
+               "1vnb2wkcmm8rnz0fqi3k7arl60mpycs8rjn8hvbgv56g3p1pgpv0"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags (list "--enable-gcc-hardening"
-- 
cgit v1.2.3


From 7fc944273d17ad0aa7dccd6eb1d730e5ea87bcfc Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 4 Mar 2018 09:48:46 +0200
Subject: gnu: masscan: Declare a source file-name.

* gnu/packages/admin.scm (masscan)[source]: Declare a source file-name.
---
 gnu/packages/admin.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 80cf8c391c..554c1679e6 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -2433,6 +2433,7 @@ on systems running the Linux kernel.")
               (method url-fetch)
               (uri (string-append "https://github.com/robertdavidgraham/masscan"
                                   "/archive/" version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
                 "1y9af345g00z83rliv6bmlqg37xwc7xpnx5xqdgmjikzcxgk9pji"))))
-- 
cgit v1.2.3


From a18ee793d7ada1bb46ecc2de91d8177ea6e15531 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 4 Mar 2018 09:52:08 +0200
Subject: gnu: papagayo: Declare a source file-name.

* gnu/packages/animation.scm (papagayo)[source]: Declare a source
file-name.
---
 gnu/packages/animation.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/animation.scm b/gnu/packages/animation.scm
index 952d3bab0d..b56a081984 100644
--- a/gnu/packages/animation.scm
+++ b/gnu/packages/animation.scm
@@ -200,6 +200,7 @@ contains the graphical user interface for synfig.")
                 (uri (git-reference
                       (url "https://github.com/LostMoho/Papagayo.git")
                       (commit commit)))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
                   "1p9gffjhbph34jhrvgpg93yha75bf88vkvlnk06x1r9601ph5321"))
-- 
cgit v1.2.3


From 35a01e67c8fd5a9d06085e56a69465881999c11c Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 4 Mar 2018 09:53:55 +0200
Subject: gnu: lv2-mda-piano: Declare a source file-name.

* gnu/packages/audio.scm (lv2-mda-piano)[source]: Declare a source
file-name.
---
 gnu/packages/audio.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index a9d29345a6..e3d3819427 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -1796,6 +1796,7 @@ software.")
               (uri (git-reference
                     (url "http://git.elephly.net/software/lv2-mdametapiano.git")
                     (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
                 "07lywf6lpfpndg3i9w752mmlg2hgn1bwp23h8b0mdj6awh67abqd"))))
-- 
cgit v1.2.3


From 6677c99a8b9d334e55e23efe9e864b90b9b9f015 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 4 Mar 2018 09:54:51 +0200
Subject: gnu: lv2-devel: Declare a source file-name.

* gnu/packages/audio.scm (lv2-devel)[source]: Declare a source file-name.
---
 gnu/packages/audio.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index e3d3819427..f00ac246c1 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -1783,6 +1783,7 @@ software.")
                 (uri (git-reference
                       (url "http://lv2plug.in/git/lv2.git")
                       (commit commit)))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
                   "1gp2rd99dfmpibvpixrqn115mrhybzf3if3h8bssf6siyi13f29r")))))))
-- 
cgit v1.2.3


From 70aa07d296f28063313d48ebcfbc6c69fec2ac82 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 4 Mar 2018 09:55:46 +0200
Subject: gnu: qjackrcd: Declare a source file-name.

* gnu/packages/audio.scm (qjackrcd)[source]: Declare a source file-name.
---
 gnu/packages/audio.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index f00ac246c1..8c48e2a0ff 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -2026,6 +2026,7 @@ into various outputs and to start, stop and configure jackd")
               (uri (git-reference
                     (url "https://github.com/orouits/qjackrcd.git")
                     (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
                 "1l5iq2mkqd4gn9yr8xbh9qlpp1clcflazychl4vhdbz0bzq4c6al"))))
-- 
cgit v1.2.3


From fdf359f82bb414754f299bc55fd314a5f107a332 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 4 Mar 2018 09:57:24 +0200
Subject: gnu: rubberband: Declare a source file-name.

* gnu/packages/audio.scm (rubberband)[source]: Declare a source
file-name.
---
 gnu/packages/audio.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 8c48e2a0ff..54bf6c1982 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -2106,6 +2106,7 @@ aimed at audio/musical applications.")
                (string-append "https://bitbucket.org/breakfastquay/rubberband/get/v"
                               version
                               ".tar.bz2"))
+              (file-name (string-append name "-" version ".tar.bz2"))
               (sha256
                (base32
                 "05amrbrxx0da3w7m237q51799r8xgs4ffqabi2qv06hq8dpcj386"))))
-- 
cgit v1.2.3


From a1eb506cf3ba5fd0ea832ae564f9c8dae5f386e7 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 4 Mar 2018 09:58:23 +0200
Subject: gnu: faust@2: Declare a source file-name.

* gnu/packages/audio.scm (faust@2)[source]: Declare a source file-name.
---
 gnu/packages/audio.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 54bf6c1982..3ae2b1ba47 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -1155,6 +1155,7 @@ PS, and DAB+.")
                                            (string-map (lambda (c)
                                                          (if (char=? c #\.) #\- c))
                                                        version)))))
+              (file-name (string-append "faust-" version "-checkout"))
               (sha256
                (base32
                 "06km0ygwxxwgw1lqldccqidxhmjfz8ck0wnbd95qk5sg8sbpc068"))))
-- 
cgit v1.2.3


From b1d4026dfb0a5f1fd12c6c0c03fe963c8fd49333 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 4 Mar 2018 11:45:40 +0200
Subject: gnu: r-dropbead: Declare a source file-name.

* gnu/packages/bioinformatics.scm (r-dropbead)[source]: Declare a source
file-name.
---
 gnu/packages/bioinformatics.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 75468aa967..6a9f13bdc6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10888,6 +10888,7 @@ memory usage and processing time is minimized.")
          (uri (git-reference
                (url "https://github.com/rajewsky-lab/dropbead.git")
                (commit commit)))
+         (file-name (git-file-name name version))
          (sha256
           (base32
            "1b2lphsc236s1rdzlijxg8yl1jnqpwcvj4x938r89rqpj93jb780"))))
-- 
cgit v1.2.3


From 51106724749a904b45738f9b4d1201ea4e11e760 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 4 Mar 2018 11:46:43 +0200
Subject: gnu: seek: Declare a source file-name.

* gnu/packages/bioinformatics.scm (seek)[source]: Declare a source
file-name.
---
 gnu/packages/bioinformatics.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6a9f13bdc6..139828111a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4846,6 +4846,7 @@ distribution, coverage uniformity, strand specificity, etc.")
                 (uri (hg-reference
                       (url "https://bitbucket.org/libsleipnir/sleipnir")
                       (changeset changeset)))
+                (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
                   "0qrvilwh18dpbhkf92qvxbmay0j75ra3jg2wrhz67gf538zzphsx"))))
-- 
cgit v1.2.3


From d9a069c2d975e37ac2f01261d1c5b4b98f856228 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 4 Mar 2018 11:47:42 +0200
Subject: gnu: libdivsufsort: Declare a source file-name.

* gnu/packages/bioinformatics.scm (libdivsufsort)[source]: Declare a
source file-name.
---
 gnu/packages/bioinformatics.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 139828111a..fd00984dd5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11650,6 +11650,7 @@ dependency like SeqAn.")
               (uri (git-reference
                     (url "https://github.com/y-256/libdivsufsort.git")
                     (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
                 "0fgdz9fzihlvjjrxy01md1bv9vh12rkgkwbm90b1hj5xpbaqp7z2"))))
-- 
cgit v1.2.3


From da49d137104229f35816bd09bf24c1756ac1613e Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 4 Mar 2018 11:48:40 +0200
Subject: gnu: piranha: Declare a source file-name.

* gnu/packages/bioinformatics.scm (piranha)[source]: Declare a source
file-name.
---
 gnu/packages/bioinformatics.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fd00984dd5..4756444d95 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8924,6 +8924,7 @@ intervals (e.g. genes, sequence alignments).")
                 (uri (git-reference
                       (url "https://github.com/smithlabcode/piranha.git")
                       (commit commit)))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
                   "117dc0zf20c61jam69sk4abl57ah6yi6i7qra7d7y5zrbgk12q5n"))))
-- 
cgit v1.2.3


From eafe96ea9e0e30e4083c001b3908fafd97394554 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 4 Mar 2018 11:50:16 +0200
Subject: gnu: sfarkxtc: Declare a source file-name.

* gnu/packages/compression.scm (sfarkxtc)[source]: Declare a source
file-name.
---
 gnu/packages/compression.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index f25c4bba3a..88b7af82d8 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -600,6 +600,7 @@ with the sfArk algorithm.")
               (uri (git-reference
                     (url "https://github.com/raboof/sfarkxtc.git")
                     (commit commit)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
                 "0f5x6i46qfl6ry21s7g2p4sd4b2r1g4fb03yqi2vv4kq3saryhvj"))))
-- 
cgit v1.2.3


From 277be74fa713654c51a4cc39b7318a2a3e15f529 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 4 Mar 2018 11:51:08 +0200
Subject: gnu: unshield: Declare a source file-name.

* gnu/packages/compression.scm (unshield)[source]: Declare a source
file-name.
---
 gnu/packages/compression.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 88b7af82d8..54c5928cb7 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -1534,6 +1534,7 @@ or junctions, and always follows hard links.")
      (origin (method url-fetch)
              (uri (string-append "http://github.com/twogood/unshield/archive/"
                                  version ".tar.gz"))
+             (file-name (string-append name "-" version ".tar.gz"))
              (sha256
               (base32
                "0x7ps644yp5dka2zhb8w0ifqmw3d255jafpzfwv8xbcpgq6fmm2x"))))
-- 
cgit v1.2.3


From c2c04cde9b8016808c45db7c4d5986d717f09604 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 4 Mar 2018 11:55:08 +0200
Subject: gnu: kurly: Declare a source file-name.

* gnu/packages/curl.scm (kurly)[source]: Declare a source file-name.
---
 gnu/packages/curl.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/curl.scm b/gnu/packages/curl.scm
index e51e014e99..32509fc3fc 100644
--- a/gnu/packages/curl.scm
+++ b/gnu/packages/curl.scm
@@ -158,6 +158,7 @@ tunneling, and so on.")
               (uri (git-reference
                      (url "https://github.com/davidjpeacock/kurly.git")
                      (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
                 "1q192f457sjypgvwq7grrf8gq8w272p3zf1d5ppc20mriqm0mbc3"))))
-- 
cgit v1.2.3


From f5c847ebd067e4b56fdeb40e64a2a44e3ae2c19d Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 4 Mar 2018 11:55:37 +0200
Subject: gnu: python-apsw: Declare a source file-name.

* gnu/packages/databases.scm (python-apsw)[source]: Declare a source
file-name.
---
 gnu/packages/databases.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index ba4ad9f9b9..7057c466d0 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -2285,6 +2285,7 @@ PickleShare.")
         (method url-fetch)
         (uri (string-append "https://github.com/rogerbinns/apsw/archive/"
                             version ".tar.gz"))
+        (file-name (string-append "apsw-" version ".tar.gz"))
         (sha256
           (base32
            "00ai7m2pqi26qaflhz314d8k5i3syw7xzr145fhfl0crhyh6adz2"))))
-- 
cgit v1.2.3


From c553b08b4949c9bb53ffd9b83b5a6de8e459ac25 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 4 Mar 2018 12:03:27 +0200
Subject: gnu: python-apsw: Use invoke.

* gnu/packages/databases.scm (python-apsw)[arguments]: Use invoke.
---
 gnu/packages/databases.scm | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 7057c466d0..269a1ffcea 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -2291,25 +2291,25 @@ PickleShare.")
            "00ai7m2pqi26qaflhz314d8k5i3syw7xzr145fhfl0crhyh6adz2"))))
     (build-system python-build-system)
     (inputs
-      `(("sqlite" ,sqlite)))
+     `(("sqlite" ,sqlite)))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
          (replace 'build
            (lambda _
-             (zero?
-              (system* "python" "setup.py" "build" "--enable-all-extensions"))))
+             (invoke "python" "setup.py" "build" "--enable-all-extensions")
+             #t))
          (add-after 'build 'build-test-helper
            (lambda _
-             (zero?
-              (system
-               (string-append "gcc -fPIC -shared -o ./testextension.sqlext "
-                              "-I. -Isqlite3 src/testextension.c") ))))
+             (invoke "gcc" "-fPIC" "-shared" "-o" "./testextension.sqlext"
+                     "-I." "-Isqlite3" "src/testextension.c")
+             #t))
          (delete 'check)
          (add-after 'install 'check
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (add-installed-pythonpath inputs outputs)
-             (zero? (system* "python" "setup.py" "test")))))))
+             (invoke "python" "setup.py" "test")
+             #t)))))
     (home-page "https://github.com/rogerbinns/apsw/")
     (synopsis "Another Python SQLite Wrapper")
     (description "APSW is a Python wrapper for the SQLite
-- 
cgit v1.2.3


From 5a6f7a68054aed1d0f75eb250d665de9706c8615 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 4 Mar 2018 12:30:08 +0200
Subject: gnu: emacs-epl: Declare a source file-name.

* gnu/packages/emacs.scm (emacs-epl)[source]: Declare a source
file-name.
---
 gnu/packages/emacs.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 67bbb153fb..73c0429095 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -3546,6 +3546,7 @@ It is recommended to use @code{clojure-mode} with paredit or smartparens.")
               (uri (string-append
                     "https://github.com/cask/epl/archive/"
                     version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
                 "1511n3a3f5gvaf2b4nh018by61ciyzi3y3603fzqma7p9hrckarc"))))
-- 
cgit v1.2.3


From aeb95f1f978cc47a04b644308a5b171ff96c6cee Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 4 Mar 2018 12:30:53 +0200
Subject: gnu: emacs-sly: Declare a source file-name.

* gnu/packages/emacs.scm (emacs-sly)[source]: Declare a source
file-name.
---
 gnu/packages/emacs.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 73c0429095..69950cc6d7 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -4301,6 +4301,7 @@ CIDER).")
          (uri (git-reference
                (url "https://github.com/joaotavora/sly.git")
                (commit commit)))
+         (file-name (git-file-name name version))
          (sha256
           (base32
            "0ib4q4k3h3qn88pymyjjmlmnpizdn1mfg5gpk5a715nqsgxlg09l"))))
-- 
cgit v1.2.3


From a1dc853ef4f0da0acc1a2c50fb3e5365bff305c9 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 4 Mar 2018 12:32:39 +0200
Subject: gnu: disorderfs: Declare a source file-name.

* gnu/packages/file-systems.scm (disorderfs)[source]: Declare a source
file-name.
---
 gnu/packages/file-systems.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/file-systems.scm b/gnu/packages/file-systems.scm
index 1d73f4aef4..0e65213c72 100644
--- a/gnu/packages/file-systems.scm
+++ b/gnu/packages/file-systems.scm
@@ -114,6 +114,7 @@ single file can be mounted.")
        (uri (git-reference
              (url "https://github.com/ReproducibleBuilds/disorderfs.git")
              (commit "0.5.2")))
+       (file-name (git-file-name name version))
        (sha256
         (base32
          "1j028dq3d4m64mn9xmfamcnnc7i2drmra4pdmxdmqdsi8p7yj4sv"))))
-- 
cgit v1.2.3


From 661ad6f0c205c64c5681d1805f42d743f316ab57 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 4 Mar 2018 12:33:55 +0200
Subject: gnu: freegish: Declare a source file-name.

* gnu/packages/games.scm (freegish)[source]: Declare a source file-name.
---
 gnu/packages/games.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index 5917bbd69c..a33da03ad5 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -3491,6 +3491,7 @@ Magic, Egypt, Indians, Norsemen, Persian or Romans.")
                 (uri (git-reference
                       (url "https://github.com/freegish/freegish.git")
                       (commit commit)))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
                   "1p1zf5qqagmcpi1db2bs02cnalpy3qiymp6yzan7k1bhmv859gsx"))
-- 
cgit v1.2.3


From fdbece74aa9582724801225e52b25e71a7a73797 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 4 Mar 2018 12:35:31 +0200
Subject: gnu: go-github-com-alsm-ioprogress: Declare a source file-name.

* gnu/packages/golang.scm (go-github-com-alsm-ioprogress)[source]:
Declare a source file-name.
---
 gnu/packages/golang.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index e201ac8e4c..3a8c889a42 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -502,6 +502,7 @@ in the style of communicating sequential processes (@dfn{CSP}).")
                 (uri (git-reference
                        (url "https://github.com/alsm/ioprogress.git")
                        (commit commit)))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
                   "10ym5qlq77nynmkxbk767f2hfwyxg2k7hrzph05hvgzv833dhivh"))))
-- 
cgit v1.2.3


From 6de107b0c907664338270a493487e7ac0f75a519 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 4 Mar 2018 12:36:34 +0200
Subject: gnu: go-github-com-davidjpeacock-cli: Declare a source file-name.

* gnu/packages/golang.scm (go-github-com-davidjpeacock-cli)[source]:
Declare a source file-name.
---
 gnu/packages/golang.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index 3a8c889a42..f3847c1b57 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -552,6 +552,7 @@ jar struct to manage the cookies added to the cookie jar.")
                 (uri (git-reference
                        (url "https://github.com/davidjpeacock/cli.git")
                        (commit commit)))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
                   "01s53ny3p0fdx64rnwcnmjj4xpc5adihnh6islsfq5z1ph2phhnj"))))
-- 
cgit v1.2.3


From 82f09c0e8ee64f39ac453fc8be94c096f7e0b266 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 4 Mar 2018 12:37:33 +0200
Subject: gnu: go-github-com-aki237-nscjar: Declare a source file-name.

* gnu/packages/golang.scm (go-github-com-aki237-nscjar)[source]: Declare
a source file-name.
---
 gnu/packages/golang.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index f3847c1b57..20a8c538be 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -528,6 +528,7 @@ writers can be supplied for alternate environments.")
                 (uri (git-reference
                        (url "https://github.com/aki237/nscjar.git")
                        (commit commit)))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
                   "03y7zzq12qvhsq86lb06sgns8xrkblbn7i7wd886wk3zr5574b96"))))
-- 
cgit v1.2.3


From 4c763b4d6792adb0a8d3f61a241e490385cc0683 Mon Sep 17 00:00:00 2001
From: Gábor Boskovits <boskovits@gmail.com>
Date: Sun, 4 Mar 2018 14:13:47 +0100
Subject: gnu: antlr3-3.1: Fix java8 issue.

* gnu/packages/java.scm (antlr3-3.1)[source]: Add patch.
* gnu/packages/patches/antlr3-3_1-fix-java8-compilation.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
---
 gnu/local.mk                                       |  1 +
 gnu/packages/java.scm                              |  4 ++-
 .../patches/antlr3-3_1-fix-java8-compilation.patch | 35 ++++++++++++++++++++++
 3 files changed, 39 insertions(+), 1 deletion(-)
 create mode 100644 gnu/packages/patches/antlr3-3_1-fix-java8-compilation.patch

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index 9684d949f6..dffecfc7e9 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -553,6 +553,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/agg-am_c_prototype.patch			\
   %D%/packages/patches/ansible-wrap-program-hack.patch		\
   %D%/packages/patches/antiword-CVE-2014-8123.patch			\
+  %D%/packages/patches/antlr3-3_1-fix-java8-compilation.patch	\
   %D%/packages/patches/ao-cad-aarch64-support.patch		\
   %D%/packages/patches/apr-skip-getservbyname-test.patch	\
   %D%/packages/patches/aspell-default-dict-dir.patch		\
diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 1e671b90bb..cda7f0e01f 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -6113,7 +6113,9 @@ import org.antlr.grammar.v2.ANTLRTreePrinter;"))
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0sfimc9cpbgrihz4giyygc8afgpma2c93yqpwb951giriri6x66z"))))
+                "0sfimc9cpbgrihz4giyygc8afgpma2c93yqpwb951giriri6x66z"))
+              (patches
+               (search-patches "antlr3-3_1-fix-java8-compilation.patch"))))
     (arguments
      `(#:jar-name (string-append "antlr3-" ,version ".jar")
        #:source-dir "src:runtime/Java/src"
diff --git a/gnu/packages/patches/antlr3-3_1-fix-java8-compilation.patch b/gnu/packages/patches/antlr3-3_1-fix-java8-compilation.patch
new file mode 100644
index 0000000000..0c4deb024b
--- /dev/null
+++ b/gnu/packages/patches/antlr3-3_1-fix-java8-compilation.patch
@@ -0,0 +1,35 @@
+Based on the upstream fix for the java8 compilation issue.
+Simplified patch.
+Upstream version of patch does not work with this source tree.
+
+The issue is that in java8 it is an error to pass null to
+removeAll. Results in null pointer exception. java7
+behaviour was to return the list unmodified.
+
+From db2a350c6d90efaa8dde949fa76005c2c5af45c4 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?G=C3=A1bor=20Boskovits?= <boskovits@gmail.com>
+Date: Fri, 5 Jan 2018 17:05:31 +0100
+Subject: [PATCH] Fix java8 compilation.
+
+---
+ src/org/antlr/tool/CompositeGrammar.java | 4 +++-
+ 1 file changed, 3 insertions(+), 1 deletion(-)
+
+diff --git a/src/org/antlr/tool/CompositeGrammar.java b/src/org/antlr/tool/CompositeGrammar.java
+index f1408e7..7e02431 100644
+--- a/src/org/antlr/tool/CompositeGrammar.java
++++ b/src/org/antlr/tool/CompositeGrammar.java
+@@ -218,7 +218,9 @@ public class CompositeGrammar {
+ 	public List<Grammar> getIndirectDelegates(Grammar g) {
+ 		List<Grammar> direct = getDirectDelegates(g);
+ 		List<Grammar> delegates = getDelegates(g);
+-		delegates.removeAll(direct);
++		if (direct != null) {
++			delegates.removeAll(direct);
++		}
+ 		return delegates;
+ 	}
+ 
+-- 
+2.15.1
+
-- 
cgit v1.2.3


From 48c8622010bd0cfc7bc82578772993178308a0b7 Mon Sep 17 00:00:00 2001
From: Gábor Boskovits <boskovits@gmail.com>
Date: Sun, 4 Mar 2018 14:16:37 +0100
Subject: gnu: antlr3-3.3: Fix java8 issue.

* gnu/packages/java.scm (antlr3-3.3)[source]: Add patch.
* gnu/packages/patches/antlr3-3_3-fix-java8-compilation.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
---
 gnu/local.mk                                       |  1 +
 gnu/packages/java.scm                              |  4 ++-
 .../patches/antlr3-3_3-fix-java8-compilation.patch | 35 ++++++++++++++++++++++
 3 files changed, 39 insertions(+), 1 deletion(-)
 create mode 100644 gnu/packages/patches/antlr3-3_3-fix-java8-compilation.patch

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index dffecfc7e9..2ef9b68590 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -554,6 +554,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/ansible-wrap-program-hack.patch		\
   %D%/packages/patches/antiword-CVE-2014-8123.patch			\
   %D%/packages/patches/antlr3-3_1-fix-java8-compilation.patch	\
+  %D%/packages/patches/antlr3-3_3-fix-java8-compilation.patch	\
   %D%/packages/patches/ao-cad-aarch64-support.patch		\
   %D%/packages/patches/apr-skip-getservbyname-test.patch	\
   %D%/packages/patches/aspell-default-dict-dir.patch		\
diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index cda7f0e01f..21e241d0fe 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -6023,7 +6023,9 @@ tree walking, and translation.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0qgg5vgsm4l1d6dj9pfbaa25dpv2ry2gny8ajy4vvgvfklw97b3m"))))
+                "0qgg5vgsm4l1d6dj9pfbaa25dpv2ry2gny8ajy4vvgvfklw97b3m"))
+              (patches
+               (search-patches "antlr3-3_3-fix-java8-compilation.patch"))))
     (arguments
      `(#:jar-name (string-append ,name "-" ,version ".jar")
        #:source-dir (string-join '("tool/src/main/java"
diff --git a/gnu/packages/patches/antlr3-3_3-fix-java8-compilation.patch b/gnu/packages/patches/antlr3-3_3-fix-java8-compilation.patch
new file mode 100644
index 0000000000..a7d6be9b6b
--- /dev/null
+++ b/gnu/packages/patches/antlr3-3_3-fix-java8-compilation.patch
@@ -0,0 +1,35 @@
+Based on the upstream fix for the java8 compilation issue.
+Simplified patch.
+Upstream version of patch does not work with this source tree.
+
+The issue is that in java8 it is an error to pass null to
+removeAll. Results in null pointer exception. java7
+behaviour was to return the list unmodified.
+
+From 43867d50c05d1c06ab7220eb974a8874ae10c308 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?G=C3=A1bor=20Boskovits?= <boskovits@gmail.com>
+Date: Fri, 5 Jan 2018 19:08:24 +0100
+Subject: [PATCH] Fix java8 complilation error.
+
+---
+ tool/src/main/java/org/antlr/tool/CompositeGrammar.java | 4 +++-
+ 1 file changed, 3 insertions(+), 1 deletion(-)
+
+diff --git a/tool/src/main/java/org/antlr/tool/CompositeGrammar.java b/tool/src/main/java/org/antlr/tool/CompositeGrammar.java
+index f34ea73..63740a6 100644
+--- a/tool/src/main/java/org/antlr/tool/CompositeGrammar.java
++++ b/tool/src/main/java/org/antlr/tool/CompositeGrammar.java
+@@ -226,7 +226,9 @@ public class CompositeGrammar {
+ 	public List<Grammar> getIndirectDelegates(Grammar g) {
+ 		List<Grammar> direct = getDirectDelegates(g);
+ 		List<Grammar> delegates = getDelegates(g);
+-		delegates.removeAll(direct);
++		if(direct != null) {
++		        delegates.removeAll(direct);
++		}
+ 		return delegates;
+ 	}
+ 
+-- 
+2.15.1
+
-- 
cgit v1.2.3


From 64cdd73c221fa43bdbde52946ed7edfe9c7b2009 Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Sun, 4 Mar 2018 15:42:41 +0100
Subject: gnu: python-funcy: Fix tests.

* gnu/packages/python.scm (python-funcy)[native-inputs]: Delete python-pytest-warnings.
---
 gnu/packages/python.scm | 1 -
 1 file changed, 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 5f701701a4..970c835de6 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -12733,7 +12733,6 @@ functions by partial application of operators.")
              (invoke "py.test"))))))
     (native-inputs
      `(("python-pytest" ,python-pytest)
-       ("python-pytest-warnings" ,python-pytest-warnings)
        ("python-whatever" ,python-whatever)))
     (home-page "http://github.com/Suor/funcy")
     (synopsis "Functional tools")
-- 
cgit v1.2.3


From 692f6e457ee2eb9cdc9d95c3f8487155ecca81d4 Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Sun, 4 Mar 2018 15:43:46 +0100
Subject: gnu: abiword: Disable duplicate icon cache generation.

* gnu/packages/abiword.scm (abiword): Disable duplicate icon cache generation.
---
 gnu/packages/abiword.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/abiword.scm b/gnu/packages/abiword.scm
index b00dac9a63..cf906c6ea4 100644
--- a/gnu/packages/abiword.scm
+++ b/gnu/packages/abiword.scm
@@ -82,7 +82,7 @@
         ;; the tests to pass.
         #:tests? #f
         #:make-flags
-        (list "CXXFLAGS=-std=c++11")))
+        (list "CXXFLAGS=-std=c++11" "gtk_update_icon_cache=true")))
     (inputs
       `(("boost" ,boost)
         ("enchant" ,enchant)
-- 
cgit v1.2.3


From 81ed306dee3b1049041edaa4b7beab8ef2743aea Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Sun, 4 Mar 2018 15:44:34 +0100
Subject: gnu: inkscape: Disable duplicate icon cache generation.

* gnu/packages/inkscape.scm (inkscape): Disable duplicate icon cache
generation.
---
 gnu/packages/inkscape.scm | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/inkscape.scm b/gnu/packages/inkscape.scm
index f1a3cb23f4..dc5a30b868 100644
--- a/gnu/packages/inkscape.scm
+++ b/gnu/packages/inkscape.scm
@@ -87,7 +87,10 @@
        ("perl" ,perl)
        ("pkg-config" ,pkg-config)))
     ;; FIXME: tests require gmock
-    (arguments `(#:tests? #f))
+    (arguments
+     `(#:tests? #f
+       #:make-flags
+       '("gtk_update_icon_cache=true")))
     (home-page "https://inkscape.org/")
     (synopsis "Vector graphics editor")
     (description "Inkscape is a vector graphics editor.  What sets Inkscape
-- 
cgit v1.2.3


From 7fa9cca84afce09d3816b70ae6d42bfc08635e9d Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 21 Feb 2018 03:06:39 +0100
Subject: gnu: rocksdb: Update to 5.10.4.

* gnu/packages/databases.scm (rocksdb): Update to 5.10.4.
[source]: Substitute the unbundled copy of GNU Parallel.
[arguments]: Add "V=1" "USE_RTTI=1" and
"ROCKSDBTESTS_END=db_tailing_iter_test" to #:make-flags.  Set #:test-target to
"check_some".  Respect parallel jobs in 'build-release-libraries' phase and
rename to 'build'.
[license]: Update for changes in 5.5.4.
---
 gnu/packages/databases.scm | 44 +++++++++++++++++++++++++++-----------------
 1 file changed, 27 insertions(+), 17 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 269a1ffcea..87f65404f8 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -17,7 +17,7 @@
 ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2016 Andy Patterson <ajpatter@uwaterloo.ca>
 ;;; Copyright © 2016 Danny Milosavljevic <dannym+a@scratchpost.org>
-;;; Copyright © 2016, 2017 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2016, 2017, 2018 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be>
 ;;; Copyright © 2017 Jelle Licht <jlicht@fsfe.org>
@@ -841,7 +841,7 @@ types are supported, as is encryption.")
 (define-public rocksdb
   (package
     (name "rocksdb")
-    (version "5.2.1")
+    (version "5.10.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/facebook/rocksdb"
@@ -849,18 +849,28 @@ types are supported, as is encryption.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1v2q05bl56sfp51m09z7g6489hkfq4vf6b4qgfg3d96ylgmay9yb"))
+                "0hp7jxr99vyc57n708hiqk4lks9a9zmjgfjc21mx6v1rmabj2944"))
               (modules '((guix build utils)))
               (snippet
                '(begin
                   ;; TODO: unbundle gtest.
                   (delete-file "build_tools/gnu_parallel")
+                  (substitute* "Makefile"
+                    (("build_tools/gnu_parallel") "parallel"))
                   #t))))
     (build-system gnu-build-system)
     (arguments
-     `(#:make-flags (list "CC=gcc"
+     `(#:make-flags (list "CC=gcc" "V=1"
+                          ;; Ceph requires that RTTI is enabled.
+                          "USE_RTTI=1"
                           (string-append "INSTALL_PATH="
-                                         (assoc-ref %outputs "out")))
+                                         (assoc-ref %outputs "out"))
+
+                          ;; Running the full test suite takes hours and require
+                          ;; a lot of disk space.  Instead we only run a subset
+                          ;; (see .travis.yml and Makefile).
+                          "ROCKSDBTESTS_END=db_tailing_iter_test")
+       #:test-target "check_some"
        ;; Many tests fail on 32-bit platforms. There are multiple reports about
        ;; this upstream, but it's not going to be supported any time soon.
        #:tests? (let ((system ,(or (%current-target-system)
@@ -872,7 +882,6 @@ types are supported, as is encryption.")
          (add-after 'unpack 'patch-Makefile
            (lambda _
              (substitute* "Makefile"
-               (("build_tools/gnu_parallel") "parallel")
                ;; Don't depend on the static library when installing.
                (("install: install-static")
                 "install: install-shared")
@@ -889,20 +898,20 @@ types are supported, as is encryption.")
          (add-before 'check 'disable-failing-tests
            (lambda _
              (substitute* "Makefile"
-               ;; This test fails with GCC-5 and is unmaintained.
-               ;; https://github.com/facebook/rocksdb/issues/2148
-               (("^[[:blank:]]+spatial_db_test[[:blank:]]+\\\\") "\\")
                ;; These tests reliably fail due to "Too many open files".
                (("^[[:blank:]]+env_test[[:blank:]]+\\\\") "\\")
                (("^[[:blank:]]+persistent_cache_test[[:blank:]]+\\\\") "\\"))
              #t))
-         (add-after 'check 'build-release-libraries
+         (add-after 'check 'build
            ;; The default build target is a debug build for tests. The
-           ;; install target depends on "shared_lib" and "static_lib"
-           ;; targets for release builds so we build them here for clarity.
-           ;; TODO: Add debug output.
-           (lambda* (#:key (make-flags '()) #:allow-other-keys)
-             (zero? (apply system* "make" "shared_lib" make-flags)))))))
+           ;; install target depends on the "shared_lib" release target
+           ;; so we build it here for clarity.
+           (lambda* (#:key (make-flags '()) parallel-build? #:allow-other-keys)
+               (apply invoke "make" "shared_lib"
+                      `(,@(if parallel-build?
+                              `("-j" ,(number->string (parallel-job-count)))
+                              '())
+                        ,@make-flags)))))))
     (native-inputs
      `(("parallel" ,parallel)
        ("perl" ,perl)
@@ -926,8 +935,9 @@ between @dfn{Write-Amplification-Factor} (WAF), @dfn{Read-Amplification-Factor}
 (RAF) and @dfn{Space-Amplification-Factor} (SAF).  It has multi-threaded
 compactions, making it specially suitable for storing multiple terabytes of
 data in a single database.  RocksDB is partially based on @code{LevelDB}.")
-    ;; RocksDB is BSD-3 and the JNI adapter is Apache 2.0.
-    (license (list license:bsd-3 license:asl2.0))))
+    ;; RocksDB is dual licensed under GPL2 and ASL 2.0.  Some header
+    ;; files carry the 3-clause BSD license.
+    (license (list license:gpl2 license:asl2.0 license:bsd-3))))
 
 (define-public sparql-query
   (package
-- 
cgit v1.2.3


From 5a4373572232a017a3579c164d37b981a370fc6f Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 21 Feb 2018 03:14:52 +0100
Subject: gnu: snappy: Update to 1.1.7.

* gnu/packages/compression.scm (snappy): Update to 1.1.7.
[source]: Change to git archive.  Set file-name.
[build-system]: Change to CMAKE-BUILD-SYSTEM.
[arguments]: Add #:configure-flags.
[description]: Fix infractions.
---
 gnu/packages/compression.scm | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 54c5928cb7..f55f0c2067 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -1071,21 +1071,23 @@ algorithm within the Numpy framework.")
 (define-public snappy
   (package
     (name "snappy")
-    (version "1.1.3")
+    (version "1.1.7")
     (source (origin
               (method url-fetch)
-              (uri (string-append
-                    "https://github.com/google/snappy/releases/download/"
-                    version "/" name "-" version ".tar.gz"))
+              (uri (string-append "https://github.com/google/snappy/archive/"
+                                  version ".tar.gz"))
+              (file-name (string-append "snappy-" version ".tar.gz"))
               (sha256
                (base32
-                "1wzf8yif5ym2gj52db6v5m1pxnmn258i38x7llk9x346y2nq47ig"))))
-    (build-system gnu-build-system)
+                "1m7rcdqzkys5lspj8jcsaah8w33zh28s771bw0ga2lgzfgl05yix"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON")))
     (home-page "https://github.com/google/snappy")
     (synopsis "Fast compressor/decompressor")
-    (description "Snappy is a compression/decompression library. It does not
+    (description "Snappy is a compression/decompression library.  It does not
 aim for maximum compression, or compatibility with any other compression library;
-instead, it aims for very high speeds and reasonable compression. For instance,
+instead, it aims for very high speeds and reasonable compression.  For instance,
 compared to the fastest mode of zlib, Snappy is an order of magnitude faster
 for most inputs, but the resulting compressed files are anywhere from 20% to
 100% bigger.")
-- 
cgit v1.2.3


From 8293d21c660a8c210a0fb3fd431e3dc7053f2326 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 21 Feb 2018 04:26:29 +0100
Subject: gnu: java-snappy: Update to 1.1.7.

* gnu/packages/compression.scm (java-snappy): Update to 1.1.7.
[arguments]: Use INVOKE instead of SYSTEM*.  Avoid CMAKE dependency.  Delete
Hadoop test.  Enable fixed test.
[native-inputs]: Add JAVA-COMMONS-LANG and JAVA-COMMONS-IO.
---
 gnu/packages/compression.scm | 25 +++++++++++++++----------
 1 file changed, 15 insertions(+), 10 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index f55f0c2067..423d3989aa 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -1133,7 +1133,7 @@ install: libbitshuffle.so
 (define-public java-snappy
   (package
     (name "java-snappy")
-    (version "1.1.4")
+    (version "1.1.7")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/xerial/snappy-java/archive/"
@@ -1141,7 +1141,7 @@ install: libbitshuffle.so
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1w58diryma7qz7aa24yv8shf3flxcbbw8jgcn2lih14wgmww58ww"))))
+                "0q4kxz2n97czf6g5gzq0d8yz22cgiaj7wp51rzsswh3bi99bpgg5"))))
     (build-system ant-build-system)
     (arguments
      `(#:jar-name "snappy.jar"
@@ -1181,7 +1181,9 @@ install: libbitshuffle.so
                (("NAME\\): \\$\\(SNAPPY_OBJ\\)")
                 "NAME): $(SNAPPY_OBJ)\n\t@mkdir -p $(@D)"))
              ;; Finally we can run the Makefile to build the dynamic library.
-             (zero? (system* "make" "native"))))
+             ;; Use the -nocmake target to avoid a dependency on cmake,
+             ;; which in turn requires the "git_unpacked" directory.
+             (invoke "make" "native-nocmake")))
          ;; Once we have built the shared library, we need to place it in the
          ;; "build" directory so it can be added to the jar file.
          (add-after 'build-jni 'copy-jni
@@ -1190,13 +1192,14 @@ install: libbitshuffle.so
                                "build/classes/org/xerial/snappy/native")))
          (add-before 'check 'fix-failing
            (lambda _
-             ;; This package assumes maven build, which puts results in "target".
-             ;; We put them in "build" instead, so fix that.
-             (substitute* "src/test/java/org/xerial/snappy/SnappyLoaderTest.java"
-               (("target/classes") "build/classes"))
-             ;; FIXME: probably an error
-             (substitute* "src/test/java/org/xerial/snappy/SnappyOutputStreamTest.java"
-               (("91080") "91013")))))))
+             (with-directory-excursion "src/test/java/org/xerial/snappy"
+               ;; This package assumes maven build, which puts results in "target".
+               ;; We put them in "build" instead, so fix that.
+               (substitute* "SnappyLoaderTest.java"
+                 (("target/classes") "build/classes"))
+               ;; This requires Hadoop, which is not in Guix yet.
+               (delete-file "SnappyHadoopCompatibleOutputStreamTest.java"))
+             #t)))))
     (inputs
      `(("osgi-framework" ,java-osgi-framework)))
     (propagated-inputs
@@ -1207,6 +1210,8 @@ install: libbitshuffle.so
        ("hamcrest" ,java-hamcrest-core)
        ("xerial-core" ,java-xerial-core)
        ("classworlds" ,java-plexus-classworlds)
+       ("commons-lang" ,java-commons-lang)
+       ("commons-io" ,java-commons-io)
        ("perl" ,perl)))
     (home-page "https://github.com/xerial/snappy-java")
     (synopsis "Compression/decompression algorithm in Java")
-- 
cgit v1.2.3


From bbce53c4b3a6576c5a13db39d558331dc0eabd29 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 24 Feb 2018 19:42:36 +0100
Subject: gnu: Add boost@1.66.0.

* gnu/packages/boost.scm (boost-1.66): New public variable.
---
 gnu/packages/boost.scm | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/boost.scm b/gnu/packages/boost.scm
index 91dd2f9156..f4ba82810a 100644
--- a/gnu/packages/boost.scm
+++ b/gnu/packages/boost.scm
@@ -110,6 +110,20 @@ across a broad spectrum of applications.")
     (license (license:x11-style "http://www.boost.org/LICENSE_1_0.txt"
                                 "Some components have other similar licences."))))
 
+(define-public boost-1.66
+  (package
+    (inherit boost)
+    (version "1.66.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "mirror://sourceforge/boost/boost/" version "/boost_"
+                    (string-map (lambda (x) (if (eq? x #\.) #\_ x)) version)
+                    ".tar.bz2"))
+              (sha256
+               (base32
+                "1aaw48cmimsskzgiclwn0iifp62a5iw9cbqrhfari876af1828ap"))))))
+
 (define-public mdds
   (package
     (name "mdds")
-- 
cgit v1.2.3


From 1568cc14fa7b8f93eb73d21be109b0e5e00cb718 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 24 Feb 2018 19:44:47 +0100
Subject: gnu: Add cmake@3.11.

* gnu/packages/cmake.scm (cmake-3.11): New public variable.
---
 gnu/packages/cmake.scm | 59 +++++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 58 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cmake.scm b/gnu/packages/cmake.scm
index a4e2d38e36..e6c5c4e793 100644
--- a/gnu/packages/cmake.scm
+++ b/gnu/packages/cmake.scm
@@ -5,7 +5,7 @@
 ;;; Copyright © 2014 Ian Denhardt <ian@zenhack.net>
 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2017, 2018 Marius Bakke <mbakke@fastmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -31,6 +31,7 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages backup)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages crypto)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages file)
   #:use-module (gnu packages libevent)
@@ -149,3 +150,59 @@ and workspaces that can be used in the compiler environment of your choice.")
                    license:bsd-2             ; cmlibarchive
                    license:expat             ; cmjsoncpp is dual MIT/public domain
                    license:public-domain)))) ; cmlibarchive/archive_getdate.c
+
+;; Recent Ceph requires Boost 1.66, which in turn requires CMake 3.11 for
+;; its updated "FindBoost.cmake" facility.
+(define-public cmake-3.11
+  (package
+    (inherit cmake)
+    (version "3.11.0-rc2")
+    (source (origin
+              (inherit (package-source cmake))
+              (uri (string-append "https://www.cmake.org/files/v"
+                                  (version-major+minor version)
+                                  "/cmake-" version ".tar.gz"))
+              (sha256
+               (base32
+                "14p6ais19nfcwl914n4n5rbzaqwafv3qkg6nd8jw54ykn6lz6mf3"))
+              (snippet
+               '(begin
+                  ;; Drop bundled software.
+                  (with-directory-excursion "Utilities"
+                    (for-each delete-file-recursively
+                              '("cmbzip2"
+                                "cmcurl"
+                                "cmexpat"
+                                "cmliblzma"
+                                "cmzlib"))
+                    #t)))))
+    (build-system gnu-build-system)
+    (arguments
+     (substitute-keyword-arguments (package-arguments cmake)
+       ((#:make-flags flags ''()) `(cons (string-append
+                                          "ARGS=-j "
+                                          (number->string (parallel-job-count))
+                                          " --output-on-failure")
+                                         ,flags))
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (replace 'patch-bin-sh
+             (lambda _
+               (substitute*
+                   '("Modules/CompilerId/Xcode-3.pbxproj.in"
+                     "Modules/CPack.RuntimeScript.in"
+                     "Source/cmakexbuild.cxx"
+                     "Source/cmGlobalXCodeGenerator.cxx"
+                     "Source/cmLocalUnixMakefileGenerator3.cxx"
+                     "Source/cmExecProgramCommand.cxx"
+                     "Utilities/Release/release_cmake.cmake"
+                     "Utilities/cmlibarchive/libarchive/archive_write_set_format_shar.c"
+                     "Tests/CMakeLists.txt"
+                     "Tests/RunCMake/File_Generate/RunCMakeTest.cmake")
+                 (("/bin/sh") (which "sh")))
+               #t))
+           ;; This is now passed through #:make-flags.
+           (delete 'set-test-environment)))))
+    (inputs
+     `(("rhash" ,rhash)
+       ,@(package-inputs cmake)))))
-- 
cgit v1.2.3


From 5b0b520e22cc4d8e08078e50e036b093efdde49c Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 21 Feb 2018 15:24:00 +0100
Subject: gnu: ceph: Update to 12.2.4.

* gnu/packages/patches/ceph-disable-cpu-optimizations.patch: Adjust to
upstream changes.
* gnu/packages/patches/ceph-disable-unittest-throttle.patch: Delete file.
* gnu/packages/patches/ceph-rocksdb-compat.patch: New file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/storage.scm (ceph): Update to 12.2.4.
[source](patches): Adjust.
[arguments]: Add "-DWITH_BABELTRACE=OFF" in #:configure-flags.  Build with
CMAKE-3.11.  Adjust file substitutions.  Wrap 'ceph' executable.
[native-inputs]: Add GPERF.
[inputs]: Replace BOOST with BOOST-1.66.  Add PYTHON2-PRETTYTABLE.
---
 gnu/local.mk                                       |  2 +-
 .../patches/ceph-disable-cpu-optimizations.patch   | 64 +++++++++-------------
 .../patches/ceph-disable-unittest-throttle.patch   | 52 ------------------
 gnu/packages/patches/ceph-rocksdb-compat.patch     | 63 +++++++++++++++++++++
 gnu/packages/storage.scm                           | 42 ++++++++------
 5 files changed, 116 insertions(+), 107 deletions(-)
 delete mode 100644 gnu/packages/patches/ceph-disable-unittest-throttle.patch
 create mode 100644 gnu/packages/patches/ceph-rocksdb-compat.patch

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index 2ef9b68590..d091a89b82 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -581,7 +581,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/cdparanoia-fpic.patch			\
   %D%/packages/patches/cdrtools-3.01-mkisofs-isoinfo.patch 	\
   %D%/packages/patches/ceph-disable-cpu-optimizations.patch	\
-  %D%/packages/patches/ceph-disable-unittest-throttle.patch	\
+  %D%/packages/patches/ceph-rocksdb-compat.patch		\
   %D%/packages/patches/ceph-skip-collect-sys-info-test.patch	\
   %D%/packages/patches/ceph-skip-unittest_blockdev.patch	\
   %D%/packages/patches/chmlib-inttypes.patch			\
diff --git a/gnu/packages/patches/ceph-disable-cpu-optimizations.patch b/gnu/packages/patches/ceph-disable-cpu-optimizations.patch
index f33eb629d6..421b1d4fe1 100644
--- a/gnu/packages/patches/ceph-disable-cpu-optimizations.patch
+++ b/gnu/packages/patches/ceph-disable-cpu-optimizations.patch
@@ -1,5 +1,4 @@
-Disable CPU optimizations not supported by all x86_64 systems. Also
-don't add anything for i686.
+Disable CPU optimizations not supported by all x86_64 systems.
 
 --- a/cmake/modules/SIMDExt.cmake	2017-03-23 22:22:58.254071694 +0100
 +++ b/cmake/modules/SIMDExt.cmake	2017-03-23 22:23:22.446848845 +0100
@@ -15,39 +14,30 @@ don't add anything for i686.
  #
  # SIMD_COMPILE_FLAGS
  #
-@@ -73,7 +68,7 @@
-     set(SIMD_COMPILE_FLAGS "${SIMD_COMPILE_FLAGS} -mfpu=neon")
-   endif()
- 
--elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "i386|i686|amd64|x86_64|AMD64")
-+elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "amd64|x86_64|AMD64")
-   set(HAVE_INTEL 1)
-   CHECK_C_COMPILER_FLAG(-msse HAVE_INTEL_SSE)
-   if(HAVE_INTEL_SSE)
-@@ -83,26 +78,6 @@
-   if(HAVE_INTEL_SSE2)
-     set(SIMD_COMPILE_FLAGS "${SIMD_COMPILE_FLAGS} -msse2")
-   endif()
--  CHECK_C_COMPILER_FLAG(-msse3 HAVE_INTEL_SSE3)
--  if(HAVE_INTEL_SSE3)
--    set(SIMD_COMPILE_FLAGS "${SIMD_COMPILE_FLAGS} -msse3")
--  endif()
--  CHECK_C_COMPILER_FLAG(-mssse3 HAVE_INTEL_SSSE3)
--  if(HAVE_INTEL_SSSE3)
--    set(SIMD_COMPILE_FLAGS "${SIMD_COMPILE_FLAGS} -mssse3")
--  endif()
--  CHECK_C_COMPILER_FLAG(-mpclmul HAVE_INTEL_PCLMUL)
--  if(HAVE_INTEL_PCLMUL)
--    set(SIMD_COMPILE_FLAGS "${SIMD_COMPILE_FLAGS} -mpclmul")
--  endif()
--  CHECK_C_COMPILER_FLAG(-msse4.1 HAVE_INTEL_SSE4_1)
--  if(HAVE_INTEL_SSE4_1)
--    set(SIMD_COMPILE_FLAGS "${SIMD_COMPILE_FLAGS} -msse4.1")
--  endif()
--  CHECK_C_COMPILER_FLAG(-msse4.2 HAVE_INTEL_SSE4_2)
--  if(HAVE_INTEL_SSE4_2)
--    set(SIMD_COMPILE_FLAGS "${SIMD_COMPILE_FLAGS} -msse4.2")
--  endif()
+@@ -85,26 +80,6 @@
+       if(HAVE_INTEL_SSE2)
+         set(SIMD_COMPILE_FLAGS "${SIMD_COMPILE_FLAGS} -msse2")
+       endif()
+-      CHECK_C_COMPILER_FLAG(-msse3 HAVE_INTEL_SSE3)
+-      if(HAVE_INTEL_SSE3)
+-        set(SIMD_COMPILE_FLAGS "${SIMD_COMPILE_FLAGS} -msse3")
+-      endif()
+-      CHECK_C_COMPILER_FLAG(-mssse3 HAVE_INTEL_SSSE3)
+-      if(HAVE_INTEL_SSSE3)
+-        set(SIMD_COMPILE_FLAGS "${SIMD_COMPILE_FLAGS} -mssse3")
+-      endif()
+-      CHECK_C_COMPILER_FLAG(-mpclmul HAVE_INTEL_PCLMUL)
+-      if(HAVE_INTEL_PCLMUL)
+-        set(SIMD_COMPILE_FLAGS "${SIMD_COMPILE_FLAGS} -mpclmul")
+-      endif()
+-      CHECK_C_COMPILER_FLAG(-msse4.1 HAVE_INTEL_SSE4_1)
+-      if(HAVE_INTEL_SSE4_1)
+-        set(SIMD_COMPILE_FLAGS "${SIMD_COMPILE_FLAGS} -msse4.1")
+-      endif()
+-      CHECK_C_COMPILER_FLAG(-msse4.2 HAVE_INTEL_SSE4_2)
+-      if(HAVE_INTEL_SSE4_2)
+-        set(SIMD_COMPILE_FLAGS "${SIMD_COMPILE_FLAGS} -msse4.2")
+-      endif()
+     endif(CMAKE_SYSTEM_PROCESSOR MATCHES "amd64|x86_64|AMD64")
+   endif(CMAKE_SYSTEM_PROCESSOR MATCHES "i686|amd64|x86_64|AMD64")
  elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "(powerpc|ppc)64le")
-   set(HAVE_PPC64LE 1)
-   message(STATUS " we are ppc64le")
diff --git a/gnu/packages/patches/ceph-disable-unittest-throttle.patch b/gnu/packages/patches/ceph-disable-unittest-throttle.patch
deleted file mode 100644
index 08ae5f9e24..0000000000
--- a/gnu/packages/patches/ceph-disable-unittest-throttle.patch
+++ /dev/null
@@ -1,52 +0,0 @@
-FIXME: This test broke after the gcc-5/glibc-2.25 core-updates merge.
-Not sure what's going on here, it hangs after spawning the first thread.
-
-diff --git a/src/test/common/Throttle.cc b/src/test/common/Throttle.cc
-index 5b6d73217d..40a477b2a3 100644
---- a/src/test/common/Throttle.cc
-+++ b/src/test/common/Throttle.cc
-@@ -216,44 +216,6 @@ TEST_F(ThrottleTest, wait) {
-   } while(!waited);
- }
- 
--TEST_F(ThrottleTest, destructor) {
--  Thread_get *t;
--  {
--    int64_t throttle_max = 10;
--    Throttle *throttle = new Throttle(g_ceph_context, "throttle", throttle_max);
--
--    ASSERT_FALSE(throttle->get(5));
--
--    t = new Thread_get(*throttle, 7);
--    t->create("t_throttle");
--    bool blocked;
--    useconds_t delay = 1;
--    do {
--      usleep(delay);
--      if (throttle->get_or_fail(1)) {
--	throttle->put(1);
--	blocked = false;
--      } else {
--	blocked = true;
--      }
--      delay *= 2;
--    } while(!blocked);
--    delete throttle;
--  }
--
--  { //
--    // The thread is left hanging, otherwise it will abort().
--    // Deleting the Throttle on which it is waiting creates a
--    // inconsistency that will be detected: the Throttle object that
--    // it references no longer exists.
--    //
--    pthread_t id = t->get_thread_id();
--    ASSERT_EQ(pthread_kill(id, 0), 0);
--    delete t;
--    ASSERT_EQ(pthread_kill(id, 0), 0);
--  }
--}
--
- std::pair<double, std::chrono::duration<double> > test_backoff(
-   double low_threshhold,
-   double high_threshhold,
diff --git a/gnu/packages/patches/ceph-rocksdb-compat.patch b/gnu/packages/patches/ceph-rocksdb-compat.patch
new file mode 100644
index 0000000000..1a3c6b0b23
--- /dev/null
+++ b/gnu/packages/patches/ceph-rocksdb-compat.patch
@@ -0,0 +1,63 @@
+Fix compatibility with newer versions of RocksDB.
+
+Adapted from this upstream patch, with some additional changes for 12.2:
+https://github.com/ceph/ceph/commit/9d73a7121fdb1ae87cb1aa6f7d9d7a13f329ae68
+
+diff --git a/src/kv/RocksDBStore.cc b/src/kv/RocksDBStore.cc
+index 8660afe1886d..bc0de79e23cb 100644
+--- a/src/kv/RocksDBStore.cc
++++ b/src/kv/RocksDBStore.cc
+@@ -505,7 +505,7 @@
+   // considering performance overhead, default is disabled
+   if (g_conf->rocksdb_perf) {
+     rocksdb::SetPerfLevel(rocksdb::PerfLevel::kEnableTimeExceptForMutex);
+-    rocksdb::perf_context.Reset();
++    rocksdb::get_perf_context()->Reset();
+   }
+ 
+   RocksDBTransactionImpl * _t =
+@@ -532,13 +532,13 @@
+     utime_t write_wal_time;
+     utime_t write_pre_and_post_process_time;
+     write_wal_time.set_from_double(
+-	static_cast<double>(rocksdb::perf_context.write_wal_time)/1000000000);
++	static_cast<double>(rocksdb::get_perf_context()->write_wal_time)/1000000000);
+     write_memtable_time.set_from_double(
+-	static_cast<double>(rocksdb::perf_context.write_memtable_time)/1000000000);
++	static_cast<double>(rocksdb::get_perf_context()->write_memtable_time)/1000000000);
+     write_delay_time.set_from_double(
+-	static_cast<double>(rocksdb::perf_context.write_delay_time)/1000000000);
++	static_cast<double>(rocksdb::get_perf_context()->write_delay_time)/1000000000);
+     write_pre_and_post_process_time.set_from_double(
+-	static_cast<double>(rocksdb::perf_context.write_pre_and_post_process_time)/1000000000);
++	static_cast<double>(rocksdb::get_perf_context()->write_pre_and_post_process_time)/1000000000);
+     logger->tinc(l_rocksdb_write_memtable_time, write_memtable_time);
+     logger->tinc(l_rocksdb_write_delay_time, write_delay_time);
+     logger->tinc(l_rocksdb_write_wal_time, write_wal_time);
+@@ -558,7 +558,7 @@
+   // considering performance overhead, default is disabled
+   if (g_conf->rocksdb_perf) {
+     rocksdb::SetPerfLevel(rocksdb::PerfLevel::kEnableTimeExceptForMutex);
+-    rocksdb::perf_context.Reset();
++    rocksdb::get_perf_context()->Reset();
+   }
+ 
+   RocksDBTransactionImpl * _t =
+@@ -586,13 +586,13 @@
+     utime_t write_wal_time;
+     utime_t write_pre_and_post_process_time;
+     write_wal_time.set_from_double(
+-	static_cast<double>(rocksdb::perf_context.write_wal_time)/1000000000);
++	static_cast<double>(rocksdb::get_perf_context()->write_wal_time)/1000000000);
+     write_memtable_time.set_from_double(
+-	static_cast<double>(rocksdb::perf_context.write_memtable_time)/1000000000);
++	static_cast<double>(rocksdb::get_perf_context()->write_memtable_time)/1000000000);
+     write_delay_time.set_from_double(
+-	static_cast<double>(rocksdb::perf_context.write_delay_time)/1000000000);
++	static_cast<double>(rocksdb::get_perf_context()->write_delay_time)/1000000000);
+     write_pre_and_post_process_time.set_from_double(
+-	static_cast<double>(rocksdb::perf_context.write_pre_and_post_process_time)/1000000000);
++	static_cast<double>(rocksdb::get_perf_context()->write_pre_and_post_process_time)/1000000000);
+     logger->tinc(l_rocksdb_write_memtable_time, write_memtable_time);
+     logger->tinc(l_rocksdb_write_delay_time, write_delay_time);
+     logger->tinc(l_rocksdb_write_wal_time, write_wal_time);
diff --git a/gnu/packages/storage.scm b/gnu/packages/storage.scm
index bee349f6f6..54d91c1f3c 100644
--- a/gnu/packages/storage.scm
+++ b/gnu/packages/storage.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2017, 2018 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -29,6 +29,7 @@
   #:use-module (gnu packages bdw-gc)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
+  #:use-module (gnu packages cmake)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages crypto)
   #:use-module (gnu packages cryptsetup)
@@ -36,6 +37,7 @@
   #:use-module (gnu packages databases)
   #:use-module (gnu packages disk)
   #:use-module (gnu packages gnuzilla)
+  #:use-module (gnu packages gperf)
   #:use-module (gnu packages jemalloc)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages lua)
@@ -50,18 +52,18 @@
 (define-public ceph
   (package
     (name "ceph")
-    (version "12.0.2")
+    (version "12.2.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://download.ceph.com/tarballs/ceph-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0l9v072ba28i984y5rwny9i11nmpyx5bl7awxg48plyadm2l3g14"))
+                "13hv8scaxc1gdvrhzbfnsk4yy3pla6n1i4j4j4zf7schmbf0j8mp"))
               (patches
                (search-patches "ceph-skip-unittest_blockdev.patch"
                                "ceph-skip-collect-sys-info-test.patch"
-                               "ceph-disable-unittest-throttle.patch"
+                               "ceph-rocksdb-compat.patch"
                                "ceph-disable-cpu-optimizations.patch"))
               (modules '((guix build utils)))
               (snippet
@@ -74,7 +76,6 @@
                               ;"src/xxHash"
                               ;"src/zstd"
                               ;"src/civetweb"
-                              ;"src/Beast"
                               "src/test/downloads"
                               "src/dpdk"
                               "src/spdk"
@@ -105,6 +106,7 @@
                "-DWITH_SYSTEM_BOOST=ON"
                "-DWITH_PYTHON3=ON"
                ;; TODO: Enable these when available in Guix.
+               "-DWITH_BABELTRACE=OFF"
                "-DWITH_LTTNG=OFF"
                "-DWITH_XFS=OFF"
                "-DWITH_XIO=OFF"
@@ -114,6 +116,7 @@
        ;; <https://bugs.gnu.org/29674> for details. Disable tests until
        ;; resolved.
        #:tests? #f
+       #:cmake ,cmake-3.11
        #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'patch-source
@@ -152,21 +155,17 @@
 
                (substitute* "src/test/test_subprocess.cc"
                  (("/bin/sh") (which "sh")))
-               (substitute* "src/test/ceph_objectstore_tool.py"
+               (substitute* "qa/standalone/special/ceph_objectstore_tool.py"
                  (("/bin/rm") (which "rm")))
                (substitute* "src/ceph-disk/ceph_disk/main.py"
                  (("/bin/mount") "mount")
                  (("/bin/umount") "umount")
                  (("/sbin/blkid") (which "blkid"))
+                 (("'cryptsetup'") (string-append "'" (which "cryptsetup") "'"))
                  (("'sgdisk'") (string-append "'" (which "sgdisk") "'"))
                  (("'parted'") (string-append "'" (which "parted") "'"))
                  (("'udevadm'") (string-append "'" (which "udevadm") "'")))
 
-               (substitute* "src/ceph-disk-udev"
-                 (("/sbin/cryptsetup") (which "cryptsetup"))
-                 (("/usr/sbin/sgdisk") (which "sgdisk"))
-                 (("/usr/sbin/ceph-disk")
-                  (string-append out "/bin/ceph-disk")))
                (substitute* "udev/50-rbd.rules"
                  (("/usr/bin/ceph-rbdnamer")
                   (string-append out "/bin/ceph-rbdnamer")))
@@ -263,23 +262,31 @@
                                       (getenv "PYTHONPATH")))
                #t)))
          (add-after 'install 'wrap-python-scripts
-           (lambda* (#:key outputs #:allow-other-keys)
+           (lambda* (#:key inputs outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
+                    (ceph (string-append out "/bin/ceph"))
                     (ceph-disk (string-append out "/bin/ceph-disk"))
                     (ceph-detect-init (string-append
                                        out "/bin/ceph-detect-init"))
-                    (PYTHONPATH (string-append
-                                 out "/lib/python2.7/site-packages")))
 
+                    (prettytable (assoc-ref inputs "python2-prettytable"))
+
+                    (sitedir (lambda (package)
+                               (string-append package
+                                              "/lib/python2.7/site-packages")))
+                    (PYTHONPATH (string-append
+                                 (sitedir out) ":"
+                                 (sitedir prettytable))))
                (for-each (lambda (executable)
                            (wrap-program executable
                              `("PYTHONPATH" ":" prefix (,PYTHONPATH))))
-                         (list ceph-disk ceph-detect-init))
+                         (list ceph ceph-disk ceph-detect-init))
                #t))))))
     (outputs
      '("out" "lib"))
     (native-inputs
-     `(("pkg-config" ,pkg-config)
+     `(("gperf" ,gperf)
+       ("pkg-config" ,pkg-config)
        ("python-cython" ,python-cython)
        ("python-sphinx" ,python-sphinx)
        ("yasm" ,yasm)
@@ -310,7 +317,7 @@
        ("python2-testtools" ,python2-testtools)
        ("python2-tox" ,python2-tox)))
     (inputs
-     `(("boost" ,boost)
+     `(("boost" ,boost-1.66)
        ("curl" ,curl)
        ("cryptsetup" ,cryptsetup)
        ("expat" ,expat)
@@ -329,6 +336,7 @@
        ("nss" ,nss)
        ("parted" ,parted)
        ("python@2" ,python-2)
+       ("python2-prettytable" ,python2-prettytable)      ;used by ceph_daemon.py
        ("python@3" ,python-3)
        ("rocksdb" ,rocksdb)
        ("snappy" ,snappy)
-- 
cgit v1.2.3


From 5275f69e6ea445f7ac7b7c3769bd652f96753817 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sun, 4 Mar 2018 04:40:38 +0100
Subject: gnu: freexl: Update to 1.0.5 [security fixes].

Fixes CVE-2018-7435, CVE-2018-7436, CVE-2018-7437, CVE-2018-7438 and
CVE-2018-7439.

* gnu/packages/xml.scm (freexl): Update to 1.0.5.
---
 gnu/packages/xml.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm
index add374c899..eabd28233a 100644
--- a/gnu/packages/xml.scm
+++ b/gnu/packages/xml.scm
@@ -1249,14 +1249,14 @@ libxls cannot write Excel files.")
 (define-public freexl
   (package
     (name "freexl")
-    (version "1.0.4")
+    (version "1.0.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://www.gaia-gis.it/gaia-sins/"
                                   name  "-" version ".tar.gz"))
               (sha256
                (base32
-                "09bwzqjc41cc8qw8qkw9wq58rg9nax8r3fg19iny5vmw1c0z23sh"))))
+                "03bmwq6hngmzwpqpb7c2amqlspz4q69iv96nlf0f5c0qs98b3j9x"))))
     (build-system gnu-build-system)
     (home-page "https://www.gaia-gis.it/fossil/freexl/index")
     (synopsis "Read Excel files")
-- 
cgit v1.2.3


From 3e57b7d99b49472470ca1134c4e6e1f7d334361e Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sun, 4 Mar 2018 05:54:48 +0100
Subject: gnu: multipath-tools: Update to 0.7.4.

* gnu/packages/linux.scm (multipath-tools): Update to 0.7.4.
[source]: Download using HTTPS.
---
 gnu/packages/linux.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 1f9e084e85..2c3a1a84c2 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -2864,15 +2864,15 @@ arrays when needed.")
 (define-public multipath-tools
   (package
     (name "multipath-tools")
-    (version "0.7.1")
+    (version "0.7.4")
     (source (origin
               (method url-fetch)
-              (uri (string-append "http://git.opensvc.com/?p=multipath-tools/"
+              (uri (string-append "https://git.opensvc.com/?p=multipath-tools/"
                                   ".git;a=snapshot;h=" version ";sf=tgz"))
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0w0rgi3lqksaki30yvd4l5rgjqb0d7js1sh7masl8aw6xbrsm26p"))
+                "02lk453wa2gfxkl8zmdws15nkcibln2yw76zm779pkngkhggl6w8"))
               (modules '((guix build utils)))
               (snippet
                '(begin
-- 
cgit v1.2.3


From 03b71957947c219a74b77b0831d9abc8d4bbfd24 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 3 Mar 2018 23:17:04 +0100
Subject: gnu: liblo: Mark up description.

* gnu/packages/audio.scm (liblo)[description]: Use @dfn.
---
 gnu/packages/audio.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 3ae2b1ba47..d8569096ab 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -1646,7 +1646,7 @@ essential distortions.")
     (synopsis "Implementation of the Open Sound Control protocol")
     (description
      "liblo is a lightweight library that provides an easy to use
-implementation of the Open Sound Control (OSC) protocol.")
+implementation of the Open Sound Control (@dfn{OSC}) protocol.")
     (license license:lgpl2.1+)))
 
 (define-public python-pyaudio
-- 
cgit v1.2.3


From 95943ed7dca205e81c22cd0723a3ab1ba67d4040 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 4 Mar 2018 01:09:57 +0100
Subject: gnu: cloc: Update to 1.76.

* gnu/packages/code.scm (cloc): Update to 1.76.
[source]: Update origin URI scheme.
[inputs]: Add perl-parallel-forkmanager.
---
 gnu/packages/code.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm
index 2067067f20..4a63cba7a0 100644
--- a/gnu/packages/code.scm
+++ b/gnu/packages/code.scm
@@ -204,23 +204,24 @@ COCOMO model or user-provided parameters.")
 (define-public cloc
   (package
     (name "cloc")
-    (version "1.74")
+    (version "1.76")
     (source
      (origin
        (method url-fetch)
        (uri (string-append
-             "https://github.com/AlDanial/cloc/releases/download/" version
+             "https://github.com/AlDanial/cloc/releases/download/v" version
              "/cloc-" version ".tar.gz"))
        (sha256
         (base32
-         "0rq5xfiln1wlv3yr9mg18ax4gskbss786iqaf0v45iv6awyl5b2m"))))
+         "05srlvzwisr7y7ymvzb5yfdsrspja27ysqdmkwhiiivy84mq2gnl"))))
     (build-system gnu-build-system)
     (inputs
      `(("coreutils" ,coreutils)
        ("perl" ,perl)
        ("perl-algorithm-diff" ,perl-algorithm-diff)
-       ("perl-regexp-common" ,perl-regexp-common)
-       ("perl-digest-md5" ,perl-digest-md5)))
+       ("perl-digest-md5" ,perl-digest-md5)
+       ("perl-parallel-forkmanager" ,perl-parallel-forkmanager)
+       ("perl-regexp-common" ,perl-regexp-common)))
     (arguments
      `(#:phases (modify-phases %standard-phases
                   (delete 'configure)
-- 
cgit v1.2.3


From 53244d1ffa544305d4b6c19907dfcaf2bff2fd21 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 4 Mar 2018 01:11:47 +0100
Subject: gnu: cloc: Update phase style.

* gnu/packages/code.scm (cloc)[arguments]: Substitute INVOKE for SYSTEM*
and end phases with #t.
---
 gnu/packages/code.scm | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm
index 4a63cba7a0..8d9c661302 100644
--- a/gnu/packages/code.scm
+++ b/gnu/packages/code.scm
@@ -229,13 +229,13 @@ COCOMO model or user-provided parameters.")
                   (replace 'install
                     (lambda* (#:key inputs outputs #:allow-other-keys)
                       (let* ((out (assoc-ref outputs "out")))
-                        (zero?
-                         (system* "make" "-C" "Unix"
-                                  (string-append "prefix=" out)
-                                  (string-append "INSTALL="
-                                                 (assoc-ref inputs "coreutils")
-                                                 "/bin/install")
-                                  "install")))))
+                        (invoke "make" "-C" "Unix"
+                                (string-append "prefix=" out)
+                                (string-append "INSTALL="
+                                               (assoc-ref inputs "coreutils")
+                                               "/bin/install")
+                                "install")
+                        #t)))
                   (add-after 'install 'wrap-program
                     (lambda* (#:key inputs outputs #:allow-other-keys)
                       (let ((out (assoc-ref outputs "out")))
-- 
cgit v1.2.3


From e0dbead5a73ffc666af38e044bb48ca94f261794 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 4 Mar 2018 01:26:07 +0100
Subject: gnu: ii: Update to 1.8.

* gnu/packages/irc.scm (ii): Update to 1.8.
---
 gnu/packages/irc.scm | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/irc.scm b/gnu/packages/irc.scm
index b00fd6cc19..3521b18dcd 100644
--- a/gnu/packages/irc.scm
+++ b/gnu/packages/irc.scm
@@ -5,7 +5,7 @@
 ;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 ng0 <ng0@infotropique.org>
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
-;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -272,22 +272,22 @@ using a mouse.  It is customizable and extensible with plugins and scripts.")
 (define-public ii
   (package
     (name "ii")
-    (version "1.7")
+    (version "1.8")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://dl.suckless.org/tools/"
                                   name "-" version ".tar.gz"))
               (sha256
                (base32
-                "176cqwnn6h7w4kbfd66hzqa243l26pqp2b06bii0nmnm0rkaqwis"))))
+                "1lk8vjl7i8dcjh4jkg8h8bkapcbs465sy8g9c0chfqsywbmf3ndr"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:tests? #f ; no tests
+     `(#:tests? #f                      ; no tests
        #:make-flags (list (string-append "PREFIX=" %output)
                           "CC=gcc")
        #:phases
        (modify-phases %standard-phases
-         (delete 'configure)))) ; no configure
+         (delete 'configure))))         ; no configure
     (home-page "http://tools.suckless.org/ii/")
     (synopsis "FIFO and file system based IRC client")
     (description
-- 
cgit v1.2.3


From d035eaa3049d58314680a3b10acbe832ca1ed22f Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 4 Mar 2018 01:27:15 +0100
Subject: gnu: ii, sic: Use HTTPS home pages.

* gnu/packages/irc.scm (ii, sic)[home-page]: Use HTTPS.
---
 gnu/packages/irc.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/irc.scm b/gnu/packages/irc.scm
index 3521b18dcd..e59b34417b 100644
--- a/gnu/packages/irc.scm
+++ b/gnu/packages/irc.scm
@@ -288,7 +288,7 @@ using a mouse.  It is customizable and extensible with plugins and scripts.")
        #:phases
        (modify-phases %standard-phases
          (delete 'configure))))         ; no configure
-    (home-page "http://tools.suckless.org/ii/")
+    (home-page "https://tools.suckless.org/ii/")
     (synopsis "FIFO and file system based IRC client")
     (description
      "ii (Irc it) is a minimalist FIFO and file system based IRC client.")
@@ -313,7 +313,7 @@ using a mouse.  It is customizable and extensible with plugins and scripts.")
        #:phases
        (modify-phases %standard-phases
          (delete 'configure)))) ; no configure
-    (home-page "http://tools.suckless.org/sic/")
+    (home-page "https://tools.suckless.org/sic/")
     (synopsis "Simple IRC client")
     (description
      "sic is a simple IRC client, even more minimalistic than ii.")
-- 
cgit v1.2.3


From 7730b7179c615319cf038f4d83939dc9bbe7b750 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 4 Mar 2018 16:56:27 +0100
Subject: gnu: gitolite: Update to 3.6.7.

* gnu/packages/version-control.scm (gitolite): Update to 3.6.7.
---
 gnu/packages/version-control.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index 05f50869a3..f6b346fff8 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -928,7 +928,7 @@ also walk each side of a merge and test those changes individually.")
 (define-public gitolite
   (package
     (name "gitolite")
-    (version "3.6.6")
+    (version "3.6.7")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -937,7 +937,7 @@ also walk each side of a merge and test those changes individually.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "07q33f86694s0x3k9lcmy1vzfw9appdrlmmb9j3bz4qkrxqdnwb9"))))
+                "1idxipg0df80bhjcxgwxs3lllqnkvhwpinmfv1xvg1l98fxiapgp"))))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f ; no tests
-- 
cgit v1.2.3


From 92793c7b0287558becefeaa4832ebcb16e34a243 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 4 Mar 2018 16:57:01 +0100
Subject: gnu: gitolite: Update phase style.

* gnu/packages/version-control.scm (gitolite): Substitute INVOKE for
SYSTEM* and end phases with #t.
---
 gnu/packages/version-control.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index f6b346fff8..209df2bb12 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -958,7 +958,8 @@ also walk each side of a merge and test those changes individually.")
                         ;; This works because gitolite-shell is in the PATH.
                         (substitute* "src/triggers/post-compile/ssh-authkeys"
                           (("\\$glshell \\$user")
-                           "gitolite-shell $user")))))
+                           "gitolite-shell $user"))
+                        #t)))
                   (replace 'install
                     (lambda* (#:key outputs #:allow-other-keys)
                       (let* ((output (assoc-ref outputs "out"))
@@ -966,7 +967,7 @@ also walk each side of a merge and test those changes individually.")
                              (bindir (string-append output "/bin")))
                         (mkdir-p sharedir)
                         (mkdir-p bindir)
-                        (system* "./install" "-to" sharedir)
+                        (invoke "./install" "-to" sharedir)
                         ;; Create symlinks for executable scripts in /bin.
                         (for-each (lambda (script)
                                     (symlink (string-append sharedir "/" script)
-- 
cgit v1.2.3


From bd128d5e880ba73ce217e864f1cce6fe1b655ff1 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 4 Mar 2018 17:06:10 +0100
Subject: gnu: footswitch: Remove redundant MKDIR-P.

* gnu/packages/accessibility.scm (footswitch)[arguments]: Remove MKDIR-P
before INSTALL-FILE.
---
 gnu/packages/accessibility.scm | 1 -
 1 file changed, 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/accessibility.scm b/gnu/packages/accessibility.scm
index 2ca4e27f81..53ea99739b 100644
--- a/gnu/packages/accessibility.scm
+++ b/gnu/packages/accessibility.scm
@@ -109,7 +109,6 @@ available to help to click.")
                       (lambda* (#:key outputs #:allow-other-keys)
                         (let ((bin (string-append (assoc-ref outputs "out")
                                                   "/bin")))
-                          (mkdir-p bin)
                           (install-file "footswitch" bin)
                           #t))))))
       (home-page "https://github.com/rgerganov/footswitch")
-- 
cgit v1.2.3


From ed36949a9d0e5fd5582cc85e533c1ef8a8b2543e Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 4 Mar 2018 17:09:27 +0100
Subject: gnu: footswitch: Update to 0.1-2.deedd87.

* gnu/packages/accessibility.scm (footswitch): Update to 0.1-2.deedd87.
---
 gnu/packages/accessibility.scm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/accessibility.scm b/gnu/packages/accessibility.scm
index 53ea99739b..f2cbfc480b 100644
--- a/gnu/packages/accessibility.scm
+++ b/gnu/packages/accessibility.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2017 ng0 <ng0@infotropique.org>
 ;;; Copyright © 2017 Stefan Reichör <stefan@xsteve.at>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -82,10 +83,11 @@ available to help to click.")
     (license license:gpl2+)))
 
 (define-public footswitch
-  (let ((commit "7cb0a9333a150c27c7e4746ee827765d244e567a"))
+  (let ((commit "deedd87fd90fad90ce342aeabafd4a3198d7d3d4")
+        (revision "2"))
     (package
       (name "footswitch")
-      (version (git-version "0.1" "1" commit))
+      (version (git-version "0.1" revision commit))
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
@@ -93,7 +95,7 @@ available to help to click.")
                       (commit commit)))
                 (file-name (git-file-name name version))
                 (sha256
-                 (base32 "0mg1vr4a9vls5y435w7wdnr1vb5059gy60lvrdfjgzhd2wwf47iw"))))
+                 (base32 "1ys90wqyz62kffa8m3hgaq1dl7f29x3mrc3zqfjrkbn2ps0k6ps0"))))
       (build-system gnu-build-system)
       (native-inputs
        `(("pkg-config" ,pkg-config)))
-- 
cgit v1.2.3


From 9539016e3addb4bd5b4adfab27334131a532a11c Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 4 Mar 2018 00:33:28 +0100
Subject: gnu: tomb: Use HTTPS home page.

* gnu/packages/crypto.scm (tomb)[home-page]: Use HTTPS.
---
 gnu/packages/crypto.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm
index 695f6ca088..7cac132b64 100644
--- a/gnu/packages/crypto.scm
+++ b/gnu/packages/crypto.scm
@@ -412,7 +412,7 @@ no man page, refer to the home page for usage details.")
              (let ((tomb (string-append (assoc-ref outputs "out")
                                         "/bin/tomb")))
                (zero? (system* tomb "dig" "-s" "10" "secrets.tomb"))))))))
-    (home-page "http://www.dyne.org/software/tomb")
+    (home-page "https://www.dyne.org/software/tomb")
     (synopsis "File encryption for secret data")
     (description
      "Tomb is an application to manage the creation and access of encrypted
-- 
cgit v1.2.3


From 635dd0cc96a5d06933a52a48bb9520efbd567550 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 4 Mar 2018 00:37:59 +0100
Subject: gnu: tomb: Update phase style.

* gnu/packages/crypto.scm (tomb)[arguments]: Substitute INVOKE for
SYSTEM* and end phases with #t.
---
 gnu/packages/crypto.scm | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm
index 7cac132b64..b498aabf4d 100644
--- a/gnu/packages/crypto.scm
+++ b/gnu/packages/crypto.scm
@@ -384,9 +384,9 @@ no man page, refer to the home page for usage details.")
          (delete 'configure)   ;no configuration to be done
          (add-after 'install 'i18n
            (lambda* (#:key make-flags #:allow-other-keys)
-             (zero? (apply system*
-                           "make" "-C" "extras/translations"
-                           "install" make-flags))))
+             (apply invoke "make" "-C" "extras/translations"
+                    "install" make-flags)
+             #t))
          (add-after 'install 'wrap
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let ((out (assoc-ref outputs "out")))
@@ -411,7 +411,8 @@ no man page, refer to the home page for usage details.")
              ;; querying `tomb -h`.
              (let ((tomb (string-append (assoc-ref outputs "out")
                                         "/bin/tomb")))
-               (zero? (system* tomb "dig" "-s" "10" "secrets.tomb"))))))))
+               (invoke tomb "dig" "-s" "10" "secrets.tomb")
+               #t))))))
     (home-page "https://www.dyne.org/software/tomb")
     (synopsis "File encryption for secret data")
     (description
-- 
cgit v1.2.3


From ac1a9ce8b07f3b80900ee08436ff6e683e8dc195 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 4 Mar 2018 17:20:03 +0100
Subject: gnu: papi: Update phase style.

* gnu/packages/profiling.scm (papi)[arguments]: Substitute INVOKE for
SYSTEM*, end phases with #t, and don't explicitly install LICENSE.txt.
---
 gnu/packages/profiling.scm | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/profiling.scm b/gnu/packages/profiling.scm
index 4fdf260c67..35f9d3884f 100644
--- a/gnu/packages/profiling.scm
+++ b/gnu/packages/profiling.scm
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2017 Dave Love <fx@gnu.org>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -84,7 +85,8 @@ stealtime lmsensors infiniband powercap"
          (add-before 'configure 'autoconf
            (lambda _
              (chdir "src")
-             (zero? (system* "autoconf"))))
+             (invoke "autoconf")
+             #t))
          ;; Amalgamating with the following clause gives double substitution.
          (add-before 'patch-source-shebangs 'patch-components
            (lambda _
@@ -95,26 +97,24 @@ stealtime lmsensors infiniband powercap"
          (add-after 'configure 'components
            (lambda*  (#:key inputs #:allow-other-keys)
              (with-directory-excursion "components"
-               (and
-                (with-directory-excursion "infiniband_umad"
-                  (zero? (system* "./configure")))
-                (with-directory-excursion "lmsensors"
-                  (let ((base  (assoc-ref inputs "lm-sensors")))
-                    (zero?
-                     (system*
-                      "./configure"
-                      (string-append "--with-sensors_incdir=" base
-                                     "/include/sensors")
-                      (string-append "--with-sensors_libdir=" base "/lib")))))))))
+               (with-directory-excursion "infiniband_umad"
+                 (invoke "./configure"))
+               (with-directory-excursion "lmsensors"
+                 (let ((base (assoc-ref inputs "lm-sensors")))
+                   (invoke "./configure"
+                           (string-append "--with-sensors_incdir="
+                                          base "/include/sensors")
+                           (string-append "--with-sensors_libdir="
+                                          base "/lib")))))
+             #t))
          (add-after 'install 'extra-doc
            (lambda* (#:key outputs #:allow-other-keys)
              (let ((doc (string-append (assoc-ref outputs "out")
                                        "/share/doc")))
-               (mkdir-p doc)
                (chdir "..")             ; we went into src above
                (for-each (lambda (file)
                            (install-file file doc))
-                         '("README" "RELEASENOTES.txt" "LICENSE.txt"))
+                         '("README" "RELEASENOTES.txt"))
                #t))))))
     (home-page "http://icl.cs.utk.edu/papi/")
     (synopsis "Performance Application Programming Interface")
-- 
cgit v1.2.3


From 16718b6776b6cb918cddb3abb3bfcf2405b0b297 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 28 Nov 2017 10:19:11 +0200
Subject: services: Add openntpd service.

* gnu/packages/ntp.scm (openntpd)[arguments]: Add 'configure-flags to
set openntpd daemon's user and localstatedir. Add a custom phase to not
try to create said directory at install time.
* gnu/services/networking.scm (<openntpd-configuration>): New record type.
(openntpd-shepherd-service, openntpd-service-activation): New procedures.
(openntpd-service-type): New variable.
* doc/guix.texi (Networking Services): Add openntpd documentation.
---
 doc/guix.texi               |  55 +++++++++++++++++++++++-
 gnu/packages/ntp.scm        |  13 +++++-
 gnu/services/networking.scm | 102 +++++++++++++++++++++++++++++++++++++++++++-
 3 files changed, 167 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/doc/guix.texi b/doc/guix.texi
index 057272df46..60703875f6 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -24,7 +24,7 @@ Copyright @copyright{} 2015, 2016, 2017 Leo Famulari@*
 Copyright @copyright{} 2015, 2016, 2017, 2018 Ricardo Wurmus@*
 Copyright @copyright{} 2016 Ben Woodcroft@*
 Copyright @copyright{} 2016, 2017 Chris Marusich@*
-Copyright @copyright{} 2016, 2017 Efraim Flashner@*
+Copyright @copyright{} 2016, 2017, 2018 Efraim Flashner@*
 Copyright @copyright{} 2016 John Darrington@*
 Copyright @copyright{} 2016, 2017 ng0@*
 Copyright @copyright{} 2016, 2017 Jan Nieuwenhuizen@*
@@ -10767,6 +10767,59 @@ make an initial adjustment of more than 1,000 seconds.
 List of host names used as the default NTP servers.
 @end defvr
 
+@cindex OpenNTPD
+@deffn {Scheme Procedure} openntpd-service-type
+Run the @command{ntpd}, the Network Time Protocol (NTP) daemon, as implemented
+by @uref{http://www.openntpd.org, OpenNTPD}.  The daemon will keep the system
+clock synchronized with that of the given servers.
+
+@example
+(service
+ openntpd-service-type
+ (openntpd-configuration
+  (listen-on '("127.0.0.1" "::1"))
+  (sensor '("udcf0 correction 70000"))
+  (constraint-from '("www.gnu.org"))
+  (constraints-from '("https://www.google.com/"))
+  (allow-large-adjustment? #t)))
+
+@end example
+@end deffn
+
+@deftp {Data Type} openntpd-configuration
+@table @asis
+@item @code{openntpd} (default: @code{(file-append openntpd "/sbin/ntpd")})
+The openntpd executable to use.
+@item @code{listen-on} (default: @code{'("127.0.0.1" "::1")})
+A list of local IP addresses or hostnames the ntpd daemon should listen on.
+@item @code{query-from} (default: @code{'()})
+A list of local IP address the ntpd daemon should use for outgoing queries.
+@item @code{sensor} (default: @code{'()})
+Specify a list of timedelta sensor devices ntpd should use.  @code{ntpd}
+will listen to each sensor that acutally exists and ignore non-existant ones.
+See @uref{https://man.openbsd.org/ntpd.conf, upstream documentation} for more
+information.
+@item @code{server} (default: @var{%ntp-servers})
+Specify a list of IP addresses or hostnames of NTP servers to synchronize to.
+@item @code{servers} (default: @code{'()})
+Specify a list of IP addresses or hostnames of NTP pools to synchronize to.
+@item @code{constraint-from} (default: @code{'()})
+@code{ntpd} can be configured to query the ‘Date’ from trusted HTTPS servers via TLS.
+This time information is not used for precision but acts as an authenticated
+constraint, thereby reducing the impact of unauthenticated NTP
+man-in-the-middle attacks.
+Specify a list of URLs, IP addresses or hostnames of HTTPS servers to provide
+a constraint.
+@item @code{constraints-from} (default: @code{'()})
+As with constraint from, specify a list of URLs, IP addresses or hostnames of
+HTTPS servers to provide a constraint.  Should the hostname resolve to multiple
+IP addresses, @code{ntpd} will calculate a median constraint from all of them.
+@item @code{allow-large-adjustment?} (default: @code{#f})
+Determines if @code{ntpd} is allowed to make an initial adjustment of more
+than 180 seconds.
+@end table
+@end deftp
+
 @cindex inetd
 @deffn {Scheme variable} inetd-service-type
 This service runs the @command{inetd} (@pxref{inetd invocation,,,
diff --git a/gnu/packages/ntp.scm b/gnu/packages/ntp.scm
index d270f513dc..1c3b8cd313 100644
--- a/gnu/packages/ntp.scm
+++ b/gnu/packages/ntp.scm
@@ -3,7 +3,7 @@
 ;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2015 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -107,6 +107,17 @@ computers over a network.")
                (base32
                 "0fn12i4kzsi0zkr4qp3dp9bycmirnfapajqvdfx02zhr4hanj0kv"))))
     (build-system gnu-build-system)
+    (arguments
+     '(#:configure-flags '("--with-privsep-user=ntpd"
+                           "--localstatedir=/var")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'modify-install-locations
+           (lambda _
+             ;; Don't try to create /var/run or /var/db
+             (substitute* "src/Makefile.in"
+               (("DESTDIR\\)\\$\\(localstatedir") "TMPDIR"))
+             #t)))))
     (inputs
      `(("libressl" ,libressl))) ; enable TLS time constraints. See ntpd.conf(5).
     (home-page "http://www.openntpd.org/")
diff --git a/gnu/services/networking.scm b/gnu/services/networking.scm
index 5ba3c5eed6..6ac440fd26 100644
--- a/gnu/services/networking.scm
+++ b/gnu/services/networking.scm
@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 John Darrington <jmd@gnu.org>
 ;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be>
@@ -64,6 +64,10 @@
             ntp-service
             ntp-service-type
 
+            openntpd-configuration
+            openntpd-configuration?
+            openntpd-service-type
+
             inetd-configuration
             inetd-entry
             inetd-service-type
@@ -446,6 +450,102 @@ make an initial adjustment of more than 1,000 seconds."
                               (allow-large-adjustment?
                                allow-large-adjustment?))))
 
+
+;;;
+;;; OpenNTPD.
+;;;
+
+(define-record-type* <openntpd-configuration>
+  openntpd-configuration make-openntpd-configuration
+  openntpd-configuration?
+  (openntpd                openntpd-configuration-openntpd
+                           (default openntpd))
+  (listen-on               openntpd-listen-on
+                           (default '("127.0.0.1"
+                                      "::1")))
+  (query-from              openntpd-query-from
+                           (default '()))
+  (sensor                  openntpd-sensor
+                           (default '()))
+  (server                  openntpd-server
+                           (default %ntp-servers))
+  (servers                 openntpd-servers
+                           (default '()))
+  (constraint-from         openntpd-constraint-from
+                           (default '()))
+  (constraints-from        openntpd-constraints-from
+                           (default '()))
+  (allow-large-adjustment? openntpd-allow-large-adjustment?
+                           (default #f))) ; upstream default
+
+(define (openntpd-shepherd-service config)
+  (match-record config <openntpd-configuration>
+    (openntpd listen-on query-from sensor server servers constraint-from
+              constraints-from allow-large-adjustment?)
+    (let ()
+      (define config
+        (string-join
+          (filter-map
+            (lambda (field value)
+              (string-join
+                (map (cut string-append field <> "\n")
+                     value)))
+            '("listen on " "query from " "sensor " "server " "servers "
+              "constraint from ")
+            (list listen-on query-from sensor server servers constraint-from))
+          ;; The 'constraints from' field needs to be enclosed in double quotes.
+          (string-join
+            (map (cut string-append "constraints from \"" <> "\"\n")
+                 constraints-from))))
+
+      (define ntpd.conf
+        (plain-file "ntpd.conf" config))
+
+      (list (shepherd-service
+              (provision '(ntpd))
+              (documentation "Run the Network Time Protocol (NTP) daemon.")
+              (requirement '(user-processes networking))
+              (start #~(make-forkexec-constructor
+                         (list (string-append #$openntpd "/sbin/ntpd")
+                               "-f" #$ntpd.conf
+                               "-d" ;; don't daemonize
+                               #$@(if allow-large-adjustment?
+                                    '("-s")
+                                    '()))
+                         ;; When ntpd is daemonized it repeatedly tries to respawn
+                         ;; while running, leading shepherd to disable it.  To
+                         ;; prevent spamming stderr, redirect output to logfile.
+                         #:log-file "/var/log/ntpd"))
+              (stop #~(make-kill-destructor)))))))
+
+(define (openntpd-service-activation config)
+  "Return the activation gexp for CONFIG."
+  (with-imported-modules '((guix build utils))
+    #~(begin
+        (use-modules (guix build utils))
+
+        (mkdir-p "/var/db")
+        (mkdir-p "/var/run")
+        (unless (file-exists? "/var/db/ntpd.drift")
+          (with-output-to-file "/var/db/ntpd.drift"
+                               (lambda _
+                                 (format #t "0.0")))))))
+
+(define openntpd-service-type
+  (service-type (name 'openntpd)
+                (extensions
+                 (list (service-extension shepherd-root-service-type
+                                          openntpd-shepherd-service)
+                       (service-extension account-service-type
+                                          (const %ntp-accounts))
+                       (service-extension activation-service-type
+                                          openntpd-service-activation)))
+                (default-value (openntpd-configuration))
+                (description
+                 "Run the @command{ntpd}, the Network Time Protocol (NTP)
+daemon, as implemented by @uref{http://www.openntpd.org, OpenNTPD}.  The
+daemon will keep the system clock synchronized with that of the given servers.")))
+
 
 ;;;
 ;;; Inetd.
-- 
cgit v1.2.3


From dc97f7e20e880f594cf2c9a16b4a1859469b9df5 Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Thu, 18 Jan 2018 22:37:59 +0000
Subject: gnu: Add emacs-hcl-mode.

* gnu/packages/emacs.scm (emacs-hcl-mode): New variable.
---
 gnu/packages/emacs.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 69950cc6d7..646aee7ba4 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -7313,3 +7313,26 @@ Features:
     (description "@code{epipe} provides an utility to use your editor in
 the pipeline, featuring the support for running @code{emacsclient}.")
     (license license:gpl3+)))
+
+(define-public emacs-hcl-mode
+  (package
+    (name "emacs-hcl-mode")
+    (version "0.03")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://github.com/syohex/emacs-hcl-mode/archive/"
+             version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0pvw74qpwh0znqzp6syp4wxjqs7dp1hbn5h7xfk97mff9l5d8k6x"))))
+    (build-system emacs-build-system)
+    (home-page "https://github.com/syohex/emacs-hcl-mode")
+    (synopsis "Major mode for the Hashicorp Configuration Language")
+    (description
+     "@code{emacs-hcl-mode} provides an Emacs major mode for working with
+@acronym{HCL, Hashicorp Configuration Language}.  It provides syntax
+highlighting and indentation support.")
+    (license license:gpl3+)))
-- 
cgit v1.2.3


From 68d70f6ae31865bba73a655e212f1cdf999d6225 Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Thu, 18 Jan 2018 22:38:12 +0000
Subject: gnu: Add emacs-terraform-mode.

* gnu/packages/emacs.scm (emacs-terraform-mode): New variable.
---
 gnu/packages/emacs.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 646aee7ba4..54eb816c15 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -7336,3 +7336,28 @@ the pipeline, featuring the support for running @code{emacsclient}.")
 @acronym{HCL, Hashicorp Configuration Language}.  It provides syntax
 highlighting and indentation support.")
     (license license:gpl3+)))
+
+(define-public emacs-terraform-mode
+  (package
+    (name "emacs-terraform-mode")
+    (version "0.06")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://github.com/syohex/emacs-terraform-mode/archive/"
+             version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0h9267ifdjmcin4sj8slxydbacx4bqicbvg8pa1qq2l72h9m5381"))))
+    (build-system emacs-build-system)
+    (propagated-inputs
+     `(("emacs-hcl-mode" ,emacs-hcl-mode)))
+    (home-page "https://github.com/syohex/emacs-terraform-mode")
+    (synopsis "Major mode for Terraform")
+    (description
+     "@code{emacs-terraform-mode} provides a major mode for working with
+@uref{https://www.terraform.io/, Terraform} configuration files.  Most of the
+functionality is inherited from @code{hcl-mode}.")
+    (license license:gpl3+)))
-- 
cgit v1.2.3


From 88b1a38e26644308cd0a53ce988cf6b344ae445d Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Mon, 5 Mar 2018 03:42:07 -0500
Subject: gnu: linux-libre@4.4: Update to 4.4.120.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.120.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 2c3a1a84c2..02fa9b3249 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -408,8 +408,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.4
-  (make-linux-libre "4.4.119"
-                    "1cicg1yxf6rvaz8jcz8mdvnkrba9hd16pkp9mm602bzgks6s1fy9"
+  (make-linux-libre "4.4.120"
+                    "17zk5dbpa3kilf8m8i6r2jifjgi4yjim42gyk9j6n4218jjcszv6"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
-- 
cgit v1.2.3


From ee483a5626ef695320ef2d5d57db4dd99da98a88 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Mon, 5 Mar 2018 03:43:02 -0500
Subject: gnu: linux-libre@4.9: Update to 4.9.86.

* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.86.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 02fa9b3249..e1ec8c0060 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -402,8 +402,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.85"
-                    "17anlawvbzw6m2lrbriy7kfncdllkl7n8vjzwl2dnrgxddavd3rf"
+  (make-linux-libre "4.9.86"
+                    "0fqixx3yyvznianygk8bfxzfqj8zpnjcalifhpfyb7rm3dyvi3wd"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
-- 
cgit v1.2.3


From 6a4eaafee06c167f5628ce06b7834d4a249a3600 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Mon, 5 Mar 2018 03:43:45 -0500
Subject: gnu: linux-libre@4.14: Update to 4.14.24.

* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.24.
(%linux-libre-4.14-hash): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index e1ec8c0060..d4b9d0d0b9 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -392,8 +392,8 @@ It has been modified to remove all non-free binary blobs.")
                     %linux-compatible-systems
                     #:configuration-file kernel-config))
 
-(define %linux-libre-4.14-version "4.14.23")
-(define %linux-libre-4.14-hash "0mz8v67zj3wn3kdjb2a781vx7nc1imi7kmlvf1h1m0f37hw0s47y")
+(define %linux-libre-4.14-version "4.14.24")
+(define %linux-libre-4.14-hash "1i14djw3rmxb6syl6vfd5w76rjksbbaviynwj2dwwp9ki1h6p1hr")
 
 (define-public linux-libre-4.14
   (make-linux-libre %linux-libre-4.14-version
-- 
cgit v1.2.3


From 0ebc1b934d39b6c924cbe17fd37ceb2b201e9ac2 Mon Sep 17 00:00:00 2001
From: Rutger Helling <rhelling@mykolab.com>
Date: Mon, 5 Mar 2018 12:28:34 +0100
Subject: gnu: xpra: Update to 2.2.5.

* gnu/packages/xorg.scm (xpra): Update to 2.2.5.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index a7099b4516..b73d7d6cd2 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -5944,7 +5944,7 @@ basic eye-candy effects.")
 (define-public xpra
   (package
     (name "xpra")
-    (version "2.2.4")
+    (version "2.2.5")
     (source
      (origin
        (method url-fetch)
@@ -5952,7 +5952,7 @@ basic eye-candy effects.")
                            version ".tar.xz"))
        (sha256
         (base32
-         "0v8yflvisk94bfj0zg4ggdfwrig0f3ss9kjnws3zflsr33cb2hxy"))))
+         "1q2l00nc3bgwlhjzkbk4a8x2l8z9w1799yn31icsx5hrgh98a1js"))))
     (build-system python-build-system)
     (inputs `(("ffmpeg" ,ffmpeg)
               ("flac" ,flac)
-- 
cgit v1.2.3


From f7c870f78afa5cdb27726ad9b0db931bbd87ca65 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 4 Mar 2018 17:28:37 +0100
Subject: gnu: papi: Fix documentation location.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/profiling.scm (papi)[arguments]: Install ‘documentation’
to a customary subdirectory of /share/doc.
---
 gnu/packages/profiling.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/profiling.scm b/gnu/packages/profiling.scm
index 35f9d3884f..e70269e9a1 100644
--- a/gnu/packages/profiling.scm
+++ b/gnu/packages/profiling.scm
@@ -66,7 +66,7 @@
      `(("autoconf" ,autoconf)
        ("gfortran" ,gfortran)))
     (arguments
-     '(#:tests? #f ; no check target
+     `(#:tests? #f ; no check target
        #:configure-flags
        ;; These are roughly per Fedora, but elide mx (assumed to be dead, even
        ;; Open-MX) and add and powercap -- I don't know the pros/cons of
@@ -110,7 +110,7 @@ stealtime lmsensors infiniband powercap"
          (add-after 'install 'extra-doc
            (lambda* (#:key outputs #:allow-other-keys)
              (let ((doc (string-append (assoc-ref outputs "out")
-                                       "/share/doc")))
+                                       "/share/doc/" ,name "-" ,version)))
                (chdir "..")             ; we went into src above
                (for-each (lambda (file)
                            (install-file file doc))
-- 
cgit v1.2.3


From 211748d4754f26a56655bea5dfcecc79ac9667c2 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 4 Mar 2018 17:16:46 +0100
Subject: gnu: papi: Use HTTPS home page.

* gnu/packages/profiling.scm (papi)[home-page]: Use HTTPS.
---
 gnu/packages/profiling.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/profiling.scm b/gnu/packages/profiling.scm
index e70269e9a1..d6f3aede28 100644
--- a/gnu/packages/profiling.scm
+++ b/gnu/packages/profiling.scm
@@ -116,7 +116,7 @@ stealtime lmsensors infiniband powercap"
                            (install-file file doc))
                          '("README" "RELEASENOTES.txt"))
                #t))))))
-    (home-page "http://icl.cs.utk.edu/papi/")
+    (home-page "https://icl.utk.edu/papi/")
     (synopsis "Performance Application Programming Interface")
     (description
      "PAPI provides the tool designer and application engineer with a consistent
-- 
cgit v1.2.3


From 0d34993a6579d294cad4fad667b0c2a0b8173d06 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 4 Mar 2018 17:32:56 +0100
Subject: gnu: openvpn: Update to 2.4.5.

* gnu/packages/vpn.scm (openvpn): Update to 2.4.5.
---
 gnu/packages/vpn.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm
index 952f12ce55..8dd3333eea 100644
--- a/gnu/packages/vpn.scm
+++ b/gnu/packages/vpn.scm
@@ -241,7 +241,7 @@ and probably others.")
 (define-public openvpn
   (package
     (name "openvpn")
-    (version "2.4.4")
+    (version "2.4.5")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -249,7 +249,7 @@ and probably others.")
                     version ".tar.xz"))
               (sha256
                (base32
-                "102an395nv8l7qfx3syydzhmd9xfbycd6gvwy0h2kjz8w67ipkcn"))))
+                "17njq59hsraqyxrbhkrxr7dvx0p066s3pn8w1mi0yd9jldis7h23"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags '("--enable-iproute2=yes")))
-- 
cgit v1.2.3


From 9599339c5982d0c446d04c1c1c7baef319ee6421 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 4 Mar 2018 17:33:56 +0100
Subject: gnu: openvpn: Mark up description.

* gnu/packages/vpn.scm (openvpn)[description]: Use @dfn.
---
 gnu/packages/vpn.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm
index 8dd3333eea..642ca1c044 100644
--- a/gnu/packages/vpn.scm
+++ b/gnu/packages/vpn.scm
@@ -262,11 +262,12 @@ and probably others.")
        ("linux-pam" ,linux-pam)))
     (home-page "https://openvpn.net/")
     (synopsis "Virtual private network daemon")
-    (description "OpenVPN implements virtual private network (VPN) techniques
+    (description
+     "OpenVPN implements virtual private network (@dfn{VPN}) techniques
 for creating secure point-to-point or site-to-site connections in routed or
 bridged configurations and remote access facilities.  It uses a custom
 security protocol that utilizes SSL/TLS for key exchange.  It is capable of
-traversing network address translators (NATs) and firewalls.")
+traversing network address translators (@dfn{NAT}s) and firewalls.")
     (license license:gpl2)))
 
 (define-public tinc
-- 
cgit v1.2.3


From 530df311ac0f04d5bddf2d538d060440b9850cd1 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 5 Mar 2018 00:03:17 +0100
Subject: gnu: perl-www-mechanize: Update to 1.87.

* gnu/packages/web.scm (perl-www-mechanize): Update to 1.87.
---
 gnu/packages/web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 23bcc5fb1c..07e4a1ad93 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -3657,7 +3657,7 @@ library.")
 (define-public perl-www-mechanize
   (package
     (name "perl-www-mechanize")
-    (version "1.86")
+    (version "1.87")
     (source
      (origin
        (method url-fetch)
@@ -3665,7 +3665,7 @@ library.")
                            "WWW-Mechanize-" version ".tar.gz"))
        (sha256
         (base32
-         "0sfl6b7mx8nannnh3ys5jk44d1s1b2d1mffrnrphkzzykaw6hm0f"))))
+         "1kxrydhl7nxlyjv0xvyiyj4igdv4fwnggv0ihlp79bysbjjl54w1"))))
     (build-system perl-build-system)
     (native-inputs                      ;only for tests
      `(("perl-cgi" ,perl-cgi)
-- 
cgit v1.2.3


From 55b7cd10c28934aaea144c06e5d4a8bb8b88bfbb Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 5 Mar 2018 00:04:17 +0100
Subject: gnu: perl-io-socket-ip: Update to 0.39.

* gnu/packages/web.scm (perl-io-socket-ip): Update to 0.39.
---
 gnu/packages/web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 07e4a1ad93..cfae9f9253 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -2933,7 +2933,7 @@ algorithm specified in section 8.2.2.1 of the draft standard.")
 (define-public perl-io-socket-ip
   (package
     (name "perl-io-socket-ip")
-    (version "0.38")
+    (version "0.39")
     (source
      (origin
        (method url-fetch)
@@ -2941,7 +2941,7 @@ algorithm specified in section 8.2.2.1 of the draft standard.")
                            "IO-Socket-IP-" version ".tar.gz"))
        (sha256
         (base32
-         "0scsnahxwnymg80a3k0p0cnr574nk7x9inn9wjniz0iycicclyhb"))))
+         "15kv5g1yb4a345sk3r5wfr99f868lhfqkddzsgpqddvccfkhv58i"))))
     (build-system perl-build-system)
     (native-inputs `(("perl-module-build" ,perl-module-build)))
     (home-page "http://search.cpan.org/dist/IO-Socket-IP")
-- 
cgit v1.2.3


From cc7a4bbd27a9d55e3c942d95ae9cfcf8157e401c Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 5 Mar 2018 00:30:42 +0100
Subject: gnu: tocc, libtocc: Use HTTPS home page.

* gnu/packages/search.scm (libtocc, tocc)[home-page]: Use HTTPS.
---
 gnu/packages/search.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/search.scm b/gnu/packages/search.scm
index 1479d1bbbb..a719819927 100644
--- a/gnu/packages/search.scm
+++ b/gnu/packages/search.scm
@@ -137,7 +137,7 @@ rich set of boolean query operators.")
                                              "-Wl,-rpath=../src/.libs")))
                             (zero? (system* "make"))
                             (zero? (system* "./libtocctests")))))))))
-    (home-page "http://t-o-c-c.com/")
+    (home-page "https://t-o-c-c.com/")
     (synopsis "Tool for Obsessive Compulsive Classifiers")
     (description
      "libtocc is the engine of the Tocc project, a tag-based file management
@@ -161,7 +161,7 @@ files and directories.")
                   (add-after
                    'unpack 'chdir-source
                    (lambda _ (chdir "cli/src"))))))
-    (home-page "http://t-o-c-c.com/")
+    (home-page "https://t-o-c-c.com/")
     (synopsis "Command-line interface to libtocc")
     (description
      "Tocc is a tag-based file management system.  This package contains the
-- 
cgit v1.2.3


From 437e5fae131d147e1b0675e5f9df9fc17439816d Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 5 Mar 2018 15:23:28 +0100
Subject: gnu: editres: Update to 1.0.7.

* gnu/packages/xorg.scm (editres): Update to 1.0.7.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index b73d7d6cd2..c63b87218a 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -357,7 +357,7 @@ provided.")
 (define-public editres
   (package
     (name "editres")
-    (version "1.0.6")
+    (version "1.0.7")
     (source
       (origin
         (method url-fetch)
@@ -367,7 +367,7 @@ provided.")
                ".tar.bz2"))
         (sha256
          (base32
-          "1w2d5hb5pw9ii2jlf4yjlp899402zfwc8hdkpdr3i1fy1cjd2riv"))))
+          "04awfwmy3f9f0bchidc4ssbgrbicn5gzasg3jydpfnp5513d76h8"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
-- 
cgit v1.2.3


From b5de208e84419ba93fdb8d265b93526ed3b27d3a Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 5 Mar 2018 15:25:54 +0100
Subject: gnu: perl-xml-rss: Update to 1.60.

* gnu/packages/xml.scm (perl-xml-rss): Update to 1.60.
---
 gnu/packages/xml.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm
index eabd28233a..5db398bce6 100644
--- a/gnu/packages/xml.scm
+++ b/gnu/packages/xml.scm
@@ -469,14 +469,14 @@ checks.")
 (define-public perl-xml-rss
   (package
     (name "perl-xml-rss")
-    (version "1.59")
+    (version "1.60")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cpan/authors/id/S/SH/SHLOMIF/"
                                   "XML-RSS-" version ".tar.gz"))
               (sha256
                (base32
-                "0v6vfizn2psy6av057kp7fv3z3y73s6b3w56jm3zr6hlq48llsx2"))))
+                "0xw6aaqka3vqwbv152sbh6fbi8j306q1gvg7v83br8miif3mjcsb"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-module-build" ,perl-module-build)
-- 
cgit v1.2.3


From 503a00597b1581db03219483fe19052ba6ee58ec Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 5 Mar 2018 15:27:51 +0100
Subject: gnu: perl-xml-compile-cache: Update to 1.06.

* gnu/packages/xml.scm (perl-xml-compile-cache): Update to 1.06.
---
 gnu/packages/xml.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm
index 5db398bce6..5f7a95463a 100644
--- a/gnu/packages/xml.scm
+++ b/gnu/packages/xml.scm
@@ -684,14 +684,14 @@ a schema.")
 (define-public perl-xml-compile-cache
   (package
     (name "perl-xml-compile-cache")
-    (version "1.05")
+    (version "1.06")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cpan/authors/id/M/MA/MARKOV/"
                                   "XML-Compile-Cache-" version ".tar.gz"))
               (sha256
                (base32
-                "0xbwlszhi9hg8sxm5ylglm2qvnb689i595p913awrj2g4mp9yfsw"))))
+                "181qf1s7ymgi7saph3cf9p6dbxkxyh1ja23na4dchhi8v5mi66sr"))))
     (build-system perl-build-system)
     (propagated-inputs
      `(("perl-log-report" ,perl-log-report)
-- 
cgit v1.2.3


From 1c3de94cff14c07b173fe391e65b1992279ba8bc Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 5 Mar 2018 15:30:12 +0100
Subject: gnu: perl-sub-quote: Update to 2.005000.

* gnu/packages/xml.scm (perl-sub-quote): Update to 2.005000.
---
 gnu/packages/perl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index e44d5c3f0f..badff6e4d1 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -7340,7 +7340,7 @@ return value is the sub.")
 (define-public perl-sub-quote
   (package
     (name "perl-sub-quote")
-    (version "2.004000")
+    (version "2.005000")
     (source
      (origin
        (method url-fetch)
@@ -7349,7 +7349,7 @@ return value is the sub.")
              version ".tar.gz"))
        (sha256
         (base32
-         "1zrh3apxsw1ks25zkh9dcn00656rsvq4mimqz3w8p37s2c1m4qaq"))))
+         "1zv45cvj4ifkbr61ydcpphnj6lvib37gfxwfh40h0yzf3c8lbca4"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-test-fatal" ,perl-test-fatal)))
-- 
cgit v1.2.3


From c8213ffc520ea34d1ca4bb5db22ec79fe23b5aa3 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 5 Mar 2018 16:42:08 +0100
Subject: gnu: perl-email-address: Update to 1.909.

* gnu/packages/perl.scm (perl-email-address): Update to 1.909.
---
 gnu/packages/mail.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index 8d3544f908..7d85d5208a 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -1375,7 +1375,7 @@ write simple, representation-independent mail handling code.")
 (define-public perl-email-address
   (package
     (name "perl-email-address")
-    (version "1.908")
+    (version "1.909")
     (source
      (origin
        (method url-fetch)
@@ -1383,7 +1383,7 @@ write simple, representation-independent mail handling code.")
                            "Email-Address-" version ".tar.gz"))
        (sha256
         (base32
-         "0i6ljdvpy279hpbqf6lgv4figr376rb2sh4yphj86xkdzsyn1y75"))))
+         "0l7x6sl06j9ffgfz5f9vgms2b5axd4cgp5fj03ivb3kia4km6b3g"))))
     (build-system perl-build-system)
     (home-page "http://search.cpan.org/dist/Email-Address")
     (synopsis "Email address parsing and creation")
-- 
cgit v1.2.3


From 0f2778029a536ceac93208f2e66af9d3e1ef44a7 Mon Sep 17 00:00:00 2001
From: Gábor Boskovits <boskovits@gmail.com>
Date: Sat, 3 Mar 2018 22:59:05 +0100
Subject: gnu: java-ops4j-pax-tinybundles: Use distribution bndlib version.

* gnu/packages/java.scm (java-ops4j-pax-tinybundles)[arguments]<#:phases>:
Modify fix-version to use the distibution version of java-aqute-bndlib.
---
 gnu/packages/java.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 21e241d0fe..5cc4a56f81 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -6980,7 +6980,8 @@ it manages project dependencies, gives diffs jars, and much more.")
              ;; packaging.  It uses the version referenced in pom.xml.  We replace
              ;; it with our own version.
              (substitute* "src/test/java/org/ops4j/pax/tinybundles/bnd/BndTest.java"
-               (("2.4.0.201411031534") "3.4.0")))))))
+               (("[0-9][0-9]*\\.[0-9][0-9]*\\.[0-9][0-9]*\\.[0-9][0-9]*")
+                ,(package-version java-aqute-bndlib))))))))
     (inputs
      `(("lang" ,java-ops4j-base-lang)
        ("io" ,java-ops4j-base-io)
-- 
cgit v1.2.3


From cee03b267cbe6e7360b106095ee2861bf010f915 Mon Sep 17 00:00:00 2001
From: Rutger Helling <rhelling@mykolab.com>
Date: Tue, 6 Mar 2018 08:24:01 +0100
Subject: gnu: ovmf: Fix build and add FIXME.

* gnu/packages/firmware.scm (ovmf): Replace 'invoke' with 'system*'. Add FIXME
about failing script.
---
 gnu/packages/firmware.scm | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm
index da7430b063..714af3df72 100644
--- a/gnu/packages/firmware.scm
+++ b/gnu/packages/firmware.scm
@@ -258,7 +258,9 @@ coreboot.")
                (setenv "WORKSPACE" cwd)
                (setenv "EDK_TOOLS_PATH" tools)
                (setenv "PATH" (string-append (getenv "PATH") ":" bin))
-               (invoke "bash" "edksetup.sh" "BaseTools")
+               ; FIXME: The below script errors out. When using 'invoke' instead
+               ; of 'system*' this causes the build to fail.
+               (system* "bash" "edksetup.sh" "BaseTools")
                (substitute* "Conf/target.txt"
                  (("^TARGET[ ]*=.*$") "TARGET = RELEASE\n")
                  (("^TOOL_CHAIN_TAG[ ]*=.*$") "TOOL_CHAIN_TAG = GCC49\n")
-- 
cgit v1.2.3


From 69611d3eacfae2d22b6b3ebc2ff4f3bfbff925b5 Mon Sep 17 00:00:00 2001
From: Oleg Pykhalov <go.wigust@gmail.com>
Date: Sun, 4 Mar 2018 12:28:52 +0300
Subject: gnu: haskell-mode: Fix find emacs-stream elisp directory.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/emacs.scm (haskell-mode)[arguments]: Find only directories with
"\\.el$" in ‘el-dir’.
---
 gnu/packages/emacs.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 54eb816c15..f27f8df8d3 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -614,7 +614,7 @@ process, passing on the arguments as command line arguments.")
           'build 'pre-build
           (lambda* (#:key inputs #:allow-other-keys)
             (define (el-dir store-dir)
-              (match (find-files store-dir)
+              (match (find-files store-dir "\\.el$")
                 ((f1 f2 ...) (dirname f1))
                 (_ "")))
 
-- 
cgit v1.2.3


From 5ad13e6cdf77311b3c1ea93d45378f7e92081145 Mon Sep 17 00:00:00 2001
From: Oleg Pykhalov <go.wigust@gmail.com>
Date: Tue, 6 Mar 2018 12:09:02 +0300
Subject: gnu: emacs-transmission: Update to 0.12.1.

* gnu/packages/emacs.scm (emacs-transmission): Update to 0.12.1.
---
 gnu/packages/emacs.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index f27f8df8d3..a6f398ac3b 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -6891,7 +6891,7 @@ in a generalized CSV (character-separated values) format.")
 (define-public emacs-transmission
   (package
     (name "emacs-transmission")
-    (version "0.12")
+    (version "0.12.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -6900,7 +6900,7 @@ in a generalized CSV (character-separated values) format.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1y0bpsy16pycp6m9aqvfjh2x1yswfb305ib7m2slcjpb6njgxfi6"))))
+                "1rrlgn96gi1ljfwbwvlyyxbq75xzamlbdhq1bpyadxxmxcvlmk3n"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/holomorph/transmission")
     (synopsis "Emacs interface to a Transmission session")
-- 
cgit v1.2.3


From 08ddb98aefc9d3831cea7c6dc6b68039836d09dd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 6 Mar 2018 10:26:59 +0100
Subject: gnu: r-gtools: Make output deterministic.

* gnu/packages/statistics.scm (r-gtools)[arguments]: Add build phase to avoid
running tempdir at build time.
---
 gnu/packages/statistics.scm | 8 ++++++++
 1 file changed, 8 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index baec1c47d2..338db28222 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4042,6 +4042,14 @@ Zurich, including many that are related to graphics.")
         (base32
          "1xknwk9xlsj027pg0nwiizigcrsc84hdrig0jn0cgcyxj8dabdl6"))))
     (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'make-deterministic
+           (lambda _
+             (substitute* "R/checkReverseDependencies.R"
+               (("tempdir\\(\\)") "\"/tmp\""))
+             #t)))))
     (home-page "https://cran.r-project.org/web/packages/gtools")
     (synopsis "Various R programming tools")
     (description
-- 
cgit v1.2.3


From fe58ab013be8b8232ed4de356b3d0cb8b1bbb847 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 6 Mar 2018 11:51:33 +0100
Subject: gnu: r-lambda-r: Run unit tests.

* gnu/packages/statistics.scm (r-lambda-r)[native-inputs]: Add r-runit.
[arguments]: Add build phase to delete test logs.
---
 gnu/packages/statistics.scm | 13 +++++++++++++
 1 file changed, 13 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 338db28222..8ebdce1376 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2814,6 +2814,19 @@ plotted and compared with the asymptotic curve.")
                 "0vql32np716dpd0kjn7s7wgawd02ysgp2a5il4kb19nlw661ii3x"))))
     (properties `((upstream-name . "lambda.r")))
     (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'check 'delete-test-log
+           ;; The test report contains time stamps and is not important for
+           ;; the installed package.
+           (lambda* (#:key outputs #:allow-other-keys)
+             (delete-file-recursively
+              (string-append (assoc-ref outputs "out")
+                             "/site-library/lambda.r/unitTests"))
+             #t)))))
+    (native-inputs
+     `(("r-runit" ,r-runit)))
     (home-page "https://cran.r-project.org/web/packages/lambda.r")
     (synopsis "Functional programming extension for R")
     (description
-- 
cgit v1.2.3


From e325c890763e89b9baeeeb78110b3a50c822b25a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 6 Mar 2018 13:55:13 +0100
Subject: gnu: r-rhdf5: Make build reproducible.

* gnu/packages/bioinformatics.scm (r-rhdf5)[arguments]: Remove timestamp and
host system information from settings file.
---
 gnu/packages/bioinformatics.scm | 10 ++++++++++
 1 file changed, 10 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4756444d95..947f99aa71 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8760,6 +8760,16 @@ of gene-level counts.")
                       "src/hdf5source/hdf5small.tgz" "-C" "src/" )
              (substitute* "src/hdf5/configure"
                (("/bin/mv") "mv"))
+             ;; Remove timestamp and host system information to make
+             ;; the build reproducible.
+             (substitute* "src/hdf5/src/libhdf5.settings.in"
+               (("Configured on: @CONFIG_DATE@")
+                "Configured on: Guix")
+               (("Uname information:.*")
+                "Uname information: Linux\n")
+               ;; Remove unnecessary store reference.
+               (("C Compiler:.*")
+                "C Compiler: GCC\n"))
              #t)))))
     (propagated-inputs
      `(("r-zlibbioc" ,r-zlibbioc)))
-- 
cgit v1.2.3


From 727d847980e61d8d0deaa4219ea730dc85e0a515 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 6 Mar 2018 15:50:08 +0100
Subject: gnu: htslib: Update to 1.7.

* gnu/packages/bioinformatics.scm (htslib): Update to 1.7.
[arguments]: Remove field.
---
 gnu/packages/bioinformatics.scm | 13 ++-----------
 1 file changed, 2 insertions(+), 11 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 947f99aa71..c098562d2d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3431,7 +3431,7 @@ The main functions of FastQC are:
 (define-public htslib
   (package
     (name "htslib")
-    (version "1.6")
+    (version "1.7")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -3439,17 +3439,8 @@ The main functions of FastQC are:
                     version "/htslib-" version ".tar.bz2"))
               (sha256
                (base32
-                "1jsca3hg4rbr6iqq6imkj4lsvgl8g9768bcmny3hlff2w25vx24m"))))
+                "1il6i2p84b0y9c93dhvzzki1ifw9bvapm2mvpr0xvb2nq8jlwgdy"))))
     (build-system gnu-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after
-          'unpack 'patch-tests
-          (lambda _
-            (substitute* "test/test.pl"
-              (("/bin/bash") (which "bash")))
-            #t)))))
     (inputs
      `(("openssl" ,openssl)
        ("curl" ,curl)
-- 
cgit v1.2.3


From c072cf57b927111d9a63b7349074052cb696280b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 6 Mar 2018 15:50:32 +0100
Subject: gnu: samtools: Update to 1.7.

* gnu/packages/bioinformatics.scm (samtools): Update to 1.7.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c098562d2d..546b240f84 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4896,7 +4896,7 @@ to the user's query of interest.")
 (define-public samtools
   (package
     (name "samtools")
-    (version "1.5")
+    (version "1.7")
     (source
      (origin
        (method url-fetch)
@@ -4905,7 +4905,7 @@ to the user's query of interest.")
                        version "/samtools-" version ".tar.bz2"))
        (sha256
         (base32
-         "1xidmv0jmfy7l0kb32hdnlshcxgzi1hmygvig0cqrq1fhckdlhl5"))))
+         "18acyqysbxpydlc44lqv2hpp57l06bs9a3yqmcvjk8va2xrrdc77"))))
     (build-system gnu-build-system)
     (arguments
      `(#:modules ((ice-9 ftw)
-- 
cgit v1.2.3


From 6f1f8d131299ce1e8cd4243df29459d86ca9a911 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 6 Mar 2018 17:38:12 +0100
Subject: gnu: python-django: Update to 1.11.11 [fixes CVE-2018-7536 and
 CVE-2018-7537].

See <https://www.djangoproject.com/weblog/2018/mar/06/security-releases/> for
more information about the vulnerabilities.

* gnu/packages/django.scm (python-django): Update to 1.11.11.
---
 gnu/packages/django.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index 0b447b5176..c52c812f00 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -36,13 +36,13 @@
 (define-public python-django
   (package
     (name "python-django")
-    (version "1.11.10")
+    (version "1.11.11")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "Django" version))
               (sha256
                (base32
-                "1ndc7axr7cz8jwhr4mz16fvwd0jcd6i81q2wi9nl172s71kkaf12"))))
+                "1p0fk0dszci9gx76hyhay3n8n0k8r4sznbdcrpd9g2xl15rps1vl"))))
     (build-system python-build-system)
     (arguments
      '(#:modules ((srfi srfi-1)
-- 
cgit v1.2.3


From 6836c228ae538a06827b47c4f7bc94b02c087be9 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 6 Mar 2018 18:16:51 +0100
Subject: gnu: iceauth: Update to 1.0.8.

* gnu/packages/xorg.scm (iceauth): Update to 1.0.8.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index c63b87218a..3ae936923c 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -918,7 +918,7 @@ rendering commands to the X server.")
 (define-public iceauth
   (package
     (name "iceauth")
-    (version "1.0.7")
+    (version "1.0.8")
     (source
       (origin
         (method url-fetch)
@@ -928,7 +928,7 @@ rendering commands to the X server.")
                ".tar.bz2"))
         (sha256
           (base32
-            "02izdyzhwpgiyjd8brzilwvwnfr72ncjb6mzz3y1icwrxqnsy5hj"))))
+            "1ik0mdidmyvy48hn8p2hwvf3535rf3m96hhf0mvcqrbj44x23vp6"))))
     (build-system gnu-build-system)
     (inputs
       `(("libice" ,libice)))
-- 
cgit v1.2.3


From 37204750b188edca17559dfc57d6f47bd9f63c62 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 6 Mar 2018 18:22:26 +0100
Subject: gnu: feh: Update to 2.25.

* gnu/packages/image-viewers.scm (feh): Update to 2.25.
---
 gnu/packages/image-viewers.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/image-viewers.scm b/gnu/packages/image-viewers.scm
index a3887ee22d..7a33f6c871 100644
--- a/gnu/packages/image-viewers.scm
+++ b/gnu/packages/image-viewers.scm
@@ -59,7 +59,7 @@
 (define-public feh
   (package
     (name "feh")
-    (version "2.24")
+    (version "2.25")
     (home-page "https://feh.finalrewind.org/")
     (source (origin
               (method url-fetch)
@@ -67,7 +67,7 @@
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "148qbxkk5m7i3cxymnfwi7aikqjyfxr306dlqm9ndp6x932js5wq"))))
+                "102rwi30n09l8rih6kv6bb7lhv3djklgzill4p2zag0h700yqfq6"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases (delete 'configure))
-- 
cgit v1.2.3


From 77412c45b1cd1dee8443d4391080f196f8b5483f Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 6 Mar 2018 18:23:42 +0100
Subject: gnu: re2: Update to 2018-03-01.

* gnu/packages/regex.scm (re2): Update to 2018-03-01.
---
 gnu/packages/regex.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/regex.scm b/gnu/packages/regex.scm
index e6fcfe304c..1294149609 100644
--- a/gnu/packages/regex.scm
+++ b/gnu/packages/regex.scm
@@ -29,7 +29,7 @@
 (define-public re2
    (package
      (name "re2")
-     (version "2018-02-01")
+     (version "2018-03-01")
      (source (origin
                (method url-fetch)
                (uri
@@ -39,7 +39,7 @@
                (file-name (string-append name "-" version ".tar.gz"))
                (sha256
                 (base32
-                 "1131hwgid76la15hh2g15gj20fzz8iq3krniwks6wxn9h4q87ay8"))))
+                 "0y21g321a802xmxdbkfz0rkcark7ypglpb3jjqhf13m6s7lpxp2i"))))
      (build-system gnu-build-system)
      (arguments
       `(#:modules ((guix build gnu-build-system)
-- 
cgit v1.2.3


From 78f19a4754628b42f4363a624bf3500c54e861cc Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Tue, 20 Feb 2018 09:01:00 -0500
Subject: gnu: Remove go-github-com-xtaci-smux.

* gnu/packages/syncthing.scm (go-github-com-xtaci-smux): Remove variable.
---
 gnu/packages/syncthing.scm | 28 ----------------------------
 1 file changed, 28 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm
index f5e5bb85be..cf7dfd6910 100644
--- a/gnu/packages/syncthing.scm
+++ b/gnu/packages/syncthing.scm
@@ -1640,34 +1640,6 @@ over UDP packets.")
     (home-page "https://github.com/templexxx/xor")
     (license expat)))
 
-(define-public go-github-com-xtaci-smux
-  (let ((commit "c3e18246ff2252a6e9d6b529fcbf22ae5c74c007")
-        (revision "0"))
-    (package
-      (name "go-github-com-xtaci-smux")
-      (version (git-version "1.0.6" revision commit))
-      (source
-        (origin
-          (method git-fetch)
-          (uri (git-reference
-                 (url "https://github.com/xtaci/smux.git")
-                 (commit commit)))
-          (file-name (git-file-name name version))
-          (sha256
-           (base32
-            "1dfmxd9g31idldhq6n7r998gi4jw51ji3xvkjrzypsw2ypbjx1dz"))))
-      (build-system go-build-system)
-      (propagated-inputs
-       `(("go-github-com-pkg-errors" ,go-github-com-pkg-errors)))
-      (arguments
-       '(#:import-path "github.com/xtaci/smux"))
-      (synopsis "Network multiplexing in Go")
-      (description "Smux ( Simple MUltipleXing) is a multiplexing library for
-Golang.  It relies on an underlying connection to provide reliability and
-ordering, such as TCP or KCP, and provides stream-oriented multiplexing.")
-      (home-page "https://github.com/xtaci/smux")
-      (license expat))))
-
 (define-public go-github-com-pkg-errors
   (let ((commit "e881fd58d78e04cf6d0de1217f8707c8cc2249bc")
         (revision "1"))
-- 
cgit v1.2.3


From bb0a84f89dd33a14062487dfd2704ff4595c07f2 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Tue, 20 Feb 2018 09:01:38 -0500
Subject: gnu: Remove go-github-com-xtaci-kcp-go.

* gnu/packages/syncthing.scm (go-github-com-xtaci-kcp-go): Remove variable.
---
 gnu/packages/syncthing.scm | 39 ---------------------------------------
 1 file changed, 39 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm
index cf7dfd6910..3d97ce09f0 100644
--- a/gnu/packages/syncthing.scm
+++ b/gnu/packages/syncthing.scm
@@ -1577,45 +1577,6 @@ rolling hash.")
       (home-page "https://github.com/chmduquesne/rollinghash")
       (license expat))))
 
-(define-public go-github-com-xtaci-kcp-go
-  (let ((commit "86eebd5cadb519b7c9306082c7eb3bcee2c49a7b")
-        (revision "0"))
-    (package
-      (name "go-github-com-xtaci-kcp-go")
-      (version (git-version "0.0.0" revision commit))
-      (source
-        (origin
-          (method git-fetch)
-          (uri (git-reference
-                 (url "https://github.com/xtaci/kcp-go")
-                 (commit commit)))
-          (file-name (git-file-name name version))
-          (sha256
-           (base32
-            "1mdfsya4y04nycfgsk9ghm67zpim5pw78si3f1566xgrv4ghl0ni"))))
-      (build-system go-build-system)
-      (propagated-inputs
-       `(("go-golang-org-x-net-ipv4" ,go-golang-org-x-net-ipv4)
-         ("go-github-com-klauspost-reedsolomon"
-          ,go-github-com-klauspost-reedsolomon)
-         ("go-github-com-tjfoc-gmsm-sm4" ,go-github-com-tjfoc-gmsm-sm4)
-         ("go-github-com-pkg-errors" ,go-github-com-pkg-errors)
-         ("go-golang-org-x-crypto" ,(go-golang-org-x-crypto-union))
-         ("go-github-com-templexxx-xor" ,go-github-com-templexxx-xor)))
-      (arguments
-       '(#:import-path "github.com/xtaci/kcp-go"
-         ;; XXX update comment
-         ;; 'TestListenerClose' is known to fail. It seems that the test suite
-         ;; is not being used upstream:
-         ;; https://github.com/AudriusButkevicius/kcp-go/pull/1
-         #:tests? #f))
-      (synopsis "Reliable UDP connections in Go")
-      (description "This package provides @code{kcp-go}, a reliable UDP library
-written in Go.  It offers fast, ordered and error-checked delivery of streams
-over UDP packets.")
-      (home-page "https://github.com/xtaci/kcp-go")
-      (license expat))))
-
 (define-public go-github-com-templexxx-xor
   (package
     (name "go-github-com-templexxx-xor")
-- 
cgit v1.2.3


From eaca421063e23b42dbac26a2957c188bcf21323a Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Tue, 20 Feb 2018 09:02:10 -0500
Subject: gnu: Remove go-github-com-ccding-go-stun.

* gnu/packages/syncthing.scm (go-github-com-ccding-go-stun): Remove variable.
---
 gnu/packages/syncthing.scm | 25 -------------------------
 1 file changed, 25 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm
index 3d97ce09f0..90389d3098 100644
--- a/gnu/packages/syncthing.scm
+++ b/gnu/packages/syncthing.scm
@@ -1526,31 +1526,6 @@ virtual connections from a single physical connection.")
       (home-page "https://github.com/AudriusButkevicius/pfilter")
       (license expat))))
 
-(define-public go-github-com-ccding-go-stun
-  (let ((commit "d9bbe8f8fa7bf7ed03e6cfc6a2796bb36139e1f4")
-        (revision "1"))
-    (package
-      (name "go-github-com-ccding-go-stun")
-      (version (git-version "0.0.0" revision commit))
-      (source
-        (origin
-          (method git-fetch)
-          (uri (git-reference
-                 (url "https://github.com/ccding/go-stun.git")
-                 (commit commit)))
-          (file-name (git-file-name name version))
-          (sha256
-           (base32
-            "04a4q69cmw6snlx54wikyj1y6gk94qzm9xv9als17inmj8z60xv7"))))
-      (build-system go-build-system)
-      (arguments
-       '(#:import-path "github.com/ccding/go-stun"))
-      (synopsis "STUN client implementation")
-      (description "Go-stun is a go implementation of the STUN client (RFC 3489
-and RFC 5389).")
-      (home-page "https://github.com/ccding/go-stun")
-      (license asl2.0))))
-
 (define-public go-github-com-chmduquesne-rollinghash-adler32
   (let ((commit "3dc7875a1f890f9bcf0619adb5571fc6f7d516bb")
         (revision "1"))
-- 
cgit v1.2.3


From abb8973544b7e27a4c17bacfbb56538974244009 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Tue, 20 Feb 2018 09:03:59 -0500
Subject: gnu: Remove go-github-com-klauspost-cpuid.

* gnu/packages/syncthing.scm (go-github-com-klauspost-cpuid): Remove variable.
---
 gnu/packages/syncthing.scm | 23 -----------------------
 1 file changed, 23 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm
index 90389d3098..e320512ed7 100644
--- a/gnu/packages/syncthing.scm
+++ b/gnu/packages/syncthing.scm
@@ -1776,29 +1776,6 @@ notification library in Go.")
       (home-page "https://github.com/zillode/notify")
       (license expat))))
 
-(define-public go-github-com-klauspost-cpuid
-  (let ((commit "eae9b3e628d72774e13bdf024e78c0802f85a5b9")
-        (revision "0"))
-  (package
-    (name "go-github-com-klauspost-cpuid")
-    (version (git-version "1.1" revision commit))
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                     (url "https://github.com/klauspost/cpuid.git")
-                     (commit commit)))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "0dgxlsxdfhfapmz1qlvc919m3kcbmfqcfpxk78zl9am5zc3zr689"))))
-    (build-system go-build-system)
-    (arguments
-     '(#:import-path "github.com/klauspost/cpuid"))
-    (synopsis "CPU feature identification library")
-    (description "This package provides @code{cpuid}, a Go library that provides information about the CPU running the current program")
-    (home-page "https://github.com/klauspost/cpuid")
-    (license expat))))
-
 (define-public go-github-com-klauspost-reedsolomon
   (let ((commit "0b30fa71cc8e4e9010c9aba6d0320e2e5b163b29")
         (revision "0"))
-- 
cgit v1.2.3


From 7915ef0bff3392f6f7773b054935c1f88704dfac Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Tue, 20 Feb 2018 09:04:33 -0500
Subject: gnu: Remove go-github-com-klauspost-reedsolomon.

* gnu/packages/syncthing.scm (go-github-com-klauspost-reedsolomon): Remove
variable.
---
 gnu/packages/syncthing.scm | 27 ---------------------------
 1 file changed, 27 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm
index e320512ed7..f67aa89e8f 100644
--- a/gnu/packages/syncthing.scm
+++ b/gnu/packages/syncthing.scm
@@ -1776,33 +1776,6 @@ notification library in Go.")
       (home-page "https://github.com/zillode/notify")
       (license expat))))
 
-(define-public go-github-com-klauspost-reedsolomon
-  (let ((commit "0b30fa71cc8e4e9010c9aba6d0320e2e5b163b29")
-        (revision "0"))
-  (package
-    (name "go-github-com-klauspost-reedsolomon")
-    (version (git-version "1.6" revision commit))
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                     (url "https://github.com/klauspost/reedsolomon.git")
-                     (commit commit)))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "04jvf65ybsa7w4d7s2n0s174p0q2fl0dqd5hhn2krw66z9i3rc6d"))))
-    (build-system go-build-system)
-    (arguments
-     '(#:import-path "github.com/klauspost/reedsolomon"))
-    (propagated-inputs
-     `(("go-github-com-klauspost-cpuid"
-        ,go-github-com-klauspost-cpuid)))
-    (synopsis "Reed-Solomon Erasure Coding in Go")
-    (description "This package provides and implemenation of Reed-Solomon
-Erasure Coding in Go.")
-    (home-page "https://github.com/klauspost/reedsolomon")
-    (license expat))))
-
 (define-public go-github-com-beorn7-perks-quantile
   (let ((commit "4c0e84591b9aa9e6dcfdf3e020114cd81f89d5f9")
         (revision "0"))
-- 
cgit v1.2.3


From 7d02ae4b85d16f34d14dfb6375b7900ca1a81b4a Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Tue, 20 Feb 2018 09:05:10 -0500
Subject: gnu: Remove go-github-com-tjfoc-gmsm-sm4.

* gnu/packages/syncthing.scm (go-github-com-tjfoc-gmsm-sm4): Remove variable.
---
 gnu/packages/syncthing.scm | 26 --------------------------
 1 file changed, 26 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm
index f67aa89e8f..9b7ea9b0c4 100644
--- a/gnu/packages/syncthing.scm
+++ b/gnu/packages/syncthing.scm
@@ -1724,32 +1724,6 @@ processor feature detection used by the Go standard libary.")
       (home-page "https://github.com/templexxx/cpufeat")
       (license bsd-3))))
 
-(define-public go-github-com-tjfoc-gmsm-sm4
-  (let ((commit "98aa888b79d8de04afe0fccf45ed10594efc858b")
-        (revision "1"))
-    (package
-      (name "go-github-com-tjfoc-gmsm-sm4")
-      (version (git-version "0.0.0" revision commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                       (url "https://github.com/tjfoc/gmsm")
-                       (commit commit)))
-                (file-name (git-file-name name version))
-                (sha256
-                 (base32
-                  "1ii4imnz3ims2s23pdv0l4ijzxjsvl82h4yzgfqm5y809ph6pjq9"))))
-      (build-system go-build-system)
-      (arguments
-       '(#:import-path "github.com/tjfoc/gmsm/sm4"
-         #:unpack-path "github.com/tjfoc/gmsm"))
-      (synopsis "SM4 block cipher")
-      (description "This package provides a Go implementation of SM4, a block
-cipher used in the Chinese National Standard for Wireless LAN WAPI (Wired
-Authentication and Privacy Infrastructure).")
-      (home-page "https://github.com/tjfoc/gmsm")
-      (license asl2.0))))
-
 (define-public go-github-com-zillode-notify
   (let ((commit "a8abcfb1ce88ee8d79a300ed65d94b8fb616ddb3")
         (revision "2"))
-- 
cgit v1.2.3


From 6482d3047247aeeac07a5a90bf6165586a039b27 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Tue, 20 Feb 2018 09:05:47 -0500
Subject: gnu: Remove go-github-com-templexxx-cpufeat.

* gnu/packages/syncthing.scm (go-github-com-templexxx-cpufeat): Remove
variable.
---
 gnu/packages/syncthing.scm | 24 ------------------------
 1 file changed, 24 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm
index 9b7ea9b0c4..17aa12782b 100644
--- a/gnu/packages/syncthing.scm
+++ b/gnu/packages/syncthing.scm
@@ -1700,30 +1700,6 @@ using sh's word-splitting rules.")
       (home-page "https://github.com/kballard/go-shellquote")
       (license expat))))
 
-(define-public go-github-com-templexxx-cpufeat
-  (let ((commit "3794dfbfb04749f896b521032f69383f24c3687e")
-        (revision "0"))
-    (package
-      (name "go-github-com-templexxx-cpufeat")
-      (version (git-version "0.0.0" revision commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                       (url "https://github.com/templexxx/cpufeat.git")
-                       (commit commit)))
-                (file-name (git-file-name name version))
-                (sha256
-                 (base32
-                  "0b9f5p6nsiv907rz5d66qzgxnsz4k68r2f45vxi2hwdbnkjfxz8j"))))
-      (build-system go-build-system)
-      (arguments
-       '(#:import-path "github.com/templexxx/cpufeat"))
-      (synopsis "CPU feature identification for Go")
-      (description "This package provides @code{cpu}, which implements
-processor feature detection used by the Go standard libary.")
-      (home-page "https://github.com/templexxx/cpufeat")
-      (license bsd-3))))
-
 (define-public go-github-com-zillode-notify
   (let ((commit "a8abcfb1ce88ee8d79a300ed65d94b8fb616ddb3")
         (revision "2"))
-- 
cgit v1.2.3


From 01794ffce0c34d3c0b5c2bded95f634bac4ffaca Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Tue, 20 Feb 2018 09:06:14 -0500
Subject: gnu: Remove go-github-com-templexxx-xor.

* gnu/packages/syncthing.scm (go-github-com-templexxx-xor): Remove variable.
---
 gnu/packages/syncthing.scm | 24 ------------------------
 1 file changed, 24 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm
index 17aa12782b..60ad23440d 100644
--- a/gnu/packages/syncthing.scm
+++ b/gnu/packages/syncthing.scm
@@ -1552,30 +1552,6 @@ rolling hash.")
       (home-page "https://github.com/chmduquesne/rollinghash")
       (license expat))))
 
-(define-public go-github-com-templexxx-xor
-  (package
-    (name "go-github-com-templexxx-xor")
-    (version "0.1.2")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/templexxx/xor.git")
-               (commit version)))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32
-          "0v1maiii0sggmxk9bgpy6pypb40j3hy2328pc4kd5bldkpdb67d5"))))
-    (build-system go-build-system)
-    (arguments
-     '(#:import-path "github.com/templexxx/xor"))
-    (propagated-inputs
-     `(("go-github-com-templexxx-cpufeat" ,go-github-com-templexxx-cpufeat)))
-    (synopsis "XOR in Go")
-    (description "This packages provides a Go implementation of XOR.")
-    (home-page "https://github.com/templexxx/xor")
-    (license expat)))
-
 (define-public go-github-com-pkg-errors
   (let ((commit "e881fd58d78e04cf6d0de1217f8707c8cc2249bc")
         (revision "1"))
-- 
cgit v1.2.3


From 3b5262865c4d5ca1d73cdda86acf1e2a0b48d470 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Tue, 20 Feb 2018 08:59:31 -0500
Subject: gnu: syncthing: Update to 0.14.45.

* gnu/packages/syncthing.scm (syncthing): Update to 0.14.45.
[inputs]: Remove go-github-com-xtaci-kcp-go,
go-github-com-ccding-go-stun, and go-github-com-xtaci-smux. Add
go-github-com-pkg-errors.
---
 gnu/packages/syncthing.scm | 10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm
index 60ad23440d..6c3792b92f 100644
--- a/gnu/packages/syncthing.scm
+++ b/gnu/packages/syncthing.scm
@@ -28,7 +28,7 @@
 (define-public syncthing
   (package
     (name "syncthing")
-    (version "0.14.44")
+    (version "0.14.45")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/syncthing/syncthing"
@@ -36,7 +36,7 @@
                                   "/syncthing-source-v" version ".tar.gz"))
               (sha256
                (base32
-                "0fxq52w1b05928xp0a333rg23fabj0nykgg7v4gz01f3vrxyydi1"))
+                "0nv5g9ymykl4316l2g3mnac77y2rx9ps4j2kg3pymxlq6qms2dij"))
               (modules '((guix build utils)))
               ;; Delete bundled ("vendored") free software source code.
               (snippet
@@ -110,8 +110,6 @@
     (inputs
      `(("go-github-com-audriusbutkevicius-cli"
         ,go-github-com-audriusbutkevicius-cli)
-       ("go-github-com-xtaci-kcp-go"
-        ,go-github-com-xtaci-kcp-go)
        ("go-github-com-audriusbutkevicius-go-nat-pmp"
         ,go-github-com-audriusbutkevicius-go-nat-pmp)
        ("go-github-com-audriusbutkevicius-pfilter"
@@ -119,8 +117,6 @@
        ("go-github-com-bkaradzic-go-lz4" ,go-github-com-bkaradzic-go-lz4)
        ("go-github-com-calmh-du" ,go-github-com-calmh-du)
        ("go-github-com-calmh-xdr" ,go-github-com-calmh-xdr)
-       ("go-github-com-ccding-go-stun"
-        ,go-github-com-ccding-go-stun)
        ("go-github-com-prometheus-union" ,(go-github-com-prometheus-union))
        ("go-github-com-chmduquesne-rollinghash-adler32"
         ,go-github-com-chmduquesne-rollinghash-adler32)
@@ -137,12 +133,12 @@
        ("go-github-com-minio-sha256-simd" ,go-github-com-minio-sha256-simd)
        ("go-github-com-oschwald-geoip2-golang"
         ,go-github-com-oschwald-geoip2-golang)
+       ("go-github-com-pkg-errors" ,go-github-com-pkg-errors)
        ("go-github-com-rcrowley-go-metrics" ,go-github-com-rcrowley-go-metrics)
        ("go-github-com-sasha-s-go-deadlock" ,go-github-com-sasha-s-go-deadlock)
        ("go-github-com-syndtr-goleveldb" ,go-github-com-syndtr-goleveldb)
        ("go-github-com-thejerf-suture" ,go-github-com-thejerf-suture)
        ("go-github-com-vitrun-qart" ,(go-github-com-vitrun-qart-union))
-       ("go-github-com-xtaci-smux" ,go-github-com-xtaci-smux)
        ("go-golang-org-x-crypto" ,(go-golang-org-x-crypto-union))
        ("go-golang-org-x-net-union" ,(go-golang-org-x-net-union))
        ("go-golang-org-x-text" ,(go-golang-org-x-text-union))
-- 
cgit v1.2.3


From 8a325748fb8c3709beb2c26966a3e3c86831f95e Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Tue, 6 Mar 2018 13:30:49 -0500
Subject: gnu: isc-dhcp: Update to 4.3.6-P1 [fixes CVE-2018-{5732,5733}].

* gnu/packages/admin.scm (isc-dhcp): Update to 4.3.6-P1.
---
 gnu/packages/admin.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 554c1679e6..78b7b64dd1 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -610,14 +610,14 @@ connection alive.")
                                       bind-release-version)))
     (package
       (name "isc-dhcp")
-      (version "4.3.6")
+      (version "4.3.6-P1")
       (source (origin
                 (method url-fetch)
                 (uri (string-append "http://ftp.isc.org/isc/dhcp/"
                                     version "/dhcp-" version ".tar.gz"))
                 (sha256
                  (base32
-                  "06vgxhm6agzkp6r1jy10467vrfw2rzcp2mnkcph7ydziciisy7m4"))))
+                  "1hx3az6ckvgvybr1ag4k9kqr8zfcpzcww4vpw5gz0mi8y2z7gl9g"))))
       (build-system gnu-build-system)
       (arguments
        `(#:parallel-build? #f
-- 
cgit v1.2.3


From 41125eaff8fd4d47bd22b3cc423b9edc1b7b918c Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Sun, 25 Feb 2018 16:06:24 +0100
Subject: gnu: Add maven-resolver-api.

* gnu/packages/maven.scm: New file.
(maven-resolver-api): New variable.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
---
 gnu/local.mk           |  1 +
 gnu/packages/maven.scm | 50 ++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 51 insertions(+)
 create mode 100644 gnu/packages/maven.scm

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index d091a89b82..d90d8a318d 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -281,6 +281,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/marst.scm			\
   %D%/packages/mate.scm             \
   %D%/packages/maths.scm			\
+  %D%/packages/maven.scm			\
   %D%/packages/mc.scm				\
   %D%/packages/mcrypt.scm			\
   %D%/packages/medical.scm			\
diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm
new file mode 100644
index 0000000000..7fcc7b4533
--- /dev/null
+++ b/gnu/packages/maven.scm
@@ -0,0 +1,50 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages maven)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix utils)
+  #:use-module (guix build-system ant)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages java))
+
+(define-public maven-resolver-api
+  (package
+    (name "maven-resolver-api")
+    (version "1.1.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/apache/maven-resolver/"
+                                  "archive/maven-resolver-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0rpvdg3qr1j88gw0ankf0wnwfyq6238mdlm7s39vf5jrcvhdgwcl"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "maven-resolver-api.jar"
+       #:source-dir "maven-resolver-api/src/main/java"
+       #:test-dir "maven-resolver-api/src/test"))
+    (native-inputs
+     `(("java-junit" ,java-junit)
+       ("java-hamcrest-core" ,java-hamcrest-core)))
+    (home-page "https://github.com/apache/maven-resolver")
+    (synopsis "Maven repository system API")
+    (description "This package contains the API for the maven repository system.")
+    (license license:asl2.0)))
-- 
cgit v1.2.3


From d85cb53924ef648ab4ad373a664dc75f4e1c3d7a Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Sun, 25 Feb 2018 16:08:57 +0100
Subject: gnu: Add maven-resolver-spi.

* gnu/packages/maven.scm (maven-resolver-spi): New variable.
---
 gnu/packages/maven.scm | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm
index 7fcc7b4533..8fa7ecc5b8 100644
--- a/gnu/packages/maven.scm
+++ b/gnu/packages/maven.scm
@@ -48,3 +48,18 @@
     (synopsis "Maven repository system API")
     (description "This package contains the API for the maven repository system.")
     (license license:asl2.0)))
+
+(define-public maven-resolver-spi
+  (package
+    (inherit maven-resolver-api)
+    (name "maven-resolver-spi")
+    (arguments
+     `(#:jar-name "maven-resolver-spi.jar"
+       #:source-dir "maven-resolver-spi/src/main/java"
+       #:test-dir "maven-resolver-spi/src/test"
+       #:jdk ,icedtea-8))
+    (inputs
+     `(("maven-resolver-api" ,maven-resolver-api)))
+    (synopsis "Maven repository system SPI")
+    (description "This package contains the service provider interface (SPI)
+for repository system implementations and repository connectors.")))
-- 
cgit v1.2.3


From 360537838ef77cdc45fc2433e108802461fa8410 Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Sun, 25 Feb 2018 16:17:40 +0100
Subject: gnu: Add maven-resolver-test-util.

* gnu/packages/maven.scm (maven-resolver-test-util): New variable.
---
 gnu/packages/maven.scm | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm
index 8fa7ecc5b8..8cc4938062 100644
--- a/gnu/packages/maven.scm
+++ b/gnu/packages/maven.scm
@@ -63,3 +63,19 @@
     (synopsis "Maven repository system SPI")
     (description "This package contains the service provider interface (SPI)
 for repository system implementations and repository connectors.")))
+
+(define-public maven-resolver-test-util
+  (package
+    (inherit maven-resolver-api)
+    (name "maven-resolver-test-util")
+    (arguments
+     `(#:jar-name "maven-resolver-test-util.jar"
+       #:source-dir "maven-resolver-test-util/src/main/java"
+       #:test-dir "maven-resolver-test-util/src/test"
+       #:jdk ,icedtea-8))
+    (inputs
+     `(("maven-resolver-api" ,maven-resolver-api)
+       ("maven-resolver-spi" ,maven-resolver-spi)))
+    (synopsis "Utility classes for testing the maven repository system")
+    (description "This package contains a collection of utility classes to
+ease testing of the repository system.")))
-- 
cgit v1.2.3


From bca6cf54f46692290aa759e3e741f812a82366ff Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Sun, 25 Feb 2018 16:19:48 +0100
Subject: gnu: Add maven-resolver-util.

gnu/packages/maven.scm (maven-resolver-util): New variable.
---
 gnu/packages/maven.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm
index 8cc4938062..6c8f4b9319 100644
--- a/gnu/packages/maven.scm
+++ b/gnu/packages/maven.scm
@@ -79,3 +79,22 @@ for repository system implementations and repository connectors.")))
     (synopsis "Utility classes for testing the maven repository system")
     (description "This package contains a collection of utility classes to
 ease testing of the repository system.")))
+
+(define-public maven-resolver-util
+  (package
+    (inherit maven-resolver-api)
+    (name "maven-resolver-util")
+    (arguments
+     `(#:jar-name "maven-resolver-util.jar"
+       #:source-dir "maven-resolver-util/src/main/java"
+       #:test-dir "maven-resolver-util/src/test"
+       #:jdk ,icedtea-8))
+    (inputs
+     `(("maven-resolver-api" ,maven-resolver-api)))
+    (native-inputs
+     `(("java-junit" ,java-junit)
+       ("java-hamcrest-core" ,java-hamcrest-core)
+       ("maven-resolver-test-util" ,maven-resolver-test-util)))
+    (synopsis "Utility classes for the maven repository system")
+    (description "This package contains a collection of utility classes to
+ease usage of the repository system.")))
-- 
cgit v1.2.3


From f70666c9ce4f463d47c4d1694ed608bfadb56cd7 Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Sun, 25 Feb 2018 16:22:49 +0100
Subject: gnu: Add maven-resolver-connector-basic.

* gnu/packages/maven.scm (maven-resolver-connector-basic): New variable.
---
 gnu/packages/maven.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm
index 6c8f4b9319..81021f6461 100644
--- a/gnu/packages/maven.scm
+++ b/gnu/packages/maven.scm
@@ -98,3 +98,33 @@ ease testing of the repository system.")))
     (synopsis "Utility classes for the maven repository system")
     (description "This package contains a collection of utility classes to
 ease usage of the repository system.")))
+
+(define-public maven-resolver-connector-basic
+  (package
+    (inherit maven-resolver-api)
+    (name "maven-resolver-connector-basic")
+    (arguments
+     `(#:jar-name "maven-resolver-connector-basic.jar"
+       #:source-dir "maven-resolver-connector-basic/src/main/java"
+       #:test-dir "maven-resolver-connector-basic/src/test"
+       #:jdk ,icedtea-8
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'generate-sisu
+           (lambda _
+             (mkdir-p "build/classes/META-INF/sisu")
+             (with-output-to-file "build/classes/META-INF/sisu/javax.inject.Named"
+               (lambda _
+                 (display "org.eclipse.aether.connector.basic.BasicRepositoryConnectorFactory\n"))))))))
+    (inputs
+     `(("maven-resolver-api" ,maven-resolver-api)
+       ("maven-resolver-spi" ,maven-resolver-spi)
+       ("maven-resolver-util" ,maven-resolver-util)
+       ("java-javax-inject" ,java-javax-inject)))
+    (native-inputs
+     `(("java-junit" ,java-junit)
+       ("java-hamcrest-core" ,java-hamcrest-core)
+       ("maven-resolver-test-util" ,maven-resolver-test-util)))
+    (synopsis "Maven repository connector implementation")
+    (description "This package contains a repository connector implementation
+for repositories using URI-based layouts.")))
-- 
cgit v1.2.3


From 2468ca04882f27ac28a427e2445a20157b9b2802 Mon Sep 17 00:00:00 2001
From: Eric Bavier <bavier@member.fsf.org>
Date: Tue, 6 Mar 2018 23:33:57 -0600
Subject: gnu: thefuck: Update to 3.25.

* gnu/packages/admin.scm (thefuck): Update to 3.25
[inputs]: Add python-pyte.
[native-inputs]: Remove python-setuptools.
* gnu/packages/patches/thefuck-test-environ.patch: Adjust to latest source.
---
 gnu/packages/admin.scm                          | 13 ++++++-------
 gnu/packages/patches/thefuck-test-environ.patch | 20 ++++++++++----------
 2 files changed, 16 insertions(+), 17 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 78b7b64dd1..26ee4aaabe 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -2,7 +2,7 @@
 ;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013 Cyril Roelandt <tipecaml@gmail.com>
 ;;; Copyright © 2014, 2015, 2016, 2018 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2014, 2015, 2016, 2017 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2014, 2015, 2016, 2017, 2018 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015, 2016 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2015 Alex Sassmannshausen <alex.sassmannshausen@gmail.com>
 ;;; Copyright © 2015 Eric Dvorsak <eric@dvorsak.fr>
@@ -75,6 +75,7 @@
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages python-web)
+  #:use-module (gnu packages terminals)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages groff)
   #:use-module (gnu packages pciutils)
@@ -1855,7 +1856,7 @@ throughput (in the same interval).")
 (define-public thefuck
   (package
     (name "thefuck")
-    (version "3.19")
+    (version "3.25")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/nvbn/thefuck/archive/"
@@ -1863,7 +1864,7 @@ throughput (in the same interval).")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "191zbvkyc02h0wwd46xwj4zzg7jhlr8xv0ji6knqkgjnk0nvqq01"))
+                "088bn2l1376qlndbpnjya4q1x3913nj3yj3wc7s2w3bz66d23skk"))
               (patches (search-patches "thefuck-test-environ.patch"))))
     (build-system python-build-system)
     (arguments
@@ -1881,14 +1882,12 @@ throughput (in the same interval).")
      `(("python-colorama" ,python-colorama)
        ("python-decorator" ,python-decorator)
        ("python-psutil" ,python-psutil)
+       ("python-pyte" ,python-pyte)
        ("python-six" ,python-six)))
     (native-inputs
      `(("python-mock" ,python-mock)
        ("python-pytest" ,python-pytest)
-       ("python-pytest-mock" ,python-pytest-mock)
-       ;; Requires setuptools >= 17.1 due to some features used, while our
-       ;; python currently only includes 12.0. TODO: Remove this input.
-       ("python-setuptools" ,python-setuptools)))
+       ("python-pytest-mock" ,python-pytest-mock)))
     (home-page "https://github.com/nvbn/thefuck")
     (synopsis "Correct mistyped console command")
     (description
diff --git a/gnu/packages/patches/thefuck-test-environ.patch b/gnu/packages/patches/thefuck-test-environ.patch
index 0c602a38c4..54194d8928 100644
--- a/gnu/packages/patches/thefuck-test-environ.patch
+++ b/gnu/packages/patches/thefuck-test-environ.patch
@@ -1,14 +1,14 @@
 Retain environment setting of "HOME" for tests that need os.path.expanduser()
 to return a readable directory in the build chroot.
 
---- thefuck-3.15/tests/test_conf.py
-+++ thefuck-3.15/tests/test_conf.py
-@@ -12,7 +12,7 @@
- 
- @pytest.fixture
- def environ(monkeypatch):
--    data = {}
-+    data = {"HOME": os.environ.get("HOME")}
-     monkeypatch.setattr('thefuck.conf.os.environ', data)
-     return data
+--- thefuck-3.25/tests/conftest.py
++++ thefuck-3.25/tests/conftest.py
+@@ -64,6 +64,7 @@ def set_shell(monkeypatch):
  
+ @pytest.fixture(autouse=True)
+ def os_environ(monkeypatch):
+-    env = {'PATH': os.environ['PATH']}
++    env = {'PATH': os.environ['PATH'],
++           'HOME': os.environ['HOME']}
+     monkeypatch.setattr('os.environ', env)
+     return env
-- 
cgit v1.2.3


From 270750d440b4b2c5f88694b5abc2c2b48046d173 Mon Sep 17 00:00:00 2001
From: Charlie Ritter <chewzerita@posteo.net>
Date: Tue, 6 Mar 2018 10:59:47 -0500
Subject: gnu: Add IBM Plex font.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/fonts.scm (font-ibm-plex): New variable.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/fonts.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm
index 8af4f8dc83..aa9e466ebb 100644
--- a/gnu/packages/fonts.scm
+++ b/gnu/packages/fonts.scm
@@ -21,6 +21,7 @@
 ;;; Copyright © 2017 Brendan Tildesley <brendan.tildesley@openmailbox.org>
 ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2017 Mohammed Sadiq <sadiq@sadiqpk.org>
+;;; Copyright © 2018 Charlie Ritter <chewzerita@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -55,6 +56,27 @@
   #:use-module (gnu packages python)
   #:use-module (gnu packages xorg))
 
+(define-public font-ibm-plex
+  (package
+    (name "font-ibm-plex")
+    (version "1.0.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/IBM/plex/releases/download/"
+                    "v" version "/OpenType.zip"))
+              (sha256
+               (base32
+                "0nzxw9z6waixslam248yr26ci3fbk83c7jf6m90hncnaj6zxx795"))))
+    (build-system font-build-system)
+    (home-page "https://github.com/IBM/plex")
+    (synopsis "IBM Plex typeface")
+    (description "This package provides the Plex font family.  It comes in a
+Sans, Serif, Mono and Sans Condensed, all with roman and true italics.  The
+fonts have been designed to work well in user interface (UI) environments as
+well as other mediums.")
+    (license license:silofl1.1)))
+
 (define-public font-inconsolata
   (package
     (name "font-inconsolata")
-- 
cgit v1.2.3


From 63d99002961c8845cd16ae4b5e9ae6b273d43a80 Mon Sep 17 00:00:00 2001
From: Alex Vong <alexvong1995@gmail.com>
Date: Fri, 2 Mar 2018 21:22:59 +0800
Subject: gnu: youtube-viewer: Add '$out/lib/perl5/site_perl/' to search path.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Fixes <https://bugs.gnu.org/30671>.
Reported by Ricardo Wurmus <rekado@elephly.net>.

* gnu/packages/video.scm (youtube-viewer)[arguments]: In 'wrap-program'
phase, add '$out/lib/perl5/site_perl/' to search path.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/video.scm | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index e4e71e9dcc..7d072009a0 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -1344,16 +1344,18 @@ audio, images) from the Web.  It can use either mpv or vlc for playback.")
                   (guix build utils)
                   (srfi srfi-26))
        #:module-build-flags '("--gtk")
-       #:phases (modify-phases %standard-phases
-                  (add-after 'install 'wrap-program
-                    (lambda* (#:key outputs #:allow-other-keys)
-                      (let ((bin-dir (string-append (assoc-ref outputs "out")
-                                                    "/bin/"))
-                            (perl-path (getenv "PERL5LIB")))
-                        (for-each (cut wrap-program <>
-                                       `("PERL5LIB" ":" prefix (,perl-path)))
-                                  (find-files bin-dir))
-                        #t))))))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'wrap-program
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin-dir (string-append out "/bin/"))
+                    (site-dir (string-append out "/lib/perl5/site_perl/"))
+                    (lib-path (getenv "PERL5LIB")))
+               (for-each (cut wrap-program <>
+                              `("PERL5LIB" ":" prefix (,lib-path ,site-dir)))
+                         (find-files bin-dir))
+               #t))))))
     (synopsis
      "Lightweight application for searching and streaming videos from YouTube")
     (description
-- 
cgit v1.2.3


From 06c15ee5856442f5520a185d0f1934b6afb1c01b Mon Sep 17 00:00:00 2001
From: Oleg Pykhalov <go.wigust@gmail.com>
Date: Fri, 9 Feb 2018 17:33:42 +0300
Subject: gnu: Add r-colorout.

* gnu/packages/statistics.scm (r-colorout): New public variable.
---
 gnu/packages/statistics.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 8ebdce1376..0ae4dddb64 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -5564,6 +5564,38 @@ inferring an appropriate positioning method.")
 shaped points?  Now you can!")
       (license license:asl2.0))))
 
+(define-public r-colorout
+  (package
+    (name "r-colorout")
+    (version "1.2-0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/jalvesaq/colorout/archive/"
+                           "v" version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "07vqx5ihgnq4dzn5jnfjfhdm3957v4prvf8vhnb3cwvlly4l7p9v"))))
+    (build-system r-build-system)
+    (home-page "https://github.com/jalvesaq/colorout")
+    (synopsis "Colorize output in the R REPL")
+    (description "@code{colorout} is an R package that colorizes R output when
+running in terminal emulator.
+
+R STDOUT is parsed and numbers, negative numbers, dates in the standard
+format, strings, and R constants are identified and wrapped by special ANSI
+scape codes that are interpreted by terminal emulators as commands to colorize
+the output.  R STDERR is also parsed to identify the expressions warning and
+error and their translations to many languages.  If these expressions are
+found, the output is colorized accordingly; otherwise, it is colorized as
+STDERROR (blue, by default).
+
+You can customize the colors according to your taste, guided by the color
+table made by the command @code{show256Colors()}.  You can also set the colors
+to any arbitrary string.  In this case, it is up to you to set valid values.")
+    (license license:gpl3+)))
+
 (define-public java-jdistlib
   (package
     (name "java-jdistlib")
-- 
cgit v1.2.3


From 7700c6ca205d6a0594a036cbbab783dca24874f1 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 7 Mar 2018 12:57:31 +0100
Subject: gnu: glibmm: Update to 2.54.1.

* gnu/packages/glib.scm (glibmm): Update to 2.54.1.
[arguments]: Add #:configure-flags.
---
 gnu/packages/glib.scm | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/glib.scm b/gnu/packages/glib.scm
index a64407a36f..e09351a788 100644
--- a/gnu/packages/glib.scm
+++ b/gnu/packages/glib.scm
@@ -499,7 +499,7 @@ has an ease of use unmatched by other C++ callback libraries.")
 (define glibmm
   (package
     (name "glibmm")
-    (version "2.50.1")
+    (version "2.54.1")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnome/sources/glibmm/"
@@ -507,10 +507,13 @@ has an ease of use unmatched by other C++ callback libraries.")
                                  "/glibmm-" version ".tar.xz"))
              (sha256
               (base32
-               "1926b3adx903hzvdp8glblsgjyadzqnwgkj8hg605d4wv98m1n0z"))))
+               "0jkapw18icz59cmlmsl00nwwz0wh291kb4hc9z9hxmq45drqrhkw"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:phases
+     `(;; XXX: Some tests uses C++14 features.  Remove this when the default
+       ;; compiler is >= GCC6.
+       #:configure-flags '("CXXFLAGS=-std=gnu++14")
+       #:phases
        (modify-phases %standard-phases
          (add-before 'build 'pre-build
            (lambda _
-- 
cgit v1.2.3


From 29c7b4d6389d7d0ae70f2d87f27433431ac74890 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 7 Mar 2018 13:10:07 +0100
Subject: gnu: gtkmm: Update to 3.22.2.

* gnu/packages/gtk.scm (gtkmm): Update to 3.22.2.
[arguments]: Set #:configure-flags.
---
 gnu/packages/gtk.scm | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm
index ceb3f4dc4e..3a67e84d2a 100644
--- a/gnu/packages/gtk.scm
+++ b/gnu/packages/gtk.scm
@@ -1053,7 +1053,7 @@ toolkit.")
 (define-public gtkmm
   (package
     (name "gtkmm")
-    (version "3.22.0")
+    (version "3.22.2")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnome/sources/" name "/"
@@ -1061,7 +1061,7 @@ toolkit.")
                                  name "-" version ".tar.xz"))
              (sha256
               (base32
-               "1x8l0ny6r3ym53z82q9d5fan4m9vi93xy3b3hj1hrclgc95lvnh5"))))
+               "1400535lhyya462pfx8bp11k3mg3jsbdghlpygskd5ai665dkbwi"))))
     (build-system gnu-build-system)
     (native-inputs `(("pkg-config" ,pkg-config)
                      ("glib" ,glib "bin")        ;for 'glib-compile-resources'
@@ -1073,7 +1073,10 @@ toolkit.")
        ("gtk+" ,gtk+)
        ("glibmm" ,glibmm)))
     (arguments
-     '(#:phases (modify-phases %standard-phases
+     '(;; XXX: Tests require C++14 or later.  Remove this when the default
+       ;; compiler is >= GCC6.
+       #:configure-flags '("CXXFLAGS=-std=gnu++14")
+       #:phases (modify-phases %standard-phases
                   (add-before 'check 'run-xvfb
                     (lambda* (#:key inputs #:allow-other-keys)
                       (let ((xorg-server (assoc-ref inputs "xorg-server")))
-- 
cgit v1.2.3


From 6a49ae786487013cecd97a372514b75c77282b50 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 7 Mar 2018 13:10:57 +0100
Subject: gnu: gtkmm: Use the for-test xorg variant for tests.

* gnu/packages/gtk.scm (gtkmm)[native-inputs]: Replace XORG-SERVER with
XORG-SERVER-1.19.3.
[arguments]: Add #:disallowed-references.
---
 gnu/packages/gtk.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm
index 3a67e84d2a..9fc9fd6015 100644
--- a/gnu/packages/gtk.scm
+++ b/gnu/packages/gtk.scm
@@ -1065,7 +1065,7 @@ toolkit.")
     (build-system gnu-build-system)
     (native-inputs `(("pkg-config" ,pkg-config)
                      ("glib" ,glib "bin")        ;for 'glib-compile-resources'
-                     ("xorg-server" ,xorg-server)))
+                     ("xorg-server" ,xorg-server-1.19.3)))
     (propagated-inputs
      `(("pangomm" ,pangomm)
        ("cairomm" ,cairomm)
@@ -1073,9 +1073,10 @@ toolkit.")
        ("gtk+" ,gtk+)
        ("glibmm" ,glibmm)))
     (arguments
-     '(;; XXX: Tests require C++14 or later.  Remove this when the default
+     `(;; XXX: Tests require C++14 or later.  Remove this when the default
        ;; compiler is >= GCC6.
        #:configure-flags '("CXXFLAGS=-std=gnu++14")
+       #:disallowed-references (,xorg-server-1.19.3)
        #:phases (modify-phases %standard-phases
                   (add-before 'check 'run-xvfb
                     (lambda* (#:key inputs #:allow-other-keys)
-- 
cgit v1.2.3


From 8e933cb36aa08843fd0187ec4c441179a1ed3695 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 7 Mar 2018 13:15:15 +0100
Subject: gnu: Use HTTPS on gtkmm.org home pages.

* gnu/packages/gtk.scm (atkmm, gtkmm)[home-page]: Use HTTPS.
* gnu/packages/gnome.scm (libgnomecanvasmm)[home-page]: Likewise.
* gnu/packages/glib.scm (glibmm)[home-page]: Likewise.
---
 gnu/packages/glib.scm  | 2 +-
 gnu/packages/gnome.scm | 2 +-
 gnu/packages/gtk.scm   | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/glib.scm b/gnu/packages/glib.scm
index e09351a788..366d615e58 100644
--- a/gnu/packages/glib.scm
+++ b/gnu/packages/glib.scm
@@ -535,7 +535,7 @@ has an ease of use unmatched by other C++ callback libraries.")
     (propagated-inputs
      `(("libsigc++" ,libsigc++)
        ("glib" ,glib)))
-    (home-page "http://gtkmm.org/")
+    (home-page "https://gtkmm.org/")
     (synopsis "C++ interface to the GLib library")
     (description
      "Glibmm provides a C++ programming interface to the part of GLib that are
diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index d6f7e9e281..2384bf2381 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -1595,7 +1595,7 @@ creating interactive structured graphics.")
     (native-inputs
      `(("gtkmm-2" ,gtkmm-2)
        ("pkg-config" ,pkg-config)))
-    (home-page "http://gtkmm.org")
+    (home-page "https://gtkmm.org")
     (synopsis "C++ bindings to the GNOME Canvas library")
     (description "C++ bindings to the GNOME Canvas library.")
     (license license:lgpl2.0+)))
diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm
index 9fc9fd6015..a1d7e548aa 100644
--- a/gnu/packages/gtk.scm
+++ b/gnu/packages/gtk.scm
@@ -1043,7 +1043,7 @@ library.")
     (native-inputs `(("pkg-config" ,pkg-config)))
     (propagated-inputs
      `(("glibmm" ,glibmm) ("atk" ,atk)))
-    (home-page "http://www.gtkmm.org")
+    (home-page "https://www.gtkmm.org")
     (synopsis "C++ interface to the ATK accessibility library")
     (description
      "ATKmm provides a C++ programming interface to the ATK accessibility
@@ -1088,7 +1088,7 @@ toolkit.")
                         ;; Don't fail because of the missing /etc/machine-id.
                         (setenv "DBUS_FATAL_WARNINGS" "0")
                         #t))))))
-    (home-page "http://gtkmm.org/")
+    (home-page "https://gtkmm.org/")
     (synopsis
      "C++ interface to the GTK+ graphical user interface library")
     (description
-- 
cgit v1.2.3


From e07a44891cd906aa071e88e355b9cc8f93b047f7 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 7 Mar 2018 13:27:09 +0100
Subject: gnu: Add gtksourceviewmm.

* gnu/packages/gtk.scm (gtksourceviewmm): New public variable.
---
 gnu/packages/gtk.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm
index a1d7e548aa..a96cb96470 100644
--- a/gnu/packages/gtk.scm
+++ b/gnu/packages/gtk.scm
@@ -1122,6 +1122,38 @@ extensive documentation, including API reference and a tutorial.")
        ("gtk+" ,gtk+-2)
        ("glibmm" ,glibmm)))))
 
+(define-public gtksourceviewmm
+  (package
+    (name "gtksourceviewmm")
+    (version "3.18.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://gnome/sources/" name "/"
+                                  (version-major+minor version)  "/"
+                                  name "-" version ".tar.xz"))
+              (sha256
+               (base32 "0fgvmhm4h4qmxig87qvangs6ijw53mi40siz7pixlxbrsgiil22i"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (propagated-inputs
+     ;; In 'Requires' of gtksourceviewmm-3.0.pc.
+     `(("glibmm" ,glibmm)
+       ("gtkmm" ,gtkmm)
+       ("gtksourceview" ,gtksourceview)))
+    (synopsis "C++ interface to the GTK+ 'GtkTextView' widget")
+    (description
+     "gtksourceviewmm is a portable C++ library that extends the standard GTK+
+framework for multiline text editing with support for configurable syntax
+highlighting, unlimited undo/redo, search and replace, a completion framework,
+printing and other features typical of a source code editor.")
+    (license license:lgpl2.1+)
+    (home-page "https://developer.gnome.org/gtksourceview/")))
+
+;;;
+;;; Python bindings.
+;;;
+
 (define-public python-pycairo
   (package
     (name "python-pycairo")
-- 
cgit v1.2.3


From 0cf985d615c6447b12ea3c784ffc3515c59ef99f Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 7 Mar 2018 13:56:26 +0100
Subject: gnu: imagemagick: Update to 6.9.9-37.

* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.9-37.
---
 gnu/packages/imagemagick.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/imagemagick.scm b/gnu/packages/imagemagick.scm
index cc03f8fc2d..d798833742 100644
--- a/gnu/packages/imagemagick.scm
+++ b/gnu/packages/imagemagick.scm
@@ -47,14 +47,14 @@
     ;; The 7 release series has an incompatible API, while the 6 series is still
     ;; maintained. Don't update to 7 until we've made sure that the ImageMagick
     ;; users are ready for the 7-series API.
-    (version "6.9.9-36")
+    (version "6.9.9-37")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://imagemagick/ImageMagick-"
                                  version ".tar.xz"))
              (sha256
               (base32
-               "1nhv3cmg4npqibhchp3qgm9pld3n94xwwzv5hgn2s7lqz0zc0vd8"))))
+               "1hmfw0jcpc3s3gz9zrzjy9amyrfz6gzzjdsyaw3xw994aq9qf4lq"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags '("--with-frozenpaths" "--without-gcc-arch")
-- 
cgit v1.2.3


From 5668a365d66d7150920822aadb12dd47ffb8d49f Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 7 Mar 2018 14:10:42 +0100
Subject: gnu: mkfontscale: Update to 1.1.3.

* gnu/packages/xorg.scm (mkfontscale): Update to 1.1.3.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index 3ae936923c..9ee7ef5bec 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -1558,7 +1558,7 @@ input from UTF-8 into the locale's encoding.")
 (define-public mkfontscale
   (package
     (name "mkfontscale")
-    (version "1.1.2")
+    (version "1.1.3")
     (source
       (origin
         (method url-fetch)
@@ -1568,7 +1568,7 @@ input from UTF-8 into the locale's encoding.")
                ".tar.bz2"))
         (sha256
           (base32
-            "081z8lwh9c1gyrx3ad12whnpv3jpfbqsc366mswpfm48mwl54vcc"))))
+            "0siag28jpm8hj62bgjvw81sjfgrc7vcy2h7127bl4iazxrlxz60y"))))
     (build-system gnu-build-system)
     (inputs
       `(("zlib" ,zlib)
-- 
cgit v1.2.3


From b5ebc1bf8cf35ae2579012319083aff29d74b9bf Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 7 Mar 2018 14:12:55 +0100
Subject: gnu: twm: Update to 1.0.10.

* gnu/packages/xorg.scm (twm): Update to 1.0.10.
[source]: Use bzip-compressed tarball.
---
 gnu/packages/xorg.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index 9ee7ef5bec..3bf2266034 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -5421,17 +5421,17 @@ Intrinsics (Xt) Library.")
 (define-public twm
   (package
     (name "twm")
-    (version "1.0.9")
+    (version "1.0.10")
     (source
      (origin
        (method url-fetch)
        (uri (string-append
              "mirror://xorg/individual/app/" name "-"
              version
-             ".tar.gz"))
+             ".tar.bz2"))
        (sha256
         (base32
-         "1s1r00x8add3f27xjqxg6q7mwplwrb72gakbh4y6j052as25wchw"))))
+         "1ms5cj1w3g26zg6bxdv1j9hl0pxr4300qnv003cz1q3cl7ffljb4"))))
     (build-system gnu-build-system)
     (inputs
      `(("libxt" ,libxt)
-- 
cgit v1.2.3


From 9dda6dadf103d6241b54ac652ccd5dec82caca00 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 7 Mar 2018 14:14:34 +0100
Subject: gnu: xdriinfo: Update to 1.0.6.

* gnu/packages/xorg.scm (xdriinfo): Update to 1.0.6.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index 3bf2266034..d1671ba8c1 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -2276,7 +2276,7 @@ available.")
 (define-public xdriinfo
   (package
     (name "xdriinfo")
-    (version "1.0.5")
+    (version "1.0.6")
     (source
       (origin
         (method url-fetch)
@@ -2286,7 +2286,7 @@ available.")
                ".tar.bz2"))
         (sha256
           (base32
-            "0681d0y8liqakkpz7mmsf689jcxrvs5291r20qi78mc9xxk3gfjc"))))
+            "0lcx8h3zd11m4w8wf7dyp89826d437iz78cyrix436bqx31x5k6r"))))
     (build-system gnu-build-system)
     (inputs
       `(("mesa" ,mesa)
-- 
cgit v1.2.3


From eaa8292e41b573adc7d4a338c8ee76918becbb9c Mon Sep 17 00:00:00 2001
From: Mark Meyer <mark@ofosos.org>
Date: Fri, 15 Dec 2017 10:09:28 +0100
Subject: gnu: Add python-pycurl.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/python-web.scm (python-pycurl, python2-pycurl): New
variables.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/python-web.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index d9721f1375..dce651246c 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -22,6 +22,7 @@
 ;;; Copyright © 2016 David Craven <david@craven.ch>
 ;;; Copyright © 2017 Oleg Pykhalov <go.wigust@gmail.com>
 ;;; Copyright © 2015, 2016 David Thompson <davet@gnu.org>
+;;; Copyright © 2017 Mark Meyer <mark@ofosos.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -45,11 +46,13 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages curl)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages django)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-crypto)
+  #:use-module (gnu packages tls)
   #:use-module (gnu packages time)
   #:use-module (gnu packages xml)
   #:use-module ((guix licenses) #:prefix license:)
@@ -238,6 +241,40 @@ C, yielding parse times that can be a thirtieth of the html5lib parse times.")
 (define-public python2-html5-parser
   (package-with-python2 python-html5-parser))
 
+(define-public python-pycurl
+  (package
+    (name "python-pycurl")
+    (version "7.43.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://dl.bintray.com/pycurl/pycurl/pycurl-"
+                           version ".tar.gz"))
+       (sha256
+        (base32 "1ali1gjs9iliwjra7w0y5hwg79a2fd0f4ydvv6k27sgxpbr1n8s3"))))
+    (build-system python-build-system)
+    (arguments
+     ;; The tests attempt to access external web servers, so we cannot run
+     ;; them.  Furthermore, they are skipped altogether when using Python 2.
+     '(#:tests? #f))
+    (native-inputs
+     `(("python-nose" ,python-nose)
+       ("python-bottle" ,python-bottle)))
+    (inputs
+     `(("curl" ,curl)
+       ("gnutls" ,gnutls)))
+    (home-page "http://pycurl.io/")
+    (synopsis "Lightweight Python wrapper around libcurl")
+    (description "Pycurl is a lightweight wrapper around libcurl.  It provides
+high-speed transfers via libcurl and frequently outperforms alternatives.")
+
+    ;; Per 'README.rst', this is dual-licensed: users can redistribute pycurl
+    ;; under the terms of LGPLv2.1+ or Expat.
+    (license (list license:lgpl2.1+ license:expat))))
+
+(define-public python2-pycurl
+  (package-with-python2 python-pycurl))
+
 (define-public python-webencodings
   (package
     (name "python-webencodings")
-- 
cgit v1.2.3


From 30e43e816b15caab97183362235d2c39ea18ec7f Mon Sep 17 00:00:00 2001
From: Mark Meyer <mark@ofosos.org>
Date: Sat, 16 Dec 2017 10:57:21 +0100
Subject: gnu: python2-gobject@2: Update to 2.28.7
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/glib.scm (python2-gobject-2): Update to 2.28.7.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/glib.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/glib.scm b/gnu/packages/glib.scm
index 366d615e58..30a22d7d59 100644
--- a/gnu/packages/glib.scm
+++ b/gnu/packages/glib.scm
@@ -547,7 +547,7 @@ useful for C++.")
     (name "python2-pygobject")
     ;; This was the last version to declare the 2.0 platform number, i.e. its
     ;; pkg-config files were named pygobject-2.0.pc
-    (version "2.28.6")
+    (version "2.28.7")
     (source
      (origin
        (method url-fetch)
@@ -556,7 +556,7 @@ useful for C++.")
                            "/pygobject-" version ".tar.xz"))
        (sha256
         (base32
-         "1f5dfxjnil2glfwxnqr14d2cjfbkghsbsn8n04js2c2icr7iv2pv"))
+         "0nkam61rsn7y3wik3vw46wk5q2cjfh2iph57hl9m39rc8jijb7dv"))
        (patches (search-patches
                  "python2-pygobject-2-gi-info-type-error-domain.patch"))))
     (build-system gnu-build-system)
-- 
cgit v1.2.3


From 2b30af95416f37f8e371d59f6a7dd8607aea6e2a Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 7 Mar 2018 13:27:48 +0100
Subject: gnu: c-reduce: Update to 2.6.0.

* gnu/packages/debug.scm (c-reduce): Update to 2.6.0.
---
 gnu/packages/debug.scm | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/debug.scm b/gnu/packages/debug.scm
index 6b566b0097..92d635332f 100644
--- a/gnu/packages/debug.scm
+++ b/gnu/packages/debug.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014, 2015, 2016, 2017 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -85,10 +86,11 @@ program to exhibit a bug.")
     ;; home-page pointing to a bsd-2 license.
     (license bsd-3)))
 
+;; Newer versions depend on LLVM and Clang >= 4, which have yet to be packaged.
 (define-public c-reduce
   (package
     (name "c-reduce")
-    (version "2.5.0")
+    (version "2.6.0")
     (source
      (origin
       (method url-fetch)
@@ -97,12 +99,12 @@ program to exhibit a bug.")
                            "creduce-" version ".tar.gz")))
       (sha256
        (base32
-        "1r23lhzq3dz8vi2dalxk5las8bf0av2w94hxxbs61pr73m77ik9d"))))
+        "0pf5q0n8vkdcr1wrkxn2jzxv0xkrir13bwmqfw3jpbm3dh2c3b6d"))))
     (build-system gnu-build-system)
     (inputs
      `(("astyle"          ,astyle)
-       ("llvm"            ,llvm)
-       ("clang"           ,clang)
+       ("llvm"            ,llvm-3.9.1)
+       ("clang"           ,clang-3.9.1)
        ("flex"            ,flex)
        ("indent"          ,indent)
        ("perl"            ,perl)
-- 
cgit v1.2.3


From 7649e4269ef2107da5fbbb1e112f4be00338d0e9 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 7 Mar 2018 13:28:32 +0100
Subject: gnu: c-reduce: Use HTTPS home page.

* gnu/packages/debug.scm (c-reduce)[home-page]: Use HTTPS.
---
 gnu/packages/debug.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/debug.scm b/gnu/packages/debug.scm
index 92d635332f..112c656ff8 100644
--- a/gnu/packages/debug.scm
+++ b/gnu/packages/debug.scm
@@ -133,7 +133,7 @@ program to exhibit a bug.")
                            "file-which"      "getopt-tabular"
                            "regex-common"    "sys-cpu")))))
              #t)))))
-    (home-page "http://embed.cs.utah.edu/creduce")
+    (home-page "https://embed.cs.utah.edu/creduce")
     (synopsis "Reducer for interesting code")
     (description
      "C-Reduce is a tool that takes a large C or C++ program that has a
-- 
cgit v1.2.3


From b11481a5428ce04da690735b24cf7fa0e994c263 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 6 Mar 2018 21:02:39 +0100
Subject: gnu: mg: Update to 20171014.

* gnu/packages/text-editors.scm (mg): Update to 20171014.
---
 gnu/packages/text-editors.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/text-editors.scm b/gnu/packages/text-editors.scm
index 0207ca36ab..64f13dd998 100644
--- a/gnu/packages/text-editors.scm
+++ b/gnu/packages/text-editors.scm
@@ -239,14 +239,14 @@ Wordstar-, EMACS-, Pico, Nedit or vi-like key bindings.  e3 can be used on
 (define-public mg
   (package
     (name "mg")
-    (version "20170401")
+    (version "20171014")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://homepage.boetes.org/software/mg/mg-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1arasswgdadbb265rahq3867r9s54jva6k4m3p5n0f8mgjqhhdha"))
+                "0hakfikzsml7z0hja8m8mcahrmfy2piy81bq9nccsjplyfc9clai"))
               (modules '((guix build utils)))
               (snippet
                '(begin
-- 
cgit v1.2.3


From c3d828855ade0d9742754339f5683ca1317baa19 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 6 Mar 2018 21:02:44 +0100
Subject: gnu: mg: Use HTTPS home page.

* gnu/packages/text-editors.scm (mg)[home-page]: Use HTTPS.
---
 gnu/packages/text-editors.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/text-editors.scm b/gnu/packages/text-editors.scm
index 64f13dd998..f1ccab9af9 100644
--- a/gnu/packages/text-editors.scm
+++ b/gnu/packages/text-editors.scm
@@ -283,7 +283,7 @@ Wordstar-, EMACS-, Pico, Nedit or vi-like key bindings.  e3 can be used on
                              (doc (string-append out "/share/doc/mg")))
                         (install-file "tutorial" doc)
                         #t))))))
-    (home-page "http://homepage.boetes.org/software/mg/")
+    (home-page "https://homepage.boetes.org/software/mg/")
     (synopsis "Microscopic GNU Emacs clone")
     (description
      "Mg (mg) is a GNU Emacs style editor, with which it is \"broadly\"
-- 
cgit v1.2.3


From 0e6c242bb7589938388983028ff55953b45d89fc Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 7 Mar 2018 00:57:40 +0100
Subject: gnu: pam-krb5: Update to 4.8.

* gnu/packages/admin.scm (pam-krb5): Update to 4.8.
---
 gnu/packages/admin.scm | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 26ee4aaabe..4b97d04804 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -1992,12 +1992,10 @@ shortcut syntax and completion options.")
       (home-page "https://github.com/TrilbyWhite/interrobang")
       (license license:gpl3+))))
 
-
-
 (define-public pam-krb5
   (package
     (name "pam-krb5")
-    (version "4.7")
+    (version "4.8")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2005,7 +2003,7 @@ shortcut syntax and completion options.")
                     version ".tar.xz"))
               (sha256
                (base32
-                "0abf8cfpkprmhw5ca8iyqgrggh65lgqvmfllc1y6qz7zw1gas894"))))
+                "1qjp8i1s9bz7g6kiqrkzzkxn5pfspa4sy53b6z40fqmdf9przdfb"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -2042,8 +2040,6 @@ Kerberos and Heimdal and FAST is supported with recent MIT Kerberos.")
     ;; clause requiring us to give all recipients a copy.
     (license license:gpl1+)))
 
-;;http://archives.eyrie.org/software/kerberos/pam-krb5-4.7.tar.xz
-
 (define-public sunxi-tools
   (package
     (name "sunxi-tools")
-- 
cgit v1.2.3


From 45298300e43d314f9001c2bdbd72f1189e20eb70 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 7 Mar 2018 01:23:55 +0100
Subject: gnu: pam-krb5: Mark up description.

* gnu/packages/admin.scm (pam-krb5)[description]: Use @code.
---
 gnu/packages/admin.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 4b97d04804..9116835d04 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -2029,8 +2029,8 @@ It supports ticket refreshing by screen savers, configurable
 authorization handling, authentication of non-local accounts for network
 services, password changing, and password expiration, as well as all the
 standard expected PAM features.  It works correctly with OpenSSH, even
-with ChallengeResponseAuthentication and PrivilegeSeparation enabled,
-and supports extensive configuration either by PAM options or in
+with @code{ChallengeResponseAuthentication} and @code{PrivilegeSeparation}
+enabled, and supports extensive configuration either by PAM options or in
 krb5.conf or both.  PKINIT is supported with recent versions of both MIT
 Kerberos and Heimdal and FAST is supported with recent MIT Kerberos.")
     (home-page "http://www.eyrie.org/~eagle/software/pam-krb5")
-- 
cgit v1.2.3


From d4f5e68e55d15f851ad4d820a5384123d9b51441 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 7 Mar 2018 02:49:23 +0100
Subject: gnu: cmdtest: Update to 0.32.

* gnu/packages/check.scm (cmdtest): Update to 0.32.
---
 gnu/packages/check.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 50b4afcaf0..686c2e2b27 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -16,7 +16,7 @@
 ;;; Copyright © 2016 Troy Sankey <sankeytms@gmail.com>
 ;;; Copyright © 2016 Lukas Gradl <lgradl@openmailbox.org>
 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
-;;; Copyright © 2016, 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2016, 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be>
 ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
@@ -202,14 +202,14 @@ multi-paradigm automated test framework for C++ and Objective-C.")
 (define-public cmdtest
   (package
     (name "cmdtest")
-    (version "0.29")
+    (version "0.32")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://git.liw.fi/cmdtest/snapshot/"
                                   name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1i6gi4yp4qqx1liax098c7nwdb24pghh11xqlrcs7lnhh079rqhb"))))
+                "1jmfiyrrqmpvwdb273bkb8hjaf4rwx9njblx29pmr7giyahskwi5"))))
     (build-system python-build-system)
     (arguments
      `(#:python ,python-2
-- 
cgit v1.2.3


From 925102bb98f3b501d5168a42ed0d7646f311257c Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 7 Mar 2018 03:23:38 +0100
Subject: gnu: cppcheck: Update to 1.82.

* gnu/packages/check.scm (cppcheck): Update to 1.82.
---
 gnu/packages/check.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 686c2e2b27..73d3efd9e1 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -271,13 +271,13 @@ format.")
 (define-public cppcheck
   (package
     (name "cppcheck")
-    (version "1.81")
+    (version "1.82")
     (source (origin
       (method url-fetch)
       (uri (string-append "https://github.com/danmar/cppcheck/archive/"
                           version ".tar.gz"))
       (sha256
-       (base32 "0miamqk7pa2dzmnmi5wb6hjp2a3zya1x8afnlcxby8jb6gp6wf8j"))
+       (base32 "0zywpd9hbsx23aj33pk5mbr0fz1ijhqzxlnqgwjfwgg6g2k48i2j"))
       (file-name (string-append name "-" version ".tar.gz"))))
     (build-system cmake-build-system)
     (home-page "http://cppcheck.sourceforge.net")
-- 
cgit v1.2.3


From b9499508b4aa6055c01cc9f2d7ff776dd5a53c1c Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 7 Mar 2018 03:31:49 +0100
Subject: gnu: keyutils: Update to 1.5.10.

* gnu/packages/crypto.scm (keyutils): Update to 1.5.10.
---
 gnu/packages/crypto.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm
index b498aabf4d..7716205947 100644
--- a/gnu/packages/crypto.scm
+++ b/gnu/packages/crypto.scm
@@ -258,7 +258,7 @@ the wrong hands.")
 (define-public keyutils
   (package
     (name "keyutils")
-    (version "1.5.9")
+    (version "1.5.10")
     (source
      (origin
        (method url-fetch)
@@ -267,7 +267,7 @@ the wrong hands.")
                        version ".tar.bz2"))
        (sha256
         (base32
-         "1bl3w03ygxhc0hz69klfdlwqn33jvzxl1zfl2jmnb2v85iawb8jd"))
+         "1dmgjcf7mnwc6h72xkvpaqpzxw8vmlnsmzz0s27pg0giwzm3sp0i"))
        (modules '((guix build utils)))
        ;; Create relative symbolic links instead of absolute ones to /lib/*
        (snippet '(substitute* "Makefile" (("\\$\\(LNS\\) \\$\\(LIBDIR\\)/")
-- 
cgit v1.2.3


From b8b34be61c663ba3dc0cefa002b7051fc47ed4c0 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 7 Mar 2018 00:52:02 +0100
Subject: gnu: links, lynx, qutebrowser: Update phase style.

* gnu/packages/web-browsers.scm (links, lynx, qutebrowser)[arguments]:
Substitute INVOKE for SYSTEM and end phases with #t.
---
 gnu/packages/web-browsers.scm | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/web-browsers.scm b/gnu/packages/web-browsers.scm
index bd4c34efb6..ef39d71411 100644
--- a/gnu/packages/web-browsers.scm
+++ b/gnu/packages/web-browsers.scm
@@ -4,6 +4,7 @@
 ;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Kei Kebreau <kkebreau@posteo.net>
 ;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -102,10 +103,10 @@ older or slower computers and embedded systems.")
                      `((setenv "CHOST" ,(%current-target-system)))
                      '())
                (setenv "CONFIG_SHELL" (which "bash"))
-               (zero?
-                (system* "./configure"
-                         (string-append "--prefix=" out)
-                         "--enable-graphics"))))))))
+               (invoke "./configure"
+                       (string-append "--prefix=" out)
+                       "--enable-graphics")
+               #t))))))
     (native-inputs `(("pkg-config" ,pkg-config)))
     (inputs `(("zlib" ,zlib)
               ("openssl" ,openssl)
@@ -175,7 +176,8 @@ features including, tables, builtin image display, bookmarks, SSL and more.")
                      #t))
          (replace 'install
            (lambda* (#:key (make-flags '()) #:allow-other-keys)
-             (zero? (apply system* "make" "install-full" make-flags)))))))
+             (apply invoke "make" "install-full" make-flags)
+             #t)))))
     (synopsis "Text Web Browser")
     (description
      "Lynx is a fully-featured World Wide Web (WWW) client for users running
@@ -223,7 +225,7 @@ access.")
              (let* ((out (assoc-ref outputs "out"))
                     (app (string-append out "/share/applications"))
                     (hicolor (string-append out "/share/icons/hicolor")))
-               (system* "a2x" "-f" "manpage" "doc/qutebrowser.1.asciidoc")
+               (invoke "a2x" "-f" "manpage" "doc/qutebrowser.1.asciidoc")
                (install-file "doc/qutebrowser.1"
                              (string-append out "/share/man/man1"))
 
-- 
cgit v1.2.3


From 6c4da3b76a7c1a92b04983a93790f3a5f3bf8284 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 7 Mar 2018 01:31:27 +0100
Subject: gnu: meson: Mark up description.

* gnu/packages/build-tools.scm (meson)[description]: Use @dfn.
---
 gnu/packages/build-tools.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/build-tools.scm b/gnu/packages/build-tools.scm
index 7c0faca9a2..2abb44fdb8 100644
--- a/gnu/packages/build-tools.scm
+++ b/gnu/packages/build-tools.scm
@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Corentin Bocquillon <corentin@nybble.fr>
-;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -90,8 +90,8 @@ makes a few sacrifices to acquire fast full and incremental build times.")
 It can compile code written in C, C++, Fortran, Java, Rust, and other
 languages.  Meson provides features comparable to those of the
 Autoconf/Automake/make combo.  Build specifications, also known as @dfn{Meson
-files}, are written in a custom domain-specific language (DSL) that resembles
-Python.")
+files}, are written in a custom domain-specific language (@dfn{DSL}) that
+resembles Python.")
     (license license:asl2.0)))
 
 (define-public meson-for-build
-- 
cgit v1.2.3


From 9dae73c31cf18779dec656fe2fb7e5eed24a35c6 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 7 Mar 2018 02:28:28 +0100
Subject: gnu: pigz: Update to 2.4.

* gnu/packages/compression.scm (pigz): Update to 2.4.
---
 gnu/packages/compression.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 423d3989aa..d77d06a642 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -844,14 +844,14 @@ extract such file systems.")
 (define-public pigz
   (package
     (name "pigz")
-    (version "2.3.3")
+    (version "2.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://zlib.net/pigz/"
                                   name "-" version ".tar.gz"))
               (sha256
                (base32
-                "172hdf26k4zmm7z8md7nl0dph2a7mhf3x7slb9bhfyff6as6g2sf"))))
+                "0wsgw5vwl23jrnpsvd8v3xcp5k4waw5mk0164fynjhkv58i1dy54"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
-- 
cgit v1.2.3


From 7f1773eaee2f10990c9c4002d383e96deb2b95c3 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 7 Mar 2018 02:31:05 +0100
Subject: gnu: Use HTTPS for zlib.net home pages.

* gnu/packages/compression.scm (zlib, pigz)[home-page]: Use HTTPS.
---
 gnu/packages/compression.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index d77d06a642..d44ae2d259 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -99,7 +99,7 @@
                (zero?
                 (system* "./configure"
                          (string-append "--prefix=" out)))))))))
-    (home-page "http://zlib.net/")
+    (home-page "https://zlib.net/")
     (synopsis "Compression library")
     (description
      "zlib is designed to be a free, general-purpose, legally unencumbered --
@@ -869,7 +869,7 @@ extract such file systems.")
        #:make-flags (list "CC=gcc")
        #:test-target "tests"))
     (inputs `(("zlib" ,zlib)))
-    (home-page "http://zlib.net/pigz/")
+    (home-page "https://zlib.net/pigz/")
     (synopsis "Parallel implementation of gzip")
     (description
      "This package provides a parallel implementation of gzip that exploits
-- 
cgit v1.2.3


From f35843674ecdfd08be710888e6e7bb1cdc0ee309 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 7 Mar 2018 13:34:47 +0100
Subject: gnu: znc: Update to 1.6.6.

* gnu/packages/messaging.scm (znc): Update to 1.6.6.
---
 gnu/packages/messaging.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index 7a4c370c99..b6323c39b2 100644
--- a/gnu/packages/messaging.scm
+++ b/gnu/packages/messaging.scm
@@ -449,14 +449,14 @@ compromised.")
 (define-public znc
   (package
     (name "znc")
-    (version "1.6.5")
+    (version "1.6.6")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://znc.in/releases/archive/znc-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1jia6kq6bp8yxfj02d5vj9vqb4pylqcldspyjj6iz82kkka2a0ig"))))
+                "09cmsnxvi7jg9a0dicf60fxnxdff4aprw7h8vjqlj5ywf6y43f3z"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
-- 
cgit v1.2.3


From 021caafa2cd213f773386af8a3226a4ad41683da Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Mar 2018 18:11:33 +0100
Subject: gnu: Add r-heatmaply.

* gnu/packages/cran.scm (r-heatmaply): New variable.
---
 gnu/packages/cran.scm | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index f8d17e1ad2..b5471d703b 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2738,3 +2738,44 @@ ordered factor data types.")
      "This package provides tools for the computation of matrix and scalar
 exponentiation.")
     (license license:gpl2)))
+
+(define-public r-heatmaply
+  (package
+    (name "r-heatmaply")
+    (version "0.14.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "heatmaply" version))
+       (sha256
+        (base32
+         "03p2caclhfgqgpx3wwck5h06jy3mxgs05gjmwkb7hmwghkjh41jc"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-assertthat" ,r-assertthat)
+       ("r-colorspace" ,r-colorspace)
+       ("r-dendextend" ,r-dendextend)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gplots" ,r-gplots)
+       ("r-htmlwidgets" ,r-htmlwidgets)
+       ("r-magrittr" ,r-magrittr)
+       ("r-plotly" ,r-plotly)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-reshape2" ,r-reshape2)
+       ("r-scales" ,r-scales)
+       ("r-seriation" ,r-seriation)
+       ("r-viridis" ,r-viridis)
+       ("r-webshot" ,r-webshot)))
+    (home-page "https://cran.r-project.org/package=heatmaply")
+    (synopsis "Interactive cluster heat maps using plotly")
+    (description
+     "This package enables you to create interactive cluster heatmaps that can
+be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
+Shiny app, and made available in the RStudio viewer pane.  Hover the mouse
+pointer over a cell to show details or drag a rectangle to zoom.  A heatmap is
+a popular graphical method for visualizing high-dimensional data, in which a
+table of numbers is encoded as a grid of colored cells.  The rows and columns
+of the matrix are ordered to highlight patterns and are often accompanied by
+dendrograms.")
+    ;; Either version of the license.
+    (license (list license:gpl2 license:gpl3))))
-- 
cgit v1.2.3


From 0fccb24765dfda3e90d7ce6981d9204f05aa6117 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Wed, 7 Mar 2018 16:57:20 +0100
Subject: gnu: commencement: 'glibc-final' now inherits from 'glibc'.

* gnu/packages/commencement.scm (glibc-final): Inherit from GLIBC
instead of GLIBC-FINAL-WITH-BOOTSTRAP-BASH.
[propagated-inputs]: New fields.
---
 gnu/packages/commencement.scm | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/commencement.scm b/gnu/packages/commencement.scm
index c38f40f618..1584f000d4 100644
--- a/gnu/packages/commencement.scm
+++ b/gnu/packages/commencement.scm
@@ -673,7 +673,12 @@ exec ~a/bin/~a-~a -B~a/lib -Wl,-dynamic-linker -Wl,~a/~a \"$@\"~%"
 
 (define glibc-final
   ;; The final glibc, which embeds the statically-linked Bash built above.
-  (package (inherit glibc-final-with-bootstrap-bash)
+  (package (inherit glibc)
+  (package
+    (inherit (package
+               (inherit glibc)
+               ;; Use the source patched with %BOOTSTRAP-GUILE.
+               (source (package-source glibc-final-with-bootstrap-bash))))
     (name "glibc")
     (inputs `(("static-bash" ,static-bash-for-glibc)
               ,@(alist-delete
@@ -684,6 +689,9 @@ exec ~a/bin/~a-~a -B~a/lib -Wl,-dynamic-linker -Wl,~a/~a \"$@\"~%"
     (native-inputs `(,@(package-native-inputs glibc-final-with-bootstrap-bash)
                      ("gettext" ,gettext-boot0)))
 
+    (propagated-inputs
+     (package-propagated-inputs glibc-final-with-bootstrap-bash))
+
     ;; The final libc only refers to itself, but the 'debug' output contains
     ;; references to GCC-BOOT0 and to the Linux headers.  XXX: Would be great
     ;; if 'allowed-references' were per-output.
-- 
cgit v1.2.3


From 7c788ed2276957ea52858d80faeca2962cd26f8d Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Wed, 7 Mar 2018 21:30:41 +0100
Subject: gnu: commencement: 'glibc-final' inherits the replacement of 'glibc'.

That was the intent of commit b672a8160755bab07fb3c13dbc43dcc26525a7b7,
but that commit left 'glibc-final' ungrafted.

Reported by Ricardo Wurmus at
<https://lists.gnu.org/archive/html/guix-devel/2018-02/msg00435.html>.

* gnu/packages/commencement.scm (glibc-final): Use 'package/inherit' so
that we inherit the 'replacement' of GLIBC.
---
 gnu/packages/commencement.scm | 53 ++++++++++++++++++++-----------------------
 1 file changed, 25 insertions(+), 28 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/commencement.scm b/gnu/packages/commencement.scm
index 1584f000d4..fe9fbebcc2 100644
--- a/gnu/packages/commencement.scm
+++ b/gnu/packages/commencement.scm
@@ -673,35 +673,32 @@ exec ~a/bin/~a-~a -B~a/lib -Wl,-dynamic-linker -Wl,~a/~a \"$@\"~%"
 
 (define glibc-final
   ;; The final glibc, which embeds the statically-linked Bash built above.
-  (package (inherit glibc)
-  (package
-    (inherit (package
-               (inherit glibc)
-               ;; Use the source patched with %BOOTSTRAP-GUILE.
-               (source (package-source glibc-final-with-bootstrap-bash))))
-    (name "glibc")
-    (inputs `(("static-bash" ,static-bash-for-glibc)
-              ,@(alist-delete
-                 "static-bash"
-                 (package-inputs glibc-final-with-bootstrap-bash))))
-
-    ;; This time we need 'msgfmt' to install all the libc.mo files.
-    (native-inputs `(,@(package-native-inputs glibc-final-with-bootstrap-bash)
-                     ("gettext" ,gettext-boot0)))
-
-    (propagated-inputs
-     (package-propagated-inputs glibc-final-with-bootstrap-bash))
-
-    ;; The final libc only refers to itself, but the 'debug' output contains
-    ;; references to GCC-BOOT0 and to the Linux headers.  XXX: Would be great
-    ;; if 'allowed-references' were per-output.
-    (arguments
-     `(#:allowed-references
-       ,(cons* `(,gcc-boot0 "lib") (kernel-headers-boot0)
-               static-bash-for-glibc
-               (package-outputs glibc-final-with-bootstrap-bash))
+  ;; Use 'package/inherit' so we get the 'replacement' of 'glibc', if any.
+  (let ((glibc (package-with-bootstrap-guile glibc)))
+    (package/inherit glibc
+      (name "glibc")
+      (inputs `(("static-bash" ,static-bash-for-glibc)
+                ,@(alist-delete
+                   "static-bash"
+                   (package-inputs glibc-final-with-bootstrap-bash))))
+
+      ;; This time we need 'msgfmt' to install all the libc.mo files.
+      (native-inputs `(,@(package-native-inputs glibc-final-with-bootstrap-bash)
+                       ("gettext" ,gettext-boot0)))
+
+      (propagated-inputs
+       (package-propagated-inputs glibc-final-with-bootstrap-bash))
+
+      ;; The final libc only refers to itself, but the 'debug' output contains
+      ;; references to GCC-BOOT0 and to the Linux headers.  XXX: Would be great
+      ;; if 'allowed-references' were per-output.
+      (arguments
+       `(#:allowed-references
+         ,(cons* `(,gcc-boot0 "lib") (kernel-headers-boot0)
+                 static-bash-for-glibc
+                 (package-outputs glibc-final-with-bootstrap-bash))
 
-       ,@(package-arguments glibc-final-with-bootstrap-bash)))))
+         ,@(package-arguments glibc-final-with-bootstrap-bash))))))
 
 (define gcc-boot0-wrapped
   ;; Make the cross-tools GCC-BOOT0 and BINUTILS-BOOT0 available under the
-- 
cgit v1.2.3


From 036ed3a8305ba0fb113666d52989cb4b009c5b72 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Wed, 7 Mar 2018 21:34:18 +0100
Subject: gnu: glibc-2.26-patch: Remove unneeded 'replacement' field.

* gnu/packages/base.scm (glibc-2.26-patched): Remove unneeded
'replacement' field.
---
 gnu/packages/base.scm | 1 -
 1 file changed, 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm
index 23107a823e..e91f7d43ef 100644
--- a/gnu/packages/base.scm
+++ b/gnu/packages/base.scm
@@ -844,7 +844,6 @@ GLIBC/HURD for a Hurd host"
 (define glibc-2.26-patched
   (package
     (inherit glibc)
-    (replacement #f)
     (source (origin
               (inherit (package-source glibc))
               (patches (cons (search-patch "glibc-allow-kernel-2.6.32.patch")
-- 
cgit v1.2.3


From 12ff7f3fc77ce6a7a3d7be9555e602be3c63704d Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Wed, 7 Mar 2018 21:36:30 +0100
Subject: gnu: glibc: Add a comment in the patch.

* gnu/packages/patches/glibc-allow-kernel-2.6.32.patch: Add a comment.
---
 gnu/packages/patches/glibc-allow-kernel-2.6.32.patch | 7 +++++++
 1 file changed, 7 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/patches/glibc-allow-kernel-2.6.32.patch b/gnu/packages/patches/glibc-allow-kernel-2.6.32.patch
index ce18b874c4..c03807323f 100644
--- a/gnu/packages/patches/glibc-allow-kernel-2.6.32.patch
+++ b/gnu/packages/patches/glibc-allow-kernel-2.6.32.patch
@@ -1,3 +1,10 @@
+This patch allows libc to be used with the heavily-patched kernel found
+on CentOS 6, which identifies itself as 2.6.32.
+
+See <https://lists.gnu.org/archive/html/guix-devel/2018-02/msg00392.html>.
+
+Patch taken from Nixpkgs.
+
 diff --git a/sysdeps/unix/sysv/linux/configure b/sysdeps/unix/sysv/linux/configure
 index cace758c01..38fe7fe0b0 100644
 --- a/sysdeps/unix/sysv/linux/configure
-- 
cgit v1.2.3


From b2dc4cb41ce107199c8899b89e1c4104d410370b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Mar 2018 18:52:18 +0100
Subject: gnu: Add r-cgdsr.

* gnu/packages/cran.scm (r-cgdsr): New variable.
---
 gnu/packages/cran.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b5471d703b..7281caf7a6 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2779,3 +2779,26 @@ of the matrix are ordered to highlight patterns and are often accompanied by
 dendrograms.")
     ;; Either version of the license.
     (license (list license:gpl2 license:gpl3))))
+
+(define-public r-cgdsr
+  (package
+    (name "r-cgdsr")
+    (version "1.2.10")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "cgdsr" version))
+       (sha256
+        (base32
+         "1xyhw7mhmjichr1l6f9y1qvfj9wm87kfbm87ji7lcwf36gxh5g23"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-r-methodss3" ,r-r-methodss3)
+       ("r-r-oo" ,r-r-oo)))
+    (home-page "https://github.com/cBioPortal/cgdsr")
+    (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
+    (description
+     "This package provides a basic set of R functions for querying the Cancer
+Genomics Data Server (CGDS), hosted by the Computational Biology Center at
+Memorial-Sloan-Kettering Cancer Center (MSKCC).")
+    (license license:lgpl3)))
-- 
cgit v1.2.3


From a00968b7a878ab5aa0d0afb000f29e713b880674 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Mar 2018 20:12:47 +0100
Subject: gnu: Add r-import.

* gnu/packages/cran.scm (r-import): New variable.
---
 gnu/packages/cran.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 7281caf7a6..b256d228d8 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2802,3 +2802,27 @@ dendrograms.")
 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
     (license license:lgpl3)))
+
+(define-public r-import
+  (package
+    (name "r-import")
+    (version "1.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "import" version))
+       (sha256
+        (base32
+         "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
+    (build-system r-build-system)
+    (home-page "https://github.com/smbache/import")
+    (synopsis "Import mechanism for R")
+    (description
+     "This is an alternative mechanism for importing objects from packages.
+The syntax allows for importing multiple objects from a package with a single
+command in an expressive way.  The import package bridges some of the gap
+between using @code{library} (or @code{require}) and direct (single-object)
+imports.  Furthermore the imported objects are not placed in the current
+environment.  It is also possible to import objects from stand-alone @code{.R}
+files.")
+    (license license:expat)))
-- 
cgit v1.2.3


From 5d9b82acfc597edfcf8ae0cce0f897c3764bb9b9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Mar 2018 20:12:54 +0100
Subject: gnu: Add r-shinyace.

* gnu/packages/cran.scm (r-shinyace): New variable.
---
 gnu/packages/cran.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b256d228d8..d0033e1685 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2826,3 +2826,25 @@ imports.  Furthermore the imported objects are not placed in the current
 environment.  It is also possible to import objects from stand-alone @code{.R}
 files.")
     (license license:expat)))
+
+(define-public r-shinyace
+  (package
+    (name "r-shinyace")
+    (version "0.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "shinyAce" version))
+       (sha256
+        (base32
+         "0ycka8rsw0178q9klfid97vdn5cbyx3r778nis5s3dqipdyazdm9"))))
+    (properties `((upstream-name . "shinyAce")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-shiny" ,r-shiny)))
+    (home-page "http://cran.r-project.org/web/packages/shinyAce")
+    (synopsis "Ace editor bindings for Shiny")
+    (description
+     "This package provides Ace editor bindings to enable a rich text editing
+environment within Shiny.")
+    (license license:expat)))
-- 
cgit v1.2.3


From f64fea1d2cbfe76882abc31f1ce1e7b917352dfb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Mar 2018 20:13:06 +0100
Subject: gnu: Add r-radiant-data.

* gnu/packages/cran.scm (r-radiant-data): New variable.
---
 gnu/packages/cran.scm | 53 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index d0033e1685..708afc0be5 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2848,3 +2848,56 @@ files.")
      "This package provides Ace editor bindings to enable a rich text editing
 environment within Shiny.")
     (license license:expat)))
+
+(define-public r-radiant-data
+  (package
+    (name "r-radiant-data")
+    (version "0.8.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "radiant.data" version))
+       (sha256
+        (base32
+         "1ylina1jlrmvjkj8pwg0ip5jv1038vnzyckmf542xl7g11x8rvw1"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           ;; Delete files that are under CC-NC-SA.
+           (delete-file-recursively "inst/app/tools/help")
+           #t))))
+    (properties `((upstream-name . "radiant.data")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-base64enc" ,r-base64enc)
+       ("r-broom" ,r-broom)
+       ("r-car" ,r-car)
+       ("r-curl" ,r-curl)
+       ("r-dplyr" ,r-dplyr)
+       ("r-dt" ,r-dt)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gridextra" ,r-gridextra)
+       ("r-import" ,r-import)
+       ("r-jsonlite" ,r-jsonlite)
+       ("r-knitr" ,r-knitr)
+       ("r-lubridate" ,r-lubridate)
+       ("r-magrittr" ,r-magrittr)
+       ("r-markdown" ,r-markdown)
+       ("r-pryr" ,r-pryr)
+       ("r-psych" ,r-psych)
+       ("r-readr" ,r-readr)
+       ("r-rmarkdown" ,r-rmarkdown)
+       ("r-rstudioapi" ,r-rstudioapi)
+       ("r-scales" ,r-scales)
+       ("r-shiny" ,r-shiny)
+       ("r-shinyace" ,r-shinyace)
+       ("r-tibble" ,r-tibble)
+       ("r-tidyr" ,r-tidyr)))
+    (home-page "https://github.com/radiant-rstats/radiant.data")
+    (synopsis "Data menu for Radiant: business analytics using R and Shiny")
+    (description
+     "The Radiant Data menu includes interfaces for loading, saving, viewing,
+visualizing, summarizing, transforming, and combining data.  It also contains
+functionality to generate reproducible reports of the analyses conducted in
+the application.")
+    (license license:agpl3)))
-- 
cgit v1.2.3


From e2cafc2449df16ccc3ca1555d5e9ed66908d846e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Mar 2018 22:43:38 +0100
Subject: gnu: Add r-algdesign.

* gnu/packages/cran.scm (r-algdesign): New variable.
---
 gnu/packages/cran.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 708afc0be5..c4cf394e6e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2901,3 +2901,26 @@ visualizing, summarizing, transforming, and combining data.  It also contains
 functionality to generate reproducible reports of the analyses conducted in
 the application.")
     (license license:agpl3)))
+
+(define-public r-algdesign
+  (package
+    (name "r-algdesign")
+    (version "1.1-7.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "AlgDesign" version))
+       (sha256
+        (base32
+         "0bl7mx4dnmkgs2x1fj7cqnrp7jx18mqwxyga0rzlniq12h8mc3fz"))))
+    (properties `((upstream-name . "AlgDesign")))
+    (build-system r-build-system)
+    (home-page "https://github.com/jvbraun/AlgDesign")
+    (synopsis "Algorithmic experimental design")
+    (description
+     "This package provides tools to calculate exact and approximate theory
+experimental designs for D, A, and I criteria.  Very large designs may be
+created.  Experimental designs may be blocked or blocked designs created from
+a candidate list, using several criteria.  The blocking can be done when whole
+and within plot factors interact.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 0bdd5b8ab7c5e618a63cac6d9aa55f9cf674deea Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 7 Mar 2018 23:07:23 +0100
Subject: gnu: Add pigx-rnaseq.

* gnu/packages/bioinformatics.scm (pigx-rnaseq): New variable.
---
 gnu/packages/bioinformatics.scm | 67 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 67 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 546b240f84..d6c7c05dd5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12646,3 +12646,70 @@ contains
 analyze RNA expression genome-wide in thousands of individual cells at
 once.  This package provides tools to perform Drop-seq analyses.")
     (license license:expat)))
+
+(define-public pigx-rnaseq
+  (package
+    (name "pigx-rnaseq")
+    (version "0.0.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/"
+                                  "releases/download/v" version
+                                  "/pigx_rnaseq-" version ".tar.gz"))
+              (sha256
+               (base32
+                "168hx2ig3rarphx3l21ay9yyg8ipaakzixnrhpbdi0sknhyvrrk8"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:parallel-tests? #f             ; not supported
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'wrap-executable
+           ;; Make sure the executable finds all R modules.
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (wrap-program (string-append out "/bin/pigx-rnaseq")
+                 `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))
+                 `("PYTHONPATH"  ":" = (,(getenv "PYTHONPATH")))))
+             #t)))))
+    (inputs
+     `(("snakemake" ,snakemake)
+       ("fastqc" ,fastqc)
+       ("multiqc" ,multiqc)
+       ("star" ,star)
+       ("trim-galore" ,trim-galore)
+       ("htseq" ,htseq)
+       ("samtools" ,samtools)
+       ("bedtools" ,bedtools)
+       ("r-minimal" ,r-minimal)
+       ("r-rmarkdown" ,r-rmarkdown)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-ggrepel" ,r-ggrepel)
+       ("r-gprofiler" ,r-gprofiler)
+       ("r-deseq2" ,r-deseq2)
+       ("r-dt" ,r-dt)
+       ("r-knitr" ,r-knitr)
+       ("r-pheatmap" ,r-pheatmap)
+       ("r-corrplot" ,r-corrplot)
+       ("r-reshape2" ,r-reshape2)
+       ("r-plotly" ,r-plotly)
+       ("r-scales" ,r-scales)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-crosstalk" ,r-crosstalk)
+       ("r-tximport" ,r-tximport)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-rjson" ,r-rjson)
+       ("salmon" ,salmon)
+       ("ghc-pandoc" ,ghc-pandoc)
+       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
+       ("python-wrapper" ,python-wrapper)
+       ("python-pyyaml" ,python-pyyaml)))
+    (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
+    (synopsis "Analysis pipeline for RNA sequencing experiments")
+    (description "PiGX RNAseq is an analysis pipeline for preprocessing and
+reporting for RNA sequencing experiments.  It is easy to use and produces high
+quality reports.  The inputs are reads files from the sequencing experiment,
+and a configuration file which describes the experiment.  In addition to
+quality control of the experiment, the pipeline produces a differential
+expression report comparing samples in an easily configurable manner.")
+    (license license:gpl3+)))
-- 
cgit v1.2.3


From f43857d65d35ba90cfe675d8e44ef05a0a593a4d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 01:24:02 +0100
Subject: gnu: emacs-slack: Update to 0-3.9272460.

* gnu/packages/emacs.scm (emacs-slack): Update to 0-3.9272460.
---
 gnu/packages/emacs.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index a6f398ac3b..c2c162c75c 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -6787,8 +6787,8 @@ want to use it.")
     (license license:gpl3+)))
 
 (define-public emacs-slack
-  (let ((commit "02ee1d7339e48c64946041f6f4e09447c3f53e82")
-        (revision "2"))
+  (let ((commit "92724604879149cf331fa8778d089813a9d4ce1a")
+        (revision "3"))
     (package
       (name "emacs-slack")
       (version (string-append "0-" revision "." (string-take commit 7)))
@@ -6800,7 +6800,7 @@ want to use it.")
                 (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
-                  "0grx95xxf314m2k35m1kf20l2pwc6j11ibvrngx4pis7wqwjas3h"))))
+                  "1fdf8s3ca356k7m7f5kqzfamfl2nrqjj2pynjv3kkrr0ad15nxmw"))))
       (build-system emacs-build-system)
       (propagated-inputs
        `(("emacs-alert" ,emacs-alert)
-- 
cgit v1.2.3


From e7988175d9a3871315fe83b9824b1be56bb18e5a Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Thu, 8 Mar 2018 00:39:58 +0100
Subject: gnu: sunxi-tools: Improve build error reporting.

* gnu/packages/admin.scm (sunxi-tools)[arguments]<#:phases>[set-environment-up]:
Improve build error reporting.
---
 gnu/packages/admin.scm | 29 +++++++++++++++++++----------
 1 file changed, 19 insertions(+), 10 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 9116835d04..b35fd8fdd4 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -2080,25 +2080,34 @@ Kerberos and Heimdal and FAST is supported with recent MIT Kerberos.")
            (lambda* (#:key make-flags #:allow-other-keys)
              (define (cross? x)
                (string-contains x "cross-arm-linux"))
+             (define (filter-environment! filter-predicate
+                                          environment-variable-names)
+               (for-each
+                (lambda (env-name)
+                  (let* ((env-value (getenv env-name))
+                         (search-path (search-path-as-string->list env-value))
+                         (new-search-path (filter filter-predicate
+                                                  search-path))
+                         (new-env-value (list->search-path-as-string
+                                         new-search-path ":")))
+                    (setenv env-name new-env-value)))
+                environment-variable-names))
              (setenv "CROSS_C_INCLUDE_PATH" (getenv "C_INCLUDE_PATH"))
              (setenv "CROSS_CPLUS_INCLUDE_PATH" (getenv "CPLUS_INCLUDE_PATH"))
              (setenv "CROSS_LIBRARY_PATH" (getenv "LIBRARY_PATH"))
-             (for-each
-              (lambda (env-name)
-                (let* ((env-value (getenv env-name))
-                       (search-path (search-path-as-string->list env-value))
-                       (new-search-path (filter (lambda (e) (not (cross? e)))
-                                                search-path))
-                       (new-env-value (list->search-path-as-string
-                                       new-search-path ":")))
-                  (setenv env-name new-env-value)))
-              '("C_INCLUDE_PATH" "CPLUS_INCLUDE_PATH" "LIBRARY_PATH"))
+             (filter-environment! cross?
+              '("CROSS_C_INCLUDE_PATH" "CROSS_CPLUS_INCLUDE_PATH"
+                "CROSS_LIBRARY_PATH"))
+             (filter-environment! (lambda (e) (not (cross? e)))
+              '("C_INCLUDE_PATH" "CPLUS_INCLUDE_PATH"
+                "LIBRARY_PATH"))
              #t))
          (replace 'build
            (lambda* (#:key make-flags #:allow-other-keys)
              (zero? (apply system* "make" "tools" "misc" make-flags))))
          (add-after 'build 'build-armhf
            (lambda* (#:key make-flags #:allow-other-keys)
+             (setenv "LIBRARY_PATH" #f)
              (zero? (apply system* "make" "target-tools" make-flags))))
          (replace 'install
            (lambda* (#:key make-flags #:allow-other-keys)
-- 
cgit v1.2.3


From e2d0cf033eb894fa8c786d0bf039fc54685d5559 Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Thu, 8 Mar 2018 00:47:46 +0100
Subject: gnu: sunxi-tools: Add cross-libc's "static" output.

* gnu/packages/admin.scm (sunxi-tools)[native-inputs]: Add cross-libc's
"static" output.
---
 gnu/packages/admin.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index b35fd8fdd4..7623693722 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -2062,7 +2062,8 @@ Kerberos and Heimdal and FAST is supported with recent MIT Kerberos.")
        ("cross-gcc" ,(cross-gcc "arm-linux-gnueabihf"
                                 #:xbinutils (cross-binutils "arm-linux-gnueabihf")
                                 #:libc (cross-libc "arm-linux-gnueabihf")))
-       ("cross-libc" ,(cross-libc "arm-linux-gnueabihf"))))
+       ("cross-libc" ,(cross-libc "arm-linux-gnueabihf")) ; header files
+       ("cross-libc-static" ,(cross-libc "arm-linux-gnueabihf") "static")))
     (inputs
      `(("libusb" ,libusb)))
     (build-system gnu-build-system)
-- 
cgit v1.2.3


From a89bf3318f81e9b190188f5f9ab9b1fa94c318db Mon Sep 17 00:00:00 2001
From: Rutger Helling <rhelling@mykolab.com>
Date: Thu, 8 Mar 2018 08:51:56 +0100
Subject: gnu: vulkan-icd-loader: Update to 1.1.70.0.

* gnu/packages/vulkan.scm (vulkan-icd-loader): Update to 1.1.70.0.
---
 gnu/packages/vulkan.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/vulkan.scm b/gnu/packages/vulkan.scm
index 1d83b6f363..478de6a444 100644
--- a/gnu/packages/vulkan.scm
+++ b/gnu/packages/vulkan.scm
@@ -158,7 +158,7 @@ interpretation of the specifications for these languages.")
 (define-public vulkan-icd-loader
   (package
     (name "vulkan-icd-loader")
-    (version "1.0.68.0")
+    (version "1.1.70.0")
     (source
      (origin
        (method url-fetch)
@@ -167,7 +167,7 @@ interpretation of the specifications for these languages.")
              "archive/sdk-" version ".tar.gz"))
        (sha256
         (base32
-         "1n5gry5zxpwi7330fmi06snalra8hkbbw68gnwbp531kd5ycyinh"))))
+         "15qkh77596v3xivnbb3l0q9zbmmsdglnaza2m1g7f8q7bbigyc5x"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f ;FIXME: 23/39 tests fail.  Try "tests/run_all_tests.sh".
-- 
cgit v1.2.3


From 254a88199f32d35e39c8913bc557ea2db69bd04e Mon Sep 17 00:00:00 2001
From: Clément Lassieur <clement@lassieur.org>
Date: Thu, 8 Mar 2018 08:58:38 +0100
Subject: gnu: global: Replace GLOBAL with GNU GLOBAL in description.

* gnu/packages/code.scm (global)[description]: Replace GLOBAL with GNU GLOBAL.
---
 gnu/packages/code.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm
index 8d9c661302..13a89c7bcc 100644
--- a/gnu/packages/code.scm
+++ b/gnu/packages/code.scm
@@ -139,10 +139,10 @@ highlighting your own code that seemed comprehensible when you wrote it.")
     (home-page "https://www.gnu.org/software/global/")
     (synopsis "Cross-environment source code tag system")
     (description
-     "GLOBAL is a source code tagging system that functions in the same way
-across a wide array of environments, such as different text editors, shells
-and web browsers.  The resulting tags are useful for quickly moving around in
-a large, deeply nested project.")
+     "GNU GLOBAL is a source code tagging system that functions in the same
+way across a wide array of environments, such as different text editors,
+shells and web browsers.  The resulting tags are useful for quickly moving
+around in a large, deeply nested project.")
     (license license:gpl3+)))
 
 (define-public sloccount
-- 
cgit v1.2.3


From 6e076b3d50f131252822286f2f9b427ae32754d8 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 8 Mar 2018 07:26:27 +0100
Subject: gnu: slurm: Update to 17.11.3.

* gnu/packages/parallel.scm (slurm): Update to 17.11.3.
---
 gnu/packages/parallel.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm
index 17423856aa..c110fab086 100644
--- a/gnu/packages/parallel.scm
+++ b/gnu/packages/parallel.scm
@@ -94,7 +94,7 @@ and they are executed on lists of files, hosts, users or other items.")
 (define-public slurm
   (package
    (name "slurm")
-   (version "17.11.2")
+   (version "17.11.3")
    (source (origin
             (method url-fetch)
             (uri (string-append
@@ -102,7 +102,7 @@ and they are executed on lists of files, hosts, users or other items.")
                   version ".tar.bz2"))
             (sha256
              (base32
-              "18yakb8kmhb16n0cv3zhjv8ahvsk9p0max8mmr2flb2c65fawks6"))
+              "1x3i6z03d9m46fvj1cslrapm1drvgyqch9pn4xf23kvbz4gkhaps"))
             (modules '((guix build utils)))
             (snippet
              '(begin
-- 
cgit v1.2.3


From f95e9a6bca75332fb71f9618b1a03a6fd455c4cf Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 8 Mar 2018 07:27:01 +0100
Subject: gnu: keepassxc: Update to 2.3.1.

* gnu/packages/password-utils.scm (keepassxc): Update to 2.3.1.
---
 gnu/packages/password-utils.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm
index 96a51f0dd4..0dde8808b6 100644
--- a/gnu/packages/password-utils.scm
+++ b/gnu/packages/password-utils.scm
@@ -92,7 +92,7 @@ human.")
 (define-public keepassxc
   (package
     (name "keepassxc")
-    (version "2.3.0")
+    (version "2.3.1")
     (source
      (origin
        (method url-fetch)
@@ -101,7 +101,7 @@ human.")
                            version "-src.tar.xz"))
        (sha256
         (base32
-         "1v6v59fnbbsssbwy4is6hh2l4qqwy3ddb6dp2jk8clx0xbd5hn7c"))))
+         "1gdrbpzwbs56anc3k5vklvcackcn214pc8gm5xh5zcymsi8q4zff"))))
     (build-system cmake-build-system)
     (arguments
      '(#:configure-flags '("-DWITH_XC_NETWORKING=YES"
-- 
cgit v1.2.3


From 3d63422c92c6931fbc688770073214b561eab723 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 8 Mar 2018 09:03:47 +0100
Subject: gnu: yapet: Update to 1.1.

* gnu/packages/password-utils.scm (yapet): Update to 1.1.
---
 gnu/packages/password-utils.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm
index 0dde8808b6..46b6e795ab 100644
--- a/gnu/packages/password-utils.scm
+++ b/gnu/packages/password-utils.scm
@@ -200,7 +200,7 @@ applications, there is xclip integration." )
 (define-public yapet
   (package
     (name "yapet")
-    (version "1.0")
+    (version "1.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://www.guengel.ch/myapps/yapet/downloads/yapet-"
@@ -208,7 +208,7 @@ applications, there is xclip integration." )
                                   ".tar.bz2"))
               (sha256
                (base32
-                "0ydbnqw6icdh07pnv2w6dhvq501bdfvrklv4xmyr8znca9d753if"))))
+                "1lq46mpxdsbl6qw4cj58hp9q7jckmyvbsi08p5zr77rjgqadxyyy"))))
     (build-system gnu-build-system)
     (inputs
      `(("ncurses" ,ncurses)
-- 
cgit v1.2.3


From ef20a6f0b469b7d86fb0d7502ecb6f7f8a78603a Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 7 Mar 2018 17:15:45 +0100
Subject: gnu: python-ddt: Mark up description.

* gnu/packages/python.scm (python-ddt)[description]: Use @dfn.
---
 gnu/packages/python.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 970c835de6..b9f6749797 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -10426,8 +10426,9 @@ convering text with ANSI color codes to HTML or LaTeX.")
     (home-page "https://github.com/txels/ddt")
     (synopsis "Data-Driven Tests")
     (description
-     "DDT (Data-Driven Tests) allows you to multiply one test case by running
-it with different test data, and make it appear as multiple test cases.")
+     "Data-Driven Tests (@dfn{DDT}) allow you to multiply one test case by
+running it with different test data, and make it appear as multiple test
+cases.")
     (license license:expat)))
 
 (define-public python2-ddt
-- 
cgit v1.2.3


From 338e2852b5d12a6d8b83e5fea1278a8a8453370f Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 7 Mar 2018 17:15:17 +0100
Subject: gnu: python-ddt: Update to 1.1.2.

* gnu/packages/python.scm (python-ddt): Update to 1.1.2.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index b9f6749797..eb25e893ff 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -10408,14 +10408,14 @@ convering text with ANSI color codes to HTML or LaTeX.")
 (define-public python-ddt
   (package
     (name "python-ddt")
-    (version "1.1.1")
+    (version "1.1.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "ddt" version))
        (sha256
         (base32
-         "1c00ikkxr7lha97c81k938bzhgd4pbwamkjn0h4nkhr3xk00zp6n"))))
+         "1wqkmz0yhanly8sif5vb02p2iik7mwxwph8ywph2kbb8ws8szdpx"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-mock" ,python-mock)
-- 
cgit v1.2.3


From ca1499ce2064c1d1015ef517cdd2ad7961160070 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Thu, 8 Mar 2018 09:43:15 +0100
Subject: gnu: intelmetool, me-cleaner: Restrict to Intel platforms.

* gnu/packages/flashing-tools.scm (intelmetool)[supported-systems]: New
field.
(me-cleaner)[supported-systems]: New field.
---
 gnu/packages/flashing-tools.scm | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/flashing-tools.scm b/gnu/packages/flashing-tools.scm
index 5309510d40..192f84c36c 100644
--- a/gnu/packages/flashing-tools.scm
+++ b/gnu/packages/flashing-tools.scm
@@ -2,7 +2,7 @@
 ;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2014 Manolis Fragkiskos Ragkousis <manolis837@gmail.com>
 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
-;;; Copyright © 2016 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Jonathan Brielmaier <jonathan.brielmaier@web.de>
 ;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu>
@@ -402,7 +402,10 @@ dump Intel Firmware Descriptor data of an image file.")
 Management Engine (ME).  You need to @code{sudo rmmod mei_me} and
 @code{sudo rmmod mei} before using this tool.  Also pass
 @code{iomem=relaxed} to the Linux kernel command line.")
-    (license license:gpl2)))
+    (license license:gpl2)
+
+    ;; This is obviously an Intel thing, plus it requires <cpuid.h>.
+    (supported-systems '("x86_64-linux" "i686-linux"))))
 
 (define-public me-cleaner
   (package
@@ -420,7 +423,7 @@ Management Engine (ME).  You need to @code{sudo rmmod mei_me} and
     (arguments
      `(#:phases
        (modify-phases %standard-phases
- (add-after 'unpack 'create-setup.py
+         (add-after 'unpack 'create-setup.py
            (lambda _
              (call-with-output-file "setup.py"
                (lambda (port)
@@ -433,4 +436,7 @@ setup(name='me_cleaner', version='~a', scripts=['me_cleaner.py'])
     (synopsis "Intel ME cleaner")
     (description "This package provides tools for disabling Intel
 ME as far as possible (it only edits ME firmware image files).")
-    (license license:gpl3+)))
+    (license license:gpl3+)
+
+    ;; This is an Intel thing.
+    (supported-systems '("x86_64-linux" "i686-linux"))))
-- 
cgit v1.2.3


From 3aab8851442713f6ad748ffebb055c5e9eae1bd4 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Thu, 8 Mar 2018 11:46:55 +0100
Subject: gnu: guile: Add 2.2.2.

* gnu/packages/guile.scm (guile-2.2.2): New variable.
---
 gnu/packages/guile.scm | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index 5dc66c1625..91a440d928 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015, 2017 Christopher Allan Webber <cwebber@dustycloud.org>
 ;;; Copyright © 2016 Alex Sassmannshausen <alex@pompo.co>
@@ -281,6 +281,21 @@ without requiring the source code to be rewritten.")
                                                ;  when heavily loaded)
     (replacement #f)))
 
+(define-public guile-2.2.2
+  ;; Keep it so that, when 'guix' runs on 2.2.2, 'guix pull' compiles objects
+  ;; with 2.2.2, thereby avoiding the ABI incompatibility issues described in
+  ;; <https://bugs.gnu.org/29570>.
+  (package
+    (inherit guile-2.2)
+    (version "2.2.2")
+    (source (origin
+              (inherit (package-source guile-2.2))
+              (uri (string-append "mirror://gnu/guile/guile-" version
+                                  ".tar.xz"))
+              (sha256
+               (base32
+                "1azm25zcmxif0skxfrp11d2wc89nrzpjaann9yxdw6pvjxhs948w"))))))
+
 (define-public guile-next
   (deprecated-package "guile-next" guile-2.2))
 
-- 
cgit v1.2.3


From 770986d5410c2f915c295c873cc8b0dec888d20d Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Thu, 8 Mar 2018 12:25:05 +0100
Subject: gnu: feh: Update to 2.25.1.

* gnu/packages/image-viewers.scm (feh): Update to 2.25.1.
---
 gnu/packages/image-viewers.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/image-viewers.scm b/gnu/packages/image-viewers.scm
index 7a33f6c871..cf612666f1 100644
--- a/gnu/packages/image-viewers.scm
+++ b/gnu/packages/image-viewers.scm
@@ -59,7 +59,7 @@
 (define-public feh
   (package
     (name "feh")
-    (version "2.25")
+    (version "2.25.1")
     (home-page "https://feh.finalrewind.org/")
     (source (origin
               (method url-fetch)
@@ -67,7 +67,7 @@
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "102rwi30n09l8rih6kv6bb7lhv3djklgzill4p2zag0h700yqfq6"))))
+                "197sm78bm33dvahr5nxqkbmpmdn4b13ahc9mrgn1l7n104bg4phc"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases (delete 'configure))
-- 
cgit v1.2.3


From 875fe4b6b625fe4626403b42da72d5c20265d41f Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Thu, 8 Mar 2018 12:40:22 +0100
Subject: gnu: nghttp2: Use a fixed variant of tzdata for tests.

* gnu/packages/web.scm (nghttp2)[native-inputs]: Replace TZDATA with TZDATA-FOR-TESTS.
---
 gnu/packages/web.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index cfae9f9253..f5e004eda5 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -6368,7 +6368,7 @@ derivation by David Revoy from the original MonsterID by Andreas Gohr.")
 
        ;; Required by tests.
        ("cunit" ,cunit)
-       ("tzdata" ,tzdata)))
+       ("tzdata" ,tzdata-for-tests)))
     (inputs
      ;; Required to build the tools (i.e. without ‘--enable-lib-only’).
      `(("c-ares" ,c-ares)
-- 
cgit v1.2.3


From 3e25d2b22e6c37ca948b67be0a5f2fc09ea50e61 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Thu, 8 Mar 2018 12:44:41 +0100
Subject: gnu: python-msgpack-transitional: Use a distinct name.

* gnu/packages/python.scm (python-msgpack-transitional)[name]: New field.
---
 gnu/packages/python.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index eb25e893ff..73b0e91327 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -5875,6 +5875,7 @@ reading and writing MessagePack data.")
 (define-public python-msgpack-transitional
   (package
     (inherit python-msgpack)
+    (name "python-msgpack-transitional")
     (arguments
      (substitute-keyword-arguments (package-arguments python-msgpack)
        ((#:phases phases)
-- 
cgit v1.2.3


From 7f2f834550a2b81bcd7d1713b3b170f981554380 Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kkebreau@posteo.net>
Date: Sun, 18 Feb 2018 14:46:26 -0500
Subject: gnu: milkytracker: Actually link with the JACK library.

* gnu/packages/music.scm (milkytracker)[arguments]: Add appropriate configure
flag.
---
 gnu/packages/music.scm | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 65dfa92896..f47749b380 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -2609,7 +2609,9 @@ of tools for manipulating and accessing your music.")
                     (("add_subdirectory\\(resources/music\\)") ""))))))
     (build-system cmake-build-system)
     (arguments
-     '(#:tests? #f)) ; no check target
+     '(#:tests? #f ; no check target
+       ;; This flag ensures that MilkyTracker links with the JACK library.
+       #:configure-flags '("-DCMAKE_CXX_FLAGS=-ljack")))
     (inputs
      `(("alsa-lib" ,alsa-lib)
        ("jack" ,jack-1)
-- 
cgit v1.2.3


From 84c195e505ce581227099e861172f5e65f3d66d7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 18:51:32 +0100
Subject: gnu: r-dropbead: Update to 0-2.d746c6f.

* gnu/packages/bioinformatics.scm (r-dropbead): Update to 0-2.d746c6f.
---
 gnu/packages/bioinformatics.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d6c7c05dd5..73765dafe7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10880,8 +10880,8 @@ memory usage and processing time is minimized.")
     (license license:expat)))
 
 (define-public r-dropbead
-  (let ((commit "cf0be5ae5302684bd03e78ab65b142900bbbb840")
-        (revision "1"))
+  (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
+        (revision "2"))
     (package
       (name "r-dropbead")
       (version (string-append "0-" revision "." (string-take commit 7)))
@@ -10894,7 +10894,7 @@ memory usage and processing time is minimized.")
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "1b2lphsc236s1rdzlijxg8yl1jnqpwcvj4x938r89rqpj93jb780"))))
+           "0sbzma49aiiyw8b0jpr7fnhzys9nsqmp4hy4hdz1gzyg1lhnca26"))))
       (build-system r-build-system)
       (propagated-inputs
        `(("r-ggplot2" ,r-ggplot2)
-- 
cgit v1.2.3


From fee7f8a94ec64943109ba9c37f75c28749fb18bd Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Thu, 8 Mar 2018 20:29:13 +0200
Subject: gnu: nano: Update to 2.9.4.

* gnu/packages/nano.scm (nano): Update to 2.9.4.
---
 gnu/packages/nano.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/nano.scm b/gnu/packages/nano.scm
index d6bef33695..07c7ed36cb 100644
--- a/gnu/packages/nano.scm
+++ b/gnu/packages/nano.scm
@@ -30,7 +30,7 @@
 (define-public nano
   (package
     (name "nano")
-    (version "2.9.3")
+    (version "2.9.4")
     (source
      (origin
       (method url-fetch)
@@ -38,7 +38,7 @@
                           version ".tar.xz"))
       (sha256
        (base32
-        "04j05nbnp8vjjwja90d83p4s6ywyl6qhggflcjzw0p9d9gyvr0vp"))))
+        "0nm3zy4azr5rkxjq7jfybbj3cnddmvxc49rxyqm9cp2zfdp75y9c"))))
     (build-system gnu-build-system)
     (inputs
      `(("gettext" ,gettext-minimal)
-- 
cgit v1.2.3


From bbf8540d43bf84349fa1c002b2d1c42ebcc02636 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 23:12:57 +0100
Subject: gnu: python-sympy, python2-sympy: Only run core tests.

* gnu/packages/python.scm (python-sympy, python2-sympy)[arguments]: Move tests
after installation; run only core tests.
---
 gnu/packages/python.scm | 25 ++++++++++++++++++++++++-
 1 file changed, 24 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 73b0e91327..c454539fef 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -5066,6 +5066,17 @@ more advanced mathematics.")
        (sha256
         (base32 "190n29sppw7g8ihilc5451y7jlfcaw56crqiqbf1jff43dlmfnxc"))))
     (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; Run the core tests after installation.  By default it would run
+         ;; *all* tests, which take a very long time to complete and are known
+         ;; to be flaky.
+         (delete 'check)
+         (add-after 'install 'check
+           (lambda* (#:key outputs #:allow-other-keys)
+             (invoke "python3" "-c" "import sympy; sympy.test(\"/core\")")
+             #t)))))
     (propagated-inputs
      `(("python-mpmath" ,python-mpmath)))
     (home-page "http://www.sympy.org/")
@@ -5077,7 +5088,19 @@ as possible in order to be comprehensible and easily extensible.")
     (license license:bsd-3)))
 
 (define-public python2-sympy
-  (package-with-python2 python-sympy))
+  (package
+    (inherit (package-with-python2 python-sympy))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; Run the core tests after installation.  By default it would run
+         ;; *all* tests, which take a very long time to complete and are known
+         ;; to be flaky.
+         (delete 'check)
+         (add-after 'install 'check
+           (lambda* (#:key outputs #:allow-other-keys)
+             (invoke "python" "-c" "import sympy; sympy.test(\"/core\")")
+             #t)))))))
 
 (define-public python-q
   (package
-- 
cgit v1.2.3


From 1b17fdbe41053a91af07f3612094096f86c926cb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 23:01:22 +0100
Subject: gnu: r-openssl: Update to 1.0.1.

* gnu/packages/statistics.scm (r-openssl): Update to 1.0.1.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 0ae4dddb64..635cf51d27 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2235,14 +2235,14 @@ collation, and NAMESPACE files.")
 (define-public r-openssl
   (package
     (name "r-openssl")
-    (version "1.0")
+    (version "1.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "openssl" version))
        (sha256
         (base32
-         "1j8smqrb79lnaf2n9icksjiy641fcazsbkhmgg916s3nnyjngjz3"))))
+         "1qyql5gpwf88bkm1qarjhbqbq4hn6w0d8j4pxb5x7i96is30ap30"))))
     (build-system r-build-system)
     (inputs
      `(("libressl" ,libressl)))
-- 
cgit v1.2.3


From 69c38faa918c7f813a75f3499d2238b6f9ad4ff1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 23:01:38 +0100
Subject: gnu: r-nmf: Update to 0.21.0.

* gnu/packages/statistics.scm (r-nmf): Update to 0.21.0.
---
 gnu/packages/statistics.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 635cf51d27..ef494dab0a 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3331,20 +3331,20 @@ memory-mapped files.")
 (define-public r-nmf
   (package
     (name "r-nmf")
-    (version "0.20.6")
+    (version "0.21.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "NMF" version))
        (sha256
         (base32
-         "0mmh9bz0zjwd8h9jplz4rq3g94npaqj8s4px51vcv47csssd9k6z"))))
+         "1qq25n3k5sgh3srlshb3ic6q92s12c1ilqf5cd5anvq6cqfchc1v"))))
     (properties `((upstream-name . "NMF")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cluster" ,r-cluster)
-       ("r-bigmemory" ,r-bigmemory)
-       ("r-synchronicity" ,r-synchronicity)
+       ("r-bigmemory" ,r-bigmemory) ; suggested
+       ("r-synchronicity" ,r-synchronicity) ; suggested
        ("r-colorspace" ,r-colorspace)
        ("r-digest" ,r-digest)
        ("r-doparallel" ,r-doparallel)
-- 
cgit v1.2.3


From b7ce825c85b474caeba67017b6e3b582f0e4c1a5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 23:01:49 +0100
Subject: gnu: r-sfsmisc: Update to 1.1-2.

* gnu/packages/statistics.scm (r-sfsmisc): Update to 1.1-2.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index ef494dab0a..7722cb3aa0 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4027,14 +4027,14 @@ existing packages provide.")
 (define-public r-sfsmisc
   (package
     (name "r-sfsmisc")
-    (version "1.1-1")
+    (version "1.1-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sfsmisc" version))
        (sha256
         (base32
-         "0jzmbywlyzfxs7hlmyd0iynghfc9qp5sa5lnhr73y8r360yv1ahf"))))
+         "0cgq2h11ngkzd6p34k6mqjnvlvc5vj4lnqrl64k05lb391j391w0"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/sfsmisc")
     (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich")
-- 
cgit v1.2.3


From 53cc59a1d86cb31fc2505ead2bf9f80b13743ecf Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 23:15:30 +0100
Subject: gnu: r-ape: Move to (gnu packages cran).

* gnu/packages/bioinformatics.scm (r-ape): Move from here...
* gnu/packages/cran.scm (r-ape): ...to here.
---
 gnu/packages/bioinformatics.scm | 26 --------------------------
 gnu/packages/cran.scm           | 27 +++++++++++++++++++++++++++
 2 files changed, 27 insertions(+), 26 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 73765dafe7..a5ad2c57e7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -110,32 +110,6 @@
   #:use-module (srfi srfi-1)
   #:use-module (ice-9 match))
 
-(define-public r-ape
-  (package
-    (name "r-ape")
-    (version "5.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "ape" version))
-       (sha256
-        (base32
-         "0q59pmxawz498cb9mv5m49lhiwxib8ak94yyydz7qg8b6lpd4bn3"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-lattice" ,r-lattice)
-       ("r-nlme" ,r-nlme)
-       ("r-rcpp" ,r-rcpp)))
-    (home-page "http://ape-package.ird.fr/")
-    (synopsis "Analyses of phylogenetics and evolution")
-    (description
-     "This package provides functions for reading, writing, plotting, and
-manipulating phylogenetic trees, analyses of comparative data in a
-phylogenetic framework, ancestral character analyses, analyses of
-diversification and macroevolution, computing distances from DNA sequences,
-and several other tools.")
-    (license license:gpl2+)))
-
 (define-public aragorn
   (package
     (name "aragorn")
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index c4cf394e6e..adcc178592 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -32,6 +33,32 @@
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages web))
 
+(define-public r-ape
+  (package
+    (name "r-ape")
+    (version "5.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ape" version))
+       (sha256
+        (base32
+         "0q59pmxawz498cb9mv5m49lhiwxib8ak94yyydz7qg8b6lpd4bn3"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-lattice" ,r-lattice)
+       ("r-nlme" ,r-nlme)
+       ("r-rcpp" ,r-rcpp)))
+    (home-page "http://ape-package.ird.fr/")
+    (synopsis "Analyses of phylogenetics and evolution")
+    (description
+     "This package provides functions for reading, writing, plotting, and
+manipulating phylogenetic trees, analyses of comparative data in a
+phylogenetic framework, ancestral character analyses, analyses of
+diversification and macroevolution, computing distances from DNA sequences,
+and several other tools.")
+    (license license:gpl2+)))
+
 (define-public r-colorspace
   (package
     (name "r-colorspace")
-- 
cgit v1.2.3


From 35b0c051c51d0d582a7ba9664c2270aae7b45f6e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 23:16:03 +0100
Subject: gnu: Add r-signal.

* gnu/packages/cran.scm (r-signal): New variable.
---
 gnu/packages/cran.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index adcc178592..c096a9d037 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2951,3 +2951,26 @@ created.  Experimental designs may be blocked or blocked designs created from
 a candidate list, using several criteria.  The blocking can be done when whole
 and within plot factors interact.")
     (license license:gpl2+)))
+
+(define-public r-signal
+  (package
+    (name "r-signal")
+    (version "0.7-6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "signal" version))
+       (sha256
+        (base32
+         "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-mass" ,r-mass)))
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "http://cran.r-project.org/web/packages/signal/")
+    (synopsis "Signal processing")
+    (description
+     "This package provides a set of signal processing functions originally
+written for Matlab and GNU Octave.  It includes filter generation utilities,
+filtering functions, resampling routines, and visualization of filter models.
+It also includes interpolation functions.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From db80dd4a1d7e2371bc3c300f48b84a817adb3550 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 23:16:11 +0100
Subject: gnu: Add r-psych.

* gnu/packages/cran.scm (r-psych): New variable.
---
 gnu/packages/cran.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index c096a9d037..84b7b244d9 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2974,3 +2974,34 @@ written for Matlab and GNU Octave.  It includes filter generation utilities,
 filtering functions, resampling routines, and visualization of filter models.
 It also includes interpolation functions.")
     (license license:gpl2)))
+
+(define-public r-psych
+  (package
+    (name "r-psych")
+    (version "1.7.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "psych" version))
+       (sha256
+        (base32
+         "0daismb8pdk392vdy304hqx0m3jx62gx3a0hygjygc125rhfla7k"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-foreign" ,r-foreign)
+       ("r-lattice" ,r-lattice)
+       ("r-mnormt" ,r-mnormt)
+       ("r-nlme" ,r-nlme)))
+    (home-page "http://cran.r-project.org/web/packages/psych")
+    (synopsis "Procedures for psychological, psychometric, and personality research")
+    (description
+     "This package provides a general purpose toolbox for personality,
+psychometric theory and experimental psychology.  The functions are primarily
+for multivariate analysis and scale construction using factor analysis,
+principal component analysis, cluster analysis and reliability analysis,
+although others provide basic descriptive statistics.  It provides functions
+for analyzing data at multiple levels within and between group statistics,
+including correlations and factor analysis; functions for simulating and
+testing particular item and test structures are included.  Several functions
+serve as a useful front end for structural equation modeling.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 3dab50d92aedeb276d7997ccf9b37535ada58454 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 23:16:19 +0100
Subject: gnu: Add r-gsubfn.

* gnu/packages/cran.scm (r-gsubfn): New variable.
---
 gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 84b7b244d9..ae7b442f64 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3005,3 +3005,29 @@ including correlations and factor analysis; functions for simulating and
 testing particular item and test structures are included.  Several functions
 serve as a useful front end for structural equation modeling.")
     (license license:gpl2+)))
+
+(define-public r-gsubfn
+  (package
+    (name "r-gsubfn")
+    (version "0.6-6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "gsubfn" version))
+       (sha256
+        (base32
+         "196x4c3ihf4q3i0v7b1xa6jm8jjld2rsx00qz03n90wfnjdx5idv"))))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-proto" ,r-proto)))
+    (home-page "http://gsubfn.googlecode.com")
+    (synopsis "Utilities for strings and function arguments.")
+    (description
+     "This package provides @code{gsubfn} which is like @code{gsub} but can
+take a replacement function or certain other objects instead of the
+replacement string.  Matches and back references are input to the replacement
+function and replaced by the function output.  @code{gsubfn} can be used to
+split strings based on content rather than delimiters and for quasi-perl-style
+string interpolation.  The package also has facilities for translating
+formulas to functions and allowing such formulas in function calls instead of
+functions.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 3a563a410ab8791dfc2a51aae4cd79c1fce1458d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 23:16:29 +0100
Subject: gnu: Add r-sqldf.

* gnu/packages/cran.scm (r-sqldf): New variable.
---
 gnu/packages/cran.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ae7b442f64..c8a4216767 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3031,3 +3031,34 @@ string interpolation.  The package also has facilities for translating
 formulas to functions and allowing such formulas in function calls instead of
 functions.")
     (license license:gpl2+)))
+
+(define-public r-sqldf
+  (package
+    (name "r-sqldf")
+    (version "0.4-11")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "sqldf" version))
+       (sha256
+        (base32
+         "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-chron" ,r-chron)
+       ("r-dbi" ,r-dbi)
+       ("r-gsubfn" ,r-gsubfn)
+       ("r-proto" ,r-proto)
+       ("r-rsqlite" ,r-rsqlite)))
+    (home-page "https://github.com/ggrothendieck/sqldf")
+    (synopsis "Manipulate R data frames using SQL")
+    (description
+     "The @code{sqldf} function is typically passed a single argument which is
+an SQL select statement where the table names are ordinary R data frame names.
+@code{sqldf} transparently sets up a database, imports the data frames into
+that database, performs the SQL statement and returns the result using a
+heuristic to determine which class to assign to each column of the returned
+data frame.  The @code{sqldf} or @code{read.csv.sql} functions can also be
+used to read filtered files into R even if the original files are larger than
+R itself can handle.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From 94e46cabc1222b82f1cef091fd955b839f2493d7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 23:16:36 +0100
Subject: gnu: Add r-abind.

* gnu/packages/cran.scm (r-abind): New variable.
---
 gnu/packages/cran.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index c8a4216767..e7e49fd519 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3062,3 +3062,25 @@ data frame.  The @code{sqldf} or @code{read.csv.sql} functions can also be
 used to read filtered files into R even if the original files are larger than
 R itself can handle.")
     (license license:gpl2)))
+
+(define-public r-abind
+  (package
+    (name "r-abind")
+    (version "1.4-5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "abind" version))
+       (sha256
+        (base32
+         "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/abind/")
+    (synopsis "Combine multidimensional arrays")
+    (description
+     "This package provides tools to combine multidimensional arrays into a
+single array.  This is a generalization of @code{cbind} and @code{rbind}.  It
+works with vectors, matrices, and higher-dimensional arrays.  It also provides
+the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
+extracting and replacing data in arrays.")
+    (license license:lgpl2.0+)))
-- 
cgit v1.2.3


From fc784b6672eb8d21e1cb52dda1fd32c1bc4ae9a2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 23:16:44 +0100
Subject: gnu: Add r-prroc.

* gnu/packages/cran.scm (r-prroc): New variable.
---
 gnu/packages/cran.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index e7e49fd519..4b63c0f644 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3084,3 +3084,27 @@ works with vectors, matrices, and higher-dimensional arrays.  It also provides
 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
 extracting and replacing data in arrays.")
     (license license:lgpl2.0+)))
+
+(define-public r-prroc
+  (package
+    (name "r-prroc")
+    (version "1.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "PRROC" version))
+       (sha256
+        (base32
+         "03hvh92lq4i4w4mla9bvwrwb4626f4hvlxgdn57hamp70960vjyc"))))
+    (properties `((upstream-name . "PRROC")))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/PRROC/")
+    (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
+    (description
+     "This package computes the areas under the @dfn{precision-recall} (PR)
+and ROC curve for weighted (e.g. soft-labeled) and unweighted data.  In
+contrast to other implementations, the interpolation between points of the PR
+curve is done by a non-linear piecewise function.  In addition to the areas
+under the curves, the curves themselves can also be computed and plotted by a
+specific S3-method.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From 661bb51e668a239372dbc4df582b73ca356e38bc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 23:29:15 +0100
Subject: gnu: Add r-vim.

* gnu/packages/cran.scm (r-vim): New variable.
---
 gnu/packages/cran.scm | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 4b63c0f644..efb612e34f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3108,3 +3108,41 @@ curve is done by a non-linear piecewise function.  In addition to the areas
 under the curves, the curves themselves can also be computed and plotted by a
 specific S3-method.")
     (license license:gpl3)))
+
+(define-public r-vim
+  (package
+    (name "r-vim")
+    (version "4.7.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "VIM" version))
+       (sha256
+        (base32
+         "1vjcs5wvjv94ln01d94h9rs4j50d3ky4n26mm3prgh13raylrmnd"))))
+    (properties `((upstream-name . "VIM")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-car" ,r-car)
+       ("r-colorspace" ,r-colorspace)
+       ("r-data-table" ,r-data-table)
+       ("r-e1071" ,r-e1071)
+       ("r-laeken" ,r-laeken)
+       ("r-mass" ,r-mass)
+       ("r-nnet" ,r-nnet)
+       ("r-rcpp" ,r-rcpp)
+       ("r-robustbase" ,r-robustbase)
+       ("r-sp" ,r-sp)
+       ("r-vcd" ,r-vcd)))
+    (home-page "https://github.com/alexkowa/VIM")
+    (synopsis "Visualization and imputation of missing values")
+    (description
+     "This package provides tools for the visualization of missing and/or
+imputed values are introduced, which can be used for exploring the data and
+the structure of the missing and/or imputed values.  Depending on this
+structure of the missing values, the corresponding methods may help to
+identify the mechanism generating the missing values and allows to explore the
+data including missing values.  In addition, the quality of imputation can be
+visually explored using various univariate, bivariate, multiple and
+multivariate plot methods.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From d10b0952ce6be1c4f172b21622184e59bb3e1020 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 23:29:44 +0100
Subject: gnu: Add r-fnn.

* gnu/packages/cran.scm (r-fnn): New variable.
---
 gnu/packages/cran.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index efb612e34f..81b791d346 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3146,3 +3146,26 @@ data including missing values.  In addition, the quality of imputation can be
 visually explored using various univariate, bivariate, multiple and
 multivariate plot methods.")
     (license license:gpl2+)))
+
+(define-public r-fnn
+  (package
+    (name "r-fnn")
+    (version "1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "FNN" version))
+       (sha256
+        (base32
+         "1kncmiaraq1mrykb9fj3fsxswabk3l71fnp1vks0x9aay5xfk8mj"))))
+    (properties `((upstream-name . "FNN")))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/FNN")
+    (synopsis "Fast nearest neighbor search algorithms and applications")
+    (description
+     "This package provides cover-tree and kd-tree fast k-nearest neighbor
+search algorithms.  Related applications including KNN classification,
+regression and information measures are implemented.")
+    ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
+    ;; later can be used.
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From be815dbdda155e1e920667a1c34bf264cb20f5b3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 23:29:53 +0100
Subject: gnu: Add r-smoother.

* gnu/packages/cran.scm (r-smoother): New variable.
---
 gnu/packages/cran.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 81b791d346..4e3a036044 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3169,3 +3169,26 @@ regression and information measures are implemented.")
     ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
     ;; later can be used.
     (license license:gpl2+)))
+
+(define-public r-smoother
+  (package
+    (name "r-smoother")
+    (version "1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "smoother" version))
+       (sha256
+        (base32
+         "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ttr" ,r-ttr)))
+    (home-page "http://cran.r-project.org/web/packages/smoother")
+    (synopsis "Functions relating to the smoothing of numerical data")
+    (description
+     "This package provides a collection of methods for smoothing numerical
+data, commencing with a port of the Matlab gaussian window smoothing function.
+In addition, several functions typically used in smoothing of financial data
+are included.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From 22a0c6596921b87dd8cc38dfbdf99e13ae719a7d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 23:29:59 +0100
Subject: gnu: Add r-phangorn.

* gnu/packages/bioinformatics.scm (r-phangorn): New variable.
---
 gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a5ad2c57e7..92549d3c75 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10853,6 +10853,34 @@ are optimized per data type and for subsetted calculations such that both
 memory usage and processing time is minimized.")
     (license license:expat)))
 
+(define-public r-phangorn
+  (package
+    (name "r-phangorn")
+    (version "2.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "phangorn" version))
+       (sha256
+        (base32
+         "0xc8k552nxczy19jr0xjjagrzc8x6lafasgk2c099ls8bc1yml1i"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ape" ,r-ape)
+       ("r-fastmatch" ,r-fastmatch)
+       ("r-igraph" ,r-igraph)
+       ("r-magrittr" ,r-magrittr)
+       ("r-matrix" ,r-matrix)
+       ("r-quadprog" ,r-quadprog)
+       ("r-rcpp" ,r-rcpp)))
+    (home-page "https://github.com/KlausVigo/phangorn")
+    (synopsis "Phylogenetic analysis in R")
+    (description
+     "Phangorn is a package for phylogenetic analysis in R.  It supports
+estimation of phylogenetic trees and networks using Maximum Likelihood,
+Maximum Parsimony, distance methods and Hadamard conjugation.")
+    (license license:gpl2+)))
+
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))
-- 
cgit v1.2.3


From 1b5905fe689716e73ad7defc1bf8c6a13966f3c1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 8 Mar 2018 23:38:41 +0100
Subject: gnu: r-fnn: Remove duplicate definition.

* gnu/packages/cran.scm (r-fnn)[home-page]: Use HTTPS.
* gnu/packages/statistics.scm (r-fnn): Remove.
---
 gnu/packages/cran.scm       |  2 +-
 gnu/packages/statistics.scm | 21 ---------------------
 2 files changed, 1 insertion(+), 22 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 4e3a036044..9b690833ce 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3160,7 +3160,7 @@ multivariate plot methods.")
          "1kncmiaraq1mrykb9fj3fsxswabk3l71fnp1vks0x9aay5xfk8mj"))))
     (properties `((upstream-name . "FNN")))
     (build-system r-build-system)
-    (home-page "http://cran.r-project.org/web/packages/FNN")
+    (home-page "https://cran.r-project.org/web/packages/FNN")
     (synopsis "Fast nearest neighbor search algorithms and applications")
     (description
      "This package provides cover-tree and kd-tree fast k-nearest neighbor
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 7722cb3aa0..1324abd1f5 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4906,27 +4906,6 @@ functions apply.  The implementation can easily be added to functions where
 showing the progress is useful e.g. bootstrap.")
     (license license:gpl2)))
 
-(define-public r-fnn
-  (package
-    (name "r-fnn")
-    (version "1.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "FNN" version))
-       (sha256
-        (base32
-         "1kncmiaraq1mrykb9fj3fsxswabk3l71fnp1vks0x9aay5xfk8mj"))))
-    (properties `((upstream-name . "FNN")))
-    (build-system r-build-system)
-    (home-page "https://cran.r-project.org/web/packages/FNN")
-    (synopsis "Fast nearest neighbor search algorithms and applications")
-    (description
-     "This package provides cover-tree and kd-tree fast k-nearest neighbor
-search algorithms and related applications including KNN classification,
-regression and information measures.")
-    (license license:gpl2+)))
-
 (define-public r-minqa
   (package
     (name "r-minqa")
-- 
cgit v1.2.3


From d8f46d52343972af6734c28cce94559e1c78481f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 9 Mar 2018 11:20:22 +0100
Subject: gnu: hdf5: Do not record the build-time kernel version.

* gnu/packages/maths.scm (hdf5)[arguments]: Patch libhdf5.settings to prevent
the kernel version on the build node from affecting the output.
---
 gnu/packages/maths.scm | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 8d0c10697f..cf3d8ae836 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -724,7 +724,11 @@ incompatible with HDF5.")
              ;; unnecessary store references to those compilers:
              (substitute* "src/libhdf5.settings"
               (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
-               (string-append prefix (string-take hash 10) "...")))
+               (string-append prefix (string-take hash 10) "..."))
+              ;; Don't record the build-time kernel version to make the
+              ;; settings file reproducible.
+              (("Uname information:.*")
+               "Uname information: Linux\n"))
              #t))
          (add-after 'install 'patch-references
            (lambda* (#:key inputs outputs #:allow-other-keys)
-- 
cgit v1.2.3


From a539ad867da9d02d50330c1454e924cf3587f7c6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 9 Mar 2018 11:40:59 +0100
Subject: gnu: r-rhdf5lib: Make build reproducible.

* gnu/packages/bioinformatics.scm (r-rhdf5lib)[arguments]: Remove timestamp
and host system kernel version.
---
 gnu/packages/bioinformatics.scm | 10 ++++++++++
 1 file changed, 10 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 92549d3c75..14e2a0daac 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10654,6 +10654,16 @@ block processing.")
                (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
                (rename-file (string-append "hdf5-" ,(package-version hdf5))
                             "hdf5")
+               ;; Remove timestamp and host system information to make
+               ;; the build reproducible.
+               (substitute* "hdf5/src/libhdf5.settings.in"
+                 (("Configured on: @CONFIG_DATE@")
+                  "Configured on: Guix")
+                 (("Uname information:.*")
+                  "Uname information: Linux\n")
+                 ;; Remove unnecessary store reference.
+                 (("C Compiler:.*")
+                  "C Compiler: GCC\n"))
                (rename-file "Makevars.in" "Makevars")
                (substitute* "Makevars"
                  (("HDF5_CXX_LIB=.*")
-- 
cgit v1.2.3


From d5f56e9089aa743e12f54163a879c17eab48380e Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Sun, 4 Mar 2018 13:23:05 +0000
Subject: gnu: Add python-djangorestframework.

* gnu/packages/django.scm (python-djangorestframework): New variable.
---
 gnu/packages/django.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index c52c812f00..f944d25b60 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -755,3 +755,27 @@ Django projects, which allows association of a number of tags with any
 
 (define-public python2-django-tagging
   (package-with-python2 python-django-tagging))
+
+(define-public python-djangorestframework
+  (package
+    (name "python-djangorestframework")
+    (version "3.7.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "djangorestframework" version))
+       (sha256
+        (base32
+         "11qv117gqwswxjljs7wafxg1hyzzlx3qrviwlk9hw41bsbl997lz"))))
+    (build-system python-build-system)
+    (arguments
+     '(;; No included tests
+       #:tests? #f))
+    (propagated-inputs
+     `(("python-django" ,python-django)))
+    (home-page "https://www.django-rest-framework.org")
+    (synopsis "Toolkit for building Web APIs with Django")
+    (description
+     "The Django REST framework is for building Web APIs with Django.  It
+provides features like a web browseable API and authentication policies.")
+    (license license:bsd-2)))
-- 
cgit v1.2.3


From cc534f0c7102f39454edec0c2cd938bff056819e Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Sun, 4 Mar 2018 13:23:15 +0000
Subject: gnu: Add python-django-crispy-forms.

* gnu/packages/django.scm (python-django-crispy-forms): New variable.
---
 gnu/packages/django.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index f944d25b60..2768ae2af1 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -779,3 +779,28 @@ Django projects, which allows association of a number of tags with any
      "The Django REST framework is for building Web APIs with Django.  It
 provides features like a web browseable API and authentication policies.")
     (license license:bsd-2)))
+
+(define-public python-django-crispy-forms
+  (package
+    (name "python-django-crispy-forms")
+    (version "1.7.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "django-crispy-forms" version))
+       (sha256
+        (base32
+         "16s05jx86jmimlvnwpq73kl0mqw1v9lryc8zi61a9qwl25krm6mj"))))
+    (build-system python-build-system)
+    (arguments
+     '(;; No included tests
+       #:tests? #f))
+    (propagated-inputs
+     `(("python-django" ,python-django)))
+    (home-page
+     "http://github.com/maraujop/django-crispy-forms")
+    (synopsis "Tool to control Django forms without custom templates")
+    (description
+     "@code{django-crispy-forms} lets you easily build, customize and reuse
+forms using your favorite CSS framework, without writing template code.")
+    (license license:expat)))
-- 
cgit v1.2.3


From da90f337b31d53d3dc293a83e069984c70cde2ad Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Sun, 4 Mar 2018 13:23:38 +0000
Subject: gnu: Update python-django-filter to 1.1.0.

* gnu/packages/django.scm (python-django-filter)[version]: Update from 0.14.0
  to 1.1.0.
  [source]: Update sha256 hash.
  [native-inputs]: Add python-djangorestframework and
  python-django-crispy-forms as native inputs, as they are used in the test
  suite.
---
 gnu/packages/django.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index 2768ae2af1..24d096bc0f 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -182,13 +182,13 @@ useful tools for testing Django applications and projects.")
 (define-public python-django-filter
   (package
     (name "python-django-filter")
-    (version "0.14.0")
+    (version "1.1.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "django-filter" version))
               (sha256
                (base32
-                "0f78hmk8c903zwfzlsiw7ivgag81ymmb5hi73rzxbhnlg2v0l3fx"))))
+                "0slpfqfhnjrzlrb6vmswyhrzn01p84s16j2x1xib35gg4fxg23pc"))))
     (build-system python-build-system)
     (arguments
      '(#:phases
@@ -198,6 +198,8 @@ useful tools for testing Django applications and projects.")
              (zero? (system* "python" "runtests.py")))))))
     (native-inputs
      `(("python-django" ,python-django)
+       ("python-djangorestframework" ,python-djangorestframework)
+       ("python-django-crispy-forms", python-django-crispy-forms)
        ("python-mock" ,python-mock)))
     (home-page "https://django-filter.readthedocs.io/en/latest/")
     (synopsis "Reusable Django application to filter querysets dynamically")
-- 
cgit v1.2.3


From 16bd3291a4ef84f6caa8fea9fd0f4715b3a8de97 Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Sun, 4 Mar 2018 13:25:32 +0000
Subject: gnu: Update python-django-gravatar2.

* gnu/packages/django.scm (python-django-gravatar2)[version]: Update from
  1.4.0 to 1.4.2.
  [source]: Update sha256 hash.
  [arguments]: Disable the tests, as the django project for the tests is
  missing.
---
 gnu/packages/django.scm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index 24d096bc0f..a901af6f14 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -267,15 +267,18 @@ account authentication.")
 (define-public python-django-gravatar2
   (package
     (name "python-django-gravatar2")
-    (version "1.4.0")
+    (version "1.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "django-gravatar2" version))
        (sha256
         (base32
-         "1v4qyj6kms321yw0z2g1kch6b2dskmv6fjd6sfxzwr4xshq9mccl"))))
+         "1qsv40xywbqsf4mkrmsswrpzqd7nfljxpfiim9an2z3dykn5rka6"))))
     (build-system python-build-system)
+    (arguments
+     '(;; TODO: The django project for the tests is missing from the release.
+       #:tests? #f))
     (inputs
      `(("python-django" ,python-django)))
     (home-page "https://github.com/twaddington/django-gravatar")
-- 
cgit v1.2.3


From ab9ad138025bdc01e286044e5de20bf03ad1c3b9 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Fri, 9 Mar 2018 16:31:32 -0500
Subject: gnu: linux-libre@4.1: Update to 4.1.50.

* gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.50.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index d4b9d0d0b9..7e49ae6ee2 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -414,8 +414,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.1
-  (make-linux-libre "4.1.49"
-                    "0dklmqj6ayjlkz97b811zdvpgb3yppahinji9l9jmkz4ssi7a1gs"
+  (make-linux-libre "4.1.50"
+                    "1hl1pk724v2waa55bhxfmxyz9nl6pkcj4dc3l80jfvqdfgr55mm2"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
-- 
cgit v1.2.3


From 464f5447396fcec9b43f7eab71d5d42b522a157f Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Fri, 9 Mar 2018 23:11:48 +0100
Subject: gnu: 'autoconf-wrapper' is no longer a procedure.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Fixes <https://bugs.gnu.org/30710>.
Suggested by Björn Höfling <bjoern.hoefling@bjoernhoefling.de>.

* gnu/packages/autotools.scm (autoconf-wrapper): Rename to...
(make-autoconf-wrapper): ... this.  Add 'properties' field.
(autoconf-wrapper): New variable.
* gnu/packages/gnunet.scm (guile-gnunet): Adjust accordingly.
* gnu/packages/gnupg.scm (signing-party): Likewise.
* gnu/packages/guile.scm (guile-ics, guile-bash): Likewise.
* gnu/packages/libevent.scm (libuv): Likewise.
* gnu/packages/logging.scm (glog): Likewise.
* gnu/packages/mail.scm (libetpan): Likewise.
* gnu/packages/mate.scm (mate-icon-theme-faenza)
(mate-screensaver): Likewise.
* gnu/packages/package-management.scm (guix): Likewise.
* gnu/packages/sawfish.scm (librep): Likewise.
* gnu/packages/video.scm (motion): Likewise.
* gnu/packages/zile.scm (zile-on-guile): Likewise.
---
 gnu/packages/autotools.scm          | 16 +++++++++++-----
 gnu/packages/gnunet.scm             |  4 ++--
 gnu/packages/gnupg.scm              |  4 ++--
 gnu/packages/guile.scm              |  4 ++--
 gnu/packages/libevent.scm           |  4 ++--
 gnu/packages/logging.scm            |  4 ++--
 gnu/packages/mail.scm               |  2 +-
 gnu/packages/mate.scm               |  4 ++--
 gnu/packages/package-management.scm |  2 +-
 gnu/packages/sawfish.scm            |  2 +-
 gnu/packages/video.scm              |  2 +-
 gnu/packages/zile.scm               |  4 ++--
 12 files changed, 29 insertions(+), 23 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/autotools.scm b/gnu/packages/autotools.scm
index 846e318aa1..33addc11a7 100644
--- a/gnu/packages/autotools.scm
+++ b/gnu/packages/autotools.scm
@@ -124,8 +124,8 @@ know anything about Autoconf or M4.")
                                (string-append "--build=" build)))))))))))
 
 
-(define* (autoconf-wrapper #:optional (autoconf autoconf))
-  "Return an wrapper around AUTOCONF that generates `configure' scripts that
+(define (make-autoconf-wrapper autoconf)
+  "Return a wrapper around AUTOCONF that generates `configure' scripts that
 use our own Bash instead of /bin/sh in shebangs.  For that reason, it should
 only be used internally---users should not end up distributing `configure'
 files with a system-specific shebang."
@@ -191,7 +191,13 @@ exec ~a --no-auto-compile \"$0\" \"$@\"
                        (patch-shebang "configure"))
                      (exit (status:exit-val result))))
                 port)))
-           (chmod (string-append bin "/autoconf") #o555)))))))
+           (chmod (string-append bin "/autoconf") #o555)))))
+
+    ;; Do not show it in the UI since it's meant for internal use.
+    (properties '((hidden? . #t)))))
+
+(define-public autoconf-wrapper
+  (make-autoconf-wrapper autoconf))
 
 (define-public autoconf-archive
   (package
@@ -253,7 +259,7 @@ output is indexed in many ways to simplify browsing.")
               (search-patches "automake-skip-amhello-tests.patch"))))
     (build-system gnu-build-system)
     (native-inputs
-     `(("autoconf" ,(autoconf-wrapper))
+     `(("autoconf" ,autoconf-wrapper)
        ("perl" ,perl)))
     (native-search-paths
      (list (search-path-specification
@@ -348,7 +354,7 @@ Makefile, simplifying the entire process for the developer.")
                      ("perl" ,perl)
                      ("help2man" ,help2man) ;because we modify ltmain.sh
                      ("automake" ,automake)      ;some tests rely on 'aclocal'
-                     ("autoconf" ,(autoconf-wrapper)))) ;others on 'autom4te'
+                     ("autoconf" ,autoconf-wrapper))) ;others on 'autom4te'
 
     (arguments
      `(;; Libltdl is provided as a separate package, so don't install it here.
diff --git a/gnu/packages/gnunet.scm b/gnu/packages/gnunet.scm
index 29bfc8199f..f4eacd3023 100644
--- a/gnu/packages/gnunet.scm
+++ b/gnu/packages/gnunet.scm
@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2014 Sree Harsha Totakura <sreeharsha@totakura.in>
-;;; Copyright © 2015, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2015, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016 Mark H Weaver <mhw@netris.org>
@@ -327,7 +327,7 @@ kinds of basic applications for the foundation of a GNU internet.")
                       (lambda _
                         (invoke "autoreconf" "-vfi"))))))
       (native-inputs `(("pkg-config" ,pkg-config)
-                       ("autoconf" ,(autoconf-wrapper))
+                       ("autoconf" ,autoconf-wrapper)
                        ("automake" ,automake)))
       (inputs `(("guile" ,guile-2.0)
                 ("gnunet" ,gnunet)))
diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm
index eeab5c5afd..28f5b58887 100644
--- a/gnu/packages/gnupg.scm
+++ b/gnu/packages/gnupg.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013, 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2014, 2015, 2016 Mark H Weaver <mhw@netris.org>
@@ -618,7 +618,7 @@ PGP keysigning parties.")
                      "1n5bpcfpl9vg1xp6r1jhbyahrgdyxp05b5pria1rh4m0qnv8sifr"))))
    (build-system gnu-build-system)
    (native-inputs
-    `(("autoconf" ,(autoconf-wrapper))
+    `(("autoconf" ,autoconf-wrapper)
       ("automake" ,automake)))
    (inputs `(("perl" ,perl)
              ("perl-text-template" ,perl-text-template)
diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index 91a440d928..bfcb32531f 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -769,7 +769,7 @@ format is also supported.")
                       (symlink "README.org" "README")
                       (zero? (system* "autoreconf" "-fi")))))))
     (native-inputs
-     `(("autoconf" ,(autoconf-wrapper))
+     `(("autoconf" ,autoconf-wrapper)
        ("automake" ,automake)
        ("texinfo" ,texinfo)
        ;; Gettext brings 'AC_LIB_LINKFLAGS_FROM_LIBS'.
@@ -1856,7 +1856,7 @@ dictionary and suggesting spelling corrections.")
                (string-append "--libdir=" (assoc-ref %outputs "out")
                               "/lib/bash"))))
       (native-inputs `(("pkg-config" ,pkg-config)
-                       ("autoconf" ,(autoconf-wrapper))
+                       ("autoconf" ,autoconf-wrapper)
                        ("automake" ,automake)
                        ("libtool" ,libtool)
                        ;; Gettext brings 'AC_LIB_LINKFLAGS_FROM_LIBS'.
diff --git a/gnu/packages/libevent.scm b/gnu/packages/libevent.scm
index 9d96e651ac..d6b70a4f17 100644
--- a/gnu/packages/libevent.scm
+++ b/gnu/packages/libevent.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015, 2016, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015, 2017 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Eric Dvorsak <eric@dvorsak.fr>
 ;;; Copyright © 2016 David Thompson <davet@gnu.org>
@@ -140,7 +140,7 @@ limited support for fork events.")
 
        ;; XXX: Some tests want /dev/tty, attempt to make connections, etc.
        #:tests? #f))
-    (native-inputs `(("autoconf" ,(autoconf-wrapper))
+    (native-inputs `(("autoconf" ,autoconf-wrapper)
                      ("automake" ,automake)
                      ("libtool" ,libtool)
 
diff --git a/gnu/packages/logging.scm b/gnu/packages/logging.scm
index 27557e1b1b..f50a2f1cbb 100644
--- a/gnu/packages/logging.scm
+++ b/gnu/packages/logging.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017 Stefan Reichör <stefan@xsteve.at>
 ;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -73,7 +73,7 @@ staying as close to their API as is reasonable.")
     (build-system gnu-build-system)
     (native-inputs
      `(("perl" ,perl)                             ;for tests
-       ("autoconf" ,(autoconf-wrapper))
+       ("autoconf" ,autoconf-wrapper)
        ("automake" ,automake)
        ("libtool" ,libtool)))
     (arguments
diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index 7d85d5208a..7986671e97 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -931,7 +931,7 @@ useful features.")
              (sha256
                (base32 "1sxnaglp5hb0z78sgnfzva4x8m4flqhicvm1dz0krkxdmfsafrsf"))))
     (build-system gnu-build-system)
-    (native-inputs `(("autoconf" ,(autoconf-wrapper))
+    (native-inputs `(("autoconf" ,autoconf-wrapper)
                      ("automake" ,automake)
                      ("libtool" ,libtool)
                      ("pkg-config" ,pkg-config)))
diff --git a/gnu/packages/mate.scm b/gnu/packages/mate.scm
index b892a768d8..0281b02daa 100644
--- a/gnu/packages/mate.scm
+++ b/gnu/packages/mate.scm
@@ -135,7 +135,7 @@ MATE applications.")
              (setenv "CONFIG_SHELL" (which "sh"))
              (invoke "sh" "autogen.sh"))))))
     (native-inputs
-     `(("autoconf" ,(autoconf-wrapper))
+     `(("autoconf" ,autoconf-wrapper)
        ("automake" ,automake)
        ("intltool" ,intltool)
        ("icon-naming-utils" ,icon-naming-utils)
@@ -1191,7 +1191,7 @@ Re-decorates windows on un-maximise.
                (("dbus-1") ""))))))))
     (native-inputs
      `(("automake" ,automake)
-       ("autoconf" ,(autoconf-wrapper))
+       ("autoconf" ,autoconf-wrapper)
        ("gettext" ,gettext-minimal)
        ("intltool" ,intltool)
        ("kbproto" ,kbproto)
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 6ec70b12fe..709cdfd0f7 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -239,7 +239,7 @@
                        ;; XXX: Keep the development inputs here even though
                        ;; they're unnecessary, just so that 'guix environment
                        ;; guix' always contains them.
-                       ("autoconf" ,(autoconf-wrapper))
+                       ("autoconf" ,autoconf-wrapper)
                        ("automake" ,automake)
                        ("gettext" ,gettext-minimal)
                        ("texinfo" ,texinfo)
diff --git a/gnu/packages/sawfish.scm b/gnu/packages/sawfish.scm
index 9f9264457d..ede725877d 100644
--- a/gnu/packages/sawfish.scm
+++ b/gnu/packages/sawfish.scm
@@ -58,7 +58,7 @@
      `(("makeinfo"   ,texinfo)
        ("pkg-config" ,pkg-config)
 
-       ("autoconf" ,(autoconf-wrapper))
+       ("autoconf" ,autoconf-wrapper)
        ("automake" ,automake)
        ("libtool"  ,libtool)))
     (inputs
diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 7d072009a0..dfd94f9d3b 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -2761,7 +2761,7 @@ It counts more than 100 plugins.")
               (file-name (string-append name "-" version ".tar.gz"))))
     (build-system gnu-build-system)
     (native-inputs
-     `(("autoconf" ,(autoconf-wrapper))
+     `(("autoconf" ,autoconf-wrapper)
        ("automake" ,automake)
        ("pkg-config" ,pkg-config)))
     (inputs
diff --git a/gnu/packages/zile.scm b/gnu/packages/zile.scm
index c0bbafdd59..fd3d168b3d 100644
--- a/gnu/packages/zile.scm
+++ b/gnu/packages/zile.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012, 2013, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2012, 2013, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;;
@@ -102,7 +102,7 @@ default Emacs configuration, but it carries a much lighter feature set.")
          ,@(package-inputs zile)))
       (native-inputs
        `(("m4" ,m4)                               ;for 'bootstrap'
-         ("autoconf" ,(autoconf-wrapper))
+         ("autoconf" ,autoconf-wrapper)
          ("automake" ,automake)
 
          ;; For some reason, 'bootstrap' insists on having these.
-- 
cgit v1.2.3


From b8605720accbc7472ab213aef48f79321da16738 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Fri, 9 Mar 2018 20:22:35 -0500
Subject: gnu: linux-libre@4.14: Update to 4.14.25.

* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.25.
(%linux-libre-4.14-hash): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 7e49ae6ee2..390e855e6c 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -392,8 +392,8 @@ It has been modified to remove all non-free binary blobs.")
                     %linux-compatible-systems
                     #:configuration-file kernel-config))
 
-(define %linux-libre-4.14-version "4.14.24")
-(define %linux-libre-4.14-hash "1i14djw3rmxb6syl6vfd5w76rjksbbaviynwj2dwwp9ki1h6p1hr")
+(define %linux-libre-4.14-version "4.14.25")
+(define %linux-libre-4.14-hash "0lrzw51ajdkc8mj9bn0lc4yx6q9sf29lcviapapqixg5hds72b94")
 
 (define-public linux-libre-4.14
   (make-linux-libre %linux-libre-4.14-version
-- 
cgit v1.2.3


From e82b61e6dda8cb979527963c913a2f72a2dfae5f Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Fri, 9 Mar 2018 20:23:24 -0500
Subject: gnu: linux-libre: Update to 4.15.8.

* gnu/packages/linux.scm (%linux-libre-version): Update to 4.15.8.
(%linux-libre-hash): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 390e855e6c..57e033f9b5 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -383,8 +383,8 @@ It has been modified to remove all non-free binary blobs.")
 ;; supports qemu "virt" machine and possibly a large number of ARM boards.
 ;; See : https://wiki.debian.org/DebianKernel/ARMMP.
 
-(define %linux-libre-version "4.15.7")
-(define %linux-libre-hash "1h17wc12lvva5vcm2z06cf57ywxb6i2snm9vxixw1lwibnksrb6l")
+(define %linux-libre-version "4.15.8")
+(define %linux-libre-hash "0178yi8k72sfv73gss2a1v7w1rmhyza3ia31jwg86gixqw74vifm")
 
 (define-public linux-libre
   (make-linux-libre %linux-libre-version
-- 
cgit v1.2.3


From fd2ebe1ed0df4e65ff1d4ed8fa512da0e93a7683 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 10 Mar 2018 09:37:47 +0100
Subject: gnu: xbitmaps: Update to 1.1.2.

* gnu/packages/xorg.scm (xbitmaps): Update to 1.1.2.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index d1671ba8c1..701992b418 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -2030,7 +2030,7 @@ the same way.")
 (define-public xbitmaps
   (package
     (name "xbitmaps")
-    (version "1.1.1")
+    (version "1.1.2")
     (source
       (origin
         (method url-fetch)
@@ -2040,7 +2040,7 @@ the same way.")
                ".tar.bz2"))
         (sha256
           (base32
-            "178ym90kwidia6nas4qr5n5yqh698vv8r02js0r4vg3b6lsb0w9n"))))
+            "1vh73sc13s7w5r6gnc6irca56s7998bja7wgdivkfn8jccawgw5r"))))
     (build-system gnu-build-system)
     (native-inputs `(("pkg-config" ,pkg-config)))
     (home-page "https://www.x.org/wiki/")
-- 
cgit v1.2.3


From 04a937f00a39538416252bc2c5c5f42bc8cb6ae4 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 10 Mar 2018 09:38:10 +0100
Subject: gnu: xcursor-themes: Update to 1.0.5.

* gnu/packages/xorg.scm (xcursor-themes): Update to 1.0.5.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index 701992b418..2409e5e521 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -2177,7 +2177,7 @@ X11 Inter-Client Communication Conventions Manual (ICCCM).")
 (define-public xcursor-themes
   (package
     (name "xcursor-themes")
-    (version "1.0.4")
+    (version "1.0.5")
     (source
       (origin
         (method url-fetch)
@@ -2187,7 +2187,7 @@ X11 Inter-Client Communication Conventions Manual (ICCCM).")
                ".tar.bz2"))
         (sha256
           (base32
-            "11mv661nj1p22sqkv87ryj2lcx4m68a04b0rs6iqh3fzp42jrzg3"))))
+            "0whjiq6d5z4z75zh37pji6llfcyrg6q3mg9zx5zqyncnj39q30xf"))))
     (build-system gnu-build-system)
     (inputs
       `(("libxcursor" ,libxcursor)
-- 
cgit v1.2.3


From 7c1119aa0f3f41b1e32c32733157ae7cb0d622d7 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 10 Mar 2018 09:38:34 +0100
Subject: gnu: xfontsel: Update to 1.0.6.

* gnu/packages/xorg.scm (xfontsel): Update to 1.0.6.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index 2409e5e521..ccacc32289 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -3962,7 +3962,7 @@ protocol.")
 (define-public xfontsel
   (package
     (name "xfontsel")
-    (version "1.0.5")
+    (version "1.0.6")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -3970,7 +3970,7 @@ protocol.")
                     version ".tar.bz2"))
               (sha256
                (base32
-                "1grir464hy52a71r3mpm9mzvkf7nwr3vk0b1vc27pd3gp588a38p"))))
+                "0700lf6hx7dg88wq1yll7zjvf9gbwh06xff20yffkxb289y0pai5"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
-- 
cgit v1.2.3


From c5b9bde5b21d81fb0cab37f58ebd8ece7a8ea2b4 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 10 Mar 2018 09:38:58 +0100
Subject: gnu: xrdb: Update to 1.1.1.

* gnu/packages/xorg.scm (xrdb): Update to 1.1.1.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index ccacc32289..ffcb9e79c8 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -4180,7 +4180,7 @@ and Reflect (RandR) extension.")
 (define-public xrdb
   (package
     (name "xrdb")
-    (version "1.1.0")
+    (version "1.1.1")
     (source
       (origin
         (method url-fetch)
@@ -4190,7 +4190,7 @@ and Reflect (RandR) extension.")
                ".tar.bz2"))
         (sha256
           (base32
-            "0nsnr90wazcdd50nc5dqswy0bmq6qcj14nnrhyi7rln9pxmpp0kk"))))
+            "1dqp486nd5sagbg572kl0k839nwvpqnb7jvppyb7jj5vrpkss8rd"))))
     (build-system gnu-build-system)
     (inputs
       `(("libxmu" ,libxmu)
-- 
cgit v1.2.3


From c609ee9f551392939e03e66ea2d53f51ba0cc94b Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 10 Mar 2018 09:39:21 +0100
Subject: gnu: xrefresh: Update to 1.0.6.

* gnu/packages/xorg.scm (xrefresh): Update to 1.0.6.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index ffcb9e79c8..9224e2ba08 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -4211,7 +4211,7 @@ file.")
 (define-public xrefresh
   (package
     (name "xrefresh")
-    (version "1.0.5")
+    (version "1.0.6")
     (source
       (origin
         (method url-fetch)
@@ -4221,7 +4221,7 @@ file.")
                ".tar.bz2"))
         (sha256
           (base32
-            "1mlinwgvql6s1rbf46yckbfr9j22d3c3z7jx3n6ix7ca18dnf4rj"))))
+            "0lv3rlshh7s0z3aqx5ahnnf8cl082m934bk7gv881mz8nydznz98"))))
     (build-system gnu-build-system)
     (inputs
       `(("libx11" ,libx11)))
-- 
cgit v1.2.3


From fdf5257e7c412fca9da4054dfeee6953c7e5efb6 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 10 Mar 2018 09:39:42 +0100
Subject: gnu: xsetroot: Update to 1.1.2.

* gnu/packages/xorg.scm (xsetroot): Update to 1.1.2.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index 9224e2ba08..9ea57d4fe7 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -4268,7 +4268,7 @@ up your screen.")
 (define-public xsetroot
   (package
     (name "xsetroot")
-    (version "1.1.1")
+    (version "1.1.2")
     (source
       (origin
         (method url-fetch)
@@ -4278,7 +4278,7 @@ up your screen.")
                ".tar.bz2"))
         (sha256
           (base32
-            "1nf3ii31m1knimbidaaym8p61fq3blv8rrdr2775yhcclym5s8ds"))))
+            "0z21mqvmdl6rl63q77479wgkfygnll57liza1i3va7sr4fx45i0h"))))
     (build-system gnu-build-system)
     (inputs
       `(("libxmu" ,libxmu)
-- 
cgit v1.2.3


From 873ee8a75038af762f175b95047cd64441cf44b3 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 10 Mar 2018 09:40:20 +0100
Subject: gnu: xwud: Update to 1.0.5.

* gnu/packages/xorg.scm (xwud): Update to 1.0.5.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index 9ea57d4fe7..0838d931cd 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -4414,7 +4414,7 @@ Various information is displayed depending on which options are selected.")
 (define-public xwud
   (package
     (name "xwud")
-    (version "1.0.4")
+    (version "1.0.5")
     (source
       (origin
         (method url-fetch)
@@ -4424,7 +4424,7 @@ Various information is displayed depending on which options are selected.")
                ".tar.bz2"))
         (sha256
           (base32
-            "1ggql6maivah58kwsh3z9x1hvzxm1a8888xx4s78cl77ryfa1cyn"))))
+            "1a8hdgy40smvblnh3s9f0vkqckl68nmivx7d48zk34m8z18p16cr"))))
     (build-system gnu-build-system)
     (inputs
       `(("xproto" ,xproto)
-- 
cgit v1.2.3


From 4a4570bea5998170b1f66e435e5c22bb16413bd5 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 10 Mar 2018 09:40:45 +0100
Subject: gnu: xinit: Update to 1.4.0.

* gnu/packages/xorg.scm (xinit): Update to 1.4.0.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index 0838d931cd..70a8b077eb 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -5650,14 +5650,14 @@ The XCB util-wm module provides the following libraries:
 (define-public xinit
   (package
     (name "xinit")
-    (version "1.3.4")
+    (version "1.4.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://xorg/individual/app/xinit-"
                                   version ".tar.bz2"))
               (sha256
                (base32
-                "1cq2g469mb2cfgr8k57960yrn90bl33vfqri4pdh2zm0jxrqvn3m"))))
+                "1vw2wlg74ig52naw0cha3pgzcwwk25l834j42cg8m5zmybp3a213"))))
     (build-system gnu-build-system)
     (inputs
      `(("xproto" ,xproto)
-- 
cgit v1.2.3


From dde360ecb238e7b1fbf501bb9ee21c7307017ece Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 10 Mar 2018 09:41:10 +0100
Subject: gnu: xmessage: Update to 1.0.5.

* gnu/packages/xorg.scm (xmessage): Update to 1.0.5.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index 70a8b077eb..78d864650f 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -5739,7 +5739,7 @@ of an X11 screen.")
 (define-public xmessage
   (package
     (name "xmessage")
-    (version "1.0.4")
+    (version "1.0.5")
     (source
      (origin
        (method url-fetch)
@@ -5749,7 +5749,7 @@ of an X11 screen.")
              ".tar.gz"))
        (sha256
         (base32
-         "1jmcac1xbwplbxfl75sr6w3zqhx1khpdzlqippjsr31cjp1rjc48"))))
+         "0sw0b0cbrjl44brw7qi1jkm61xd7a1lpj04418c6iqk6mf83llwr"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
-- 
cgit v1.2.3


From f20348549f214f2367ddad9a2c276389fe9ddfd7 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 10 Mar 2018 09:50:32 +0100
Subject: gnu: xlsclients: Update to 1.1.4.

* gnu/packages/xorg.scm (xlsclients): Update to 1.1.4.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index 78d864650f..fdaa73389c 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -3908,7 +3908,7 @@ programs that have displayed undesired windows on a user's screen.")
 (define-public xlsclients
   (package
     (name "xlsclients")
-    (version "1.1.3")
+    (version "1.1.4")
     (source
       (origin
         (method url-fetch)
@@ -3918,7 +3918,7 @@ programs that have displayed undesired windows on a user's screen.")
                ".tar.bz2"))
         (sha256
           (base32
-            "0g9x7rrggs741x9xwvv1k9qayma980d88nhdqw7j3pn3qvy6d5jx"))))
+            "1h8931sn34mcip6vpi4v7hdmr1r58gkbw4s2p97w98kykks2lgvp"))))
     (build-system gnu-build-system)
     (inputs
       `(("libxcb" ,libxcb)))
-- 
cgit v1.2.3


From a4f48cc59ad5d5ba1f8983d9169f29680efa6677 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 10 Mar 2018 09:50:52 +0100
Subject: gnu: xwd: Update to 1.0.7.

* gnu/packages/xorg.scm (xwd): Update to 1.0.7.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index fdaa73389c..e10332274d 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -4353,7 +4353,7 @@ extension.")
 (define-public xwd
   (package
     (name "xwd")
-    (version "1.0.6")
+    (version "1.0.7")
     (source
       (origin
         (method url-fetch)
@@ -4363,7 +4363,7 @@ extension.")
                ".tar.bz2"))
         (sha256
           (base32
-            "0ybx48agdvjp9lgwvcw79r1x6jbqbyl3fliy3i5xwy4d4si9dcrv"))))
+            "1537i8q8pgf0sjklakzfvjwrq5b246qjywrx9ll8xfg0p6w1as6d"))))
     (build-system gnu-build-system)
     (inputs
       `(("libxt" ,libxt)
-- 
cgit v1.2.3


From 61c70e54857d3283e1aedd6a955e183b1d881660 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 10 Mar 2018 09:51:15 +0100
Subject: gnu: xset: Update to 1.2.4.

* gnu/packages/xorg.scm (xset): Update to 1.2.4.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index e10332274d..46a09f089b 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -4239,7 +4239,7 @@ up your screen.")
 (define-public xset
   (package
     (name "xset")
-    (version "1.2.3")
+    (version "1.2.4")
     (source
       (origin
         (method url-fetch)
@@ -4249,7 +4249,7 @@ up your screen.")
                ".tar.bz2"))
         (sha256
           (base32
-            "0qw0iic27bz3yz2wynf1gxs70hhkcf9c4jrv7zhlg1mq57xz90j3"))))
+            "0my987wjvra7l92ry6q44ky383yg3phzxhdbn3lqhapm1ll9bzg4"))))
     (build-system gnu-build-system)
     (inputs
       `(("xproto" ,xproto)
-- 
cgit v1.2.3


From 79b0f0b7cd1649d3280b596f3ea33ca7159f5c4d Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 10 Mar 2018 09:51:37 +0100
Subject: gnu: xwininfo: Update to 1.1.4.

* gnu/packages/xorg.scm (xwininfo): Update to 1.1.4.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index 46a09f089b..ca877eacb2 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -4386,7 +4386,7 @@ dump and twice whenthe dump is completed.")
 (define-public xwininfo
   (package
     (name "xwininfo")
-    (version "1.1.3")
+    (version "1.1.4")
     (source
       (origin
         (method url-fetch)
@@ -4396,7 +4396,7 @@ dump and twice whenthe dump is completed.")
                ".tar.bz2"))
         (sha256
           (base32
-            "1y1zn8ijqslb5lfpbq4bb78kllhch8in98ps7n8fg3dxjpmb13i1"))))
+            "00avrpw4h5mr1klp41lv2j4dmq465v6l5kb5bhm4k5ml8sm9i543"))))
     (build-system gnu-build-system)
     (inputs
       `(("libx11" ,libx11)
-- 
cgit v1.2.3


From 19ec5a05a8140f684a9f2a7781b20e346f76155f Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 10 Mar 2018 09:53:27 +0100
Subject: gnu: xbacklight: Update to 1.2.2.

* gnu/packages/xorg.scm (xbacklight): Update to 1.2.2.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index ca877eacb2..b0ac4d3bcc 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -2000,7 +2000,7 @@ information used in connecting to the X server.")
 (define-public xbacklight
   (package
     (name "xbacklight")
-    (version "1.2.1")
+    (version "1.2.2")
     (source
       (origin
         (method url-fetch)
@@ -2010,7 +2010,7 @@ information used in connecting to the X server.")
                ".tar.bz2"))
         (sha256
           (base32
-            "0arnd1j8vzhzmw72mqhjjcb2qwcbs9qphsy3ps593ajyld8wzxhp"))))
+            "0pmzaz4kp38qv2lqiw5rnqhwzmwrq65m1x5j001mmv99wh9isnk1"))))
     (build-system gnu-build-system)
     (inputs
      `(("libxcb" ,libxcb)
-- 
cgit v1.2.3


From 060c82c113e550de98ffc1baa8127b08b63c5c58 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 10 Mar 2018 09:54:21 +0100
Subject: gnu: xkill: Update to 1.0.5.

* gnu/packages/xorg.scm (xkill): Update to 1.0.5.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index b0ac4d3bcc..217547da15 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -3853,7 +3853,7 @@ can be combined together using the 'rules' component of this database.")
 (define-public xkill
   (package
     (name "xkill")
-    (version "1.0.4")
+    (version "1.0.5")
     (source
       (origin
         (method url-fetch)
@@ -3863,7 +3863,7 @@ can be combined together using the 'rules' component of this database.")
                ".tar.bz2"))
         (sha256
           (base32
-            "0bl1ky8ps9jg842j4mnmf4zbx8nkvk0h77w7bqjlpwij9wq2mvw8"))))
+            "0szzd9nzn0ybkhnfyizb876irwnjsnb78rcaxx6prb71jmmbpw65"))))
     (build-system gnu-build-system)
     (inputs
       `(("libxmu" ,libxmu)
-- 
cgit v1.2.3


From cafda73f7e2804c986a892f20b09ca1e87b5fdbd Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 10 Mar 2018 09:54:45 +0100
Subject: gnu: xlsfonts: Update to 1.0.6.

* gnu/packages/xorg.scm (xlsfonts): Update to 1.0.6.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index 217547da15..c8d4d4cd2e 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -3935,7 +3935,7 @@ running on X server.")
 (define-public xlsfonts
   (package
     (name "xlsfonts")
-    (version "1.0.5")
+    (version "1.0.6")
     (source
      (origin
        (method url-fetch)
@@ -3945,7 +3945,7 @@ running on X server.")
              ".tar.bz2"))
        (sha256
         (base32
-         "1yi774g6r1kafsbnxbkrwyndd3i60362ck1fps9ywz076pn5naa0"))))
+         "0s6kxgv78chkwsqmhw929f4pf91gq63f4yvixxnan1h00cx0pf49"))))
     (build-system gnu-build-system)
     (inputs
      `(("xproto" ,xproto)
-- 
cgit v1.2.3


From 505a65dccf1c30df6c94ffa336f0f8427f7212dd Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 10 Mar 2018 09:58:55 +0100
Subject: gnu: xpr: Update to 1.0.5.

* gnu/packages/xorg.scm (xpr): Update to 1.0.5.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index c8d4d4cd2e..4dda27b9f1 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -4094,7 +4094,7 @@ refers to the included common xorg.css stylesheet.")
 (define-public xpr
   (package
     (name "xpr")
-    (version "1.0.4")
+    (version "1.0.5")
     (source
       (origin
         (method url-fetch)
@@ -4104,7 +4104,7 @@ refers to the included common xorg.css stylesheet.")
                ".tar.bz2"))
         (sha256
           (base32
-            "1dbcv26w2yand2qy7b3h5rbvw1mdmdd57jw88v53sgdr3vrqvngy"))))
+            "07qy9lwjvxighcmg6qvjkgagad3wwvidrfx0jz85lgynz3qy0dmr"))))
     (build-system gnu-build-system)
     (inputs
       `(("xproto" ,xproto)
-- 
cgit v1.2.3


From 8e3b852ad0c53612828bc1c10bf7f2014eaa5ba4 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 10 Mar 2018 09:59:18 +0100
Subject: gnu: xprop: Update to 1.2.3.

* gnu/packages/xorg.scm (xprop): Update to 1.2.3.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index 4dda27b9f1..46a9a3b85f 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -4123,7 +4123,7 @@ it for output on various types of printers.")
 (define-public xprop
   (package
     (name "xprop")
-    (version "1.2.2")
+    (version "1.2.3")
     (source
       (origin
         (method url-fetch)
@@ -4133,7 +4133,7 @@ it for output on various types of printers.")
                ".tar.bz2"))
         (sha256
           (base32
-            "1ilvhqfjcg6f1hqahjkp8qaay9rhvmv2blvj3w9asraq0aqqivlv"))))
+            "06sjgahjiz85v0k0pmv5x05chc591xynl5ah1bqzz1bdr0lgnanj"))))
     (build-system gnu-build-system)
     (inputs
       `(("xproto" ,xproto)
-- 
cgit v1.2.3


From 0fa4702c041a5746ec3a58b39e4276c39d18e7da Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 9 Mar 2018 22:25:40 +0100
Subject: gnu: r-minimal: Respect SOURCE_DATE_EPOCH in srcfile.

Fixes <https://bugs.gnu.org/30729>.

* gnu/packages/statistics.scm (r-minimal)[arguments]: Replace timestamp hack
with patch to "srcfile" and "srcfilecopy".
---
 gnu/packages/statistics.scm | 24 +++++++++---------------
 1 file changed, 9 insertions(+), 15 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 1324abd1f5..af69703d90 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -172,21 +172,15 @@ be output in text, PostScript, PDF or HTML.")
              ;; queries the mtime of a given file and records it in an object.
              ;; This is acceptable at runtime to detect stale source files,
              ;; but it destroys reproducibility at build time.
-             ;;
-             ;; Instead of disabling this feature, which may have unexpected
-             ;; consequences, we reset the mtime of generated files before
-             ;; passing them to the "srcfile" procedure.
-             (substitute* "src/library/Makefile.in"
-               (("@\\(cd base && \\$\\(MAKE\\) mkdesc\\)" line)
-                (string-append line "\n	find $(top_builddir)/library/tools | xargs touch -d '1970-01-01'; \n"))
-               (("@\\$\\(MAKE\\) Rdobjects" line)
-                (string-append "@find $(srcdir)/tools | xargs touch -d '1970-01-01'; \n	"
-                               line)))
-             (substitute* "src/library/tools/Makefile.in"
-               (("@\\$\\(INSTALL_DATA\\) all.R \\$\\(top_builddir\\)/library/\\$\\(pkg\\)/R/\\$\\(pkg\\)" line)
-                (string-append
-                 line
-                 "\n	find $(srcdir)/$(pkg) $(top_builddir)/library/$(pkg) | xargs touch -d \"1970-01-01\"; \n")))
+
+             ;; Similarly, the "srcfilecopy" procedure records the current
+             ;; time.  We change both of them to respect SOURCE_DATE_EPOCH.
+             (substitute* "src/library/base/R/srcfile.R"
+               (("timestamp <- (timestamp.*|file.mtime.*)" _ time)
+                (string-append "timestamp <- \
+as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
+  as.numeric(Sys.getenv(\"SOURCE_DATE_EPOCH\"))\
+} else { " time "}, origin=\"1970-01-01\")\n")))
 
              ;; This library is installed using "install_package_description",
              ;; so we need to pass the "builtStamp" argument.
-- 
cgit v1.2.3


From f55aa0c7b72c6e4f08f77aa84e196895182860e7 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Fri, 9 Mar 2018 20:06:39 -0500
Subject: gnu: zsh: Fix CVE-2018-{7548,7549}.

* gnu/packages/patches/zsh-CVE-2018-7548.patch,
gnu/packages/patches/zsh-CVE-2018-7549.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/shells.scm (zsh)[source]: Use them.
---
 gnu/local.mk                                 |  4 +-
 gnu/packages/patches/zsh-CVE-2018-7548.patch | 48 ++++++++++++++++++++++++
 gnu/packages/patches/zsh-CVE-2018-7549.patch | 56 ++++++++++++++++++++++++++++
 gnu/packages/shells.scm                      |  2 +
 4 files changed, 109 insertions(+), 1 deletion(-)
 create mode 100644 gnu/packages/patches/zsh-CVE-2018-7548.patch
 create mode 100644 gnu/packages/patches/zsh-CVE-2018-7549.patch

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index d90d8a318d..fbf7b2a7c7 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1181,7 +1181,9 @@ dist_patch_DATA =						\
   %D%/packages/patches/xinetd-CVE-2013-4342.patch		\
   %D%/packages/patches/xmodmap-asprintf.patch 			\
   %D%/packages/patches/libyaml-CVE-2014-9130.patch 		\
-  %D%/packages/patches/zathura-plugindir-environment-variable.patch
+  %D%/packages/patches/zathura-plugindir-environment-variable.patch	\
+  %D%/packages/patches/zsh-CVE-2018-7548.patch			\
+  %D%/packages/patches/zsh-CVE-2018-7549.patch
 
 MISC_DISTRO_FILES =				\
   %D%/packages/ld-wrapper.in
diff --git a/gnu/packages/patches/zsh-CVE-2018-7548.patch b/gnu/packages/patches/zsh-CVE-2018-7548.patch
new file mode 100644
index 0000000000..1ee15fad73
--- /dev/null
+++ b/gnu/packages/patches/zsh-CVE-2018-7548.patch
@@ -0,0 +1,48 @@
+Fix CVE-2018-7548:
+
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-7548
+
+Patch copied from upstream source repository:
+
+https://sourceforge.net/p/zsh/code/ci/110b13e1090bc31ac1352b28adc2d02b6d25a102
+
+From 110b13e1090bc31ac1352b28adc2d02b6d25a102 Mon Sep 17 00:00:00 2001
+From: Joey Pabalinas <joeypabalinas@gmail.com>
+Date: Tue, 23 Jan 2018 22:28:08 -0800
+Subject: [PATCH] 42313: avoid null-pointer deref when using ${(PA)...} on an
+ empty array result
+
+---
+ ChangeLog   | 5 +++++
+ Src/subst.c | 2 +-
+ 2 files changed, 6 insertions(+), 1 deletion(-)
+
+#diff --git a/ChangeLog b/ChangeLog
+#index d2ba94afc..3037edda4 100644
+#--- a/ChangeLog
+#+++ b/ChangeLog
+#@@ -1,3 +1,8 @@
+#+2018-01-23  Barton E. Schaefer  <schaefer@zsh.org>
+#+
+#+       * Joey Pabalinas: 42313: Src/subst.c: avoid null-pointer deref
+#+       when using ${(PA)...} on an empty array result
+#+
+# 2018-01-23  Oliver Kiddle  <okiddle@yahoo.co.uk>
+# 
+#        * 42317: Completion/Linux/Command/_cryptsetup,
+diff --git a/Src/subst.c b/Src/subst.c
+index d027e3d83..a265a187e 100644
+--- a/Src/subst.c
++++ b/Src/subst.c
+@@ -2430,7 +2430,7 @@ paramsubst(LinkList l, LinkNode n, char **str, int qt, int pf_flags,
+ 		val = aval[0];
+ 		isarr = 0;
+ 	    }
+-	    s = dyncat(val, s);
++	    s = val ? dyncat(val, s) : dupstring(s);
+ 	    /* Now behave po-faced as if it was always like that... */
+ 	    subexp = 0;
+ 	    /*
+-- 
+2.16.2
+
diff --git a/gnu/packages/patches/zsh-CVE-2018-7549.patch b/gnu/packages/patches/zsh-CVE-2018-7549.patch
new file mode 100644
index 0000000000..abefcdf2f9
--- /dev/null
+++ b/gnu/packages/patches/zsh-CVE-2018-7549.patch
@@ -0,0 +1,56 @@
+Fix CVE-2018-7549:
+
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-7549
+
+Patch copied from upstream source repository:
+
+https://sourceforge.net/p/zsh/code/ci/c2cc8b0fbefc9868fa83537f5b6d90fc1ec438dd
+
+From c2cc8b0fbefc9868fa83537f5b6d90fc1ec438dd Mon Sep 17 00:00:00 2001
+From: Stephane Chazelas <stephane.chazelas@gmail.com>
+Date: Fri, 22 Dec 2017 22:17:09 +0000
+Subject: [PATCH] Avoid crash copying empty hash table.
+
+Visible with typeset -p.
+---
+ ChangeLog    |  2 ++
+ Src/params.c | 11 +++++++----
+ 2 files changed, 9 insertions(+), 4 deletions(-)
+
+#diff --git a/ChangeLog b/ChangeLog
+#index f74c26b88..e3628cfa7 100644
+#--- a/ChangeLog
+#+++ b/ChangeLog
+#@@ -1,5 +1,7 @@
+# 2018-01-04  Peter Stephenson  <p.stephenson@samsung.com>
+# 
+#+       * Stephane: 42159: Src/params.c: avoid crash copying empty hash table.
+#+
+#        * Sebastian: 42188: Src/Modules/system.c: It is necessary to
+#        close the lock descriptor in some failure cases.
+#
+diff --git a/Src/params.c b/Src/params.c
+index 31ff0445b..de7730ae7 100644
+--- a/Src/params.c
++++ b/Src/params.c
+@@ -549,10 +549,13 @@ scancopyparams(HashNode hn, UNUSED(int flags))
+ HashTable
+ copyparamtable(HashTable ht, char *name)
+ {
+-    HashTable nht = newparamtable(ht->hsize, name);
+-    outtable = nht;
+-    scanhashtable(ht, 0, 0, 0, scancopyparams, 0);
+-    outtable = NULL;
++    HashTable nht = 0;
++    if (ht) {
++	nht = newparamtable(ht->hsize, name);
++	outtable = nht;
++	scanhashtable(ht, 0, 0, 0, scancopyparams, 0);
++	outtable = NULL;
++    }
+     return nht;
+ }
+ 
+-- 
+2.16.2
+
diff --git a/gnu/packages/shells.scm b/gnu/packages/shells.scm
index f4a38b8779..685f6d2df4 100644
--- a/gnu/packages/shells.scm
+++ b/gnu/packages/shells.scm
@@ -300,6 +300,8 @@ history mechanism, job control and a C-like syntax.")
                          (string-append
                            "http://www.zsh.org/pub/old/zsh-" version
                            ".tar.gz")))
+              (patches (search-patches "zsh-CVE-2018-7548.patch"
+                                       "zsh-CVE-2018-7549.patch"))
               (sha256
                (base32
                 "1jdcfinzmki2w963msvsanv29vqqfmdfm4rncwpw0r3zqnrcsywm"))))
-- 
cgit v1.2.3


From 440b16290076b660347c2196a346a0538cb35577 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sat, 10 Mar 2018 22:55:17 +0200
Subject: gnu: enlightenment: Use 'loginctl' for system actions.

* gnu/packages/enlightenment.scm (enlightenment)[arguments]: Use
'loginctl' functions when powering off, sleeping, rebooting or
suspending the system.
---
 gnu/packages/enlightenment.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/enlightenment.scm b/gnu/packages/enlightenment.scm
index 8550a89640..a0bf841415 100644
--- a/gnu/packages/enlightenment.scm
+++ b/gnu/packages/enlightenment.scm
@@ -286,9 +286,10 @@ Libraries with some extra bells and whistles.")
                  (("/bin/mount") (string-append utils "/bin/mount"))
                  (("/bin/umount") (string-append utils "/bin/umount"))
                  (("/usr/bin/eject") (string-append utils "/bin/eject"))
-                 ; TODO: Replace suspend and hibernate also.
-                 (("/sbin/shutdown -h now") "/run/current-system/profile/sbin/halt")
-                 (("/sbin/shutdown -r now") "/run/current-system/profile/sbin/reboot"))
+                 (("/etc/acpi/sleep.sh force") "/run/current-system/profile/bin/loginctl suspend")
+                 (("/etc/acpi/hibernate.sh force") "/run/current-system/profile/bin/loginctl hibernate")
+                 (("/sbin/shutdown -h now") "/run/current-system/profile/bin/loginctl poweroff now")
+                 (("/sbin/shutdown -r now") "/run/current-system/profile/bin/loginctl reboot now"))
                #t))))))
     (native-inputs
      `(("gettext" ,gettext-minimal)
-- 
cgit v1.2.3


From 3c90c7ae37db57580f89e39468225d2901b2a513 Mon Sep 17 00:00:00 2001
From: David Thompson <dthompson2@worcester.edu>
Date: Sat, 10 Mar 2018 21:30:35 -0500
Subject: gnu: guile-syntax-highlight: Update to 0.1.

* gnu/packages/guile.scm (guile-syntax-highlight): Update to 0.1.
---
 gnu/packages/guile.scm | 48 +++++++++++++++++++-----------------------------
 1 file changed, 19 insertions(+), 29 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index bfcb32531f..d39285460b 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -2008,40 +2008,30 @@ manipulate repositories of the Git version control system.")
   (package-for-guile-2.0 guile-git))
 
 (define-public guile-syntax-highlight
-  (let ((commit "a047675e66861b647426372aa2ba7820f749616d")
-        (revision "0"))
-    (package
-      (name "guile-syntax-highlight")
-      (version (string-append "0.0." revision "."
-                              (string-take commit 7)))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "git://dthompson.us/guile-syntax-highlight.git")
-                      (commit commit)))
-                (file-name (string-append name "-" version "-checkout"))
-                (sha256
-                 (base32
-                  "1zjr6sg3n7xbdsliy45i39dqanxvcms58ayx36wxrz72zpq58vq3"))))
-      (build-system gnu-build-system)
-      (arguments
-       '(#:phases (modify-phases %standard-phases
-                    (add-after 'unpack 'bootstrap
-                      (lambda _
-                        (zero? (system* "sh" "bootstrap")))))))
-      (native-inputs
-       `(("autoconf" ,autoconf)
-         ("automake" ,automake)
-         ("pkg-config" ,pkg-config)))
-      (inputs
-       `(("guile" ,guile-2.2)))
+  (package
+    (name "guile-syntax-highlight")
+    (version "0.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://files.dthompson.us/"
+                                  "guile-syntax-highlight/"
+                                  "guile-syntax-highlight-"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "1p771kq15x83483m23bhah1sz6vkalg3drm7x279f4j1cxligkzi"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("guile" ,guile-2.2)))
       (synopsis "General-purpose syntax highlighter for GNU Guile")
       (description "Guile-syntax-highlight is a general-purpose syntax
 highlighting library for GNU Guile.  It can parse code written in various
 programming languages into a simple s-expression that can be converted to
 HTML (via SXML) or any other format for rendering.")
-      (home-page "http://dthompson.us/software/guile-syntax-highlight")
-      (license license:lgpl3+))))
+    (home-page "http://dthompson.us/projects/guile-syntax-highlight.html")
+    (license license:lgpl3+)))
 
 (define-public guile-sjson
   (package
-- 
cgit v1.2.3


From 907254e513b8b50b0440b21d4deb34e7c4722ceb Mon Sep 17 00:00:00 2001
From: David Thompson <dthompson2@worcester.edu>
Date: Sat, 10 Mar 2018 21:31:00 -0500
Subject: gnu: haunt: Update to 0.2.2.

* gnu/packages/guile.scm (haunt): Update to 0.2.2.
---
 gnu/packages/guile.scm | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index d39285460b..1e8aca1acf 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -1259,14 +1259,14 @@ Guile's foreign function interface.")
 (define-public haunt
   (package
     (name "haunt")
-    (version "0.2.1")
+    (version "0.2.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://files.dthompson.us/haunt/haunt-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1fpaf1vm6s7j13fs35barjh5yajcc2rc3pi8r7278wpgp4i2vs3w"))))
+                "0nm00krmqq4zmqi2irh35dbf2cn6al58s620hijmhfvhgvdqznlp"))))
     (build-system gnu-build-system)
     (arguments
      `(#:modules ((ice-9 match) (ice-9 ftw)
@@ -1283,12 +1283,15 @@ Guile's foreign function interface.")
                                     out "/share/guile/site")))
                         (match (scandir site)
                           (("." ".." version)
-                           (let ((modules (string-append site "/" version)))
+                           (let ((modules (string-append site "/" version))
+                                 (compiled-modules (string-append
+                                                    out "/lib/guile/" version
+                                                    "/site-ccache")))
                              (wrap-program (string-append bin "/haunt")
                                `("GUILE_LOAD_PATH" ":" prefix
                                  (,modules))
                                `("GUILE_LOAD_COMPILED_PATH" ":" prefix
-                                 (,modules)))
+                                 (,compiled-modules)))
                              #t)))))))))
     (native-inputs
      `(("pkg-config" ,pkg-config)
-- 
cgit v1.2.3


From 4f55b39fa7b33646b898031be48fed761ffda4ee Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 10 Mar 2018 00:08:12 +0100
Subject: gnu: archivemount: Update to 0.8.9.

* gnu/packages/linux.scm (archivemount): Update to 0.8.9.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 57e033f9b5..e30453ba2f 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -1758,7 +1758,7 @@ file system is as easy as logging into the server with an SSH client.")
 (define-public archivemount
   (package
     (name "archivemount")
-    (version "0.8.7")
+    (version "0.8.9")
     (source
      (origin
        (method url-fetch)
@@ -1766,7 +1766,7 @@ file system is as easy as logging into the server with an SSH client.")
                            "archivemount-" version ".tar.gz"))
        (sha256
         (base32
-         "1diiw6pnlnrnikn6l5ld92dx59lhrxjlqms8885vwbynsjl5q127"))))
+         "0v4si1ri6lhnq9q87gkx7fsh6lv6xz4bynknwndqncpvfp5cy1jg"))))
     (build-system gnu-build-system)
     (inputs `(("fuse", fuse)
               ("libarchive", libarchive)))
-- 
cgit v1.2.3


From 26cd470d3c568487550b82ae5776a024a14333d7 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 10 Mar 2018 23:24:54 +0100
Subject: gnu: git-remote-gcrypt: Update to 1.0.3.

* gnu/packages/version-control.scm (git-remote-gcrypt): Update to 1.0.3.
---
 gnu/packages/version-control.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index 209df2bb12..34c1852a22 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -473,7 +473,7 @@ to lock down your entire repository.")
 (define-public git-remote-gcrypt
   (package
    (name "git-remote-gcrypt")
-   (version "1.0.2")
+   (version "1.0.3")
    (source (origin
              (method git-fetch)
              (uri (git-reference
@@ -482,7 +482,7 @@ to lock down your entire repository.")
              (file-name (string-append name "-" version "-checkout"))
              (sha256
               (base32
-               "0kc6qi5gavziqlwnzpy7v4ah7yw860v3i8pyna6way0cfr0qnpr2"))))
+               "1vay3204729c7wajgn3nxf0s0hzwpdrw14pl6kd8w2ss25gvw2k1"))))
    (build-system trivial-build-system)
    (arguments
     `(#:modules ((guix build utils))
-- 
cgit v1.2.3


From 1bc11c5ddb3d5dde66da7d61d5fd6ac1ed20f502 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 10 Mar 2018 23:40:23 +0100
Subject: gnu: sssd: Update to 1.16.1.

* gnu/packages/sssd.scm (sssd): Update to 1.16.1.
---
 gnu/packages/sssd.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/sssd.scm b/gnu/packages/sssd.scm
index 70ea5fe9e2..28a364ebd5 100644
--- a/gnu/packages/sssd.scm
+++ b/gnu/packages/sssd.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -81,14 +81,14 @@ fundamental object types for C.")
 (define-public sssd
   (package
     (name "sssd")
-    (version "1.16.0")
+    (version "1.16.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://releases.pagure.org/SSSD/sssd/"
                                   "sssd-" version ".tar.gz"))
               (sha256
                (base32
-                "03wllgbxxz2zv14dcqr8d2xssppi7ibckh0rlky8gvsw6vjsd0f5"))))
+                "0vjh1c5960wh86zjsamdjhljls7bb5fz5jpcazgzrpmga5w6ggrd"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags
-- 
cgit v1.2.3


From 387428def11c59867eb528bcf622f3144617033a Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 11 Mar 2018 00:03:45 +0100
Subject: gnu: gambit-c: Update to 4.8.9.

* gnu/packages/scheme.scm (gambit-c): Update to 4.8.9.
---
 gnu/packages/scheme.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/scheme.scm b/gnu/packages/scheme.scm
index 8947509cb1..657ca875d5 100644
--- a/gnu/packages/scheme.scm
+++ b/gnu/packages/scheme.scm
@@ -519,7 +519,7 @@ of libraries.")
 (define-public gambit-c
   (package
     (name "gambit-c")
-    (version "4.8.8")
+    (version "4.8.9")
     (source
      (origin
        (method url-fetch)
@@ -529,7 +529,7 @@ of libraries.")
              (string-map (lambda (c) (if (char=? c #\.) #\_ c)) version)
              ".tgz"))
        (sha256
-        (base32 "1plw1id94mpg2c4y6q9z39ndcz1hbxfnp3i08szsg6794rasmgkk"))))
+        (base32 "16sg1s8myzxqpimj5ry6lfza0qfs157zj28bvmxwwgy89jd9m5v7"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags
-- 
cgit v1.2.3


From f2785bd657c55cd36f436b1f6ee1af5d72683162 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 10 Mar 2018 18:35:31 +0100
Subject: gnu: icedtea-8: Build "out" reproducibly.

Partially fixes <https://bugs.gnu.org/30730>.

* gnu/packages/java.scm (icedtea-8)[arguments]: Add phases
"patch-keystore" and "strip-jar-timestamps".
[source]: Also patch DIST_ID in "configure" script.
---
 gnu/packages/java.scm | 146 +++++++++++++++++++++++++++++---------------------
 1 file changed, 86 insertions(+), 60 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 5cc4a56f81..bb20b1d464 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -1591,7 +1591,8 @@ IcedTea build harness.")
                 (modules '((guix build utils)))
                 (snippet
                  '(begin
-                    (substitute* "acinclude.m4"
+                    (substitute* '("configure"
+                                   "acinclude.m4")
                       ;; Do not embed build time
                       (("(DIST_ID=\"Custom build).*$" _ prefix)
                        (string-append prefix "\"\n"))
@@ -1600,65 +1601,90 @@ IcedTea build harness.")
                        "DIST_NAME=\"guix\""))
                     #t))))
       (arguments
-       (substitute-keyword-arguments (package-arguments icedtea-7)
-         ((#:configure-flags flags)
-          `(let ((jdk (assoc-ref %build-inputs "jdk")))
-             `(;;"--disable-bootstrap"
-               "--enable-bootstrap"
-               "--enable-nss"
-               "--disable-downloading"
-               "--disable-system-pcsc"
-               "--disable-system-sctp"
-               "--disable-tests"      ;they are run in the check phase instead
-               "--with-openjdk-src-dir=./openjdk.src"
-               ,(string-append "--with-jdk-home=" jdk))))
-         ((#:phases phases)
-          `(modify-phases ,phases
-             (delete 'fix-x11-extension-include-path)
-             (delete 'patch-paths)
-             (delete 'set-additional-paths)
-             (delete 'patch-patches)
-             (add-after 'unpack 'patch-jni-libs
-               ;; Hardcode dynamically loaded libraries.
-               (lambda _
-                 (let* ((library-path (search-path-as-string->list
-                                       (getenv "LIBRARY_PATH")))
-                        (find-library (lambda (name)
-                                        (search-path
-                                         library-path
-                                         (string-append "lib" name ".so")))))
-                   (for-each
-                    (lambda (file)
-                      (catch 'decoding-error
-                        (lambda ()
-                          (substitute* file
-                            (("VERSIONED_JNI_LIB_NAME\\(\"(.*)\", \"(.*)\"\\)"
-                              _ name version)
-                             (format #f "\"~a\""  (find-library name)))
-                            (("JNI_LIB_NAME\\(\"(.*)\"\\)" _ name)
-                             (format #f "\"~a\"" (find-library name)))))
-                        (lambda _
-                          ;; Those are safe to skip.
-                          (format (current-error-port)
-                                  "warning: failed to substitute: ~a~%"
-                                  file))))
-                    (find-files "openjdk.src/jdk/src/solaris/native"
-                                "\\.c|\\.h"))
-                   #t)))
-             (replace 'install
-               (lambda* (#:key outputs #:allow-other-keys)
-                 (let ((doc (string-append (assoc-ref outputs "doc")
-                                           "/share/doc/icedtea"))
-                       (jre (assoc-ref outputs "out"))
-                       (jdk (assoc-ref outputs "jdk")))
-                   (copy-recursively "openjdk.build/docs" doc)
-                   (copy-recursively "openjdk.build/images/j2re-image" jre)
-                   (copy-recursively "openjdk.build/images/j2sdk-image" jdk)
-                   ;; Install the nss.cfg file to JRE to enable SSL/TLS
-                   ;; support via NSS.
-                   (copy-file (string-append jdk "/jre/lib/security/nss.cfg")
-                              (string-append jre "/lib/security/nss.cfg"))
-                   #t)))))))
+       `(#:imported-modules
+         ((guix build ant-build-system)
+          (guix build syscalls)
+          ,@%gnu-build-system-modules)
+         ,@(substitute-keyword-arguments (package-arguments icedtea-7)
+             ((#:modules modules)
+              `((guix build utils)
+                (guix build gnu-build-system)
+                ((guix build ant-build-system) #:prefix ant:)
+                (ice-9 match)
+                (ice-9 popen)
+                (srfi srfi-19)
+                (srfi srfi-26)))
+             ((#:configure-flags flags)
+              `(let ((jdk (assoc-ref %build-inputs "jdk")))
+                 `( ;;"--disable-bootstrap"
+                   "--enable-bootstrap"
+                   "--enable-nss"
+                   "--disable-downloading"
+                   "--disable-system-pcsc"
+                   "--disable-system-sctp"
+                   "--disable-tests"  ;they are run in the check phase instead
+                   "--with-openjdk-src-dir=./openjdk.src"
+                   ,(string-append "--with-jdk-home=" jdk))))
+             ((#:phases phases)
+              `(modify-phases ,phases
+                 (delete 'fix-x11-extension-include-path)
+                 (delete 'patch-paths)
+                 (delete 'set-additional-paths)
+                 (delete 'patch-patches)
+                 ;; Prevent the keytool from recording the current time when
+                 ;; adding certificates at build time.
+                 (add-after 'unpack 'patch-keystore
+                   (lambda _
+                     (substitute* "openjdk.src/jdk/src/share/classes/sun/security/provider/JavaKeyStore.java"
+                       (("date = new Date\\(\\);")
+                        "\
+date = (System.getenv(\"SOURCE_DATE_EPOCH\") != null) ?\
+new Date(Long.parseLong(System.getenv(\"SOURCE_DATE_EPOCH\"))) :\
+new Date();"))
+                     #t))
+                 (add-after 'unpack 'patch-jni-libs
+                   ;; Hardcode dynamically loaded libraries.
+                   (lambda _
+                     (let* ((library-path (search-path-as-string->list
+                                           (getenv "LIBRARY_PATH")))
+                            (find-library (lambda (name)
+                                            (search-path
+                                             library-path
+                                             (string-append "lib" name ".so")))))
+                       (for-each
+                        (lambda (file)
+                          (catch 'decoding-error
+                            (lambda ()
+                              (substitute* file
+                                (("VERSIONED_JNI_LIB_NAME\\(\"(.*)\", \"(.*)\"\\)"
+                                  _ name version)
+                                 (format #f "\"~a\""  (find-library name)))
+                                (("JNI_LIB_NAME\\(\"(.*)\"\\)" _ name)
+                                 (format #f "\"~a\"" (find-library name)))))
+                            (lambda _
+                              ;; Those are safe to skip.
+                              (format (current-error-port)
+                                      "warning: failed to substitute: ~a~%"
+                                      file))))
+                        (find-files "openjdk.src/jdk/src/solaris/native"
+                                    "\\.c|\\.h"))
+                       #t)))
+                 (replace 'install
+                   (lambda* (#:key outputs #:allow-other-keys)
+                     (let ((doc (string-append (assoc-ref outputs "doc")
+                                               "/share/doc/icedtea"))
+                           (jre (assoc-ref outputs "out"))
+                           (jdk (assoc-ref outputs "jdk")))
+                       (copy-recursively "openjdk.build/docs" doc)
+                       (copy-recursively "openjdk.build/images/j2re-image" jre)
+                       (copy-recursively "openjdk.build/images/j2sdk-image" jdk)
+                       ;; Install the nss.cfg file to JRE to enable SSL/TLS
+                       ;; support via NSS.
+                       (copy-file (string-append jdk "/jre/lib/security/nss.cfg")
+                                  (string-append jre "/lib/security/nss.cfg"))
+                       #t)))
+                 (add-after 'install 'strip-jar-timestamps
+                   (assoc-ref ant:%standard-phases 'strip-jar-timestamps)))))))
       (native-inputs
        `(("jdk" ,icedtea-7 "jdk")
          ("openjdk-src"
-- 
cgit v1.2.3


From 531afc8a892512487251a03be24d9833b86179f1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Mar 2018 19:52:52 +0100
Subject: gnu: Add pigx-chipseq.

* gnu/packages/bioinformatics.scm (pigx-chipseq): New variable.
---
 gnu/packages/bioinformatics.scm | 66 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 66 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 14e2a0daac..50d3568987 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12725,3 +12725,69 @@ and a configuration file which describes the experiment.  In addition to
 quality control of the experiment, the pipeline produces a differential
 expression report comparing samples in an easily configurable manner.")
     (license license:gpl3+)))
+
+(define-public pigx-chipseq
+  (package
+    (name "pigx-chipseq")
+    (version "0.0.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/"
+                                  "releases/download/v" version
+                                  "/pigx_chipseq-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1jliwhifnjgl9x0z730bzpxswi2s84fyg5y8cagbyzpw509452f5"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'wrap-executable
+           ;; Make sure the executable finds all R modules.
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (wrap-program (string-append out "/bin/pigx-chipseq")
+                 `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))
+                 `("PYTHONPATH"  ":" = (,(getenv "PYTHONPATH")))))
+             #t)))))
+    (inputs
+     `(("r-minimal" ,r-minimal)
+       ("r-argparser" ,r-argparser)
+       ("r-chipseq" ,r-chipseq)
+       ("r-data-table" ,r-data-table)
+       ("r-genomation" ,r-genomation)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-rcas" ,r-rcas)
+       ("r-stringr" ,r-stringr)
+       ("r-jsonlite" ,r-jsonlite)
+       ("r-heatmaply" ,r-heatmaply)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-plotly" ,r-plotly)
+       ("python-wrapper" ,python-wrapper)
+       ("python-pyyaml" ,python-pyyaml)
+       ("snakemake" ,snakemake)
+       ("macs" ,macs)
+       ("multiqc" ,multiqc)
+       ("perl" ,perl)
+       ("ghc-pandoc" ,ghc-pandoc)
+       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
+       ("fastqc" ,fastqc)
+       ("bowtie" ,bowtie)
+       ("idr" ,idr)
+       ("snakemake" ,snakemake)
+       ("samtools" ,samtools)
+       ("bedtools" ,bedtools)
+       ("kentutils" ,kentutils)))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)))
+    (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
+    (synopsis "Analysis pipeline for ChIP sequencing experiments")
+    (description "PiGX ChIPseq is an analysis pipeline for preprocessing, peak
+calling and reporting for ChIP sequencing experiments.  It is easy to use and
+produces high quality reports.  The inputs are reads files from the sequencing
+experiment, and a configuration file which describes the experiment.  In
+addition to quality control of the experiment, the pipeline enables to set up
+multiple peak calling analysis and allows the generation of a UCSC track hub
+in an easily configurable manner.")
+    (license license:gpl3+)))
-- 
cgit v1.2.3


From fb94174fc39cfbdddf23aa58a12b1ee62674122d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Mar 2018 19:53:11 +0100
Subject: gnu: Add pigx-bsseq.

* gnu/packages/bioinformatics.scm (pigx-bsseq): New variable.
---
 gnu/packages/bioinformatics.scm | 64 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 64 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 50d3568987..567dd2c24b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12791,3 +12791,67 @@ addition to quality control of the experiment, the pipeline enables to set up
 multiple peak calling analysis and allows the generation of a UCSC track hub
 in an easily configurable manner.")
     (license license:gpl3+)))
+
+(define-public pigx-bsseq
+  (package
+    (name "pigx-bsseq")
+    (version "0.0.5")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/"
+                                  "releases/download/v" version
+                                  "/pigx_bsseq-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1h8ma99vi7hs83nafvjpq8jmaq9977j3n11c4zd95hai0cf7zxmp"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'set-timezone
+           ;; The readr package is picky about timezones.
+           (lambda* (#:key inputs #:allow-other-keys)
+             (setenv "TZ" "UTC+1")
+             (setenv "TZDIR"
+                     (string-append (assoc-ref inputs "tzdata")
+                                    "/share/zoneinfo"))
+             #t))
+         (add-after 'install 'wrap-executable
+           ;; Make sure the executable finds all R modules.
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (wrap-program (string-append out "/bin/pigx-bsseq")
+                 `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))
+                 `("PYTHONPATH"  ":" = (,(getenv "PYTHONPATH")))))
+             #t)))))
+    (native-inputs
+     `(("tzdata" ,tzdata)))
+    (inputs
+     `(("r-minimal" ,r-minimal)
+       ("r-annotationhub" ,r-annotationhub)
+       ("r-dt" ,r-dt)
+       ("r-genomation" ,r-genomation)
+       ("r-methylkit" ,r-methylkit)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-rmarkdown" ,r-rmarkdown)
+       ("r-bookdown" ,r-bookdown)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-ggbio" ,r-ggbio)
+       ("ghc-pandoc" ,ghc-pandoc)
+       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
+       ("python-wrapper" ,python-wrapper)
+       ("python-pyyaml" ,python-pyyaml)
+       ("snakemake" ,snakemake)
+       ("bismark" ,bismark)
+       ("fastqc" ,fastqc)
+       ("bowtie" ,bowtie)
+       ("trim-galore" ,trim-galore)
+       ("cutadapt" ,cutadapt)
+       ("samtools" ,samtools)))
+    (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
+    (synopsis "Bisulfite sequencing pipeline from fastq to methylation reports")
+    (description "PiGx BSseq is a data processing pipeline for raw fastq read
+data of bisulfite experiments; it produces reports on aggregate methylation
+and coverage and can be used to produce information on differential
+methylation and segmentation.")
+    (license license:gpl3+)))
-- 
cgit v1.2.3


From bfc007e13e055ca2d535a02aa7fc4ba7f6183150 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 11 Mar 2018 20:02:10 +0100
Subject: gnu: java-hamcrest-all: Build with icedtea-8.

* gnu/packages/java.scm (java-hamcrest-all)[arguments]: Build with icedtea-8;
do not disable tests.
[inputs]: Remove java-hamcrest-core.
---
 gnu/packages/java.scm | 49 ++++++++++++++++++++-----------------------------
 1 file changed, 20 insertions(+), 29 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index bb20b1d464..43a3a62889 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -3886,39 +3886,30 @@ The jMock library
   (package (inherit java-hamcrest-core)
     (name "java-hamcrest-all")
     (arguments
-     (substitute-keyword-arguments (package-arguments java-hamcrest-core)
-       ;; FIXME: a unit test fails because org.hamcrest.SelfDescribing is not
-       ;; found, although it is part of the hamcrest-core library that has
-       ;; just been built.
-       ;;
-       ;; Fixing this one test is insufficient, though, and upstream confirmed
-       ;; that the latest hamcrest release fails its unit tests when built
-       ;; with Java 7.  See https://github.com/hamcrest/JavaHamcrest/issues/30
-       ((#:tests? _) #f)
-       ((#:build-target _) "bigjar")
-       ((#:phases phases)
-        `(modify-phases ,phases
-           ;; Some build targets override the classpath, so we need to patch
-           ;; the build.xml to ensure that required dependencies are on the
-           ;; classpath.
-           (add-after 'unpack 'patch-classpath-for-integration
-             (lambda* (#:key inputs #:allow-other-keys)
-               (substitute* "build.xml"
-                 ((" build/hamcrest-library-\\$\\{version\\}.jar" line)
-                  (string-join
-                   (cons line
-                         (append
-                          (find-files (assoc-ref inputs "java-hamcrest-core") "\\.jar$")
-                          (find-files (assoc-ref inputs "java-junit") "\\.jar$")
-                          (find-files (assoc-ref inputs "java-jmock") "\\.jar$")
-                          (find-files (assoc-ref inputs "java-easymock") "\\.jar$")))
-                   ";")))
-               #t))))))
+     `(#:jdk ,icedtea-8
+       ,@(substitute-keyword-arguments (package-arguments java-hamcrest-core)
+           ((#:build-target _) "bigjar")
+           ((#:phases phases)
+            `(modify-phases ,phases
+               ;; Some build targets override the classpath, so we need to patch
+               ;; the build.xml to ensure that required dependencies are on the
+               ;; classpath.
+               (add-after 'unpack 'patch-classpath-for-integration
+                 (lambda* (#:key inputs #:allow-other-keys)
+                   (substitute* "build.xml"
+                     ((" build/hamcrest-library-\\$\\{version\\}.jar" line)
+                      (string-join
+                       (cons line
+                             (append
+                              (find-files (assoc-ref inputs "java-junit") "\\.jar$")
+                              (find-files (assoc-ref inputs "java-jmock") "\\.jar$")
+                              (find-files (assoc-ref inputs "java-easymock") "\\.jar$")))
+                       ";")))
+                   #t)))))))
     (inputs
      `(("java-junit" ,java-junit)
        ("java-jmock" ,java-jmock-1)
        ("java-easymock" ,java-easymock)
-       ("java-hamcrest-core" ,java-hamcrest-core)
        ,@(package-inputs java-hamcrest-core)))))
 
 (define-public java-jopt-simple
-- 
cgit v1.2.3


From 594bd3a08aeac24cf4939a4f06f2551ff8f61167 Mon Sep 17 00:00:00 2001
From: Gábor Boskovits <boskovits@gmail.com>
Date: Sat, 10 Mar 2018 11:45:36 +0100
Subject: gnu: java-jeromq: Fix tests.

* gnu/packages/patches/java-jeromq-fix-tests.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/java.scm (java-jeromq)[source](patches): Add it.
[arguments](#test-exclude): Disable more failing tests.
---
 gnu/local.mk                                     |   1 +
 gnu/packages/java.scm                            |  11 +-
 gnu/packages/patches/java-jeromq-fix-tests.patch | 253 +++++++++++++++++++++++
 3 files changed, 263 insertions(+), 2 deletions(-)
 create mode 100644 gnu/packages/patches/java-jeromq-fix-tests.patch

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index fbf7b2a7c7..5c95cdae21 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -785,6 +785,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/intltool-perl-compatibility.patch	\
   %D%/packages/patches/isl-0.11.1-aarch64-support.patch	\
   %D%/packages/patches/jacal-fix-texinfo.patch			\
+  %D%/packages/patches/java-jeromq-fix-tests.patch		\
   %D%/packages/patches/java-powermock-fix-java-files.patch		\
   %D%/packages/patches/java-xerces-bootclasspath.patch	\
   %D%/packages/patches/java-xerces-build_dont_unzip.patch	\
diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 43a3a62889..bdfd3fd41b 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -8578,7 +8578,8 @@ protocol-independent framework to build mail and messaging applications.")
               (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "1gxkp7lv2ahymgrqdw94ncq54bmp4m4sw5m1x9gkp7l5bxn0xsyj"))))
+                "1gxkp7lv2ahymgrqdw94ncq54bmp4m4sw5m1x9gkp7l5bxn0xsyj"))
+              (patches (search-patches "java-jeromq-fix-tests.patch"))))
     (build-system ant-build-system)
     (arguments
      `(#:jar-name "java-jeromq.jar"
@@ -8592,7 +8593,13 @@ protocol-independent framework to build mail and messaging applications.")
          ;; Failures
          "**/DealerSpecTest.java"
          "**/CustomDecoderTest.java"
-         "**/CustomEncoderTest.java")))
+         "**/CustomEncoderTest.java"
+         "**/ConnectRidTest.java"
+         "**/ReqSpecTest.java"
+         "**/PushPullSpecTest.java"
+         "**/PubSubHwmTest.java"
+         "**/RouterSpecTest.java"
+         "**/ProxyTest.java")))
     (inputs
      `(("java-jnacl" ,java-jnacl)))
     (native-inputs
diff --git a/gnu/packages/patches/java-jeromq-fix-tests.patch b/gnu/packages/patches/java-jeromq-fix-tests.patch
new file mode 100644
index 0000000000..5466b92707
--- /dev/null
+++ b/gnu/packages/patches/java-jeromq-fix-tests.patch
@@ -0,0 +1,253 @@
+From 5803aadd3f209eba1ffbb2cf7bf16778019dbee1 Mon Sep 17 00:00:00 2001
+From: fredoboulo <fredoboulo@users.noreply.github.com>
+Date: Fri, 23 Feb 2018 23:55:57 +0100
+Subject: [PATCH] Fix #524 : V1 and V2 protocol downgrades handle received data
+ in handshake buffer
+
+This patch is upstream pull request, see:
+https://gihub.com/zeromq/jeromq/pull/527.
+
+It is merged on commit c2afa9c, and we can drop it on the
+0.4.4 release.
+
+---
+ src/main/java/zmq/io/StreamEngine.java            | 21 ++++++++++--
+ src/test/java/zmq/io/AbstractProtocolVersion.java | 41 +++++++++++++----------
+ src/test/java/zmq/io/V0ProtocolTest.java          | 12 +++++++
+ src/test/java/zmq/io/V1ProtocolTest.java          | 16 +++++++--
+ src/test/java/zmq/io/V2ProtocolTest.java          | 16 +++++++--
+ 5 files changed, 81 insertions(+), 25 deletions(-)
+
+diff --git a/src/main/java/zmq/io/StreamEngine.java b/src/main/java/zmq/io/StreamEngine.java
+index b8933c92..fe2f2d8d 100644
+--- a/src/main/java/zmq/io/StreamEngine.java
++++ b/src/main/java/zmq/io/StreamEngine.java
+@@ -816,9 +816,7 @@ private boolean handshake()
+             assert (bufferSize == headerSize);
+ 
+             //  Make sure the decoder sees the data we have already received.
+-            greetingRecv.flip();
+-            inpos = greetingRecv;
+-            insize = greetingRecv.limit();
++            decodeDataAfterHandshake(0);
+ 
+             //  To allow for interoperability with peers that do not forward
+             //  their subscriptions, we inject a phantom subscription message
+@@ -846,6 +844,8 @@ else if (greetingRecv.get(revisionPos) == Protocol.V1.revision) {
+             }
+             encoder = new V1Encoder(errno, Config.OUT_BATCH_SIZE.getValue());
+             decoder = new V1Decoder(errno, Config.IN_BATCH_SIZE.getValue(), options.maxMsgSize, options.allocator);
++
++            decodeDataAfterHandshake(V2_GREETING_SIZE);
+         }
+         else if (greetingRecv.get(revisionPos) == Protocol.V2.revision) {
+             //  ZMTP/2.0 framing.
+@@ -859,6 +859,8 @@ else if (greetingRecv.get(revisionPos) == Protocol.V2.revision) {
+             }
+             encoder = new V2Encoder(errno, Config.OUT_BATCH_SIZE.getValue());
+             decoder = new V2Decoder(errno, Config.IN_BATCH_SIZE.getValue(), options.maxMsgSize, options.allocator);
++
++            decodeDataAfterHandshake(V2_GREETING_SIZE);
+         }
+         else {
+             zmtpVersion = Protocol.V3;
+@@ -904,6 +906,19 @@ else if (greetingRecv.get(revisionPos) == Protocol.V2.revision) {
+         return true;
+     }
+ 
++    private void decodeDataAfterHandshake(int greetingSize)
++    {
++        final int pos = greetingRecv.position();
++        if (pos > greetingSize) {
++            // data is present after handshake
++            greetingRecv.position(greetingSize).limit(pos);
++
++            //  Make sure the decoder sees this extra data.
++            inpos = greetingRecv;
++            insize = greetingRecv.remaining();
++        }
++    }
++
+     private Msg identityMsg()
+     {
+         Msg msg = new Msg(options.identitySize);
+diff --git a/src/test/java/zmq/io/AbstractProtocolVersion.java b/src/test/java/zmq/io/AbstractProtocolVersion.java
+index e60db403..aa06b4a7 100644
+--- a/src/test/java/zmq/io/AbstractProtocolVersion.java
++++ b/src/test/java/zmq/io/AbstractProtocolVersion.java
+@@ -18,15 +18,18 @@
+ import zmq.SocketBase;
+ import zmq.ZError;
+ import zmq.ZMQ;
++import zmq.ZMQ.Event;
+ import zmq.util.Utils;
+ 
+ public abstract class AbstractProtocolVersion
+ {
++    protected static final int REPETITIONS = 1000;
++
+     static class SocketMonitor extends Thread
+     {
+-        private final Ctx             ctx;
+-        private final String          monitorAddr;
+-        private final List<ZMQ.Event> events = new ArrayList<>();
++        private final Ctx         ctx;
++        private final String      monitorAddr;
++        private final ZMQ.Event[] events = new ZMQ.Event[1];
+ 
+         public SocketMonitor(Ctx ctx, String monitorAddr)
+         {
+@@ -41,15 +44,15 @@ public void run()
+             boolean rc = s.connect(monitorAddr);
+             assertThat(rc, is(true));
+             // Only some of the exceptional events could fire
+-            while (true) {
+-                ZMQ.Event event = ZMQ.Event.read(s);
+-                if (event == null && s.errno() == ZError.ETERM) {
+-                    break;
+-                }
+-                assertThat(event, notNullValue());
+-
+-                events.add(event);
++
++            ZMQ.Event event = ZMQ.Event.read(s);
++            if (event == null && s.errno() == ZError.ETERM) {
++                s.close();
++                return;
+             }
++            assertThat(event, notNullValue());
++
++            events[0] = event;
+             s.close();
+         }
+     }
+@@ -69,11 +72,12 @@ public void run()
+         boolean rc = ZMQ.setSocketOption(receiver, ZMQ.ZMQ_LINGER, 0);
+         assertThat(rc, is(true));
+ 
+-        SocketMonitor monitor = new SocketMonitor(ctx, "inproc://monitor");
+-        monitor.start();
+         rc = ZMQ.monitorSocket(receiver, "inproc://monitor", ZMQ.ZMQ_EVENT_HANDSHAKE_PROTOCOL);
+         assertThat(rc, is(true));
+ 
++        SocketMonitor monitor = new SocketMonitor(ctx, "inproc://monitor");
++        monitor.start();
++
+         rc = ZMQ.bind(receiver, host);
+         assertThat(rc, is(true));
+ 
+@@ -81,17 +85,18 @@ public void run()
+         OutputStream out = sender.getOutputStream();
+         for (ByteBuffer raw : raws) {
+             out.write(raw.array());
+-            ZMQ.msleep(100);
+         }
+ 
+         Msg msg = ZMQ.recv(receiver, 0);
+         assertThat(msg, notNullValue());
+         assertThat(new String(msg.data(), ZMQ.CHARSET), is(payload));
+ 
+-        ZMQ.msleep(500);
+-        assertThat(monitor.events.size(), is(1));
+-        assertThat(monitor.events.get(0).event, is(ZMQ.ZMQ_EVENT_HANDSHAKE_PROTOCOL));
+-        assertThat((Integer) monitor.events.get(0).arg, is(version));
++        monitor.join();
++
++        final Event event = monitor.events[0];
++        assertThat(event, notNullValue());
++        assertThat(event.event, is(ZMQ.ZMQ_EVENT_HANDSHAKE_PROTOCOL));
++        assertThat((Integer) event.arg, is(version));
+ 
+         InputStream in = sender.getInputStream();
+         byte[] data = new byte[255];
+diff --git a/src/test/java/zmq/io/V0ProtocolTest.java b/src/test/java/zmq/io/V0ProtocolTest.java
+index bd547d23..1a5b7aef 100644
+--- a/src/test/java/zmq/io/V0ProtocolTest.java
++++ b/src/test/java/zmq/io/V0ProtocolTest.java
+@@ -10,6 +10,18 @@
+ 
+ public class V0ProtocolTest extends AbstractProtocolVersion
+ {
++    @Test
++    public void testFixIssue524() throws IOException, InterruptedException
++    {
++        for (int idx = 0; idx < REPETITIONS; ++idx) {
++            if (idx % 100 == 0) {
++                System.out.print(idx + " ");
++            }
++            testProtocolVersion0short();
++        }
++        System.out.println();
++    }
++
+     @Test(timeout = 2000)
+     public void testProtocolVersion0short() throws IOException, InterruptedException
+     {
+diff --git a/src/test/java/zmq/io/V1ProtocolTest.java b/src/test/java/zmq/io/V1ProtocolTest.java
+index e1045f34..764159d0 100644
+--- a/src/test/java/zmq/io/V1ProtocolTest.java
++++ b/src/test/java/zmq/io/V1ProtocolTest.java
+@@ -10,7 +10,19 @@
+ 
+ public class V1ProtocolTest extends AbstractProtocolVersion
+ {
+-    @Test(timeout = 2000)
++    @Test
++    public void testFixIssue524() throws IOException, InterruptedException
++    {
++        for (int idx = 0; idx < REPETITIONS; ++idx) {
++            if (idx % 100 == 0) {
++                System.out.print(idx + " ");
++            }
++            testProtocolVersion1short();
++        }
++        System.out.println();
++    }
++
++    @Test
+     public void testProtocolVersion1short() throws IOException, InterruptedException
+     {
+         List<ByteBuffer> raws = raws(0);
+@@ -25,7 +37,7 @@ public void testProtocolVersion1short() throws IOException, InterruptedException
+         assertProtocolVersion(1, raws, "abcdefg");
+     }
+ 
+-    @Test(timeout = 2000)
++    @Test
+     public void testProtocolVersion1long() throws IOException, InterruptedException
+     {
+         List<ByteBuffer> raws = raws(0);
+diff --git a/src/test/java/zmq/io/V2ProtocolTest.java b/src/test/java/zmq/io/V2ProtocolTest.java
+index d5e64bce..7fda31bc 100644
+--- a/src/test/java/zmq/io/V2ProtocolTest.java
++++ b/src/test/java/zmq/io/V2ProtocolTest.java
+@@ -21,7 +21,19 @@ protected ByteBuffer identity()
+                 .put((byte) 0);
+     }
+ 
+-    @Test(timeout = 2000)
++    @Test
++    public void testFixIssue524() throws IOException, InterruptedException
++    {
++        for (int idx = 0; idx < REPETITIONS; ++idx) {
++            if (idx % 100 == 0) {
++                System.out.print(idx + " ");
++            }
++            testProtocolVersion2short();
++        }
++        System.out.println();
++    }
++
++    @Test
+     public void testProtocolVersion2short() throws IOException, InterruptedException
+     {
+         List<ByteBuffer> raws = raws(1);
+@@ -38,7 +50,7 @@ public void testProtocolVersion2short() throws IOException, InterruptedException
+         assertProtocolVersion(2, raws, "abcdefg");
+     }
+ 
+-    @Test(timeout = 2000)
++    @Test
+     public void testProtocolVersion2long() throws IOException, InterruptedException
+     {
+         List<ByteBuffer> raws = raws(1);
-- 
cgit v1.2.3


From b37f005c6ba0bfddb2069ed8523eaa5cd9910531 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 10 Mar 2018 05:20:05 +0100
Subject: gnu: python-tqdm: Update to 4.19.6.

* gnu/packages/python.scm (python-tqdm): Update to 4.19.6.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index c454539fef..968ef32e30 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -12080,14 +12080,14 @@ ignoring formatting changes.")
 (define-public python-tqdm
   (package
     (name "python-tqdm")
-    (version "4.19.5")
+    (version "4.19.6")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "tqdm" version))
          (sha256
            (base32
-             "0xvkffm77nqckk29xjy5fkqvig5b97vk7nzafp3cn36w4zqyccnz"))))
+             "1pw0ngm0zn9papdmkwipi3yih5c3di6d0w849bdmrraq4d2d9h2y"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-flake8" ,python-flake8)
-- 
cgit v1.2.3


From 4b61374b1b6601d36a68bbbdbab47bce06cee6ac Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 10 Mar 2018 06:01:11 +0100
Subject: gnu: python-colorama: Update to 0.3.9.

* gnu/packages/python.scm (python-colorama): Update to 0.3.9.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 968ef32e30..aab2d3082a 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -7407,14 +7407,14 @@ concurrent.futures package from Python 3.2")
 (define-public python-colorama
   (package
    (name "python-colorama")
-   (version "0.3.7")
+   (version "0.3.9")
    (source
     (origin
      (method url-fetch)
      (uri (pypi-uri "colorama" version))
      (sha256
       (base32
-       "0avqkn6362v7k2kg3afb35g4sfdvixjgy890clip4q174p9whhz0"))))
+       "1wd1szk0z3073ghx26ynw43gnc140ibln1safgsis6s6z3s25ss8"))))
    (build-system python-build-system)
    (synopsis "Colored terminal text rendering for Python")
    (description "Colorama is a Python library for rendering colored terminal
-- 
cgit v1.2.3


From e5c98075f240343c6b611f42926cde52b41a05f1 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 10 Mar 2018 16:16:48 +0100
Subject: gnu: python-rply: Update to 0.7.5.

* gnu/packages/python.scm (python-rply): Update to 0.7.5.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index aab2d3082a..e0d88f094e 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -7231,13 +7231,13 @@ Abstract Syntax Tree.")
 (define-public python-rply
   (package
     (name "python-rply")
-    (version "0.7.4")
+    (version "0.7.5")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "rply" version))
               (sha256
                (base32
-                "12rp1d9ba7nvd5rhaxi6xzx1rm67r1k1ylsrkzhpwnphqpb06cvj"))))
+                "0lv428895zxsz43968qx0q9bimwqnfykndz4dpjbq515w2gvzhjh"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-appdirs" ,python-appdirs)))
-- 
cgit v1.2.3


From cd5b6816f84fd3dfb58b9c345d0e051e0fa181ff Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 10 Mar 2018 16:19:17 +0100
Subject: gnu: python-ly: Update to 0.9.5.

* gnu/packages/python.scm (python-ly): Update to 0.9.5.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index e0d88f094e..1c9848e3da 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -5766,7 +5766,7 @@ from an XML-based format.")
 (define-public python-ly
   (package
     (name "python-ly")
-    (version "0.9.4")
+    (version "0.9.5")
     (source
      (origin
        (method url-fetch)
@@ -5775,7 +5775,7 @@ from an XML-based format.")
                            "/python-ly-" version ".tar.gz"))
        (sha256
         (base32
-         "0g6n288l83sfwavxh1aryi0aqvsr3sp7v6f903mckwqa4scpky62"))))
+         "0x98dv7p8mg26p4816yy8hz4f34zf6hpnnfmr56msgh9jnsm2qfl"))))
     (build-system python-build-system)
     (arguments
      ;; FIXME: Some tests need network access.
-- 
cgit v1.2.3


From 8a19a81768027ef2762b9f0ed68ca2849a7b180f Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 10 Mar 2018 16:20:12 +0100
Subject: gnu: python-jmespath: Update to 0.9.3.

* gnu/packages/python.scm (python-jmespath): Update to 0.9.3.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 1c9848e3da..828beba495 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -7510,14 +7510,14 @@ servers.")
 (define-public python-jmespath
   (package
    (name "python-jmespath")
-   (version "0.9.0")
+   (version "0.9.3")
    (source
     (origin
      (method url-fetch)
      (uri (pypi-uri "jmespath" version))
      (sha256
       (base32
-       "0g9xvl69y7nr3w7ag4fsp6sm4fqf6vrqjw7504x2hzrrsh3ampq8"))))
+       "0r7wc7fsxmlwzxx9j1j7rms06c6xs6d4sysirdhz1jk2mb4x90ba"))))
    (build-system python-build-system)
    (native-inputs
     `(("python-nose" ,python-nose)))
-- 
cgit v1.2.3


From 47772a4e3b2ffe6cde85362911f61fc03ff4d491 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 10 Mar 2018 16:36:07 +0100
Subject: gnu: python-pycryptodome: Update to 3.5.1.

* gnu/packages/python-crypto.scm (python-pycryptodome): Update to 3.5.1.
---
 gnu/packages/python-crypto.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm
index b898f088be..b4f75e5997 100644
--- a/gnu/packages/python-crypto.scm
+++ b/gnu/packages/python-crypto.scm
@@ -720,14 +720,14 @@ protocol (Javascript Object Signing and Encryption).")
 (define-public python-pycryptodome
   (package
     (name "python-pycryptodome")
-    (version "3.4.7")
+    (version "3.5.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pycryptodome" version))
        (sha256
         (base32
-         "1xrsd6ql4w0ypkxnsg3fivs3r3z6dd93x44lhvam7jzh3gixzn0q"))))
+         "15mc1h5ij1b6hcqvb048kb4k0ip64n2ky0zz0rml2s78ylv7g5dp"))))
     (build-system python-build-system)
     (home-page "https://www.pycryptodome.org")
     (synopsis "Cryptographic library for Python")
-- 
cgit v1.2.3


From b9d84721238d8d6de074177fc61786f846de823b Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 10 Mar 2018 16:40:27 +0100
Subject: gnu: python-tblib: Update to 1.3.2.

* gnu/packages/python.scm (python-tblib): Update to 1.3.2.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 828beba495..de3e659d84 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -8609,12 +8609,12 @@ own code, responding to click events and updating clock every second.")
 (define-public python-tblib
   (package
     (name "python-tblib")
-    (version "1.3.0")
+    (version "1.3.2")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "tblib" version))
               (sha256 (base32
-                       "02iahfkfa927hb4jq2bak36ldihwapzacfiq5lyxg8llwn98a1yi"))))
+                       "1rsg8h069kqgncyv8fgzyj6qflk6j10cb78pa5jk34ixwq044vj3"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
-- 
cgit v1.2.3


From 0fe227350621c4bc36db8a05838875d11f7372eb Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 10 Mar 2018 16:53:54 +0100
Subject: gnu: python-markdown: Update to 2.6.11.

* gnu/packages/python.scm (python-markdown): Update to 2.6.11.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index de3e659d84..dce67be755 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -5580,14 +5580,14 @@ Python.")
 (define-public python-markdown
   (package
     (name "python-markdown")
-    (version "2.6.8")
+    (version "2.6.11")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "Markdown" version))
        (sha256
         (base32
-         "0cqfhr1km2s5d8jm6hbwgkrrj9hvkjf2gab3s2axlrw1clgaij0a"))))
+         "108g80ryzykh8bj0i7jfp71510wrcixdi771lf2asyghgyf8cmm8"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
-- 
cgit v1.2.3


From 6de86fd5aa59302b027d57c5827755280de07576 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 10 Mar 2018 23:20:08 +0100
Subject: gnu: python-pyaes: Update to 1.6.1.

* gnu/packages/python-crypto.scm (python-pyaes): Update to 1.6.1.
---
 gnu/packages/python-crypto.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm
index b4f75e5997..701e23c2ac 100644
--- a/gnu/packages/python-crypto.scm
+++ b/gnu/packages/python-crypto.scm
@@ -510,14 +510,14 @@ faster ones are not available.")
 (define-public python-pyaes
   (package
     (name "python-pyaes")
-    (version "1.6.0")
+    (version "1.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pyaes" version))
        (sha256
         (base32
-         "0bp9bjqy1n6ij1zb86wz9lqa1dhla8qr1d7w2kxyn7jbj56sbmcw"))))
+         "13vdaff15k0jyfcss4b4xvfgm8xyv0nrbyw5n1qc7lrqbi0b3h82"))))
     (build-system python-build-system)
     (home-page "https://github.com/ricmoo/pyaes")
     (synopsis "Implementation of AES in Python")
-- 
cgit v1.2.3


From a992423775323045154eefb85cbcf207a0e4a226 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 10 Mar 2018 23:20:17 +0100
Subject: gnu: python-kitchen: Update to 1.2.5.

* gnu/packages/python.scm (python-kitchen): Update to 1.2.5.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index dce67be755..0fd5299702 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -1935,14 +1935,14 @@ something else) to Python data-types.")
 (define-public python-kitchen
   (package
     (name "python-kitchen")
-    (version "1.2.4")
+    (version "1.2.5")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "kitchen" version))
        (sha256
         (base32
-         "0ggv3p4x8jvmmzhp0xm00h6pvh1g0gmycw71rjwagnrj8n23vxrq"))))
+         "1zakh6l0yjvwic9p0nkvmbidpnkygkxbigh2skmb5gccyrhbp7xg"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-chardet" ,python-chardet)))
-- 
cgit v1.2.3


From 197babfb9d8ee4afe40a22e8e98fb4c6e2dd0d15 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 10 Mar 2018 23:57:13 +0100
Subject: gnu: python-ipaddress: Update to 1.0.19.

* gnu/packages/python.scm (python-ipaddress): Update to 1.0.19.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 0fd5299702..895a8bde3a 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -6132,13 +6132,13 @@ implementations of ASN.1-based codecs and protocols.")
 (define-public python-ipaddress
   (package
     (name "python-ipaddress")
-    (version "1.0.18")
+    (version "1.0.19")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "ipaddress" version))
               (sha256
                (base32
-                "1q8klj9d84cmxgz66073x1j35cplr3r77vx1znhxiwl5w74391ax"))))
+                "10agaa1cys1bk1ycpl2w8lky9vjx8h1xh1z29mg0niqx0638c390"))))
     (build-system python-build-system)
     (home-page "https://github.com/phihag/ipaddress")
     (synopsis "IP address manipulation library")
-- 
cgit v1.2.3


From bb5ca93625c5a1c94a535fe946c472ecce1c89cb Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 11 Mar 2018 18:41:34 +0100
Subject: gnu: youtube-dl: Update to 2018.03.10.

* gnu/packages/video.scm (youtube-dl): Update to 2018.03.10.
---
 gnu/packages/video.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index dfd94f9d3b..984d2f183d 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -1158,7 +1158,7 @@ access to mpv's powerful playback capabilities.")
 (define-public youtube-dl
   (package
     (name "youtube-dl")
-    (version "2018.02.26")
+    (version "2018.03.10")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://yt-dl.org/downloads/"
@@ -1166,7 +1166,7 @@ access to mpv's powerful playback capabilities.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0ijjnx8qjxk07v5dbz3n5z3cvz8dlkmh7jkyvgng7inl74c29zq5"))))
+                "1ibmz91anli1vzkgw2i3h4wf1i8arzd74730ylwcwyg3375xryjb"))))
     (build-system python-build-system)
     (arguments
      ;; The problem here is that the directory for the man page and completion
-- 
cgit v1.2.3


From 8aaba500713df6d0ccd806caff4f24f4c9fcce49 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 11 Mar 2018 22:34:07 +0100
Subject: gnu: mingw-w64: Fix home page and avoid further confusion.

MinGW-w64 was forked (in rather dramatic fashion) from the original
MinGW.  The two projects remain distinct and MinGW-w64 seems by far the
actively developed of the two.

* gnu/packages/mingw.scm (mingw-w64)[home-page]: Point to the correct
upstream.  Use HTTPS.
[description]: Expand and briefly note the relationship between the
two projects.  Use @dfn.
---
 gnu/packages/mingw.scm | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/mingw.scm b/gnu/packages/mingw.scm
index c7bc5c025d..cd58883b1f 100644
--- a/gnu/packages/mingw.scm
+++ b/gnu/packages/mingw.scm
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -76,9 +77,16 @@
        #:make-flags (list "DEFS=-DHAVE_CONFIG_H -D__MINGW_HAS_DXSDK=1")
        #:tests? #f ; compiles and includes glibc headers
        #:strip-binaries? #f))
-    (home-page "http://mingw.org")
+    (home-page "https://mingw-w64.org")
     (synopsis "Minimalist GNU for Windows")
-    (description "MinGW provides a complete programming tool set which is
-suitable for the development of native MS-Windows applications, and which does
-not depend on any 3rd-party C-Runtime dlls.")
+    (description
+     "Minimalist GNU for Windows (@dfn{MinGW}) is a complete software
+development environment for creating native Microsoft Windows applications.
+
+It includes a set of Windows-specific header files and static import libraries
+which enable the use of the Windows API.  It does not rely on any third-party C
+runtime dynamic-link libraries (@dfn{DLL}s).
+
+Mingw-w64 is an advancement of the original mingw.org project and provides
+several new APIs such as DirectX and DDK, and 64-bit support.")
     (license license:fdl1.3+)))
-- 
cgit v1.2.3


From 5dacc645b8830d5f65a677bb23a2c93241b165fb Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 11 Mar 2018 23:00:00 +0100
Subject: gnu: mingw-w64: Update to 5.0.3.

* gnu/packages/mingw.scm (mingw-w64): Update to 5.0.3.
---
 gnu/packages/mingw.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/mingw.scm b/gnu/packages/mingw.scm
index cd58883b1f..f7f34e9dc3 100644
--- a/gnu/packages/mingw.scm
+++ b/gnu/packages/mingw.scm
@@ -37,14 +37,14 @@
 (define-public mingw-w64
   (package
     (name "mingw-w64")
-    (version "5.0-rc2")
+    (version "5.0.3")
     (source (origin
               (method url-fetch)
               (uri (string-append
                     "https://sourceforge.net/projects/mingw-w64/files/mingw-w64/"
                     "mingw-w64-release/mingw-w64-v" version ".tar.bz2"))
               (sha256
-               (base32 "0imdary8j07if8ih73pfgxiclpf2ax8h3mz8mxln07i8sbbd30c9"))
+               (base32 "1d4wrjfdlq5xqpv9zg6ssw4lm8jnv6522xf7d6zbjygmkswisq1a"))
               (patches (search-patches "mingw-w64-5.0rc2-gcc-4.9.3.patch"))))
     (native-inputs `(("xgcc-core" ,(cross-gcc %mingw-triplet))
                      ("xbinutils" ,(cross-binutils %mingw-triplet))))
-- 
cgit v1.2.3


From bd971438bed00909def54c2114041f218e9983ca Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 11 Mar 2018 19:35:55 +0100
Subject: gnu: criu: Update to 3.7.

* gnu/packages/virtualization.scm (criu): Update to 3.7.
---
 gnu/packages/virtualization.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm
index f8f9de16fc..24f7333cd8 100644
--- a/gnu/packages/virtualization.scm
+++ b/gnu/packages/virtualization.scm
@@ -613,14 +613,14 @@ domains, their live performance and resource utilization statistics.")
 (define-public criu
   (package
     (name "criu")
-    (version "3.5")
+    (version "3.7")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://download.openvz.org/criu/criu-"
                                   version ".tar.bz2"))
               (sha256
                (base32
-                "1w0ybla7ac0ql0jzh0vxdf2w9amqp88jcg0na3b33r3hq8acry6x"))))
+                "0qrpz7pvnks34v7d8lb73flz3mb7qwnib94pdwaxh0mskn8470fq"))))
     (build-system gnu-build-system)
     (arguments
      `(#:test-target "test"
-- 
cgit v1.2.3


From fe0523d4579e7bdeb9771ba9527545e802598d9d Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 11 Mar 2018 20:15:57 +0100
Subject: gnu: msgpack: Use HTTPS home page.

* gnu/packages/serialization.scm (msgpack)[home-page]: Use HTTPS.
---
 gnu/packages/serialization.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm
index 8df4841eae..a0361c76fd 100644
--- a/gnu/packages/serialization.scm
+++ b/gnu/packages/serialization.scm
@@ -132,7 +132,7 @@ such as compact binary encodings, XML, or JSON.")
          (add-after 'unpack 'autoconf
            (lambda _
              (system* "autoreconf" "-vfi"))))))
-    (home-page "http://www.msgpack.org")
+    (home-page "https://www.msgpack.org")
     (synopsis "Binary serialization library")
     (description "Msgpack is a library for C/C++ that implements binary
 serialization.")
-- 
cgit v1.2.3


From 778fb47bcd1a595c0cd9e9d47f984f6d0bfaccf7 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 11 Mar 2018 20:30:44 +0100
Subject: gnu: msgpack: Update phase style.

* gnu/packages/serialization.scm (msgpack)[arguments]: Substitute INVOKE
for SYSTEM* and end phase with #t.
---
 gnu/packages/serialization.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm
index a0361c76fd..131d68242c 100644
--- a/gnu/packages/serialization.scm
+++ b/gnu/packages/serialization.scm
@@ -131,7 +131,8 @@ such as compact binary encodings, XML, or JSON.")
        (modify-phases %standard-phases
          (add-after 'unpack 'autoconf
            (lambda _
-             (system* "autoreconf" "-vfi"))))))
+             (invoke "autoreconf" "-vfi")
+             #t)))))
     (home-page "https://www.msgpack.org")
     (synopsis "Binary serialization library")
     (description "Msgpack is a library for C/C++ that implements binary
-- 
cgit v1.2.3


From 3592937550affcfe1dc1b5de46d159e834c3a74f Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 11 Mar 2018 20:14:47 +0100
Subject: gnu: cereal: Update phase style.

* gnu/packages/serialization.scm (cereal)[arguments]: Substitute INVOKE
for SYSTEM* and end phases with #t.
---
 gnu/packages/serialization.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm
index 131d68242c..9bbac3ac22 100644
--- a/gnu/packages/serialization.scm
+++ b/gnu/packages/serialization.scm
@@ -70,7 +70,8 @@
           (lambda _
             (substitute* "doc/doxygen.in"
               (("@CMAKE_CURRENT_SOURCE_DIR@") "."))
-            (zero? (system* "doxygen" "doc/doxygen.in"))))
+            (invoke "doxygen" "doc/doxygen.in")
+            #t))
          ;; There is no "install" target, so we have to provide our own
          ;; "install" phase.
          (replace 'install
-- 
cgit v1.2.3


From a23b131c2d2e9c008fdad9fe1fe19ab61da3ac22 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 11 Mar 2018 23:45:50 +0100
Subject: gnu: perl-io-tty: Update to 1.12.

* gnu/packages/perl.scm (perl-io-tty): Update to 1.12.
---
 gnu/packages/perl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index badff6e4d1..9e3dcb1a74 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -4062,14 +4062,14 @@ filehandles; in particular, IO::Scalar, IO::ScalarArray, and IO::Lines.")
 (define-public perl-io-tty
   (package
     (name "perl-io-tty")
-    (version "1.11")
+    (version "1.12")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cpan/authors/id/T/TO/TODDR/IO-Tty-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0lgd9xcbi4gf4gw1ka6fj94my3w1f3k1zamb4pfln0qxz45zlxx4"))))
+                "0399anjy3bc0w8xzsc3qx5vcyqryc9gc52lc7wh7i49hsdq8gvx2"))))
     (build-system perl-build-system)
     (home-page "http://search.cpan.org/~toddr/IO-Tty//")
     (synopsis "Perl interface to pseudo ttys")
-- 
cgit v1.2.3


From 6d2f72cd58541bee77e1624555726cf525dc71e9 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 11 Mar 2018 23:48:27 +0100
Subject: gnu: perl-json-maybexs: Update to 1.003010.

* gnu/packages/perl.scm (perl-json-maybexs): Update to 1.003010.
[source]: Update source URI.
---
 gnu/packages/perl.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 9e3dcb1a74..2d0c4c3570 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -4249,15 +4249,15 @@ installed.")
 (define-public perl-json-maybexs
   (package
     (name "perl-json-maybexs")
-    (version "1.003003")
+    (version "1.003010")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "mirror://cpan/authors/id/E/ET/ETHER/"
+       (uri (string-append "mirror://cpan/authors/id/H/HA/HAARG/"
                            "JSON-MaybeXS-" version ".tar.gz"))
        (sha256
         (base32
-         "0q21wzz87drrvblxcm2py8fcvkzwx1hxzfybynz8ln7wv66vbx3f"))))
+         "0hs504x5zsa2vl6r7b3rvbygsak1ly24m1lg636bqp3x7jirmb30"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-test-without-module" ,perl-test-without-module)))
-- 
cgit v1.2.3


From a304f3a2c1d147ed8fcae82177f7e23404c19633 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 11 Mar 2018 23:55:10 +0100
Subject: gnu: perl-datetime: Update to 1.46.

* gnu/packages/perl.scm (perl-datetime): Update to 1.46.
---
 gnu/packages/perl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 2d0c4c3570..ac65ac481c 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -2091,7 +2091,7 @@ hours, minutes, seconds, and time zones.")
 (define-public perl-datetime
   (package
     (name "perl-datetime")
-    (version "1.43")
+    (version "1.46")
     (source
      (origin
        (method url-fetch)
@@ -2099,7 +2099,7 @@ hours, minutes, seconds, and time zones.")
                            "DateTime-" version ".tar.gz"))
        (sha256
         (base32
-         "0xgrcqs7zza7646g81j54z3fcxb8rw11ynlfm02afr436lgfnfql"))))
+         "1247d2q2gm912bxj88a0sr5gvj2nx4a7n6z1smkq16iy21cziz79"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-cpan-meta-check" ,perl-cpan-meta-check)
-- 
cgit v1.2.3


From f372c9faf002028ce77d54d978c11dbe75547df2 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 11 Mar 2018 23:59:27 +0100
Subject: gnu: perl-datetime-locale: Update to 1.17.

* gnu/packages/perl.scm (perl-datetime-locale): Update to 1.17.
---
 gnu/packages/perl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index ac65ac481c..48999dca55 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -2361,7 +2361,7 @@ takes a string and a pattern and returns the `DateTime` object associated.")
 (define-public perl-datetime-locale
   (package
     (name "perl-datetime-locale")
-    (version "1.16")
+    (version "1.17")
     (source
      (origin
        (method url-fetch)
@@ -2369,7 +2369,7 @@ takes a string and a pattern and returns the `DateTime` object associated.")
                            "DateTime-Locale-" version ".tar.gz"))
        (sha256
         (base32
-         "1zkc0wggbsczbj4qadahh197imr9fa6knxr10zl241lw2i14rbyz"))))
+         "1jawnci23kik5x4gln6ixvv9bxznd5f6ira024yjxsc97y5mk9hc"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-file-sharedir" ,perl-file-sharedir)
-- 
cgit v1.2.3


From 6cafe347582916ad3d6c27cefd3a35f72a9eed74 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 12 Mar 2018 00:03:22 +0100
Subject: gnu: perl-datetime-timezone: Update to 2.17.

* gnu/packages/perl.scm (perl-datetime-timezone): Update to 2.17.
---
 gnu/packages/perl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 48999dca55..b2e8a8ab82 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -2392,7 +2392,7 @@ the DateTime.pm class.")
 (define-public perl-datetime-timezone
   (package
     (name "perl-datetime-timezone")
-    (version "2.13")
+    (version "2.17")
     (source
      (origin
        (method url-fetch)
@@ -2400,7 +2400,7 @@ the DateTime.pm class.")
                            "DateTime-TimeZone-" version ".tar.gz"))
        (sha256
         (base32
-         "1371sk4p9clygfwxzvivfqz6q9dy8gn3n4dr1424d0xqsv63jg9k"))))
+         "1ckhjw7h545306b02p6ra60y8zxqnbqr2lsy7c1wib8libf0l2hx"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-test-fatal" ,perl-test-fatal)
-- 
cgit v1.2.3


From ce2c11e9b19b0ba154f680e380a489638a5ac93c Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 12 Mar 2018 00:06:32 +0100
Subject: gnu: perl-getopt-long-descriptive: Update to 0.102.

* gnu/packages/perl.scm (perl-getopt-long-descriptive): Update to 0.102.
---
 gnu/packages/perl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index b2e8a8ab82..bf558043c6 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -3722,7 +3722,7 @@ single-letter approach, is provided but not enabled by default.")
 (define-public perl-getopt-long-descriptive
   (package
     (name "perl-getopt-long-descriptive")
-    (version "0.100")
+    (version "0.102")
     (source
      (origin
        (method url-fetch)
@@ -3730,7 +3730,7 @@ single-letter approach, is provided but not enabled by default.")
                            "Getopt-Long-Descriptive-" version ".tar.gz"))
        (sha256
         (base32
-         "1dpz5nhg5glmrpq46nkc90dg19cfqfjspqwhfvihsqyi229yfl8l"))))
+         "0ii8xafvlph5vzcqp3dpc83lg7nkg3l1l2hmqdf5382a567vkm4s"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-cpan-meta-check" ,perl-cpan-meta-check)
-- 
cgit v1.2.3


From 3b6903495ae485763cd2c0811a3e8c0896093330 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 12 Mar 2018 00:12:34 +0100
Subject: gnu: perl-io-stringy: Update to 2.111.

* gnu/packages/perl.scm (perl-io-stringy): Update to 2.111.
---
 gnu/packages/perl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index bf558043c6..8f2786124c 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -4042,7 +4042,7 @@ that reads or writes data from in-core strings.")
 (define-public perl-io-stringy
   (package
     (name "perl-io-stringy")
-    (version "2.110")
+    (version "2.111")
     (source
      (origin
        (method url-fetch)
@@ -4050,7 +4050,7 @@ that reads or writes data from in-core strings.")
                            "IO-stringy-" version ".tar.gz"))
        (sha256
         (base32
-         "1vh4n0k22hx20rwvf6h7lp25wb7spg0089shrf92d2lkncwg8g3y"))))
+         "178rpx0ym5l2m9mdmpnr92ziscvchm541w94fd7ygi6311kgsrwc"))))
     (build-system perl-build-system)
     (home-page "http://search.cpan.org/dist/IO-stringy/")
     (synopsis "IO:: interface for reading/writing an array of lines")
-- 
cgit v1.2.3


From 631efa496cc4d0983d67e6d9fb2493a78e5011fd Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 12 Mar 2018 00:19:25 +0100
Subject: gnu: perl-scope-guard: Update to 0.21.

* gnu/packages/perl.scm (perl-scope-guard): Update to 0.21.
---
 gnu/packages/perl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 8f2786124c..86c5718ea5 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -6880,7 +6880,7 @@ safely on things that may not be objects.")
 (define-public perl-scope-guard
   (package
     (name "perl-scope-guard")
-    (version "0.20")
+    (version "0.21")
     (source
      (origin
        (method url-fetch)
@@ -6888,7 +6888,7 @@ safely on things that may not be objects.")
                            "Scope-Guard-" version ".tar.gz"))
        (sha256
         (base32
-         "1lsagnz6pli035zvx5c1x4qm9fabi773vns86yd8lzfpldhfv3sv"))))
+         "0y6jfzvxiz8h5yfz701shair0ilypq2mvimd7wn8wi2nbkm1p6wc"))))
     (build-system perl-build-system)
     (home-page "http://search.cpan.org/dist/Scope-Guard/")
     (synopsis "Lexically-scoped resource management")
-- 
cgit v1.2.3


From d437a60f3ee6b4596d12b0d484a53202f5b90ff4 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 12 Mar 2018 00:24:00 +0100
Subject: gnu: perl-data-dump: Update to 1.23.

* gnu/packages/perl.scm (perl-data-dump): Update to 1.23.
---
 gnu/packages/perl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 86c5718ea5..1f1be8d600 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -1681,7 +1681,7 @@ short and handy (e.g. to use it as part of a URL).")
 (define-public perl-data-dump
   (package
     (name "perl-data-dump")
-    (version "1.22")
+    (version "1.23")
     (source
      (origin
        (method url-fetch)
@@ -1689,7 +1689,7 @@ short and handy (e.g. to use it as part of a URL).")
                            "Data-Dump-" version ".tar.gz"))
        (sha256
         (base32
-         "1ciqlwsy1q35s94dry9bjy1pwanbq6b7q4rhxm9z8prgkzbslg2k"))))
+         "0r9ba52b7p8nnn6nw0ygm06lygi8g68piri78jmlqyrqy5gb0lxg"))))
     (build-system perl-build-system)
     (home-page "http://search.cpan.org/dist/Data-Dump/")
     (synopsis "Pretty printing of data structures")
-- 
cgit v1.2.3


From 09000b6b6dd429f79e0a906dd50237cc17e51196 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 12 Mar 2018 00:33:06 +0100
Subject: gnu: perl-path-tiny: Update to 0.104.

* gnu/packages/perl.scm (perl-path-tiny): Update to 0.104.
---
 gnu/packages/perl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 1f1be8d600..1f8cbb291e 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -6577,14 +6577,14 @@ directory specifications in a cross-platform manner.")
 (define-public perl-path-tiny
   (package
     (name "perl-path-tiny")
-    (version "0.096")
+    (version "0.104")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cpan/authors/id/D/DA/DAGOLDEN/"
                                   "Path-Tiny-" version ".tar.gz"))
               (sha256
                (base32
-                "08dmr6ijjg3dp7h9dxix0nmad0fw16c6qzs4qc0hdz500gd64sr2"))))
+                "1vxaczi44d2acfyyzwa7p6c5gx3rgm6c36zbdl40982axg7iv7y6"))))
     (build-system perl-build-system)
     (arguments
      `(#:tests? #f)) ; Tests require additional test modules to be packaged
-- 
cgit v1.2.3


From 387a8fd7d06e05faab4ac896aae32229df0bf1a3 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 12 Mar 2018 00:35:47 +0100
Subject: gnu: perl-class-accessor: Update to 0.51.

* gnu/packages/perl.scm (perl-class-accessor): Update to 0.51.
---
 gnu/packages/perl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 1f8cbb291e..457a51e738 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -831,7 +831,7 @@ the Carp.pm module doesn't help.")
 (define-public perl-class-accessor
   (package
     (name "perl-class-accessor")
-    (version "0.34")
+    (version "0.51")
     (source
      (origin
        (method url-fetch)
@@ -839,7 +839,7 @@ the Carp.pm module doesn't help.")
                            "Class-Accessor-" version ".tar.gz"))
        (sha256
         (base32
-         "1z6fqg0yz8gay15r1iasslv8f1n1mzjkrhs47fvbj3rqz36y1cfd"))))
+         "07215zzr4ydf49832vn54i3gf2q5b97lydkv8j56wb2svvjs64mz"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-sub-name" ,perl-sub-name)))
-- 
cgit v1.2.3


From 221ff3c0971219813d8a10b2093e2af9f45b9086 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 12 Mar 2018 00:44:04 +0100
Subject: gnu: perl-ref-util-xs: Update to 0.117.

* gnu/packages/perl.scm (perl-ref-util-xs): Update to 0.117.
---
 gnu/packages/perl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 457a51e738..00ef99da02 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -6757,7 +6757,7 @@ variables that should not be changed.")
 (define-public perl-ref-util-xs
   (package
     (name "perl-ref-util-xs")
-    (version "0.116")
+    (version "0.117")
     (source
      (origin
        (method url-fetch)
@@ -6765,7 +6765,7 @@ variables that should not be changed.")
                            "Ref-Util-XS-" version ".tar.gz"))
        (sha256
         (base32
-         "0l5dzbd71iclv8fdjk7685rq6pbfiiydh0n70br6g9l9iy2smr6f"))))
+         "0g33cndhj353h5xjihvgjc2h6vxwkyyzw63r4l06czvq4flcar7v"))))
     (build-system perl-build-system)
     (home-page "http://search.cpan.org/dist/Ref-Util-XS/")
     (synopsis "XS implementation for Ref::Util")
-- 
cgit v1.2.3


From b8b7bd05ae6a48533642da2797508d39aafcac02 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 12 Mar 2018 03:36:10 +0100
Subject: gnu: perl-task-weaken: Update to 1.05.

* gnu/packages/perl.scm (perl-task-weaken): Update to 1.05.
[source]: Update source URI.
---
 gnu/packages/perl.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 00ef99da02..754f1fe43b 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -7521,15 +7521,15 @@ of a system.")
 (define-public perl-task-weaken
   (package
     (name "perl-task-weaken")
-    (version "1.04")
+    (version "1.05")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "mirror://cpan/authors/id/A/AD/ADAMK/"
+       (uri (string-append "mirror://cpan/authors/id/E/ET/ETHER/"
                            "Task-Weaken-" version ".tar.gz"))
        (sha256
         (base32
-         "1i7kd9v8fjsqyhr4rx4a1jv7n5vfjjm1v4agb24pizh0b72p3qk7"))))
+         "0p5ryr3421p5rqj6dk5dcvxsml5gl9skbn7gv4szk50fimrvzww5"))))
     (build-system perl-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases
-- 
cgit v1.2.3


From 162189361e87996e2156598c3fe264fb5e918824 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 12 Mar 2018 03:42:47 +0100
Subject: gnu: perl-datetime-format-strptime: Update to 1.75.

* gnu/packages/perl.scm (perl-datetime-format-strptime): Update to 1.75.
---
 gnu/packages/perl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 754f1fe43b..cf9f21dbc9 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -2332,7 +2332,7 @@ parsing logic.")
 (define-public perl-datetime-format-strptime
   (package
     (name "perl-datetime-format-strptime")
-    (version "1.73")
+    (version "1.75")
     (source
      (origin
        (method url-fetch)
@@ -2340,7 +2340,7 @@ parsing logic.")
                            "DateTime-Format-Strptime-" version ".tar.gz"))
        (sha256
         (base32
-         "1gmjcmvh81cla6yn2pvlkr7i25bspg90pzzsizrfb0c5xc37h1vd"))))
+         "069wmgbchydgx3nm9klqw0g6ksnja28g61d4allgzmvr9ynb5ksg"))))
     (build-system perl-build-system)
     (propagated-inputs
      `(("perl-datetime" ,perl-datetime)
-- 
cgit v1.2.3


From f6246195e57d6e50b202bba6777cd70c64b36ce2 Mon Sep 17 00:00:00 2001
From: Rutger Helling <rhelling@mykolab.com>
Date: Mon, 12 Mar 2018 10:32:45 +0100
Subject: gnu: Add wine-staging-patchset-data.

* gnu/packages/wine.scm (wine-staging-patchset-data): New variable.
---
 gnu/packages/wine.scm | 47 +++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/wine.scm b/gnu/packages/wine.scm
index e71538f1b0..df16b99280 100644
--- a/gnu/packages/wine.scm
+++ b/gnu/packages/wine.scm
@@ -26,9 +26,12 @@
   #:use-module (guix download)
   #:use-module (guix utils)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system trivial)
   #:use-module (gnu packages)
   #:use-module (gnu packages admin)
   #:use-module (gnu packages audio)
+  #:use-module (gnu packages base)
+  #:use-module (gnu packages bash)
   #:use-module (gnu packages bison)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cups)
@@ -212,6 +215,50 @@ integrate Windows applications into your desktop.")
     (synopsis "Implementation of the Windows API (WoW64 version)")
     (supported-systems '("x86_64-linux" "aarch64-linux"))))
 
+(define-public wine-staging-patchset-data
+  (package
+   (name "wine-staging-patchset-data")
+   (version "3.3")
+   (source
+    (origin
+     (method url-fetch)
+     (uri (string-append "https://github.com/wine-staging/wine-staging/archive/v"
+                         version ".zip"))
+     (file-name (string-append name "-" version ".zip"))
+     (sha256
+      (base32
+       "16l28vrhqn27kipqwms622jz1prfky8qkjb8pj747k3qjnm2k1g9"))))
+   (build-system trivial-build-system)
+   (native-inputs
+    `(("bash" ,bash)
+      ("coreutils" ,coreutils)
+      ("unzip" ,unzip)))
+   (arguments
+    `(#:modules ((guix build utils))
+      #:builder
+      (begin
+        (use-modules (guix build utils))
+        (let* ((out (assoc-ref %outputs "out"))
+               (wine-staging (string-append out "/share/wine-staging"))
+               (source (assoc-ref %build-inputs "source"))
+               (sh (string-append (assoc-ref %build-inputs "bash") "/bin/bash"))
+               (env (string-append (assoc-ref %build-inputs "coreutils") "/bin/env"))
+               (unzip (string-append (assoc-ref %build-inputs "unzip") "/bin/unzip")))
+          (copy-file source (string-append ,name "-" ,version ".zip"))
+          (invoke unzip (string-append ,name "-" ,version ".zip"))
+          (substitute* (string-append "wine-staging-" ,version
+                                      "/patches/patchinstall.sh") (("/bin/sh") sh))
+          (substitute* (string-append "wine-staging-" ,version
+                                      "/patches/gitapply.sh") (("/usr/bin/env") env))
+          (mkdir-p wine-staging)
+          (copy-recursively (string-append "wine-staging-" ,version)
+                            wine-staging)))))
+   (home-page "https://github.com/wine-staging")
+   (synopsis "Patchset for Wine")
+   (description
+    "wine-staging-patchset-data contains the patchset to build Wine-Staging.")
+   (license license:lgpl2.1+)))
+
 (define-public wine-staging
   (package
     (inherit wine)
-- 
cgit v1.2.3


From b53b9c8dd12820a28775b295895fb0d32b8e0ed4 Mon Sep 17 00:00:00 2001
From: Rutger Helling <rhelling@mykolab.com>
Date: Mon, 12 Mar 2018 10:40:59 +0100
Subject: gnu: wine-staging: Update to 3.3.

* gnu/packages/wine.scm (wine-staging): Update to 3.3.
[inputs]: Add autoconf, python, util-linux, wine-staging-patchset-data.
[arguments]: Remove 'hardcode-libvulkan-path phase. Add
'patch-source-wine-staging phase.
[home-page]: Change URL.
---
 gnu/packages/wine.scm | 32 +++++++++++++++++++-------------
 1 file changed, 19 insertions(+), 13 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/wine.scm b/gnu/packages/wine.scm
index df16b99280..836ed0666e 100644
--- a/gnu/packages/wine.scm
+++ b/gnu/packages/wine.scm
@@ -30,6 +30,7 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages admin)
   #:use-module (gnu packages audio)
+  #:use-module (gnu packages autotools)
   #:use-module (gnu packages base)
   #:use-module (gnu packages bash)
   #:use-module (gnu packages bison)
@@ -50,6 +51,7 @@
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pulseaudio)
   #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages python)
   #:use-module (gnu packages mp3)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages photo)
@@ -263,30 +265,34 @@ integrate Windows applications into your desktop.")
   (package
     (inherit wine)
     (name "wine-staging")
-    (version "2.21")
+    (version (package-version wine-staging-patchset-data))
     (source (origin
               (method url-fetch)
               (uri (string-append
-                    "https://github.com/wine-compholio/wine-patched/archive/"
-                    "staging-" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+                    "https://dl.winehq.org/wine/source/3.x/wine-" version
+                    ".tar.xz"))
+              (file-name (string-append name "-" version ".tar.xz"))
               (sha256
                (base32
-                "1pjaxj7h3q6y356np908fvsx0bf7yx5crqvgl4hza6gfssdmsr5r"))))
-    (inputs `(("gtk+", gtk+)
+                "0cx31jsll7mxd9r7v0vpahajqwb6da6cpwybv06l5ydkgfrbv505"))))
+    (inputs `(("autoconf" ,autoconf) ; for autoreconf
+              ("gtk+", gtk+)
               ("libva", libva)
+              ("python" ,python)
+              ("util-linux" ,util-linux) ; for hexdump
               ("vulkan-icd-loader" ,vulkan-icd-loader)
+              ("wine-staging-patchset-data" ,wine-staging-patchset-data)
               ,@(package-inputs wine)))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (add-before 'configure 'hardcode-libvulkan-path
+         (add-before 'configure 'patch-source-wine-staging
            (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((libvulkan (string-append (assoc-ref %build-inputs
-                               "vulkan-icd-loader") "/lib/libvulkan.so")))
-               ;; Hard-code the path to libvulkan.so.
-               (substitute* "dlls/vulkan/vulkan_thunks.c" (("libvulkan.so")
-                            libvulkan))
+             (let* ((source (assoc-ref %build-inputs "source"))
+                    (script (string-append (assoc-ref %build-inputs
+                            "wine-staging-patchset-data")
+                            "/share/wine-staging/patches/patchinstall.sh")))
+               (invoke script (string-append "DESTDIR=" ".") "--all")
                #t)))
          (add-after 'configure 'patch-dlopen-paths
            ;; Hardcode dlopened sonames to absolute paths.
@@ -308,7 +314,7 @@ the development branch yet.  The idea of Wine-Staging is to provide
 experimental features faster to end users and to give developers the
 possibility to discuss and improve their patches before they are
 integrated into the main branch.")
-    (home-page "https://wine-staging.com")
+    (home-page "https://github.com/wine-staging")
     ;; In addition to the regular Wine license (lgpl2.1+), Wine-Staging
     ;; provides Liberation and WenQuanYi Micro Hei fonts.  Those use
     ;; different licenses.  In particular, the latter is licensed under
-- 
cgit v1.2.3


From 3139f18524334c4ba373f5f031dbab7f44c94650 Mon Sep 17 00:00:00 2001
From: Rutger Helling <rhelling@mykolab.com>
Date: Mon, 12 Mar 2018 10:41:51 +0100
Subject: gnu: wine64-staging: Update to 3.3.

* gnu/packages/wine.scm (wine64-staging): Update to 3.3.
[arguments]: Remove 'hardcode-libvulkan-path phase. Add
'patch-source-wine-staging phase.
---
 gnu/packages/wine.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/wine.scm b/gnu/packages/wine.scm
index 836ed0666e..e23dcc55f1 100644
--- a/gnu/packages/wine.scm
+++ b/gnu/packages/wine.scm
@@ -334,13 +334,13 @@ integrated into the main branch.")
              (string-append "libdir=" %output "/lib/wine64"))
        #:phases
        (modify-phases %standard-phases
-         (add-before 'configure 'hardcore-libvulkan-path
+         (add-before 'configure 'patch-source-wine-staging
            (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((libvulkan (string-append (assoc-ref %build-inputs
-                               "vulkan-icd-loader") "/lib/libvulkan.so")))
-               ;; Hard-code the path to libvulkan.so.
-               (substitute* "dlls/vulkan/vulkan_thunks.c" (("libvulkan.so")
-                            libvulkan))
+             (let* ((source (assoc-ref %build-inputs "source"))
+                    (script (string-append (assoc-ref %build-inputs
+                            "wine-staging-patchset-data")
+                            "/share/wine-staging/patches/patchinstall.sh")))
+               (invoke script (string-append "DESTDIR=" ".") "--all")
                #t)))
          (add-after 'install 'copy-wine32-binaries
            (lambda* (#:key outputs #:allow-other-keys)
-- 
cgit v1.2.3


From 51158d83d86d9f969c52f7baf513160a8d9fbd78 Mon Sep 17 00:00:00 2001
From: Rutger Helling <rhelling@mykolab.com>
Date: Mon, 12 Mar 2018 11:30:30 +0100
Subject: gnu: wine-staging: Add SDL2 support.

* gnu/packages/wine.scm (wine-staging)[inputs]: Add sdl2.
---
 gnu/packages/wine.scm | 2 ++
 1 file changed, 2 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/wine.scm b/gnu/packages/wine.scm
index e23dcc55f1..0327deaf24 100644
--- a/gnu/packages/wine.scm
+++ b/gnu/packages/wine.scm
@@ -57,6 +57,7 @@
   #:use-module (gnu packages photo)
   #:use-module (gnu packages samba)
   #:use-module (gnu packages scanner)
+  #:use-module (gnu packages sdl)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages video)
   #:use-module (gnu packages vulkan)
@@ -279,6 +280,7 @@ integrate Windows applications into your desktop.")
               ("gtk+", gtk+)
               ("libva", libva)
               ("python" ,python)
+              ("sdl2" ,sdl2)
               ("util-linux" ,util-linux) ; for hexdump
               ("vulkan-icd-loader" ,vulkan-icd-loader)
               ("wine-staging-patchset-data" ,wine-staging-patchset-data)
-- 
cgit v1.2.3


From 93f3b7762ea872e0e72d62aa14b417d324fdeed8 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Mon, 12 Mar 2018 14:41:06 +0100
Subject: gnu: automake@1.16: Update to 1.16.1.

* gnu/packages/autotools.scm (automake-1.16): Update to 1.16.1.
---
 gnu/packages/autotools.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/autotools.scm b/gnu/packages/autotools.scm
index 33addc11a7..9394ee014f 100644
--- a/gnu/packages/autotools.scm
+++ b/gnu/packages/autotools.scm
@@ -325,14 +325,14 @@ Makefile, simplifying the entire process for the developer.")
   ;; Make this the default on the next rebuild cycle.
   (package
     (inherit automake)
-    (version "1.16")
+    (version "1.16.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnu/automake/automake-"
                                   version ".tar.xz"))
               (sha256
                (base32
-                "12jvcmkcmd5p14b41w9f7ixd3sca97pymd6lqbkwnl8qn6bjv3zr"))
+                "08g979ficj18i1w6w5219bgmns7czr03iadf20mk3lrzl8wbn1ax"))
               (patches
                (search-patches "automake-skip-amhello-tests.patch"))))))
 
-- 
cgit v1.2.3


From c0edb5b5430a5278a3ebc9aeea9d3c8ae9a2e1f1 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludovic.courtes@inria.fr>
Date: Mon, 12 Mar 2018 16:06:17 +0100
Subject: gnu: arpack-ng: Update to 3.5.0; use 3.3.0 for julia.

Partly fixes <https://bugs.gnu.org/30282>.

* gnu/packages/maths.scm (arpack-ng): Update to 3.5.0.
[native-inputs]: New field.
(arpack-ng-3.3.0): New variable.
* gnu/packages/julia.scm (julia)[inputs]: Use ARPACK-NG-3.3.0.
---
 gnu/packages/julia.scm |  7 ++++++-
 gnu/packages/maths.scm | 35 +++++++++++++++++++++++++++++------
 2 files changed, 35 insertions(+), 7 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm
index 41bbc66dd2..7a44abdec2 100644
--- a/gnu/packages/julia.scm
+++ b/gnu/packages/julia.scm
@@ -315,7 +315,12 @@
         "USE_SYSTEM_OPENSPECFUN=1")))
     (inputs
      `(("llvm" ,llvm)
-       ("arpack-ng" ,arpack-ng)
+
+       ;; The bundled version is 3.3.0 so stick to that version.  With other
+       ;; versions, we get test failures in 'linalg/arnoldi' as described in
+       ;; <https://bugs.gnu.org/30282>.
+       ("arpack-ng" ,arpack-ng-3.3.0)
+
        ("coreutils" ,coreutils) ;for bindings to "mkdir" and the like
        ("lapack" ,lapack)
        ("openblas" ,openblas) ;Julia does not build with Atlas
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index cf3d8ae836..f9e5d2c3a2 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -12,7 +12,7 @@
 ;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2016 Kei Kebreau <kkebreau@posteo.net>
-;;; Copyright © 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
 ;;; Copyright © 2017 Paul Garlick <pgarlick@tourbillion-technology.com>
@@ -418,18 +418,26 @@ computing convex hulls.")
 (define-public arpack-ng
   (package
     (name "arpack-ng")
-    (version "3.2.0")
+    (version "3.5.0")
+    (home-page "https://github.com/opencollab/arpack-ng")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://github.com/opencollab/arpack-ng/archive/"
-                           version ".tar.gz"))
+       (uri (string-append home-page "/archive/" version ".tar.gz"))
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1fwch6vipms1ispzg2djvbzv5wag36f1dmmr3xs3mbp6imfyhvff"))))
+         "0f8jx3fifmj9qdp289zr7r651y1q48k1jya859rqxq62mvis7xsh"))))
     (build-system gnu-build-system)
-    (home-page "https://github.com/opencollab/arpack-ng")
+    (arguments
+     '(#:phases (modify-phases %standard-phases
+                  (add-after 'unpack 'autoreconf
+                    (lambda _
+                      (invoke "autoreconf" "-vfi"))))))
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)))
     (inputs
      `(("lapack" ,lapack)
        ("fortran" ,gfortran)))
@@ -440,6 +448,21 @@ large scale eigenvalue problems.")
     (license (license:non-copyleft "file://COPYING"
                                 "See COPYING in the distribution."))))
 
+(define-public arpack-ng-3.3.0
+  (package
+    (inherit arpack-ng)
+    (version "3.3.0")
+    (name (package-name arpack-ng))
+    (home-page (package-home-page arpack-ng))
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append home-page "/archive/" version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1cz53wqzcf6czmcpfb3vb61xi0rn5bwhinczl65hpmbrglg82ndd"))))))
+
 (define-public arpack-ng-openmpi
   (package (inherit arpack-ng)
     (name "arpack-ng-openmpi")
-- 
cgit v1.2.3


From f06e391338346cae54d23071f49e572b4b6e5bb3 Mon Sep 17 00:00:00 2001
From: Jelle Licht <jlicht@fsfe.org>
Date: Mon, 12 Mar 2018 17:42:48 +0100
Subject: gnu: node: Update to 9.8.0.

* gnu/packages/node.scm (node): Update to 9.8.0.
[arguments]: Remove 'doc-only' workaround. Re-enable fixed tests.
---
 gnu/packages/node.scm | 32 ++++----------------------------
 1 file changed, 4 insertions(+), 28 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/node.scm b/gnu/packages/node.scm
index 982d3f905c..ea98f28efd 100644
--- a/gnu/packages/node.scm
+++ b/gnu/packages/node.scm
@@ -41,14 +41,14 @@
 (define-public node
   (package
     (name "node")
-    (version "9.4.0")
+    (version "9.8.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://nodejs.org/dist/v" version
                                   "/node-v" version ".tar.gz"))
               (sha256
                (base32
-                "0rx947ibcfpa0lf93nayfrmjls7r7svqsq87z0xmjzf8fb9361r4"))))
+                "1mjr1rm5w26c0yb4zq6z5yv3zbvqk18lwbswhwn1sha8hapinjp8"))))
     (build-system gnu-build-system)
     (arguments
      ;; TODO: Purge the bundled copies from the source.
@@ -77,29 +77,13 @@
                (("'/usr/bin/env'")
                 (string-append "'" (which "env") "'")))
 
-
-             ;; test-make-doc needs doc-only target, which is inhibited below
-             (for-each delete-file
-                       '("test/doctool/test-make-doc.js"))
              ;; FIXME: These tests depend on being able to install eslint.
              ;; See https://github.com/nodejs/node/issues/17098.
              (for-each delete-file
-                       '("test/parallel/test-eslint-crypto-check.js"
-                         "test/parallel/test-eslint-alphabetize-errors.js"
+                       '("test/parallel/test-eslint-alphabetize-errors.js"
                          "test/parallel/test-eslint-buffer-constructor.js"
                          "test/parallel/test-eslint-documented-errors.js"
-                         "test/parallel/test-eslint-inspector-check.js"
-                         "test/parallel/test-eslint-lowercase-name-for-primitive.js"
-                         "test/parallel/test-eslint-no-unescaped-regexp-dot.js"
-                         "test/parallel/test-eslint-no-let-in-for-declaration.js"
-                         "test/parallel/test-eslint-number-isnan.js"
-                         "test/parallel/test-eslint-prefer-assert-iferror.js"
-                         "test/parallel/test-eslint-prefer-assert-methods.js"
-                         "test/parallel/test-eslint-prefer-common-expectserror.js"
-                         "test/parallel/test-eslint-prefer-common-mustnotcall.js"
-                         "test/parallel/test-eslint-prefer-util-format-errors.js"
-                         "test/parallel/test-eslint-require-buffer.js"
-                         "test/parallel/test-eslint-required-modules.js"))
+                         "test/parallel/test-eslint-inspector-check.js"))
 
              ;; FIXME: These tests fail in the build container, but they don't
              ;; seem to be indicative of real problems in practice.
@@ -135,14 +119,6 @@
                              (string-append (assoc-ref inputs "python")
                                             "/bin/python")
                              "configure" flags)))))
-         (add-before 'check 'skip-check-doc-only
-           (lambda _
-             (substitute* "Makefile"
-               ;; requires js-yaml, which is not part of the distribution,
-               ;; and falls back to using npm to download it
-               (("\\$\\(MAKE\\) doc-only" all)
-                (string-append "#" all)))
-             #t))
          (add-after 'patch-shebangs 'patch-npm-shebang
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((bindir (string-append (assoc-ref outputs "out")
-- 
cgit v1.2.3


From fe5d4f81be40e68b8cbb846595e6f40d6cdbca13 Mon Sep 17 00:00:00 2001
From: Jelle Licht <jlicht@fsfe.org>
Date: Mon, 12 Mar 2018 17:46:03 +0100
Subject: gnu: node: Use more unbundled dependencies.

* gnu/packages/node.scm (node)[inputs]: Add icu4c and nghttp2.
[native-inputs]: Add pkg-config.
[arguments]: Add configure flags for using system libraries.
[source]: Remove bundled dependencies.
---
 gnu/packages/node.scm | 37 +++++++++++++++++++++++++++++++------
 1 file changed, 31 insertions(+), 6 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/node.scm b/gnu/packages/node.scm
index ea98f28efd..976d0c048a 100644
--- a/gnu/packages/node.scm
+++ b/gnu/packages/node.scm
@@ -31,9 +31,11 @@
   #:use-module (gnu packages base)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages gcc)
+  #:use-module (gnu packages icu4c)
   #:use-module (gnu packages libevent)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages perl)
+  #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages web))
@@ -48,16 +50,36 @@
                                   "/node-v" version ".tar.gz"))
               (sha256
                (base32
-                "1mjr1rm5w26c0yb4zq6z5yv3zbvqk18lwbswhwn1sha8hapinjp8"))))
+                "1mjr1rm5w26c0yb4zq6z5yv3zbvqk18lwbswhwn1sha8hapinjp8"))
+              (modules '((guix build utils)))
+              (snippet
+               `(begin
+                  ;; Remove bundled software.
+                  (for-each delete-file-recursively
+                            '("deps/cares"
+                              "deps/http_parser"
+                              "deps/icu-small"
+                              "deps/nghttp2"
+                              "deps/openssl"
+                              "deps/uv"
+                              "deps/zlib"))
+                  (substitute* "Makefile"
+                    ;; Remove references to bundled software
+                    (("deps/http_parser/http_parser.gyp") "")
+                    (("deps/uv/include/\\*.h") "")
+                    (("deps/uv/uv.gyp") "")
+                    (("deps/zlib/zlib.gyp") ""))))))
     (build-system gnu-build-system)
     (arguments
      ;; TODO: Purge the bundled copies from the source.
-     '(#:configure-flags '("--shared-openssl"
-                           "--shared-zlib"
-                           "--shared-libuv"
-                           "--shared-cares"
+     '(#:configure-flags '("--shared-cares"
                            "--shared-http-parser"
-                           "--without-snapshot")
+                           "--shared-libuv"
+                           "--shared-nghttp2"
+                           "--shared-openssl"
+                           "--shared-zlib"
+                           "--without-snapshot"
+                           "--with-intl=system-icu")
        #:phases
        (modify-phases %standard-phases
          (add-before 'configure 'patch-files
@@ -131,6 +153,7 @@
     (native-inputs
      `(("python" ,python-2)
        ("perl" ,perl)
+       ("pkg-config" ,pkg-config)
        ("procps" ,procps)
        ("util-linux" ,util-linux)
        ("which" ,which)))
@@ -141,7 +164,9 @@
     (inputs
      `(("c-ares" ,c-ares)
        ("http-parser" ,http-parser)
+       ("icu4c" ,icu4c)
        ("libuv" ,libuv)
+       ("nghttp2" ,nghttp2 "lib")
        ("openssl" ,openssl)
        ("zlib" ,zlib)))
     (synopsis "Evented I/O for V8 JavaScript")
-- 
cgit v1.2.3


From 2f17e93974416966bc2b7c1e3286a90a92ee06db Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 12 Mar 2018 15:39:57 +0100
Subject: gnu: gtk-vnc: Update to 0.7.1.

* gnu/packages/gnome.scm (gtk-vnc): Update to 0.7.1.
[native-inputs]: Add python-wrapper.
---
 gnu/packages/gnome.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 2384bf2381..48298e47cc 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -5600,7 +5600,7 @@ like switching to windows and launching applications.")
 (define-public gtk-vnc
   (package
     (name "gtk-vnc")
-    (version "0.7.0")
+    (version "0.7.1")
     (source
      (origin
        (method url-fetch)
@@ -5609,7 +5609,7 @@ like switching to windows and launching applications.")
                            name "-" version ".tar.xz"))
        (sha256
         (base32
-         "0gj8dpy3sj4dp810gy67spzh5f0jd8aqg69clcwqjcskj1yawbiw"))))
+         "1cdaywj5lqnl5b22qzd7k7lmacsnmk8b8rc4drk6gvqmcrlsljzk"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags '("--with-gtk=3.0")))
@@ -5625,6 +5625,7 @@ like switching to windows and launching applications.")
        ("gobject-introspection" ,gobject-introspection)
        ("intltool" ,intltool)
        ("pkg-config" ,pkg-config)
+       ("python-wrapper" ,python-wrapper)
        ("vala" ,vala)))
     (home-page "https://wiki.gnome.org/Projects/gtk-vnc")
     (synopsis "VNC viewer widget for GTK+")
-- 
cgit v1.2.3


From f63d6188d3e27fffd9f29395b189be65082ace4e Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 12 Mar 2018 16:53:57 +0100
Subject: gnu: ogre: Update to 1.10.11.

* gnu/packages/graphics.scm (ogre): Update to 1.10.11.
---
 gnu/packages/graphics.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm
index d6feab1197..8504b2f11e 100644
--- a/gnu/packages/graphics.scm
+++ b/gnu/packages/graphics.scm
@@ -6,7 +6,7 @@
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2017 Manolis Fragkiskos Ragkousis <manolis837@gmail.com>
-;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
+;;; Copyright © 2017, 2018 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;;
@@ -251,7 +251,7 @@ exception-handling library.")
 (define-public ogre
   (package
     (name "ogre")
-    (version "1.10.7")
+    (version "1.10.11")
     (source
      (origin
        (method url-fetch)
@@ -259,7 +259,7 @@ exception-handling library.")
                            "/archive/v" version ".tar.gz"))
        (sha256
         (base32
-         "1p0c91cc7zg3c00wjaibnxb0a0xm14mkg0h65pzpw93m0d6nc8wd"))
+         "13bdh9v4026qf8w8rbfln2rmwf0rby1a8fz55zpdvpy105i6cbpz"))
        (file-name (string-append name "-" version ".tar.gz"))))
     (build-system cmake-build-system)
     (arguments
-- 
cgit v1.2.3


From a440a6af09d530a841b814051f4efb423c65ae21 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 12 Mar 2018 05:15:23 +0100
Subject: gnu: nspr: Mark up description.

* gnu/packages/gnuzilla.scm (nspr)[description]: Use @dfn.
---
 gnu/packages/gnuzilla.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm
index 457a8fbcdc..323743d089 100644
--- a/gnu/packages/gnuzilla.scm
+++ b/gnu/packages/gnuzilla.scm
@@ -274,7 +274,7 @@ in C/C++.")
     (home-page
      "https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR")
     (synopsis "Netscape API for system level and libc-like functions")
-    (description "Netscape Portable Runtime (NSPR) provides a
+    (description "Netscape Portable Runtime (@dfn{NSPR}) provides a
 platform-neutral API for system level and libc-like functions.  It is used
 in the Mozilla clients.")
     (license license:mpl2.0)))
-- 
cgit v1.2.3


From 5400fdfd5d3c2201ee3ea8ec0d55690c221a91d8 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 12 Mar 2018 18:08:04 +0100
Subject: gnu: lrzip: Fix CVE-2017-8842.

* gnu/packages/compression.scm (lrzip)[source]: Add patch.
* gnu/packages/patches/lrzip-CVE-2017-8842.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
---
 gnu/local.mk                                   |  1 +
 gnu/packages/compression.scm                   |  3 ++-
 gnu/packages/patches/lrzip-CVE-2017-8842.patch | 23 +++++++++++++++++++++++
 3 files changed, 26 insertions(+), 1 deletion(-)
 create mode 100644 gnu/packages/patches/lrzip-CVE-2017-8842.patch

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index 5c95cdae21..97d5e00c2b 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -885,6 +885,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/llvm-3.5-fix-clang-build-with-gcc5.patch	\
   %D%/packages/patches/llvm-for-extempore.patch			\
   %D%/packages/patches/lm-sensors-hwmon-attrs.patch		\
+  %D%/packages/patches/lrzip-CVE-2017-8842.patch		\
   %D%/packages/patches/lua-CVE-2014-5461.patch                      \
   %D%/packages/patches/lua-pkgconfig.patch                      \
   %D%/packages/patches/lua51-liblua-so.patch                    \
diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index d44ae2d259..86efe2a40e 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -1017,7 +1017,8 @@ human-readable output.")
              "http://ck.kolivas.org/apps/lrzip/lrzip-" version ".tar.bz2"))
        (sha256
         (base32
-         "0mb449vmmwpkalq732jdyginvql57nxyd31sszb108yps1lf448d"))))
+         "0mb449vmmwpkalq732jdyginvql57nxyd31sszb108yps1lf448d"))
+       (patches (search-patches "lrzip-CVE-2017-8842.patch"))))
     (build-system gnu-build-system)
     (native-inputs
      `(;; nasm is only required when building for 32-bit x86 platforms
diff --git a/gnu/packages/patches/lrzip-CVE-2017-8842.patch b/gnu/packages/patches/lrzip-CVE-2017-8842.patch
new file mode 100644
index 0000000000..89b4f2f5d9
--- /dev/null
+++ b/gnu/packages/patches/lrzip-CVE-2017-8842.patch
@@ -0,0 +1,23 @@
+From 38386bd482c0a8102a79958cb3eddcb97a167ca3 Mon Sep 17 00:00:00 2001
+From: Con Kolivas <kernel@kolivas.org>
+Date: Fri, 9 Mar 2018 17:39:40 +1100
+Subject: [PATCH] CVE-2017-8842 Fix divide-by-zero in bufRead::get
+
+---
+ libzpaq/libzpaq.h | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/libzpaq/libzpaq.h b/libzpaq/libzpaq.h
+index 93387da..cbe211d 100644
+--- a/libzpaq/libzpaq.h
++++ b/libzpaq/libzpaq.h
+@@ -465,7 +465,8 @@ struct bufRead: public libzpaq::Reader {
+ 
+ 	int get() {
+ 		if (progress && !(*s_len % 128)) {
+-			int pct = (total_len - *s_len) * 100 / total_len;
++			int pct = (total_len > 0) ?
++				(total_len - *s_len) * 100 / total_len : 100;
+ 
+ 			if (pct / 10 != *last_pct / 10) {
+ 				int i;
-- 
cgit v1.2.3


From a3a7eb2fe22ec7567d036d174ef65bea4011575c Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sun, 11 Mar 2018 18:50:30 +0100
Subject: gnu: rofi: Update to 1.5.0.

* gnu/packages/xdisorg.scm (rofi): Update to 1.5.0.
[native-inputs]: Add GLIB:BIN.
[arguments]: Add phase to create missing test files.
---
 gnu/packages/xdisorg.scm | 29 ++++++++++++++++++++++++++---
 1 file changed, 26 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm
index a3630b3cb9..173de8e5a2 100644
--- a/gnu/packages/xdisorg.scm
+++ b/gnu/packages/xdisorg.scm
@@ -1101,7 +1101,7 @@ connectivity of the X server running on a particular @code{DISPLAY}.")
 (define-public rofi
   (package
     (name "rofi")
-    (version "1.4.2")
+    (version "1.5.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/DaveDavenport/rofi/"
@@ -1109,7 +1109,7 @@ connectivity of the X server running on a particular @code{DISPLAY}.")
                                   version "/rofi-" version ".tar.xz"))
               (sha256
                (base32
-                "1129cbg76g56c6ckzj5y5haf92jxhx3b71cr3qmhrb0n8g4gi38s"))))
+                "0li2hl55sxzdpbxxiwgxsvkhyy6bh8qd2j1r8xh8y6q8a318zsz9"))))
     (build-system gnu-build-system)
     (inputs
      `(("pango" ,pango)
@@ -1126,6 +1126,7 @@ connectivity of the X server running on a particular @code{DISPLAY}.")
      `(("bison" ,bison)
        ("check" ,check)
        ("flex" ,flex)
+       ("glib:bin" ,glib "bin")
        ("pkg-config" ,pkg-config)))
     (arguments
      `(#:parallel-tests? #f ; May fail in some circumstances.
@@ -1136,7 +1137,29 @@ connectivity of the X server running on a particular @code{DISPLAY}.")
              (substitute* '("test/helper-expand.c")
                (("~root") "/root")
                (("~") "")
-               (("g_get_home_dir \\(\\)") "\"/\"")))))))
+               (("g_get_home_dir \\(\\)") "\"/\""))
+             #t))
+         (add-before 'check 'add-missing-configuration-files
+           (lambda _
+             ;; These files are missing in the 1.5.0 release, causing a test
+             ;; failure: <https://github.com/DaveDavenport/rofi/issues/782>.
+             (with-directory-excursion "subprojects/libnkutils/tests"
+               (mkdir "gtk-3.0")
+               (call-with-output-file "gtk-3.0/settings.ini"
+                 (lambda (port)
+                   (format port "[Settings]
+gtk-double-click-time = 300
+gtk-cursor-theme-name = gnome
+")))
+               (mkdir "gtk-4.0")
+               (call-with-output-file "gtk-4.0/settings.ini"
+                 (lambda (port)
+                   (format port "[Settings]
+gtk-double-click-time = 300
+gtk-icon-theme-name = nothing-like-this-theme
+gtk-enable-primary-paste = true
+")))
+               #t))))))
     (home-page "https://davedavenport.github.io/rofi/")
     (synopsis "Application launcher")
     (description "Rofi is a minimalist application launcher.  It memorizes which
-- 
cgit v1.2.3


From 06229f184fad7a7e997852c58781aa4f9baa773d Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Mon, 12 Mar 2018 03:13:52 +0100
Subject: gnu: rofi: Update redirected home page.

* gnu/packages/xdisorg.scm (rofi)[home-page]: Change to repository URL.
---
 gnu/packages/xdisorg.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm
index 173de8e5a2..07a9b390fa 100644
--- a/gnu/packages/xdisorg.scm
+++ b/gnu/packages/xdisorg.scm
@@ -1160,7 +1160,7 @@ gtk-icon-theme-name = nothing-like-this-theme
 gtk-enable-primary-paste = true
 ")))
                #t))))))
-    (home-page "https://davedavenport.github.io/rofi/")
+    (home-page "https://github.com/DaveDavenport/rofi")
     (synopsis "Application launcher")
     (description "Rofi is a minimalist application launcher.  It memorizes which
 applications you regularly use and also allows you to search for an application
-- 
cgit v1.2.3


From 1a5459ca23cf3198d33345d7bf269a4126e7179e Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Mon, 12 Mar 2018 12:42:29 +0100
Subject: gnu: i3-wm: Update to 4.15.

* gnu/packages/wm.scm (i3-wm): Update to 4.15.
---
 gnu/packages/wm.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm
index 888173313b..b38b3caa25 100644
--- a/gnu/packages/wm.scm
+++ b/gnu/packages/wm.scm
@@ -175,14 +175,14 @@ commands would.")
 (define-public i3-wm
   (package
     (name "i3-wm")
-    (version "4.14.1")
+    (version "4.15")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://i3wm.org/downloads/i3-"
                                   version ".tar.bz2"))
               (sha256
                (base32
-                "1cazmfbbx6n8c81h6x6pdayq3mxs2ml3adz165z8vapkc72kl1nh"))))
+                "09jk70hsdxab24lqvj2f30ijrkbv3f6q9xi5dcsax1dw3x6m4z91"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags
-- 
cgit v1.2.3


From 607d280ec82e8c4849926a380f4c717585a4ce80 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Mon, 5 Mar 2018 11:03:28 +0200
Subject: gnu: Add jetring.

* gnu/packages/gnupg.scm (jetring): New variable.
---
 gnu/packages/gnupg.scm | 57 +++++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 56 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm
index 28f5b58887..2696e332de 100644
--- a/gnu/packages/gnupg.scm
+++ b/gnu/packages/gnupg.scm
@@ -4,7 +4,7 @@
 ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2014, 2015, 2016 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
-;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016 Christopher Allan Webber <cwebber@dustycloud.org>
 ;;; Copyright © 2016, 2017 ng0 <ng0@infotropique.org>
@@ -929,3 +929,58 @@ keyring content.  Parcimonie is a daemon that fetches one key at a time using
 the Tor network, waits a bit, changes the Tor circuit being used, and starts
 over.")
     (license license:gpl1+)))
+
+(define-public jetring
+  (package
+    (name "jetring")
+    (version "0.25")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "mirror://debian/pool/main/j/" name "/"
+                            name "_" version ".tar.xz"))
+        (sha256
+         (base32
+          "0shcnnw0h31b08vmnvf18ni33dg40w18wv9smb69vkklz3h4jhpw"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (delete 'configure) ; no configure script
+         (add-before 'install 'hardlink-gnupg
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((gpg (string-append (assoc-ref inputs "gnupg")
+                                       "/bin/gpg")))
+               (substitute* (find-files "." "jetring-[[:alpha:]]+$")
+                 (("gpg -") (string-append gpg " -"))
+                 (("\\\"gpg\\\"") (string-append "\"" gpg "\"")))
+               #t)))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (man (string-append out "/share/man")))
+               (for-each (lambda (file)
+                           (install-file file (string-append out "/bin/")))
+                         (find-files "." "jetring-[[:alpha:]]+$"))
+               (for-each (lambda (file)
+                           (install-file file (string-append man "/man1/")))
+                         (find-files "." ".*\\.1$"))
+               (install-file "jetring.7" (string-append man "/man7/"))
+               #t))))
+       #:tests? #f)) ; no test phase
+    (inputs
+     `(("gnupg" ,gnupg)
+       ("perl" ,perl)))
+    (home-page "https://joeyh.name/code/jetring/")
+    (synopsis "GnuPG keyring maintenance using changesets")
+    (description
+     "Jetring is a collection of tools that allow for gpg keyrings to be
+maintained using changesets.  It was developed with the Debian keyring in mind,
+and aims to solve the problem that a gpg keyring is a binary blob that's hard
+for multiple people to collaboratively edit.
+
+With jetring, changesets can be submitted, reviewed to see exactly what they
+will do, applied, and used to build a keyring.  The origin of every change made
+to the keyring is available for auditing, and gpg signatures can be used for
+integrity guarantees.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 8e1cd1a2c53a2944012d5b2c1670e7203cdf91b6 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Mon, 5 Mar 2018 11:08:32 +0200
Subject: gnu: Add debian-archive-keyring.

* gnu/packages/debian.scm (debian-archive-keyring): New variable.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
---
 gnu/local.mk            |  1 +
 gnu/packages/debian.scm | 62 +++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 63 insertions(+)
 create mode 100644 gnu/packages/debian.scm

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index 97d5e00c2b..5a3ae502f2 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -120,6 +120,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/datastructures.scm		\
   %D%/packages/dav.scm				\
   %D%/packages/dc.scm				\
+  %D%/packages/debian.scm			\
   %D%/packages/debug.scm			\
   %D%/packages/dejagnu.scm			\
   %D%/packages/dico.scm				\
diff --git a/gnu/packages/debian.scm b/gnu/packages/debian.scm
new file mode 100644
index 0000000000..70131ff451
--- /dev/null
+++ b/gnu/packages/debian.scm
@@ -0,0 +1,62 @@
+;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages debian)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix download)
+  #:use-module (guix packages)
+  #:use-module (guix build-system gnu)
+  #:use-module (gnu packages gnupg))
+
+(define-public debian-archive-keyring
+  (package
+    (name "debian-archive-keyring")
+    (version "2017.7")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "mirror://debian/pool/main/d/" name "/"
+                            name "_" version ".tar.xz"))
+        (sha256
+         (base32
+          "1pdwgipfi0y4svhxlw8arhq792f1g3vlmw4raphizy7sa65vd4ca"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:test-target "verify-results"
+       #:parallel-build? #f ; has race conditions
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure) ; no configure script
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (apt (string-append out "/etc/apt/trusted.gpg.d/"))
+                    (key (string-append out "/share/keyrings/")))
+               (install-file "keyrings/debian-archive-keyring.gpg" key)
+               (install-file "keyrings/debian-archive-removed-keys.gpg" key)
+               (for-each (lambda (file)
+                           (install-file file apt))
+                         (find-files "trusted.gpg" "\\.gpg$")))
+             #t)))))
+    (native-inputs
+     `(("gnupg" ,gnupg)
+       ("jetring" ,jetring)))
+    (home-page "https://packages.qa.debian.org/d/debian-archive-keyring.html")
+    (synopsis "GnuPG archive keys of the Debian archive")
+    (description
+     "The Debian project digitally signs its Release files.  This package
+contains the archive keys used for that.")
+    (license (list license:public-domain ; the keys
+                   license:gpl2+)))) ; see debian/copyright
-- 
cgit v1.2.3


From b3230c287ae244df518c78cc65b5f20cdb5f0885 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Mon, 5 Mar 2018 11:15:20 +0200
Subject: gnu: Add ubuntu-keyring.

* gnu/packages/debian.scm (ubuntu-keyring): New variable.
---
 gnu/packages/debian.scm | 45 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/debian.scm b/gnu/packages/debian.scm
index 70131ff451..15d4429939 100644
--- a/gnu/packages/debian.scm
+++ b/gnu/packages/debian.scm
@@ -18,6 +18,9 @@
   #:use-module (guix download)
   #:use-module (guix packages)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system trivial)
+  #:use-module (gnu packages base)
+  #:use-module (gnu packages compression)
   #:use-module (gnu packages gnupg))
 
 (define-public debian-archive-keyring
@@ -60,3 +63,45 @@
 contains the archive keys used for that.")
     (license (list license:public-domain ; the keys
                    license:gpl2+)))) ; see debian/copyright
+
+(define-public ubuntu-keyring
+  (package
+    (name "ubuntu-keyring")
+    (version "2018.02.28")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "https://launchpad.net/ubuntu/+archive/primary/"
+                            "+files/" name "_" version ".tar.gz"))
+        (sha256
+         (base32
+          "1zj3012cz7rlx9pm39wnwa0lmi1h38n6bkgbz81vnmcsvqsc9a3a"))))
+    (build-system trivial-build-system)
+    (arguments
+     `(#:modules ((guix build utils))
+       #:builder (begin
+                   (use-modules (guix build utils))
+                   (let* ((out (assoc-ref %outputs "out"))
+                          (apt (string-append out "/etc/apt/trusted.gpg.d/"))
+                          (key (string-append out "/share/keyrings/")))
+                     (setenv "PATH" (string-append
+                                      (assoc-ref %build-inputs "gzip") "/bin:"
+                                      (assoc-ref %build-inputs "tar") "/bin"))
+                     (invoke "tar" "xvf" (assoc-ref %build-inputs "source"))
+                     (for-each (lambda (file)
+                                 (install-file file apt))
+                               (find-files "." "ubuntu-[^am].*\\.gpg$"))
+                     (for-each (lambda (file)
+                                 (install-file file key))
+                               (find-files "." "ubuntu-[am].*\\.gpg$")))
+                   #t)))
+    (native-inputs
+     `(("tar" ,tar)
+       ("gzip" ,gzip)))
+    (home-page "https://launchpad.net/ubuntu/+source/ubuntu-keyring")
+    (synopsis "GnuPG keys of the Ubuntu archive")
+    (description
+     "The Ubuntu project digitally signs its Release files.  This package
+contains the archive keys used for that.")
+    (license (list license:public-domain ; the keys
+                   license:gpl2+)))) ; see debian/copyright
-- 
cgit v1.2.3


From 298a2c1e669f1782f3e3d92c96bb55e9000163ce Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Mon, 5 Mar 2018 11:17:45 +0200
Subject: gnu: Add debootstrap.

* gnu/packages/debian.scm (debootstrap): New variable.
---
 gnu/packages/debian.scm | 65 ++++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 64 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/debian.scm b/gnu/packages/debian.scm
index 15d4429939..3c3189e073 100644
--- a/gnu/packages/debian.scm
+++ b/gnu/packages/debian.scm
@@ -21,7 +21,9 @@
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages base)
   #:use-module (gnu packages compression)
-  #:use-module (gnu packages gnupg))
+  #:use-module (gnu packages gnupg)
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages wget))
 
 (define-public debian-archive-keyring
   (package
@@ -105,3 +107,64 @@ contains the archive keys used for that.")
 contains the archive keys used for that.")
     (license (list license:public-domain ; the keys
                    license:gpl2+)))) ; see debian/copyright
+
+(define-public debootstrap
+  (package
+    (name "debootstrap")
+    (version "1.0.93")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "mirror://debian/pool/main/d/" name "/"
+                            name "_" version ".tar.gz"))
+        (sha256
+         (base32
+          "1nyp9fwb7xrk1vin81dmgx2g9rb52yg4gwz4rcx97gamw4mlvbfd"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (add-after 'unpack 'patch-source
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out    (assoc-ref outputs "out"))
+                   (wget   (assoc-ref inputs "wget"))
+                   (debian (assoc-ref inputs "debian-keyring"))
+                   (ubuntu (assoc-ref inputs "ubuntu-keyring")))
+               (substitute* "Makefile"
+                 (("/usr") "")
+                 (("-o root -g root") "")
+                 (("chown root.*") "\n"))
+               (substitute* "scripts/sid"
+                 (("/usr") debian))
+               (substitute* "scripts/gutsy"
+                 (("/usr") ubuntu))
+               (substitute* "debootstrap"
+                 (("=/usr") (string-append "=" out)))
+               (substitute* "functions"
+                 (("wget ") (string-append wget "/bin/wget ")))
+               #t)))
+         (add-after 'install 'install-man-file
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (install-file "debootstrap.8"
+                             (string-append out "/share/man/man8"))
+               #t))))
+       #:make-flags (list (string-append "DESTDIR=" (assoc-ref %outputs "out")))
+       #:tests? #f)) ; no tests
+    (inputs
+     `(("debian-keyring" ,debian-archive-keyring)
+       ("ubuntu-keyring" ,ubuntu-keyring)
+       ("wget" ,wget)))
+    ;; The following are required for debootstrap to work correctly
+    (propagated-inputs
+     `(("binutils" ,binutils)
+       ("gnupg" ,gnupg)
+       ("perl" ,perl)))
+    (home-page "https://anonscm.debian.org/cgit/d-i/debootstrap.git")
+    (synopsis "Bootstrap a basic Debian system")
+    (description "Debootstrap is used to create a Debian base system from
+scratch, without requiring the availability of @code{dpkg} or @code{apt}.
+It does this by downloading .deb files from a mirror site, and carefully
+unpacking them into a directory which can eventually be chrooted into.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From 7d20d9832699529e9dc094ea94d7b94dc360aa3b Mon Sep 17 00:00:00 2001
From: Rutger Helling <rhelling@mykolab.com>
Date: Tue, 13 Mar 2018 08:19:45 +0100
Subject: gnu: gnome-sudoku: Update to 3.28.0.

* gnu/packages/gnome.scm (gnome-sudoku): Update to 3.28.0.
---
 gnu/packages/gnome.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 48298e47cc..30be123f4d 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -2689,7 +2689,7 @@ floating in an ocean using only your brain and a little bit of luck.")
 (define-public gnome-sudoku
   (package
     (name "gnome-sudoku")
-    (version "3.26.0")
+    (version "3.28.0")
     (source
      (origin
        (method url-fetch)
@@ -2698,7 +2698,7 @@ floating in an ocean using only your brain and a little bit of luck.")
                            name "-" version ".tar.xz"))
        (sha256
         (base32
-         "186k2axryn3ic8blc9ddnvyrqqf88khg2hlisfa1n4wp784wfx47"))))
+         "07b4lzniaf3gjsss6zl1lslv18smwc4nrijykvn2z90f423q2xav"))))
     (build-system glib-or-gtk-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)
-- 
cgit v1.2.3


From 0982e5c7f1616ecef8ce61128ddf417df609d79f Mon Sep 17 00:00:00 2001
From: Rutger Helling <rhelling@mykolab.com>
Date: Tue, 13 Mar 2018 08:36:16 +0100
Subject: gnu: gedit: Update to 3.28.0.

* gnu/packages/gnome.scm (gedit): Update to 3.28.0.
---
 gnu/packages/gnome.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 30be123f4d..4eb52066c5 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -4645,7 +4645,7 @@ javascript engine and the GObject introspection framework.")
 (define-public gedit
   (package
     (name "gedit")
-    (version "3.22.1")
+    (version "3.28.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/" name "/"
@@ -4653,7 +4653,7 @@ javascript engine and the GObject introspection framework.")
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "0as9r5zvnyrxh699q6jnd0p9ddqy5qamfbxggpdjzagzixhw6yxa"))))
+                "0pyam0zi44xq776x20ycqnvmf86l98jns8ldv4m81gnp9wnhmycv"))))
     (build-system glib-or-gtk-build-system)
     (arguments
      `(#:phases
-- 
cgit v1.2.3


From 8456765772cb48a428a15719e32ab49c9d4d7a53 Mon Sep 17 00:00:00 2001
From: Oleg Pykhalov <go.wigust@gmail.com>
Date: Thu, 1 Mar 2018 18:51:17 +0300
Subject: gnu: Add flameshot.

* gnu/packages/image.scm (flameshot): New public variable.
---
 gnu/packages/image.scm | 43 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm
index e3e3a3ccc7..b576c508ec 100644
--- a/gnu/packages/image.scm
+++ b/gnu/packages/image.scm
@@ -58,6 +58,7 @@
   #:use-module (gnu packages python)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg)
+  #:use-module (gnu packages qt)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix download)
@@ -1250,3 +1251,45 @@ such as images.  This metadata can include captions and keywords, often used by
 popular photo management applications.  The library provides routines for
 parsing, viewing, modifying, and saving this metadata.")
     (license license:lgpl2.0+)))
+
+(define-public flameshot
+  (package
+    (name "flameshot")
+    (version "0.5.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/lupoDharkael/flameshot/archive/"
+                           "v" version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0kp451bqgssvg8n3sg60s3fifplm9l5kxiij0yxkl864p2mhw8im"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("qttools" ,qttools)))
+    (inputs
+     `(("qtbase" ,qtbase)))
+    (arguments
+     `(#:tests? #f ; no tests
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'configure
+           (lambda* (#:key outputs #:allow-other-keys)
+             (invoke "qmake"
+                     "CONFIG+=packaging"
+                     (string-append "BASEDIR=" (assoc-ref outputs "out"))
+                     "PREFIX=/"))))))
+    (home-page "https://github.com/lupoDharkael/flameshot")
+    (synopsis "Powerful yet simple to use screenshot software")
+    (description "Flameshot is a screenshot program.
+Features:
+
+@itemize
+@item Customizable appearance.
+@item Easy to use.
+@item In-app screenshot edition.
+@item DBus interface.
+@item Upload to Imgur.
+@end itemize\n")
+    (license license:gpl3+)))
-- 
cgit v1.2.3


From 906dcb20f2847d4f886e482642e2a5d361c5c59c Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Sat, 3 Mar 2018 22:02:27 +0000
Subject: gnu: Add makefile2graph.

* gnu/packages/code.scm (makefile2graph): New variable.
---
 gnu/packages/code.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm
index 13a89c7bcc..979c7a72b8 100644
--- a/gnu/packages/code.scm
+++ b/gnu/packages/code.scm
@@ -37,6 +37,7 @@
   #:use-module (gnu packages databases)
   #:use-module (gnu packages emacs)
   #:use-module (gnu packages gcc)
+  #:use-module (gnu packages graphviz)
   #:use-module (gnu packages pcre)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages perl)
@@ -497,3 +498,32 @@ importantly we give you proper follow-symbol and find-references support.")
     (description "This package provides a wrapper around @command{make} to
 produce colored output.")
     (license license:gpl2+)))
+
+(define-public makefile2graph
+  (package
+    (name "makefile2graph")
+    (version "1.5.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/lindenb/" name
+                                  "/archive/v" version ".tar.gz"))
+              (sha256
+               (base32
+                "0h1vchkpmm9h6s87p5nf0ksjxcmsxpx8k62a508w428n570wcr4l"))
+              (file-name (string-append name "-" version ".tar.gz"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:test-target "test"
+       #:make-flags (list "CC=gcc" (string-append "prefix=" %output))
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure))))
+    (native-inputs
+     `(("graphviz" ,graphviz)))
+    (home-page "https://github.com/lindenb/makefile2graph")
+    (synopsis "Creates a graph of dependencies from GNU Make")
+    (description
+     "@code{make2graph} creates a graph of dependencies from GNU Make.  The
+output is a graphviz-dot file, a Gexf-XML file or a list of the deepest
+independent targets.")
+    (license license:expat)))
-- 
cgit v1.2.3


From 64f925cb4bb726b07e1d115e1132688ca47bdefe Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 19:47:32 +0200
Subject: gnu: time: Update to 1.9.

* gnu/packages/time.scm (time): Update to 1.9.
* tests/guix-build.sh: Update time package to 1.9.
---
 gnu/packages/time.scm | 6 +++---
 tests/guix-build.sh   | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/time.scm b/gnu/packages/time.scm
index 59414f6d7c..c7a285079c 100644
--- a/gnu/packages/time.scm
+++ b/gnu/packages/time.scm
@@ -2,7 +2,7 @@
 ;;; Copyright © 2012 Nikita Karetnikov <nikita@karetnikov.org>
 ;;; Copyright © 2013, 2017 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013, 2015 Andreas Enge <andreas@enge.fr>
-;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2015, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2015, 2017 Cyril Roelandt <tipecaml@gmail.com>
 ;;; Copyright © 2016 Sou Bunnbu <iyzsong@gmail.com>
@@ -43,7 +43,7 @@
 (define-public time
   (package
     (name "time")
-    (version "1.8")
+    (version "1.9")
     (source
      (origin
       (method url-fetch)
@@ -51,7 +51,7 @@
                           version ".tar.gz"))
       (sha256
        (base32
-        "06rfg8dn0q2r8pdq8i6brrs6rqrsgvkwbbl4kfx3a6lnal0m8bwa"))))
+        "07jj7cz6lc13iqrpgn81ivqh8rkm73p4rnivwgrrshk23v4g1b7v"))))
     (build-system gnu-build-system)
     (home-page "https://www.gnu.org/software/time/")
     (synopsis "Run a command, then display its resource usage")
diff --git a/tests/guix-build.sh b/tests/guix-build.sh
index 004a40dee2..b84723fa43 100644
--- a/tests/guix-build.sh
+++ b/tests/guix-build.sh
@@ -184,7 +184,7 @@ test "`guix build superseded -d`" = "`guix build bar -d`"
 
 # Parsing package names and versions.
 guix build -n time		# PASS
-guix build -n time@1.8		# PASS, version found
+guix build -n time@1.9		# PASS, version found
 if guix build -n time@3.2;	# FAIL, version not found
 then false; else true; fi
 if guix build -n something-that-will-never-exist; # FAIL
-- 
cgit v1.2.3


From 671249b934728b25bc4ccc710e78273981af5c1c Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 19:51:41 +0200
Subject: gnu: tinyxml: Declare a source file-name.

* gnu/packages/xml.scm (tinyxml)[source]: Declare a source file-name.
---
 gnu/packages/xml.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm
index 5f7a95463a..80933a872b 100644
--- a/gnu/packages/xml.scm
+++ b/gnu/packages/xml.scm
@@ -993,6 +993,7 @@ UTF-8 and UTF-16 encoding.")
                                   version "/tinyxml_"
                                   (string-join (string-split version #\.) "_")
                                   ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
                 "14smciid19lvkxqznfig77jxn5s4iq3jpb47vh5a6zcaqp7gvg8m"))
-- 
cgit v1.2.3


From 0efb64524bf3abaf8f4de9514fd0fb083300b2f6 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 19:57:14 +0200
Subject: gnu: tinyxml: Use 'invoke'.

* gnu/packages/xml.scm (tinyxml)[arguments]: Replace 'system*' calls
with 'invoke'.
---
 gnu/packages/xml.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm
index 80933a872b..bde959a284 100644
--- a/gnu/packages/xml.scm
+++ b/gnu/packages/xml.scm
@@ -5,7 +5,7 @@
 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
 ;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015, 2016, 2017 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2015 Raimon Grau <raimonster@gmail.com>
 ;;; Copyright © 2016 Mathieu Lirzin <mthl@gnu.org>
 ;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name>
@@ -1007,12 +1007,12 @@ UTF-8 and UTF-16 encoding.")
          (delete 'configure)
          (add-after 'build 'build-shared-library
            (lambda _
-             (zero? (system* "g++" "-Wall" "-O2" "-shared" "-fpic"
-                             "tinyxml.cpp" "tinyxmlerror.cpp"
-                             "tinyxmlparser.cpp" "tinystr.cpp"
-                             "-o" "libtinyxml.so"))))
+             (invoke "g++" "-Wall" "-O2" "-shared" "-fpic"
+                     "tinyxml.cpp" "tinyxmlerror.cpp"
+                     "tinyxmlparser.cpp" "tinystr.cpp"
+                     "-o" "libtinyxml.so")))
          (replace 'check
-           (lambda _ (zero? (system "./xmltest"))))
+           (lambda _ (invoke "./xmltest")))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
-- 
cgit v1.2.3


From 87d868cc7ca3efdfc1ec6ace076e8eb9096af4e5 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 20:01:03 +0200
Subject: gnu: gpscorrelate: Declare a source file-name.

* gnu/packages/gps.scm (gpscorrelate)[source]: Declare a source file-name.
---
 gnu/packages/gps.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gps.scm b/gnu/packages/gps.scm
index 211a33ef89..e07c9f4acb 100644
--- a/gnu/packages/gps.scm
+++ b/gnu/packages/gps.scm
@@ -108,6 +108,7 @@ manipulate maps.")
                 (uri (git-reference
                       (url "https://github.com/freefoote/gpscorrelate")
                       (commit commit)))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
                   "006a6l8p38a4h7y2959sqrmjjn29d8pd50zj9nypcp5ph18nybjb"))))
-- 
cgit v1.2.3


From 4a885c650db278515fd5ae143a97cdb9d0f3b4fc Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 20:03:45 +0200
Subject: gnu: ganv-devel: Declare a source file-name.

* gnu/packages/gtk.scm (ganv-devel)[source]: Declare a source file-name.
---
 gnu/packages/gtk.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm
index a96cb96470..0e98a7c9d5 100644
--- a/gnu/packages/gtk.scm
+++ b/gnu/packages/gtk.scm
@@ -322,6 +322,7 @@ diagrams.")
                 (uri (git-reference
                       (url "http://git.drobilla.net/ganv.git")
                       (commit commit)))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
                   "1cr8w02lr6bk9mkxa12j3imq721b2an2yn4bj5wnwmpm91ddn2gi")))))))
-- 
cgit v1.2.3


From 6c34ad73d5190b2793a1bb80bb42eeb2850f45c5 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 20:05:27 +0200
Subject: gnu: java-jnacl: Declare a source file-name.

* gnu/packages/java.scm (java-jnacl)[source]: Declare a source
file-name.
---
 gnu/packages/java.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index bdfd3fd41b..e2c4b2c1e6 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -7982,6 +7982,7 @@ to use.")
                 (uri (git-reference
                       (url "https://github.com/neilalexander/jnacl.git")
                       (commit commit)))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
                   "1d6g6xhn83byv5943n7935wwjsk0ibk0qdvqgr699qqgqqmwisbb"))))
-- 
cgit v1.2.3


From 307856cdfa58d72434be06de12d79e2dce25189d Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 20:06:29 +0200
Subject: gnu: java-snakeyaml: Declare a source file-name.

* gnu/packages/java.scm (java-snakeyaml)[source]: Declare a source
file-name.
---
 gnu/packages/java.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index e2c4b2c1e6..521293da48 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -7307,6 +7307,7 @@ configuration.")
               (method url-fetch)
               (uri (string-append "https://bitbucket.org/asomov/snakeyaml/get/v"
                                   version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
                 "0rf5ha6w0waz50jz2479jsrbgmd0dnx0gs337m126j5z7zlmg7mg"))))
-- 
cgit v1.2.3


From 8cf57bc1c6a938fd62deb0e4bf9ef5e460c24669 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 20:07:51 +0200
Subject: gnu: libusb4java: Declare a source file-name.

* gnu/packages/libusb.scm (libusb4java)[source]: Declare a source
file-name.
---
 gnu/packages/libusb.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/libusb.scm b/gnu/packages/libusb.scm
index 10a5a91db4..e5a63803d8 100644
--- a/gnu/packages/libusb.scm
+++ b/gnu/packages/libusb.scm
@@ -124,6 +124,7 @@ version of libusb to run with newer libusb.")
                 (uri (git-reference
                       (url "https://github.com/usb4java/libusb4java.git")
                       (commit commit)))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
                   "0wqgapalhfh9v38ycbl6i2f5lh1wpr6fzwn5dwd0rdacypkd1gml"))))
-- 
cgit v1.2.3


From 03e8182b8ea0e5be756416198a3ef49f45b6116c Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 20:10:08 +0200
Subject: gnu: sbcl-cl-uglify-js: Declare a source file-name.

* gnu/packages/lisp.scm (sbcl-cl-uglify-js)[source]: Declare a source
file-name.
---
 gnu/packages/lisp.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index a506566a05..1cda606c20 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -1370,6 +1370,7 @@ It is similar to the @code{CL:LOOP} macro, with these distinguishing marks:
          (uri (git-reference
                (url "https://github.com/mishoo/cl-uglify-js.git")
                (commit commit)))
+         (file-name (git-file-name name version))
          (sha256
           (base32
            "0k39y3c93jgxpr7gwz7w0d8yknn1fdnxrjhd03057lvk5w8js27a"))))
-- 
cgit v1.2.3


From 7b5f8a998a7d0ab7e8509a51b32f82ddbbb70713 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 20:11:09 +0200
Subject: gnu: hydrogen: Declare a source file-name.

* gnu/packages/music.scm (hydrogen)[source]: Declare a source file-name.
---
 gnu/packages/music.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index f47749b380..4bd58d9733 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -441,6 +441,7 @@ background while you work.")
               (uri (string-append
                     "https://github.com/hydrogen-music/hydrogen/archive/"
                     version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
                 "1dy2jfkdw0nchars4xi4isrz66fqn53a9qk13bqza7lhmsg3s3qy"))))
-- 
cgit v1.2.3


From f45ceced511c1902133255a52f78de637d173be2 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 20:12:24 +0200
Subject: gnu: pulsemixer: Declare a source file-name.

* gnu/packages/pulseaudio.scm (pulsemixer)[source]: Declare a source
file-name.
---
 gnu/packages/pulseaudio.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/pulseaudio.scm b/gnu/packages/pulseaudio.scm
index 903b22529d..8a45137a7f 100644
--- a/gnu/packages/pulseaudio.scm
+++ b/gnu/packages/pulseaudio.scm
@@ -280,6 +280,7 @@ sinks.")
               (method url-fetch)
               (uri (string-append "https://github.com/GeorgeFilipkin/"
                                   "pulsemixer/archive/" version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
                 "1lpad90ifr2xfldyf39sbwx1v85rif2gm9w774gwwpjv53zfgk1g"))))
-- 
cgit v1.2.3


From c819558227eeb686765c116afe1d67f40d5b8066 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 20:13:56 +0200
Subject: gnu: python-asn1crypto: Declare a source file-name.

* gnu/packages/python-crypto.scm (python-asn1crypto)[source]: Declare a
source file-name.
---
 gnu/packages/python-crypto.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm
index 701e23c2ac..3734b6ba10 100644
--- a/gnu/packages/python-crypto.scm
+++ b/gnu/packages/python-crypto.scm
@@ -538,6 +538,7 @@ ECB and OFB).")
         (method url-fetch)
         (uri (string-append "https://github.com/wbond/asn1crypto/archive/"
                             version ".tar.gz"))
+        (file-name (string-append name "-" version ".tar.gz"))
         (sha256
          (base32
           "1kn910896l3knmilla1c9ly20q181s43w1ah08lzkbm1h3j6pcz0"))))
-- 
cgit v1.2.3


From 7896e6c219b22bf001501198b1ce574944921de8 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 20:15:14 +0200
Subject: gnu: python-dukpy: Declare a source file-name.

* gnu/packages/python.scm (python-dukpy)[source]: Declare a source
file-name.
---
 gnu/packages/python.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 895a8bde3a..5c7588767e 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -12263,6 +12263,7 @@ executed more than a given number of times during a given period.")
        (method url-fetch)
        (uri (string-append "https://github.com/kovidgoyal/dukpy/archive/v"
                            version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
          "0pj39rfwlzivqm5hkrsza7gssg6ggpxlq5ivc8f3h7x5pfgc6y6c"))))
-- 
cgit v1.2.3


From 79f450a120068ac1d2fc4e5b4b33ae938b604f95 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 20:16:20 +0200
Subject: gnu: python-mwclient: Declare a source file-name.

* gnu/packages/python.scm (python-mwclient)[source]: Declare a source
file-name.
---
 gnu/packages/python.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 5c7588767e..22fbdf6720 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -11015,6 +11015,7 @@ exception message with a traceback that points to the culprit.")
        ;; The PyPI version wouldn't contain tests.
        (uri (string-append "https://github.com/mwclient/mwclient/archive/"
                            "v" version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
          "1jj0yhilkjir00719fc7w133x7hdyhkxhk6xblla4asig45klsfv"))))
-- 
cgit v1.2.3


From 0efd09acd402e1d333e21df35fe64cb9ee8d6811 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 13 Mar 2018 19:57:35 +0100
Subject: gnu: Add r-riverplot.

* gnu/packages/cran.scm (r-riverplot): New variable.
---
 gnu/packages/cran.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 9b690833ce..b7126518c1 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3192,3 +3192,25 @@ data, commencing with a port of the Matlab gaussian window smoothing function.
 In addition, several functions typically used in smoothing of financial data
 are included.")
     (license license:gpl2)))
+
+(define-public r-riverplot
+  (package
+    (name "r-riverplot")
+    (version "0.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "riverplot" version))
+       (sha256
+        (base32
+         "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
+    (build-system r-build-system)
+    (home-page "https://logfc.wordpress.com")
+    (synopsis "Sankey or ribbon plots")
+    (description
+     "Sankey plots are a type of diagram that is convenient to illustrate how
+flow of information, resources etc. separates and joins, much like observing
+how rivers split and merge.  For example, they can be used to compare
+different clusterings.  This package provides an implementation of Sankey
+plots for R.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 379cb3893d15ce00f76d0eb5c477670019d47b42 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 13 Mar 2018 17:21:37 +0100
Subject: gnu: Add ghc-aeson-for-pandoc-1.

* gnu/packages/haskell-web.scm (ghc-aeson-for-pandoc-1): New variable.
---
 gnu/packages/haskell-web.scm | 12 ++++++++++++
 1 file changed, 12 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index f1b50b29bd..1190bc63a5 100644
--- a/gnu/packages/haskell-web.scm
+++ b/gnu/packages/haskell-web.scm
@@ -777,6 +777,18 @@ for Haskell, optimized for ease of use and high performance.  (A note on
 naming: in Greek mythology, Aeson was the father of Jason.)")
     (license license:bsd-3)))
 
+(define-public ghc-aeson-for-pandoc-1
+  (package (inherit ghc-aeson)
+    (version "1.1.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/aeson/aeson-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "1zy5z8pzvh53qkjm0nm3f4rwqfqg3867ck8ncd6mrxpcyvxqqj1p"))))))
+
 (define-public ghc-aeson-pretty
   (package
     (name "ghc-aeson-pretty")
-- 
cgit v1.2.3


From 0f1fef71938371a24743501e267cfd8c36893d09 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 13 Mar 2018 17:21:55 +0100
Subject: gnu: Add ghc-pandoc-types-for-pandoc-1.

* gnu/packages/haskell.scm (ghc-pandoc-types-for-pandoc-1): New variable.
---
 gnu/packages/haskell.scm | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index e7401e5cf4..6c8b33ae4d 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -4980,6 +4980,22 @@ pandoc to represent structured documents.  It also provides functions for
 building up, manipulating and serialising @code{Pandoc} structures.")
     (license license:bsd-3)))
 
+(define-public ghc-pandoc-types-for-pandoc-1
+  (package (inherit ghc-pandoc-types)
+    (version "1.17.0.5")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://hackage.haskell.org/package/"
+                                  "pandoc-types/pandoc-types-"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "1csipjdq00iiq77k2wlrg4i7afrzlh8nl585q785xzw7nn45b0n8"))))
+    (inputs
+     `(("ghc-syb" ,ghc-syb)
+       ("ghc-aeson" ,ghc-aeson-for-pandoc-1)
+       ("ghc-string-qq" ,ghc-string-qq)))))
+
 (define-public ghc-texmath
   (package
     (name "ghc-texmath")
-- 
cgit v1.2.3


From dcf8e2ab30afd76754126a54059a60dd7c128e10 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 13 Mar 2018 17:22:09 +0100
Subject: gnu: Add ghc-texmath-for-pandoc-1.

* gnu/packages/haskell.scm (ghc-texmath-for-pandoc-1): New variable.
---
 gnu/packages/haskell.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 6c8b33ae4d..3359a196cf 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -5029,6 +5029,27 @@ markup formats).  The TeX reader supports basic LaTeX and AMS extensions, and
 it can parse and apply LaTeX macros.")
     (license license:gpl2+)))
 
+(define-public ghc-texmath-for-pandoc-1
+  (package (inherit ghc-texmath)
+    (version "0.9.4.4")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://hackage.haskell.org/package/"
+                                  "texmath/texmath-" version ".tar.gz"))
+              (sha256
+               (base32
+                "129q33m56diiv35kdwfb07838wrg0mm88kxdqxfyl1zvf9nzkqkd"))))
+    (inputs
+     `(("ghc-mtl" ,ghc-mtl)
+       ("ghc-network-uri" ,ghc-network-uri)
+       ("ghc-pandoc-types" ,ghc-pandoc-types-for-pandoc-1)
+       ("ghc-parsec" ,ghc-parsec)
+       ("ghc-split" ,ghc-split)
+       ("ghc-syb" ,ghc-syb)
+       ("ghc-temporary" ,ghc-temporary)
+       ("ghc-utf8-string" ,ghc-utf8-string)
+       ("ghc-xml" ,ghc-xml)))))
+
 (define-public ghc-regex-pcre-builtin
   (package
     (name "ghc-regex-pcre-builtin")
-- 
cgit v1.2.3


From f45c86b555820b4ddfe4705f052eca480da03ae1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 13 Mar 2018 17:22:30 +0100
Subject: gnu: Add ghc-hslua-for-pandoc-1.

* gnu/packages/haskell.scm (ghc-hslua-for-pandoc-1): New variable.
---
 gnu/packages/haskell.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 3359a196cf..a222e1b4ae 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -5703,6 +5703,27 @@ TIFF and GIF formats.")
 described in @url{https://www.lua.org/}.")
     (license license:expat)))
 
+(define-public ghc-hslua-for-pandoc-1
+  (package (inherit ghc-hslua)
+    (version "0.4.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://hackage.haskell.org/package/"
+                                  "hslua/hslua-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0gqp6qhp4v24kzv2j49kgk7bxqzw0w10x0zr0r2j9wkfavqb9wid"))))
+    (inputs
+     `(("lua" ,lua-5.1)
+       ("ghc-text" ,ghc-text)))
+    (native-inputs
+     `(("ghc-quickcheck" ,ghc-quickcheck)
+       ("ghc-quickcheck-instances" ,ghc-quickcheck-instances)
+       ("ghc-hspec" ,ghc-hspec)
+       ("ghc-hspec-contrib" ,ghc-hspec-contrib)
+       ("ghc-hunit" ,ghc-hunit)
+       ("hspec-discover" ,hspec-discover)))))
+
 (define-public ghc-hslua-module-text
   (package
     (name "ghc-hslua-module-text")
-- 
cgit v1.2.3


From 6c055278514c1374a4fe6e803ab618bfc797cf58 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 13 Mar 2018 17:22:54 +0100
Subject: gnu: Add ghc-doctemplates-for-pandoc-1.

* gnu/packages/haskell.scm (ghc-doctemplates-for-pandoc-1): New variable.
---
 gnu/packages/haskell.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index a222e1b4ae..5cee8623f3 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -5981,6 +5981,29 @@ provided.  Skylighting is intended to be the successor to highlighting-kate.")
      "This package provides a simple text templating system used by pandoc.")
     (license license:bsd-3)))
 
+(define-public ghc-doctemplates-for-pandoc-1
+  (package (inherit ghc-doctemplates)
+    (version "0.1.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "doctemplates/doctemplates-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "0swal6rjya1293mwvl63jch5fx9ghpsil7qs4v7rpansa0izalmp"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-aeson" ,ghc-aeson-for-pandoc-1)
+       ("ghc-blaze-markup" ,ghc-blaze-markup)
+       ("ghc-blaze-html" ,ghc-blaze-html)
+       ("ghc-text" ,ghc-text)
+       ("ghc-vector" ,ghc-vector)
+       ("ghc-parsec" ,ghc-parsec)
+       ("ghc-unordered-containers" ,ghc-unordered-containers)
+       ("ghc-scientific" ,ghc-scientific)))))
+
 (define-public ghc-pandoc
   (package
     (name "ghc-pandoc")
-- 
cgit v1.2.3


From 8e3149eeb273fe66fac55119e37e96f725d99074 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 13 Mar 2018 17:23:30 +0100
Subject: gnu: Add ghc-yaml-for-pandoc-1.

* gnu/packages/haskell.scm (ghc-yaml-for-pandoc-1): New variable.
---
 gnu/packages/haskell.scm | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 5cee8623f3..12dbe2f000 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -63,7 +63,8 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix utils)
-  #:use-module (ice-9 regex))
+  #:use-module (ice-9 regex)
+  #:use-module ((srfi srfi-1) #:select (alist-delete)))
 
 (define-public cl-yale-haskell
   (let ((commit "85f94c72a16c5f70301dd8db04cde9de2d7dd270")
@@ -5599,6 +5600,12 @@ back-ends.")
      "This package provides a library to parse and render YAML documents.")
     (license license:bsd-3)))
 
+(define-public ghc-yaml-for-pandoc-1
+  (package (inherit ghc-yaml)
+    (inputs
+     `(("ghc-aeson" ,ghc-aeson-for-pandoc-1)
+       ,@(alist-delete "ghc-aeson" (package-inputs ghc-yaml))))))
+
 (define-public ghc-filemanip
   (package
     (name "ghc-filemanip")
-- 
cgit v1.2.3


From 08eaa0d877869d6e54ddb97a48fe9d8f90da16d2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 13 Mar 2018 17:23:46 +0100
Subject: gnu: Add ghc-skylighting-for-pandoc-1.

* gnu/packages/haskell.scm (ghc-skylighting-for-pandoc-1): New variable.
---
 gnu/packages/haskell.scm | 51 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 51 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 12dbe2f000..aa8c0352b6 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -5957,6 +5957,57 @@ supported by that framework can be added.  An optional command-line program is
 provided.  Skylighting is intended to be the successor to highlighting-kate.")
     (license license:gpl2)))
 
+(define-public ghc-skylighting-for-pandoc-1
+  (package (inherit ghc-skylighting)
+    (version "0.1.1.5")
+    (source (origin
+              (method git-fetch)
+              ;; We take the sources from Github, because the tarball on
+              ;; hackage does not include the XML files.
+              (uri (git-reference
+                    (url "https://github.com/jgm/skylighting.git")
+                    (commit version)))
+              (file-name (string-append "ghc-skylighting-" version "-checkout"))
+              (sha256
+               (base32
+                "0z3yv8v2fqqgv6lsf0ff3ld0h2vkg97b2jiry9wn2f1rizwdqmzl"))))
+    (arguments
+     `(#:configure-flags '("-fbootstrap")
+       #:phases
+       (modify-phases %standard-phases
+         ;; After building the skylighting-extract tool we use it to generate
+         ;; syntax source files from the included XML files.  These are then
+         ;; added to the skylighting.cabal file.
+         (add-after 'build 'extract-xml
+           (lambda _
+             (make-file-writable "skylighting.cabal")
+             (apply invoke "./dist/build/skylighting-extract/skylighting-extract"
+                    (find-files "xml" "\\.xml$"))
+             #t))
+         ;; Reconfigure without bootstrap flag
+         (add-after 'extract-xml 'configure-again
+           (lambda* (#:key outputs inputs tests? #:allow-other-keys)
+             ((assoc-ref %standard-phases 'configure)
+              #:outputs outputs
+              #:inputs inputs
+              #:tests? tests?
+              #:configure-flags '("-f-bootstrap"))))
+         (add-after 'configure-again 'build-again
+           (assoc-ref %standard-phases 'build)))))
+    (inputs
+     `(("ghc-aeson" ,ghc-aeson-for-pandoc-1)
+       ("ghc-ansi-terminal" ,ghc-ansi-terminal)
+       ("ghc-blaze-html" ,ghc-blaze-html)
+       ("ghc-case-insensitive" ,ghc-case-insensitive)
+       ("ghc-diff" ,ghc-diff)
+       ("ghc-hxt" ,ghc-hxt)
+       ("ghc-mtl" ,ghc-mtl)
+       ("ghc-pretty-show" ,ghc-pretty-show)
+       ("ghc-regex-pcre-builtin" ,ghc-regex-pcre-builtin)
+       ("ghc-safe" ,ghc-safe)
+       ("ghc-text" ,ghc-text)
+       ("ghc-utf8-string" ,ghc-utf8-string)))))
+
 (define-public ghc-doctemplates
   (package
     (name "ghc-doctemplates")
-- 
cgit v1.2.3


From 8b1e1e4c33a5b799f700759957a375d60f4ca7a9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 13 Mar 2018 17:24:00 +0100
Subject: gnu: Add ghc-pandoc-1.

* gnu/packages/haskell.scm (ghc-pandoc-1): New variable.
---
 gnu/packages/haskell.scm | 61 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 61 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index aa8c0352b6..c5408f8627 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -6138,6 +6138,67 @@ definition lists, tables, and other features.  A compatibility mode is
 provided for those who need a drop-in replacement for Markdown.pl.")
     (license license:gpl2+)))
 
+;; This is the last version of Pandoc 1.x, which is preferred for Rmarkdown.
+(define-public ghc-pandoc-1
+  (package (inherit ghc-pandoc)
+    (version "1.19.2.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/pandoc/pandoc-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "0mim429mpakrcnm50csxyqk3ljcx2l26r5grk6w9isnggwgqrq5v"))))
+    (arguments
+     `(#:configure-flags (list "--allow-newer=skylighting")))
+    (inputs
+     `(("ghc-aeson" ,ghc-aeson-for-pandoc-1)
+       ("ghc-ansi-terminal" ,ghc-ansi-terminal)
+       ("ghc-base64-bytestring" ,ghc-base64-bytestring)
+       ("ghc-blaze-html" ,ghc-blaze-html)
+       ("ghc-blaze-markup" ,ghc-blaze-markup)
+       ("ghc-cmark" ,ghc-cmark)
+       ("ghc-data-default" ,ghc-data-default)
+       ("ghc-deepseq-generics" ,ghc-deepseq-generics)
+       ("ghc-diff" ,ghc-diff)
+       ("ghc-doctemplates" ,ghc-doctemplates-for-pandoc-1)
+       ("ghc-executable-path" ,ghc-executable-path)
+       ("ghc-extensible-exceptions" ,ghc-extensible-exceptions)
+       ("ghc-filemanip" ,ghc-filemanip)
+       ("ghc-haddock-library" ,ghc-haddock-library)
+       ("ghc-hslua" ,ghc-hslua-for-pandoc-1)
+       ("ghc-http" ,ghc-http)
+       ("ghc-http-client" ,ghc-http-client)
+       ("ghc-http-client-tls" ,ghc-http-client-tls)
+       ("ghc-http-types" ,ghc-http-types)
+       ("ghc-juicypixels" ,ghc-juicypixels)
+       ("ghc-mtl" ,ghc-mtl)
+       ("ghc-network" ,ghc-network)
+       ("ghc-network-uri" ,ghc-network-uri)
+       ("ghc-old-time" ,ghc-old-time)
+       ("ghc-pandoc-types" ,ghc-pandoc-types-for-pandoc-1)
+       ("ghc-parsec" ,ghc-parsec)
+       ("ghc-random" ,ghc-random)
+       ("ghc-scientific" ,ghc-scientific)
+       ("ghc-sha" ,ghc-sha)
+       ("ghc-skylighting" ,ghc-skylighting-for-pandoc-1)
+       ("ghc-syb" ,ghc-syb)
+       ("ghc-tagsoup" ,ghc-tagsoup)
+       ("ghc-temporary" ,ghc-temporary)
+       ("ghc-texmath" ,ghc-texmath-for-pandoc-1)
+       ("ghc-text" ,ghc-text)
+       ("ghc-unordered-containers" ,ghc-unordered-containers)
+       ("ghc-vector" ,ghc-vector)
+       ("ghc-xml" ,ghc-xml)
+       ("ghc-yaml" ,ghc-yaml-for-pandoc-1)
+       ("ghc-zip-archive" ,ghc-zip-archive)
+       ("ghc-zlib" ,ghc-zlib)))
+    (native-inputs
+     `(("ghc-test-framework" ,ghc-test-framework)
+       ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)
+       ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)))))
+
 (define-public ghc-hs-bibutils
   (package
     (name "ghc-hs-bibutils")
-- 
cgit v1.2.3


From 5e51c268e46710b76c1d2fdb9b48ffea91f80584 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 13 Mar 2018 17:26:14 +0100
Subject: gnu: r-rmarkdown: Use Pandoc 1.

* gnu/packages/statistics.scm (r-rmarkdown)[propagated-inputs]: Replace
"ghc-pandoc" with "ghc-pandoc-1".
---
 gnu/packages/statistics.scm | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index af69703d90..5a7e76c21b 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2592,7 +2592,11 @@ certain criterion, e.g., it contains a certain regular file.")
        ("r-rprojroot" ,r-rprojroot)
        ("r-stringr" ,r-stringr)
        ("r-yaml" ,r-yaml)
-       ("ghc-pandoc" ,ghc-pandoc)))
+       ;; rmarkdown works with the 2.x release of Pandoc, but with degraded
+       ;; functionality.  For example, tabbed plots do not currently work with
+       ;; Pandoc 2.  The authors of rmarkdown recommend the use of Pandoc 1
+       ;; for the time being.
+       ("ghc-pandoc" ,ghc-pandoc-1)))
     (home-page "http://rmarkdown.rstudio.com")
     (synopsis "Convert R Markdown documents into a variety of formats")
     (description
-- 
cgit v1.2.3


From 9a7b5784633b168009ec2e7199c42ac5f789a362 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 13 Mar 2018 17:55:14 +0100
Subject: gnu: r-minimal: Add bash to inputs.

* gnu/packages/statistics.scm (r-minimal)[inputs]: Add bash-minimal.
---
 gnu/packages/statistics.scm | 4 ++++
 1 file changed, 4 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 5a7e76c21b..f4a1e0545f 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -39,6 +39,7 @@
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages)
   #:use-module (gnu packages algebra)
+  #:use-module (gnu packages bash)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cran)
@@ -261,6 +262,9 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
        ("libxt" ,libxt)
        ("pcre" ,pcre)
        ("readline" ,readline)
+       ;; This avoids a reference to the ungraftable static bash.  R uses the
+       ;; detected shell for the "system" procedure.
+       ("bash" ,bash-minimal)
        ("which" ,which)
        ("zlib" ,zlib)))
     (native-search-paths
-- 
cgit v1.2.3


From 79234c0a690e9fef5e695a43aa906741c9d223fb Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 21:12:18 +0200
Subject: gnu: ocaml-qtest: Declare a source file-name.

* gnu/packages/ocaml.scm (ocaml-qtest)[source]: Declare a source
file-name.
---
 gnu/packages/ocaml.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index 2ec67ba7be..d84348111d 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -1128,6 +1128,7 @@ instances and printing them.")
               (method url-fetch)
               (uri (string-append "https://github.com/vincent-hugot/iTeML/"
                                   "archive/v" version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
                 "1hw3jqir7w79payy4knc38fa3nxcvl7ap6y6hnqavrhpi8zqb59j"))))
-- 
cgit v1.2.3


From fdb3fba30fd4d01f912bcd2914b7a10d6b1511cd Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 21:19:34 +0200
Subject: gnu: ocaml-qtest: Update to 2.8.

* gnu/packages/ocaml.scm (ocaml-qtest): Update to 2.8.
[source]: Update source uri, declare a source file-name.
[home-page]: Update home-page.
---
 gnu/packages/ocaml.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index d84348111d..6430310fa1 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -5,7 +5,7 @@
 ;;; Copyright © 2015 David Hashe <david.hashe@dhashe.com>
 ;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org>
-;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2017 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -1123,15 +1123,15 @@ instances and printing them.")
 (define-public ocaml-qtest
   (package
     (name "ocaml-qtest")
-    (version "2.5")
+    (version "2.8")
     (source (origin
               (method url-fetch)
-              (uri (string-append "https://github.com/vincent-hugot/iTeML/"
-                                  "archive/v" version ".tar.gz"))
+              (uri (string-append "https://github.com/vincent-hugot/qtest/"
+                                  "archive/" version ".tar.gz"))
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1hw3jqir7w79payy4knc38fa3nxcvl7ap6y6hnqavrhpi8zqb59j"))))
+                "1ff4if64mc9c7wmhjdgnlnh6k6a713piqzr4043zzj4s5pw7smxk"))))
     (build-system ocaml-build-system)
     (native-inputs
      `(("findlib" ,ocaml-findlib)))
@@ -1145,7 +1145,7 @@ instances and printing them.")
        #:phases
        (modify-phases %standard-phases
          (delete 'configure))))
-    (home-page "https://github.com/vincent-hugot/iTeML")
+    (home-page "https://github.com/vincent-hugot/qtest")
     (synopsis "Inline (Unit) Tests for OCaml")
     (description "Qtest extracts inline unit tests written using a special
 syntax in comments.  Those tests are then run using the oUnit framework and the
-- 
cgit v1.2.3


From b965c1ca62043495b531e3ec3d5eaa33be062334 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 21:21:43 +0200
Subject: gnu: ocaml-stringext: Declare a source file-name.

* gnu/packages/ocaml.scm (ocaml-stringext)[source]: Declare a source
file-name.
---
 gnu/packages/ocaml.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index 6430310fa1..2fccb12a2e 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -1164,6 +1164,7 @@ to use -- to sophisticated random generation of test cases.")
               (method url-fetch)
               (uri (string-append "https://github.com/rgrinberg/stringext"
                                   "/archive/v" version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
                 "19g6lfn03iki9f8h91hi0yiqn0b3wkxyq08b3y23wgv6jw6mssfh"))))
-- 
cgit v1.2.3


From 232557c1592718455977ab35e946085eeaf6cced Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 21:22:48 +0200
Subject: gnu: ocaml-result: Declare a source file-name.

* gnu/packages/ocaml.scm (ocaml-result)[source]: Declare a source
file-name.
---
 gnu/packages/ocaml.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index 2fccb12a2e..ccf27610a7 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -1309,6 +1309,7 @@ powerful.")
               (method url-fetch)
               (uri (string-append "https://github.com/janestreet/result"
                                   "/archive/" version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
                 "1pgpfsgvhxnh0i37fkvp9j8nadns9hz9iqgabj4dr519j2gr1xvw"))))
-- 
cgit v1.2.3


From 597beb8a5dc20d0d21cba916df7d04134ab590a7 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 21:23:57 +0200
Subject: gnu: ocaml-piqi: Declare a source file-name.

* gnu/packages/ocaml.scm (ocaml-piqi)[source]: Declare a source
file-name.
---
 gnu/packages/ocaml.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index ccf27610a7..951cb89f42 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -3451,6 +3451,7 @@ and 4 (random based) according to RFC 4122.")
               (method url-fetch)
               (uri (string-append "https://github.com/alavrik/piqi-ocaml/"
                                   "archive/v" version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
                 "0ngz6y8i98i5v2ma8nk6mc83pdsmf2z0ks7m3xi6clfg3zqbddrv"))))
-- 
cgit v1.2.3


From 0aee7fdc8c42a931e8741c1bd8fabd97fd896484 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 21:25:10 +0200
Subject: gnu: ocaml-bitstring: Declare a source file-name.

* gnu/packages/ocaml.scm (ocaml-bitstring)[source]: Declare a source
file-name.
---
 gnu/packages/ocaml.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index 951cb89f42..613baedf5c 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -1244,6 +1244,7 @@ coverage information.")
               (method url-fetch)
               (uri (string-append "https://github.com/xguerin/bitstring"
                                   "/archive/v" version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
                 "0vy8ibrxccii1jbsk5q6yh1kxjigqvi7lhhcmizvd5gfhf7mfyc8"))
-- 
cgit v1.2.3


From 14ebf2fc5f72f5dafd8f811f6c628e33a4026689 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 21:26:06 +0200
Subject: gnu: ocaml-lwt: Declare a source file-name.

* gnu/packages/ocaml.scm (ocaml-lwt)[source]: Declare a source
file-name.
---
 gnu/packages/ocaml.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index 613baedf5c..be18766ba2 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -1682,6 +1682,7 @@ through Transport Layer Security (@dfn{TLS}) encrypted connections.")
         (method url-fetch)
         (uri (string-append "https://github.com/ocsigen/lwt/archive/" version
                             ".tar.gz"))
+        (file-name (string-append name "-" version ".tar.gz"))
         (sha256 (base32
                   "1gbw0g8a5a4b16diqrmlhc8ilnikrm4w3jjm1zq310maqg8z0zxz"))))
     (build-system ocaml-build-system)
-- 
cgit v1.2.3


From 04eecf4bdb6b3002ef9951864a6fdba2c4d1675b Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 21:27:04 +0200
Subject: gnu: ocaml-ssl: Declare a source file-name.

* gnu/packages/ocaml.scm (ocaml-ssl)[source]: Declare a source
file-name.
---
 gnu/packages/ocaml.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index be18766ba2..24f402128c 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -1648,6 +1648,7 @@ lets the client choose the concrete timeline.")
         (method url-fetch)
         (uri (string-append "https://github.com/savonet/ocaml-ssl/archive/"
                             version ".tar.gz"))
+        (file-name (string-append name "-" version ".tar.gz"))
         (sha256 (base32
                   "15p7652cvzdrlqxc1af11mg07wasxr1fsaj44gcmmh6bmav7wfzq"))))
     (build-system ocaml-build-system)
-- 
cgit v1.2.3


From 96dcb8a037e8dd4997096217f7f77110265b2ede Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 21:29:28 +0200
Subject: gnu: usbredir: Declare a source file-name.

* gnu/packages/spice.scm (usbredir)[source]: Declare a source file-name.
---
 gnu/packages/spice.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/spice.scm b/gnu/packages/spice.scm
index 58450e6a3e..fb3b11ba2d 100644
--- a/gnu/packages/spice.scm
+++ b/gnu/packages/spice.scm
@@ -69,6 +69,7 @@
                 (uri (git-reference
                         (url "https://anongit.freedesktop.org/git/spice/usbredir.git")
                         (commit commit)))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
                   "052fywgi72j68dr5ybldncg4vk8iqfrh58la7iazyxxpph9aag1g"))))
-- 
cgit v1.2.3


From 76b27f427a71e10895b4fb4d7b58af3404224a66 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 21:30:50 +0200
Subject: gnu: r-tgstat: Declare a source file-name.

* gnu/packages/statistics.scm (r-tgstat)[source]: Declare a source
file-name.
---
 gnu/packages/statistics.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index f4a1e0545f..72cdf7ff3f 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -5450,6 +5450,7 @@ manually \"recoding\").")
          (uri (hg-reference
                (url "https://bitbucket.org/tanaylab/tgstat")
                (changeset changeset)))
+         (file-name (string-append name "-" version "-checkout"))
          (sha256
           (base32
            "0ilkkyximy77zbncm91kdfqbxf0qyndg16pd3q3p6a3xc9qcmxvn"))))
-- 
cgit v1.2.3


From 4510f976dcbff4b509ba635c9c8d2950660b343b Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 21:31:49 +0200
Subject: gnu: r-tgconfig: Declare a source file-name.

* gnu/packages/statistics.scm (r-tgconfig)[source]: Declare a source
file-name.
---
 gnu/packages/statistics.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 72cdf7ff3f..b7a12d907a 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -5485,6 +5485,7 @@ tools.")
          (uri (hg-reference
                (url "https://bitbucket.org/tanaylab/tgconfig")
                (changeset changeset)))
+         (file-name (string-append name "-" version "-checkout"))
          (sha256
           (base32
            "0xy6c7s7mn1yx191154bwbv1bl424bnvc80syqpl1vdl28ba46rj"))))
-- 
cgit v1.2.3


From 29a3905452a35f4e6e59c4e0eb3e9a27178d15fc Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 21:33:44 +0200
Subject: gnu: tinyxml2: Declare a source file-name.

* gnu/packages/xml.scm (tinyxml2)[source]: Declare a source file-name.
---
 gnu/packages/xml.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm
index bde959a284..729fa56a30 100644
--- a/gnu/packages/xml.scm
+++ b/gnu/packages/xml.scm
@@ -1061,9 +1061,10 @@ C++ programming language.")
        (method url-fetch)
        (uri (string-append "https://github.com/leethomason/tinyxml2/archive/"
                            version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
        (sha256
-       (base32
-        "083z4r4khcndxi9k840lcr48sqxvar4gpsnf749xfdn1bkr8xcql"))))
+        (base32
+         "083z4r4khcndxi9k840lcr48sqxvar4gpsnf749xfdn1bkr8xcql"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f))    ; no tests
-- 
cgit v1.2.3


From da0baf117d740320b0e2733137611a8059b0abba Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 21:35:31 +0200
Subject: gnu: mod-wsgi: Declare a source file-name.

* gnu/packages/web.scm (mod-wsgi)[source]: Declare a source file-name.
---
 gnu/packages/web.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index f5e004eda5..3fb860a8e3 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -159,6 +159,7 @@ and its related documentation.")
               (uri (string-append
                     "https://github.com/GrahamDumpleton/mod_wsgi/archive/"
                     version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
                 "0n1yhmrfp8mjbsngmyjl937c6rc0069p6wdi1lknrbn1q42hzw6q"))))
-- 
cgit v1.2.3


From 716a39bcf15e2d05709d8757e994a1613cefc95e Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 21:36:22 +0200
Subject: gnu: tidy: Declare a source file-name.

* gnu/packages/web.scm (tidy)[source]: Declare a source file-name.
---
 gnu/packages/web.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 3fb860a8e3..1cf426b5c0 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -846,6 +846,7 @@ UTS#46.")
                      ":pserver:anonymous@tidy.cvs.sourceforge.net:/cvsroot/tidy")
                     (module "tidy")
                     (revision "2009-12-23")))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "14dsnmirjcrvwsffqp3as70qr6bbfaig2fv3zvs5g7005jrsbvpb"))
-- 
cgit v1.2.3


From 728ee9d6f7257baa51eb6fccd25d62fe2134d9fe Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 21:39:42 +0200
Subject: gnu: vpnc-scripts: Declare a source file-name.

* gnu/packages/vpn.scm (vpnc-scripts)[source]: Declare a source
file-name.
---
 gnu/packages/vpn.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm
index 642ca1c044..0fc3197077 100644
--- a/gnu/packages/vpn.scm
+++ b/gnu/packages/vpn.scm
@@ -128,6 +128,7 @@ Only \"Universal TUN/TAP device driver support\" is needed in the kernel.")
                  (git-reference
                   (url "git://git.infradead.org/users/dwmw2/vpnc-scripts.git")
                   (commit commit)))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
                   "0pa36w4wlyyvfb66cayhans99wsr2j5si2fvfr7ldfm512ajwn8h"))))
-- 
cgit v1.2.3


From d36df187e05d570b9da8e1d09be0a7ab2ac907a3 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 21:41:34 +0200
Subject: gnu: git-flow: Declare a source file-name.

* gnu/packages/version-control.scm (git-flow)[source]: Declare a source
file-name.
---
 gnu/packages/version-control.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index 34c1852a22..b55ba5370a 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -785,6 +785,7 @@ will work.")
               (uri (git-reference
                     (url "https://github.com/nvie/gitflow/")
                     (commit "15aab26490facf285acef56cb5d61025eacb3a69")))
+              (file-name (git-file-name name version))
               (sha256
                (base32
                 "01fs97q76fdfnvmrh2cyjhywcs3pykf1dg58sy0frflnsdzs6prx"))))
-- 
cgit v1.2.3


From 348f8c8553a0a9ae7815cfb51a1d0aed564ccb7f Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 21:42:37 +0200
Subject: gnu: git-test-sequence: Declare a source file-name.

* gnu/packages/version-control.scm (git-test-sequence)[source]: Declare
a source file-name.
---
 gnu/packages/version-control.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index b55ba5370a..a3f4a4dd4b 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -903,6 +903,7 @@ though this can be overridden.")
                       ;; are interested in just one for this package.
                       (url "https://github.com/dustin/bindir")
                       (commit commit)))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
                   "1dcq0y16yznbv4k9h8gg90kv1gkn8r8dbvl4m2rpfd7q5nqhn617"))))
-- 
cgit v1.2.3


From 54335b59f08b83cda22ee0ee5157528ad8833e40 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 21:44:16 +0200
Subject: gnu: python-editdistance: Declare a source file-name.

* gnu/packages/textutils.scm (python-editdistance)[source]: Declare a
source file-name.
---
 gnu/packages/textutils.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm
index d75ba7766e..be8dd086a2 100644
--- a/gnu/packages/textutils.scm
+++ b/gnu/packages/textutils.scm
@@ -632,6 +632,7 @@ source code.")
          (uri (git-reference
                (url "https://github.com/aflc/editdistance.git")
                (commit commit)))
+         (file-name (git-file-name name version))
          (sha256
           (base32
            "1l43svsv12crvzphrgi6x435z6xg8m086c64armp8wzb4l8ccm7g"))))
-- 
cgit v1.2.3


From 54d5b27e92d8cc4e3195ce859f3c79bb676dc9df Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 21:46:48 +0200
Subject: gnu: python-editdistance: Use 'invoke'.

* gnu/packages/textutils.scm (python-editdistance)[arguments]: Use
'invoke' instead of 'system*'.
---
 gnu/packages/textutils.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm
index be8dd086a2..2d8a104d54 100644
--- a/gnu/packages/textutils.scm
+++ b/gnu/packages/textutils.scm
@@ -644,7 +644,7 @@ source code.")
              (lambda _
                (with-directory-excursion "editdistance"
                  (delete-file "bycython.cpp")
-                 (zero? (system* "cython" "--cplus" "bycython.pyx"))))))))
+                 (invoke "cython" "--cplus" "bycython.pyx")))))))
       (native-inputs
        `(("python-cython" ,python-cython)))
       (home-page "https://www.github.com/aflc/editdistance")
-- 
cgit v1.2.3


From ebd43a2a45f9ac0ce702ef5810eddafd0830db5f Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Wed, 7 Mar 2018 02:05:43 +0100
Subject: gnu: Add python2-langkit.

* gnu/packages/ada.scm: New file.
---
 gnu/packages/ada.scm | 61 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 61 insertions(+)
 create mode 100644 gnu/packages/ada.scm

(limited to 'gnu/packages')

diff --git a/gnu/packages/ada.scm b/gnu/packages/ada.scm
new file mode 100644
index 0000000000..d6cd1e9787
--- /dev/null
+++ b/gnu/packages/ada.scm
@@ -0,0 +1,61 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2018 Danny Milosavljevic <dannym@scratchpost.org>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages ada)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix build-system gnu)
+  #:use-module (guix build-system python)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix git-download)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages check)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages python))
+
+(define-public python2-langkit
+  (let ((commit "fe0bc8bf60dbd2937759810df76ac420d99fc15f")
+        (revision "0"))
+    (package
+      (name "python2-langkit")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/AdaCore/langkit.git")
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "1abqgw2p8pb1pm54my5kkbbixfhc6l0bwajdv1xlzyrh31xki3wx"))
+                (file-name (string-append name "-" version "-checkout"))))
+      (build-system python-build-system)
+      (propagated-inputs
+       `(("python2-docutils" ,python2-docutils)
+         ("python2-enum34" ,python2-enum34)
+         ("python2-funcy" ,python2-funcy)
+         ("python2-mako" ,python2-mako)))
+      (arguments
+       `(#:python ,python-2
+         #:tests? #f))           ; Tests would requite gprbuild (Ada).
+      (synopsis "Semantic analysis tool generator in Python")
+      (description "@code{Langkit} is a tool whose purpose is to make it easy
+to create syntactic and semantic analysis engines.  Write a language
+specification in our Python DSL and Langkit will generate for you an
+Ada library with bindings for the C and Python programming languages.")
+      (home-page "https://github.com/AdaCore/langkit/")
+      (license license:gpl3+))))   ; and gcc runtime library exception
-- 
cgit v1.2.3


From 80b58d15bc659d5d0b4565b9fa700eabfc38fd83 Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Tue, 13 Mar 2018 21:11:48 +0100
Subject: gnu: Add python2-quex@0.67.3.

* gnu/packages/python.scm (python2-quex-0.67.3): New variable.
---
 gnu/packages/python.scm | 42 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 22fbdf6720..2272f15b54 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -12992,3 +12992,45 @@ filesystem events on Linux.")
 
 (define-public python2-pyinotify
   (package-with-python2 python-pyinotify))
+
+;; Ada parser uses this version.
+(define-public python2-quex-0.67.3
+  (package
+    (name "python2-quex")
+    (version "0.67.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://sourceforge/quex/HISTORY/0.67/quex-" version ".zip"))
+       (sha256
+        (base32
+         "14gv8ll3ipqv4kyc2xiy891nrmjl4ic823zfyx8hassagyclyppw"))
+       (file-name (string-append name "-" version ".zip"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("unzip" ,unzip)))
+    (arguments
+     `(#:python ,python-2
+       #:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (delete 'build)
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (share/quex (string-append out "/share/quex"))
+                    (bin (string-append out "/bin")))
+               (copy-recursively "." share/quex)
+               (mkdir-p bin)
+               (symlink (string-append share/quex "/quex-exe.py")
+                        (string-append bin "/quex"))
+               #t))))))
+    (native-search-paths
+     (list (search-path-specification
+            (variable "QUEX_PATH")
+            (files '("share/quex")))))
+    (home-page "http://quex.sourceforge.net/")
+    (synopsis "Lexical analyzer generator in Python")
+    (description "@code{quex} is a lexical analyzer generator in Python.")
+    (license license:lgpl2.1+)))        ; Non-military
-- 
cgit v1.2.3


From 6c7017269228c1766c62aa425d35f27870c5724c Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Tue, 13 Mar 2018 21:14:39 +0100
Subject: gnu: Add python-quex.

* gnu/packages/python.scm (python-quex): New variable.
---
 gnu/packages/python.scm | 13 +++++++++++++
 1 file changed, 13 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 2272f15b54..8db00dbf37 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -13034,3 +13034,16 @@ filesystem events on Linux.")
     (synopsis "Lexical analyzer generator in Python")
     (description "@code{quex} is a lexical analyzer generator in Python.")
     (license license:lgpl2.1+)))        ; Non-military
+
+(define-public python2-quex
+  (package (inherit python2-quex-0.67.3)
+    (name "python2-quex")
+    (version "0.68.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://sourceforge/quex/DOWNLOAD/quex-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0svc9nla3b9145d6b7fb9dizx412l3difzqw0ilh9lz52nsixw8j"))
+       (file-name (string-append name "-" version ".tar.gz"))))))
-- 
cgit v1.2.3


From 2cdd9729fac5d3fc1e700e55e4a6bbf93a990c8a Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 22:00:57 +0200
Subject: gnu: texlive-dvips: Declare a source file-name.

* gnu/packages/tex.scm (texlive-dvips)[source]: Declare a source
file-name.
[native-inputs]: Declare source file-names for native-inputs.
---
 gnu/packages/tex.scm | 3 +++
 1 file changed, 3 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index 764f4fff15..9a6d8ec344 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -214,6 +214,7 @@ This package contains the binaries.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/dvips"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0fcy2hpapbj01ncpjj3v39yhr0jjxb6rm13qaxjjw66s3vydxls1"))))
@@ -244,6 +245,7 @@ This package contains the binaries.")
                                      %texlive-tag "/Master/texmf-dist/"
                                      "/fonts/map/dvips/tetex"))
                  (revision %texlive-revision)))
+           (file-name (string-append "dvips-font-maps-" version "-checkout"))
            (sha256
             (base32
              "100208pg7q6lj7swiq9p9287nn6b64bl62bnlaxpjni9y2kdrqy5"))))
@@ -255,6 +257,7 @@ This package contains the binaries.")
                                      %texlive-tag "/Master/texmf-dist/"
                                      "/fonts/enc/dvips/base"))
                  (revision %texlive-revision)))
+           (file-name (string-append "dvips-base-enc-" version "-checkout"))
            (sha256
             (base32
              "1xnf6ms0h87r55kxik4vicwr1907scj789lhqflqns8svvsli5iy"))))))
-- 
cgit v1.2.3


From b8d8806b52543e7e5d7f578fb6adb632683d8b4f Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 22:18:00 +0200
Subject: gnu: Use https for www.ctan.org.

* gnu/packages/tex.scm: Use https for ctan.org.
---
 gnu/packages/tex.scm | 186 +++++++++++++++++++++++++--------------------------
 1 file changed, 93 insertions(+), 93 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index 9a6d8ec344..93788a1c50 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -3,7 +3,7 @@
 ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Federico Beffa <beffa@fbengineering.ch>
 ;;; Copyright © 2016 Thomas Danckaert <post@thomasdanckaert.be>
 ;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
@@ -261,7 +261,7 @@ This package contains the binaries.")
            (sha256
             (base32
              "1xnf6ms0h87r55kxik4vicwr1907scj789lhqflqns8svvsli5iy"))))))
-    (home-page "http://www.ctan.org/pkg/dvips")
+    (home-page "https://www.ctan.org/pkg/dvips")
     (synopsis "DVI to PostScript drivers")
     (description "This package provides files needed for converting DVI files
 to PostScript.")
@@ -295,7 +295,7 @@ to PostScript.")
              (mkdir-p target)
              (copy-recursively (assoc-ref %build-inputs "source") target)
              #t))))
-    (home-page "http://www.ctan.org/pkg/unicode-data")
+    (home-page "https://www.ctan.org/pkg/unicode-data")
     (synopsis "Unicode data and loaders for TeX")
     (description "This bundle provides generic access to Unicode Consortium
 data for TeX use.  It contains a set of text files provided by the Unicode
@@ -368,7 +368,7 @@ bundle.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://ctan.org/pkg/tex-ini-files")
+    (home-page "https://www.ctan.org/pkg/tex-ini-files")
     (synopsis "Files for creating TeX formats")
     (description "This bundle provides a collection of model \".ini\" files
 for creating TeX formats.  These files are commonly used to introduced
@@ -402,7 +402,7 @@ to adapt the plain e-TeX source file to work with XeTeX and LuaTeX.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://ctan.org/pkg/hyph-utf8")
+    (home-page "https://ctan.org/pkg/hyph-utf8")
     (synopsis "Hyphenation patterns expressed in UTF-8")
     (description "Modern native UTF-8 engines such as XeTeX and LuaTeX need
 hyphenation patterns in UTF-8 format, whereas older systems require
@@ -478,7 +478,7 @@ converters, will completely supplant the older patterns.")
                #t))))))
     (native-inputs
      `(("texlive-bin" ,texlive-bin)))
-    (home-page "http://www.ctan.org/pkg/metafont")
+    (home-page "https://www.ctan.org/pkg/metafont")
     (synopsis "Metafont base files")
     (description "This package provides the Metafont base files needed to
 build fonts using the Metafont system.")
@@ -578,7 +578,7 @@ documents.")
     (native-inputs
      `(("texlive-bin" ,texlive-bin)
        ("texlive-metafont-base" ,texlive-metafont-base)))
-    (home-page "http://www.ctan.org/pkg/cm")
+    (home-page "https://www.ctan.org/pkg/cm")
     (synopsis "Computer Modern fonts for TeX")
     (description "This package provides the Computer Modern fonts by Donald
 Knuth.  The Computer Modern font family is a large collection of text,
@@ -715,7 +715,7 @@ fonts.")
      `(("texlive-bin" ,texlive-bin)
        ("texlive-metafont-base" ,texlive-metafont-base)
        ("texlive-fonts-cm" ,texlive-fonts-cm)))
-    (home-page "http://www.ctan.org/pkg/latex-fonts")
+    (home-page "https://www.ctan.org/pkg/latex-fonts")
     (synopsis "Collection of fonts used in LaTeX distributions")
     (description "This is a collection of fonts for use with standard LaTeX
 packages and classes. It includes invisible fonts (for use with the slides
@@ -793,7 +793,7 @@ symbol fonts.")
      `(("texlive-fonts-cm" ,texlive-fonts-cm)
        ("texlive-metafont-base" ,texlive-metafont-base)
        ("texlive-bin" ,texlive-bin)))
-    (home-page "http://www.ctan.org/pkg/amsfonts")
+    (home-page "https://www.ctan.org/pkg/amsfonts")
     (synopsis "TeX fonts from the American Mathematical Society")
     (description
      "This package provides an extended set of fonts for use in mathematics,
@@ -823,7 +823,7 @@ details can be found in the documentation.")
     (native-inputs
      `(("texlive-fonts-cm" ,texlive-fonts-cm)
        ("texlive-metafont-base" ,texlive-metafont-base)))
-    (home-page "http://www.ctan.org/pkg/amsfonts")
+    (home-page "https://www.ctan.org/pkg/amsfonts")
     (synopsis "TeX fonts from the American Mathematical Society")
     (description
      "This package provides basic LaTeX support for the symbol fonts provides
@@ -1006,7 +1006,7 @@ book).")
          ("texlive-fonts-cm" ,texlive-fonts-cm)
          ("texlive-fonts-latex" ,texlive-fonts-latex)
          ("texlive-fonts-knuth-lib" ,texlive-fonts-knuth-lib)))
-      (home-page "http://www.ctan.org/pkg/latex-base")
+      (home-page "https://www.ctan.org/pkg/latex-base")
       (synopsis "Base sources of LaTeX")
       (description
        "This bundle comprises the source of LaTeX itself, together with several
@@ -1027,7 +1027,7 @@ contain.")
                 "0swkbxv8vg0yizadfnvrwjb4cj0pn34v9wm6v7wqq903fdav7k7q"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/filecontents"))
-    (home-page "http://www.ctan.org/pkg/filecontents")
+    (home-page "https://www.ctan.org/pkg/filecontents")
     (synopsis "Extended filecontents and filecontents* environments")
     (description
      "LaTeX2e's @code{filecontents} and @code{filecontents*} environments
@@ -1055,7 +1055,7 @@ overwrite existing files and letting you use @code{filecontents} /
        #:tex-format "xelatex"))
     (inputs
      `(("texlive-latex-filecontents" ,texlive-latex-filecontents)))
-    (home-page "http://www.ctan.org/pkg/ifxetex")
+    (home-page "https://www.ctan.org/pkg/ifxetex")
     (synopsis "Am I running under XeTeX?")
     (description
      "This is a simple package which provides an @code{\\ifxetex} conditional,
@@ -1088,7 +1088,7 @@ requires the e-TeX extensions to the TeX primitive set.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/epsf")
+    (home-page "https://www.ctan.org/pkg/epsf")
     (synopsis "Simple macros for EPS inclusion")
     (description
      "This package provides the original (and now obsolescent) graphics
@@ -1115,7 +1115,7 @@ users, via its Plain TeX version.)")
        ;; We exclude "fvrb-ex" to avoid a dependency on texlive-luaotfload and
        ;; thus texlive-luatex-lualibs.
        #:build-targets '("fancyvrb.ins")))
-    (home-page "http://www.ctan.org/pkg/fancyvrb")
+    (home-page "https://www.ctan.org/pkg/fancyvrb")
     (synopsis "Sophisticated verbatim text")
     (description
      "This package provides tools for the flexible handling of verbatim text
@@ -1179,7 +1179,7 @@ verbatim source).")
            (sha256
             (base32
              "0gi4qv6378nl84s8n1yx3hjqvv7r4lza7hpbymbl5rzwgw8qrnyb"))))))
-    (home-page "http://www.ctan.org/pkg/latex-graphics")
+    (home-page "https://www.ctan.org/pkg/latex-graphics")
     (synopsis "LaTeX standard graphics bundle")
     (description
      "This is a collection of LaTeX packages for producing color, including
@@ -1202,7 +1202,7 @@ keyval, and lscape.")
                 "01n613s7bcrd2n4jfawm0k4nn2ny3aaifp2jjfif3lz4sbv31494"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/xcolor"))
-    (home-page "http://www.ctan.org/pkg/xcolor")
+    (home-page "https://www.ctan.org/pkg/xcolor")
     (synopsis "Driver-independent color extensions for LaTeX and pdfLaTeX")
     (description
      "The package starts from the basic facilities of the colorcolor package,
@@ -1230,7 +1230,7 @@ tables.")
                 "1d3rmjgzh0025a1dza55zb6nzzlgd1y9snwx45wq1c1vf42m79h2"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/hyperref"))
-    (home-page "http://www.ctan.org/pkg/hyperref")
+    (home-page "https://www.ctan.org/pkg/hyperref")
     (synopsis "Extensive support for hypertext in LaTeX")
     (description
      "The @code{hyperref} package is used to handle cross-referencing commands
@@ -1265,7 +1265,7 @@ pdf and HTML backends.  The package is distributed with the @code{backref} and
              (substitute* "oberdiek.ins"
                (("ifpdf.ins") "ifpdf.dtx"))
              #t)))))
-    (home-page "http://www.ctan.org/pkg/oberdiek")
+    (home-page "https://www.ctan.org/pkg/oberdiek")
     (synopsis "Bundle of packages submitted by Heiko Oberdiek")
     (description
      "The bundle comprises various LaTeX packages, providing among others:
@@ -1287,7 +1287,7 @@ arrows; record information about document class(es) used; and many more.")
     (arguments
      '(#:tex-directory "latex/tools"
        #:build-targets '("tools.ins")))
-    (home-page "http://www.ctan.org/pkg/latex-tools")
+    (home-page "https://www.ctan.org/pkg/latex-tools")
     (synopsis "LaTeX standard tools bundle")
     (description
      "This package is a collection of (variously) simple tools provided as
@@ -1350,7 +1350,7 @@ of file names.")
     (build-system texlive-build-system)
     (arguments
      '(#:tex-directory "latex/l3kernel"))
-    (home-page "http://www.ctan.org/pkg/l3kernel")
+    (home-page "https://www.ctan.org/pkg/l3kernel")
     (synopsis "LaTeX3 programmers’ interface")
     (description
      "The l3kernel bundle provides an implementation of the LaTeX3
@@ -1389,7 +1389,7 @@ that the LaTeX3 conventions can be used with regular LaTeX 2e packages.")
              #t)))))
     (inputs
      `(("texlive-latex-l3kernel" ,texlive-latex-l3kernel)))
-    (home-page "http://www.ctan.org/pkg/l3packages")
+    (home-page "https://www.ctan.org/pkg/l3packages")
     (synopsis "High-level LaTeX3 concepts")
     (description
      "This bundle holds prototype implementations of concepts for a LaTeX
@@ -1423,7 +1423,7 @@ programming tools and kernel sup­port.  Packages provided in this release are:
        #:build-targets '("fontspec.dtx")))
     (inputs
      `(("texlive-latex-l3kernel" ,texlive-latex-l3kernel)))
-    (home-page "http://www.ctan.org/pkg/fontspec")
+    (home-page "https://www.ctan.org/pkg/fontspec")
     (synopsis "Advanced font selection in XeLaTeX and LuaLaTeX")
     (description
      "Fontspec is a package for XeLaTeX and LuaLaTeX.  It provides an
@@ -1481,7 +1481,7 @@ this bundle for use independent of ConTeXt.")
                 "178ywjpdlv78qmfzqdyn6gy14620zjsn2q9wap76fbr9s4hw6dba"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/amsmath"))
-    (home-page "http://www.ctan.org/pkg/amsmath")
+    (home-page "https://www.ctan.org/pkg/amsmath")
     (synopsis "AMS mathematical facilities for LaTeX")
     (description
      "This is the principal package in the AMS-LaTeX distribution.  It adapts
@@ -1510,7 +1510,7 @@ definitions.")
     (build-system texlive-build-system)
     (arguments
      `(#:tex-directory "latex/amscls"))
-    (home-page "http://www.ctan.org/pkg/amscls")
+    (home-page "https://www.ctan.org/pkg/amscls")
     (synopsis "AMS document classes for LaTeX")
     (description
      "This bundle contains three AMS classes: @code{amsartamsart} (for writing
@@ -1542,7 +1542,7 @@ distribution.")
              (substitute* "babel.ins"
                (("askonceonly") "askforoverwritefalse"))
              #t)))))
-    (home-page "http://www.ctan.org/pkg/babel")
+    (home-page "https://www.ctan.org/pkg/babel")
     (synopsis "Multilingual support for Plain TeX or LaTeX")
     (description
      "The package manages culturally-determined typographical (and other)
@@ -1567,7 +1567,7 @@ polyglossia package rather than Babel.")
                 "1s404wbx91z5w65hm024kyl4h56zsa096irx18vsx8jvlmwsr5wc"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "generic/babel-english"))
-    (home-page "http://www.ctan.org/pkg/babel-english")
+    (home-page "https://www.ctan.org/pkg/babel-english")
     (synopsis "Babel support for English")
     (description
      "This package provides the language definition file for support of
@@ -1589,7 +1589,7 @@ for Canadian and USA text.")
     (build-system texlive-build-system)
     (arguments
      '(#:tex-directory "latex/cyrillic"))
-    (home-page "http://www.ctan.org/pkg/latex-cyrillic")
+    (home-page "https://www.ctan.org/pkg/latex-cyrillic")
     (synopsis "Support for Cyrillic fonts in LaTeX")
     (description
      "This bundle of macros files provides macro support (including font
@@ -1610,7 +1610,7 @@ language that is written in a Cyrillic alphabet.")
                 "1920dcq8613yzprasbg80fh4fcjcidvvl54wkx438nimyxcri7qz"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/psnfss"))
-    (home-page "http://www.ctan.org/pkg/psnfss")
+    (home-page "https://www.ctan.org/pkg/psnfss")
     (synopsis "Font support for common PostScript fonts")
     (description
      "The PSNFSS collection includes a set of files that provide a complete
@@ -1730,7 +1730,7 @@ It includes little more than the required set of LaTeX packages.")))
                 "15i4k479dwrpr0kspmm70g1yn4p3dkh0whyzmr93hph9bggnh1i1"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/amsrefs"))
-    (home-page "http://www.ctan.org/pkg/amsrefs")
+    (home-page "https://www.ctan.org/pkg/amsrefs")
     (synopsis "LaTeX-based replacement for BibTeX")
     (description
      "Amsrefs is a LaTeX package for bibliographies that provides an archival
@@ -1759,7 +1759,7 @@ conjunction with BibTeX or as a replacement for BibTeX.")
            (lambda _
              (for-each delete-file (find-files "." "\\.drv$"))
              #t)))))
-    (home-page "http://www.ctan.org/pkg/bigfoot")
+    (home-page "https://www.ctan.org/pkg/bigfoot")
     (synopsis "Footnotes for critical editions")
     (description
      "This package aims to provide a one-stop solution to requirements for
@@ -1787,7 +1787,7 @@ documentation.  The bigfoot bundle also provides the @code{perpage} and
                 "1jrja9b1pzdh9zgv1jh807w4xijqja58n2mqny6dkwicv8qfgbfg"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/blindtext"))
-    (home-page "http://www.ctan.org/pkg/blindtext")
+    (home-page "https://www.ctan.org/pkg/blindtext")
     (synopsis "Producing 'blind' text for testing")
     (description
      "The package provides the commands @code{\\blindtext} and
@@ -1819,7 +1819,7 @@ ipsum\" text, see the @code{lipsum} package).")
            (lambda _
              (delete-file "dinbrief.drv")
              #t)))))
-    (home-page "http://www.ctan.org/pkg/dinbrief")
+    (home-page "https://www.ctan.org/pkg/dinbrief")
     (synopsis "German letter DIN style")
     (description
      "This package implements a document layout for writing letters according
@@ -1845,7 +1845,7 @@ package.")
                 "1zyl2pcz2x529gzj5m93a1s4ipymdabf7qdjl3l1673pizd4hfyv"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/draftwatermark"))
-    (home-page "http://www.ctan.org/pkg/draftwatermark")
+    (home-page "https://www.ctan.org/pkg/draftwatermark")
     (synopsis "Put a grey textual watermark on document pages")
     (description
      "This package provides a means to add a textual, light grey watermark on
@@ -1869,7 +1869,7 @@ on everypage.")
                 "06h28b26dyjkj9shksphgqfv4130jfkwhbw737hxn7d3yvdfffyd"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/environ"))
-    (home-page "http://www.ctan.org/pkg/environ")
+    (home-page "https://www.ctan.org/pkg/environ")
     (synopsis "New interface for environments in LaTeX")
     (description
      "This package provides the @code{\\collect@@body} command (as in
@@ -1891,7 +1891,7 @@ define a new author interface to creating new environments.")
                 "0pvmhsd4xmpil0m3c7qcgwilbk266mlkzv03g0jr8r3zd8jxlyzq"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/eqparbox"))
-    (home-page "http://www.ctan.org/pkg/eqparbox")
+    (home-page "https://www.ctan.org/pkg/eqparbox")
     (synopsis "Create equal-widthed parboxes")
     (description
      "LaTeX users sometimes need to ensure that two or more blocks of text
@@ -1927,7 +1927,7 @@ also provided.")
              (for-each delete-file
                        (find-files "." "\\.drv$"))
              #t)))))
-    (home-page "http://www.ctan.org/pkg/expdlist")
+    (home-page "https://www.ctan.org/pkg/expdlist")
     (synopsis "Expanded description environments")
     (description
      "The package provides additional features for the LaTeX
@@ -1962,7 +1962,7 @@ without affecting the structure of the list (this works for @code{itemize} and
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/filemod")
+    (home-page "https://www.ctan.org/pkg/filemod")
     (synopsis "Provide file modification times, and compare them")
     (description
      "This package provides macros to read and compare the modification dates
@@ -1988,7 +1988,7 @@ but non-expandable ones.")
                 "11gvvjvmdfs9b7mm19yf80zwkx49jqcbq6g8qb9y5ns1r1qvnixp"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/ifplatform"))
-    (home-page "http://www.ctan.org/pkg/ifplatform")
+    (home-page "https://www.ctan.org/pkg/ifplatform")
     (synopsis "Conditionals to test which platform is being used")
     (description
      "This package uses the (La)TeX extension @code{-shell-escape} to
@@ -2012,7 +2012,7 @@ classes of systems.")
                 "0aqliq0nwblxyrzhwhv77pnmk7qh2y3prgq7z7qhwcbgz5kisld7"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/natbib"))
-    (home-page "http://www.ctan.org/pkg/natbib")
+    (home-page "https://www.ctan.org/pkg/natbib")
     (synopsis "Flexible bibliography support")
     (description
      "This bundle provides a package that implements both author-year and
@@ -2036,7 +2036,7 @@ designed from the start to be compatible with @code{natbib}.")
                 "1dxbl5il7wbbsp0v45vk884xi1192wxw03849pb1g5q4x808n352"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/psfrag"))
-    (home-page "http://www.ctan.org/pkg/psfrag")
+    (home-page "https://www.ctan.org/pkg/psfrag")
     (synopsis "Replace strings in encapsulated PostScript figures")
     (description
      "This package allows LaTeX constructions (equations, picture
@@ -2074,7 +2074,7 @@ rotated.")
        ("texlive-latex-oberdiek" ,texlive-latex-oberdiek)
        ("texlive-latex-psfrag" ,texlive-latex-psfrag)
        ("texlive-latex-trimspaces" ,texlive-latex-trimspaces)))
-    (home-page "http://www.ctan.org/pkg/pstool")
+    (home-page "https://www.ctan.org/pkg/pstool")
     (synopsis "Process PostScript graphisc within pdfLaTeX documents")
     (description
      "This is a package for processing PostScript graphics with @code{psfrag}
@@ -2099,7 +2099,7 @@ re-processing.")
                 "0y4i651b75y6006n03x8n86bsqvjsailvvz9bhzy51dzsznqidq0"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/seminar"))
-    (home-page "http://www.ctan.org/pkg/seminar")
+    (home-page "https://www.ctan.org/pkg/seminar")
     (synopsis "Make overhead slides")
     ;; TODO: This package may need fancybox and xcomment at runtime.
     (description
@@ -2134,7 +2134,7 @@ recent classes such as powerdot or beamer, both of which are tuned to
              #t)))))
     (inputs
      `(("texlive-latex-filecontents" ,texlive-latex-filecontents)))
-    (home-page "http://www.ctan.org/pkg/trimspaces")
+    (home-page "https://www.ctan.org/pkg/trimspaces")
     (synopsis "Trim spaces around an argument or within a macro")
     (description
      "This very short package allows you to expandably remove spaces around a
@@ -2169,7 +2169,7 @@ space-stripped macros.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/capt-of")
+    (home-page "https://www.ctan.org/pkg/capt-of")
     (synopsis "Captions on more than floats")
     (description
      "This package defines a command @code{\\captionof} for putting a caption
@@ -2202,7 +2202,7 @@ to something that's not a float.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/etoolbox")
+    (home-page "https://www.ctan.org/pkg/etoolbox")
     (synopsis "e-TeX tools for LaTeX")
     (description
      "This package is a toolbox of programming facilities geared primarily
@@ -2240,7 +2240,7 @@ of the LaTeX kernel.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/fncychap")
+    (home-page "https://www.ctan.org/pkg/fncychap")
     (synopsis "Seven predefined chapter heading styles")
     (description
      "This package provides seven predefined chapter heading styles.  Each
@@ -2275,7 +2275,7 @@ headings.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/framed")
+    (home-page "https://www.ctan.org/pkg/framed")
     (synopsis "Framed or shaded regions that can break across pages")
     (description
      "The package creates three environments: @code{framed}, which puts an
@@ -2309,7 +2309,7 @@ course of the framed/shaded matter.  There is also a command
            (lambda _
              (delete-file "g-brief.drv")
              #t)))))
-    (home-page "http://www.ctan.org/pkg/g-brief")
+    (home-page "https://www.ctan.org/pkg/g-brief")
     (synopsis "Letter document class")
     (description
      "This package is designed for formatting formless letters in German; it
@@ -2331,7 +2331,7 @@ are LaTeX 2.09 @code{documentstyle} and LaTeX 2e class files for both an
                 "0d4l0msk8j5pi95xnmm9wygv1vbpkwkv5amx9l0km86cs79jpp1h"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/galois"))
-    (home-page "http://www.ctan.org/pkg/galois")
+    (home-page "https://www.ctan.org/pkg/galois")
     (synopsis "Typeset Galois connections")
     (description
      "The package deals with connections in two-dimensional style, optionally
@@ -2351,7 +2351,7 @@ in colour.")
                 "03g9by54yrypn599y98r1xh7qw0bbbmpzq0bfwpj6j5q5rkl1mfa"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/gcite"))
-    (home-page "http://www.ctan.org/pkg/gcite")
+    (home-page "https://www.ctan.org/pkg/gcite")
     (synopsis "Citations in a reader-friendly style")
     (description
      "The package allows citations in the German style, which is considered by
@@ -2375,7 +2375,7 @@ BibLaTeX, and is considered experimental.")
                 "1r2kfcwclg33yk5z8mvlagwxj7nr1mc3w4bdpmhrwv6dn8mrbvw8"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/geometry"))
-    (home-page "http://www.ctan.org/pkg/geometry")
+    (home-page "https://www.ctan.org/pkg/geometry")
     (synopsis "Flexible and complete interface to document dimensions")
     (description
      "This package provides an easy and flexible user interface to customize
@@ -2400,7 +2400,7 @@ ability to communicate the paper size it's set up to the output.")
                 "0caxs74hla28hc67csf5i5ahadx97w8vxh3mdmsprxbpd1mr7ssg"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/mdwtools"))
-    (home-page "http://www.ctan.org/pkg/mdwtools")
+    (home-page "https://www.ctan.org/pkg/mdwtools")
     (synopsis "Miscellaneous tools by Mark Wooding")
     (description
      "This collection of tools includes: @code{atsupport} for short commands
@@ -2424,7 +2424,7 @@ array environments; verbatim handling; and syntax diagrams.")
                 "09mvszd5qgqg4cfglpj5qxyzjz190ppb9p8gnsnjydwp1akvhayf"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/polyglossia"))
-    (home-page "http://www.ctan.org/pkg/polyglossia")
+    (home-page "https://www.ctan.org/pkg/polyglossia")
     (synopsis "Alternative to babel for XeLaTeX and LuaLaTeX")
     (description
      "This package provides a complete Babel replacement for users of LuaLaTeX
@@ -2444,7 +2444,7 @@ and XeLaTeX; it relies on the @code{fontspec} package, version 2.0 at least.")
                 "14b2bc7cqz4ckxxycim9sw6jkrr1pahivm1rdbpz5k6hl967w1s3"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/supertabular"))
-    (home-page "http://www.ctan.org/pkg/supertabular")
+    (home-page "https://www.ctan.org/pkg/supertabular")
     (synopsis "Multi-page tables package")
     (description
      "This package was a predecessor of @code{longtable}; the newer
@@ -2478,7 +2478,7 @@ situations where longtable has problems.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/texinfo")
+    (home-page "https://www.ctan.org/pkg/texinfo")
     (synopsis "TeX macros to handle Texinfo files")
     (description
      "Texinfo is the preferred format for documentation in the GNU project;
@@ -2501,7 +2501,7 @@ hypertext linkages in some cases).")
                 "0d1050i973wnxigy0xpky5l7vn4ff7ldhkjpdqsw5s653gagwixp"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/upquote"))
-    (home-page "http://www.ctan.org/pkg/upquote")
+    (home-page "https://www.ctan.org/pkg/upquote")
     (synopsis "Show \"realistic\" quotes in verbatim")
     (description
      "Typewriter-style fonts are best for program listings, but Computer
@@ -2541,7 +2541,7 @@ does not affect @code{\\tt}, @code{\\texttt}, etc.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/anysize")
+    (home-page "https://www.ctan.org/pkg/anysize")
     (synopsis "Simple package to set up document margins")
     (description
      "This is a simple package to set up document margins.  This package is
@@ -2561,7 +2561,7 @@ considered obsolete; alternatives are the @code{typearea} package from the
                 "0rxfpr8vq3brwx5rc7qn91ixlp9zva4zrms8a579fqa1g5yva7vg"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/appendix"))
-    (home-page "http://www.ctan.org/pkg/appendix")
+    (home-page "https://www.ctan.org/pkg/appendix")
     (synopsis "Extra control of appendices")
     (description
      "The appendix package provides various ways of formatting the titles of
@@ -2583,7 +2583,7 @@ command.")
                 "1ik4m8pzfsn1grlda6fniqqfwmgj7rfxwg63jdw0p0qv002vc7ik"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/changebar"))
-    (home-page "http://www.ctan.org/pkg/changebar")
+    (home-page "https://www.ctan.org/pkg/changebar")
     (synopsis "Generate changebars in LaTeX documents")
     (description
      "Identify areas of text to be marked with changebars with the
@@ -2639,7 +2639,7 @@ copy-and-paste functions work properly.")
                 "190pmq8la2rq07xry8bn8z8yywzxv6fqyqaj7yjfj5rgw6x0mas8"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/colortbl"))
-    (home-page "http://www.ctan.org/pkg/colortbl")
+    (home-page "https://www.ctan.org/pkg/colortbl")
     (synopsis "Add colour to LaTeX tables")
     (description
      "This package allows rows, columns, and even individual cells in LaTeX
@@ -2671,7 +2671,7 @@ tables to be coloured.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/fancybox")
+    (home-page "https://www.ctan.org/pkg/fancybox")
     (synopsis "Variants of \\fbox and other games with boxes")
     (description
      "This package provides variants of @code{\\fbox}: @code{\\shadowbox},
@@ -2705,7 +2705,7 @@ floats, center, flushleft, and flushright, lists, and pages.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/fancyhdr")
+    (home-page "https://www.ctan.org/pkg/fancyhdr")
     (synopsis "Extensive control of page headers and footers in LaTeX2e")
     (description
      "The package provides extensive facilities, both for constructing headers
@@ -2725,7 +2725,7 @@ would automatically change the heading style in use).")
                 "0nbl7wylkv22fcdv4p8byhhj575fli6jnqjpkhrkbv8dzwah84nq"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/float"))
-    (home-page "http://www.ctan.org/pkg/float")
+    (home-page "https://www.ctan.org/pkg/float")
     (synopsis "Improved interface for floating objects")
     (description
      "This package improves the interface for defining floating objects such
@@ -2748,7 +2748,7 @@ with @code{\\floatplacement{figure}{H}}.")
                 "03x61wwql8nh6zrqiiiq3rb0x7m3pn48c606zapy19y21fybwdxs"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/footmisc"))
-    (home-page "http://www.ctan.org/pkg/footmisc")
+    (home-page "https://www.ctan.org/pkg/footmisc")
     (synopsis "Range of footnote options")
     (description
      "This is a collection of ways to change the typesetting of footnotes.
@@ -2773,7 +2773,7 @@ footnotes with symbols rather than numbers.")
     (arguments
      '(#:tex-directory "latex/listings"
        #:build-targets '("listings.ins")))
-    (home-page "http://www.ctan.org/pkg/listings")
+    (home-page "https://www.ctan.org/pkg/listings")
     (synopsis "Typeset source code listings using LaTeX")
     (description
      "The package enables the user to typeset programs (programming code)
@@ -2807,7 +2807,7 @@ styles.  Support for @code{hyperref} is provided.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/jknappen")
+    (home-page "https://www.ctan.org/pkg/jknappen")
     (synopsis "Miscellaneous packages by Joerg Knappen")
     (description
      "This package provides miscellaneous macros by Joerg Knappen, including:
@@ -2882,7 +2882,7 @@ in SGML; use maths minus in text as appropriate; simple Young tableaux.")
      `(("texlive-bin" ,texlive-bin)
        ("texlive-metafont-base" ,texlive-metafont-base)
        ("texlive-fonts-cm" ,texlive-fonts-cm)))
-    (home-page "http://www.ctan.org/pkg/ec")
+    (home-page "https://www.ctan.org/pkg/ec")
     (synopsis "Computer modern fonts in T1 and TS1 encodings")
     (description
      "The EC fonts are European Computer Modern Fonts, supporting the complete
@@ -2963,7 +2963,7 @@ texlive-2017.1/Master/texmf-dist/doc/fonts/ec/copyrite.txt"))))
      `(("texlive-bin" ,texlive-bin)
        ("texlive-metafont-base" ,texlive-metafont-base)
        ("texlive-fonts-cm" ,texlive-fonts-cm)))
-    (home-page "http://www.ctan.org/pkg/rsfs")
+    (home-page "https://www.ctan.org/pkg/rsfs")
     (synopsis "Ralph Smith's Formal Script font")
     (description
      "The fonts provide uppercase formal script letters for use as symbols in
@@ -2986,7 +2986,7 @@ one of the packages @code{calrsfs} and @code{mathrsfs}.")
                 "1xvmms28mvvfpks9x7lfya2xhh5k8jy3qnlih1mzcnf156xnb89z"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/eso-pic"))
-    (home-page "http://www.ctan.org/pkg/eso-pic")
+    (home-page "https://www.ctan.org/pkg/eso-pic")
     (synopsis "Add picture commands (or backgrounds) to every page")
     (description
      "The package adds one or more user commands to LaTeX's @code{shipout}
@@ -3019,7 +3019,7 @@ routine, which may be used to place the output at fixed positions.  The
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/eepic")
+    (home-page "https://www.ctan.org/pkg/eepic")
     (synopsis "Extensions to epic and the LaTeX drawing tools")
     (description
      "Extensions to @code{epic} and the LaTeX picture drawing environment,
@@ -3056,7 +3056,7 @@ splines, and filled circles and ellipses.  The package uses @code{tpic}
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/enumitem")
+    (home-page "https://www.ctan.org/pkg/enumitem")
     (synopsis "Customize basic list environments")
     (description
      "This package is intended to ease customizing the three basic list
@@ -3078,7 +3078,7 @@ in the form @code{key=value} are available, for example:
                 "0qlxy47f1f8plgch3jqfsnrdgpyz20sz46yp33i2jwvf9hvfczf0"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/multirow"))
-    (home-page "http://www.ctan.org/pkg/multirow")
+    (home-page "https://www.ctan.org/pkg/multirow")
     (synopsis "Create tabular cells spanning multiple rows")
     (description
      "The package provides tools for creating tabular cells spanning multiple
@@ -3111,7 +3111,7 @@ entry at the \"natural\" width of its text.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/overpic")
+    (home-page "https://www.ctan.org/pkg/overpic")
     (synopsis "Combine LaTeX commands over included graphics")
     (description
      "The @code{overpic} environment is a cross between the LaTeX
@@ -3147,7 +3147,7 @@ positions; a grid for orientation is available.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/parskip")
+    (home-page "https://www.ctan.org/pkg/parskip")
     (synopsis "Layout with zero \\parindent, non-zero \\parskip")
     (description
      "Simply changing @code{\\parskip} and @code{\\parindent} leaves a layout
@@ -3167,7 +3167,7 @@ designed class) helps alleviate this untidiness.")
                 "06p5smfq66559ppdnmkl3hp8534x84ywbscimsiir4gllpya3i9h"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/pdfpages"))
-    (home-page "http://www.ctan.org/pkg/pdfpages")
+    (home-page "https://www.ctan.org/pkg/pdfpages")
     (synopsis "Include PDF documents in LaTeX")
     (description
      "This package simplifies the inclusion of external multi-page PDF
@@ -3200,7 +3200,7 @@ use this package to insert PostScript files, in addition to PDF files.")
                (("fontdef\\}\\}" line)
                 (string-append line "\n\\endbatchfile")))
              #t)))))
-    (home-page "http://www.ctan.org/pkg/stmaryrd")
+    (home-page "https://www.ctan.org/pkg/stmaryrd")
     (synopsis "St Mary Road symbols for theoretical computer science")
     (description
      "The fonts were originally distributed as Metafont sources only, but
@@ -3222,7 +3222,7 @@ the whole font.")
                 "15spcl5wb7w269qd6y596vp4yi8sa5ppcx8w4z2i9kyp02r3a0yb"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/subfigure"))
-    (home-page "http://www.ctan.org/pkg/subfigure")
+    (home-page "https://www.ctan.org/pkg/subfigure")
     (synopsis "Figures divided into subfigures")
     (description
      "This (deprecated) package provides support for the manipulation and
@@ -3249,7 +3249,7 @@ the more recent @code{subcaption} package more satisfactory.")
                 "1adkdx2zkk42g82nqf57lv1nc1z7kwl13jmy8vpcsizsa0xdnx9n"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/tabulary"))
-    (home-page "http://www.ctan.org/pkg/tabulary")
+    (home-page "https://www.ctan.org/pkg/tabulary")
     (synopsis "Tabular with variable width columns balanced")
     (description
      "The package defines a @code{tabular*}-like environment, @code{tabulary},
@@ -3286,7 +3286,7 @@ according to the natural width of the widest cell in the column.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/threeparttable")
+    (home-page "https://www.ctan.org/pkg/threeparttable")
     (synopsis "Tables with captions and notes all the same width")
     (description
      "This package facilitates tables with titles (captions) and notes.  The
@@ -3409,7 +3409,7 @@ environment.")
            (sha256
             (base32
              "1bal5fhw0xlhl37ayv8vlnqnsn1y82kadzfjhbgr223blspp4zsj"))))))
-    (home-page "http://www.ctan.org/pkg/threeparttable")
+    (home-page "https://www.ctan.org/pkg/threeparttable")
     (synopsis "Times-like fonts in support of mathematics")
     (description
      "Txfonts supplies virtual text roman fonts using Adobe Times (or URW
@@ -3493,7 +3493,7 @@ of ink traps which typify the Kurier font.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/titlesec")
+    (home-page "https://www.ctan.org/pkg/titlesec")
     (synopsis "Select alternative section titles")
     (description
      "This package provides an interface to sectioning commands for selection
@@ -3516,7 +3516,7 @@ floats in a page.  You may assign headers/footers to individual floats, too.")
                 "1lvxrqfwcwa4p31zyfm80gr05v8c28xybv5ri79zi2ngz6834z12"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/type1cm"))
-    (home-page "http://www.ctan.org/pkg/type1cm")
+    (home-page "https://www.ctan.org/pkg/type1cm")
     (synopsis "Arbitrary size font selection in LaTeX")
     (description
      "LaTeX, by default, restricts the sizes at which you can use its default
@@ -3544,7 +3544,7 @@ now contains a package @code{fix-cm},f which performs the task of
                 "00gdiwh3sfhh1iimjhpja7lm7k4vzqzql2irgwnpz94qvh25zwi5"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/lh"))
-    (home-page "http://www.ctan.org/pkg/lh")
+    (home-page "https://www.ctan.org/pkg/lh")
     (synopsis "Cyrillic fonts that support LaTeX standard encodings")
     (description
      "The LH fonts address the problem of the wide variety of alphabets that
@@ -3583,7 +3583,7 @@ OT2 encoded fonts, CM bright shaped fonts and Concrete shaped fonts.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/metapost")
+    (home-page "https://www.ctan.org/pkg/metapost")
     (synopsis "Create scalable illustrations")
     (description
      "MetaPost uses a language based on that of Metafont to produce precise
@@ -3604,7 +3604,7 @@ than the bitmaps Metafont creates.")
               (file-name (string-append name "-" version "-checkout"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/acmart"))
-    (home-page "http://www.ctan.org/pkg/acmart")
+    (home-page "https://www.ctan.org/pkg/acmart")
     (synopsis "Class for typesetting publications of ACM")
     (description
      "This package provides a class for typesetting publications of the
@@ -3637,7 +3637,7 @@ Association for Computing Machinery (ACM).")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/varwidth")
+    (home-page "https://www.ctan.org/pkg/varwidth")
     (synopsis "Variable-width minipage")
     (description
      "The @code{varwidth} environment is superficially similar to
@@ -3657,7 +3657,7 @@ get a narrower “natural” width.")
                 "1sgwbfwjjf70g54hh93gsd9jp9nm67w6n74x9d72a56n07jbk5hv"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/wasysym"))
-    (home-page "http://www.ctan.org/pkg/wasysym")
+    (home-page "https://www.ctan.org/pkg/wasysym")
     (synopsis "LaTeX support file to use the WASY2 fonts")
     (description
      "The wasy2WASY2 (Waldi Symbol) font by Roland Waldi provides many glyphs
@@ -3692,7 +3692,7 @@ to use interface for these symbols.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/wrapfig")
+    (home-page "https://www.ctan.org/pkg/wrapfig")
     (synopsis "Produces figures which text can flow around")
     (description
      "This package allows figures or tables to have text wrapped around them.
@@ -3726,7 +3726,7 @@ It does not work in combination with list environments, but can be used in a
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/ucs")
+    (home-page "https://www.ctan.org/pkg/ucs")
     (synopsis "Extended UTF-8 input encoding support for LaTeX")
     (description
      "The bundle provides the @code{ucs} package, and @code{utf8x.def},
@@ -3760,7 +3760,7 @@ package of that name now exists.")
            (lambda _
              (delete-file "preview.drv")
              #t)))))
-    (home-page "http://www.ctan.org/pkg/preview")
+    (home-page "https://www.ctan.org/pkg/preview")
     (synopsis "Extract bits of a LaTeX source for output")
     (description
      "The main purpose of the preview package is the extraction of selected
@@ -3785,7 +3785,7 @@ files.")
                 "0jmasg40bk53zdd2jc8nc18jvdai3p2wmamy7hwli8gls4nf25qp"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/acronym"))
-    (home-page "http://www.ctan.org/pkg/acronym")
+    (home-page "https://www.ctan.org/pkg/acronym")
     (synopsis "Expand acronyms at least once")
     (description
      "This package ensures that all acronyms used in the text are spelled out
@@ -3820,7 +3820,7 @@ e-TeX.")
            (mkdir-p target)
            (copy-recursively (assoc-ref %build-inputs "source") target)
            #t))))
-    (home-page "http://www.ctan.org/pkg/pdftex")
+    (home-page "https://www.ctan.org/pkg/pdftex")
     (synopsis "TeX extension for direct creation of PDF")
     (description
      "This package provides an extension of TeX which can be configured to
-- 
cgit v1.2.3


From f569e9174f4a7b45619486878c4c7ab721a08c4d Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 22:19:30 +0200
Subject: gnu: texlive-generic-unicode-data: Declare a source file-name.

* gnu/packages/tex.scm (texlive-generic-unicode-data)[source]: Declare a
source file-name.
---
 gnu/packages/tex.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index 93788a1c50..c57ae1d6ba 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -281,6 +281,7 @@ to PostScript.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/tex/generic/unicode-data"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0ivrhp6jz31pl4z841g4ws41lmvdiwz4sslmhf02inlib79gz6r2"))))
-- 
cgit v1.2.3


From ddc0bbc875aa46b3af449a020db4392fef03154e Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 22:20:57 +0200
Subject: gnu: texlive-generic-dehyph-exptl: Declare a source file-name.

* gnu/packages/tex.scm (texlive-generic-dehyph-exptl)[source]: Declare a
source file-name.
---
 gnu/packages/tex.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index c57ae1d6ba..a574b01209 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -320,6 +320,7 @@ out to date by @code{unicode-letters.tex}. ")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/tex/generic/dehyph-exptl"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "1l9wgv99qq0ysvlxqpj4g8bl0dywbzra4g8m2kmpg2fb0i0hczap"))))
-- 
cgit v1.2.3


From ac0529ddec796b970439d00f7a33070ff6bc7483 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 22:21:52 +0200
Subject: gnu: texlive-generic-tex-ini-files: Declare a source file-name.

* gnu/packages/tex.scm (texlive-generic-tex-ini-files)[source]: Declare
a source file-name.
---
 gnu/packages/tex.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index a574b01209..ce73dcf448 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -356,6 +356,7 @@ bundle.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/tex/generic/tex-ini-files"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "1wh42n1lmzcvi3g6mm31nm3yd5ha5bl260xqc444jg1m9fdp3wz5"))))
-- 
cgit v1.2.3


From a6acd6113c4c8ce2092d86f0ab9ffd5907cef853 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 22:23:16 +0200
Subject: gnu: texlive-generic-hyph-utf8: Declare a source file-name.

* gnu/packages/tex.scm (texlive-generic-hyph-utf8)[source]: Declare a
source file-name.
---
 gnu/packages/tex.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index ce73dcf448..276634a2e6 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -391,6 +391,7 @@ to adapt the plain e-TeX source file to work with XeTeX and LuaTeX.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/tex/generic/hyph-utf8"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0ghizcz7ps16dzfqf66wwg5i181assc6qsm0g7g5dbmp909931vi"))))
-- 
cgit v1.2.3


From 1dec413ae0c731c23ec9286e56c711af7f9a4e5b Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 22:23:54 +0200
Subject: gnu: texlive-metafont-base: Declare a source file-name.

* gnu/packages/tex.scm (texlive-metafont-base)[source]: Declare a source
file-name.
---
 gnu/packages/tex.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index 276634a2e6..e743143be9 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -448,6 +448,7 @@ converters, will completely supplant the older patterns.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/metafont"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "1yl4n8cn5xqk2nc22zgzq6ymd7bhm6xx1mz3azip7i3ki4bhb5q5"))))
-- 
cgit v1.2.3


From b8e213cb2f0c388f7ce41be48409ec28a5adf763 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 22:24:52 +0200
Subject: gnu: texlive-fontname: Fix source file-name.

* gnu/packages/tex.scm (texlive-fontname)[source]: Correct source
file-name.
---
 gnu/packages/tex.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index e743143be9..bc0dc6c71b 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -500,7 +500,7 @@ build fonts using the Metafont system.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/fonts/map/fontname"))
                     (revision %texlive-revision)))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0cssbzcx15221dynp5sii72qh4l18mwkr14n8w1xb19j8pbaqasz"))))
-- 
cgit v1.2.3


From a4015c206540cf3e75df592a1fbe76b94565a05b Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 22:25:45 +0200
Subject: gnu: texlive-fonts-cm: Declare a source file-name.

* gnu/packages/tex.scm (texlive-fonts-cm)[source]: Declare a source
file-name.
---
 gnu/packages/tex.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index bc0dc6c71b..b0211c7924 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -534,6 +534,7 @@ documents.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/fonts/source/public/cm"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "045k5b9rdmbxpy1a3006l1x96z1rd18vg3cwrvnld9bqybw5qz44"))))
-- 
cgit v1.2.3


From 6b286e424a1c7feeeb6ca581a597ab4037002f1d Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 22:26:33 +0200
Subject: gnu: texlive-fonts-knuth-lib: Declare a source file-name.

* gnu/packages/tex.scm (texlive-fonts-knuth-lib)[source]: Declare a
source file-name.
---
 gnu/packages/tex.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index b0211c7924..48b4d1f3bd 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -603,6 +603,7 @@ display, and mathematical fonts in a range of styles, based on Monotype Modern
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/fonts/source/public/knuth-lib"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0in9aqyi8jkyf9d16z0li50z5fpwj1iwgwm83gmvwqcf7chfs04y"))))
-- 
cgit v1.2.3


From a4550e7d664b317bcaf8c4fa0d4d8642c7b96cec Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 22:27:13 +0200
Subject: gnu: texlive-fonts-latex: Declare a source file-name.

* gnu/packages/tex.scm (texlive-fonts-latex)[source]: Declare a source
file-name.
---
 gnu/packages/tex.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index 48b4d1f3bd..10b48f13bd 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -667,6 +667,7 @@ fonts.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/fonts/source/public/latex-fonts"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0ypsm4xv9cw0jckk2qc7gi9hcmhf31mrg56pz3llyx3yd9vq2lps"))))
-- 
cgit v1.2.3


From 5fe9233eb4c52b669342c74598d4480c2c20d8bf Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 22:27:54 +0200
Subject: gnu: texlive-fonts-amsfonts: Declare a source file-name.

* gnu/packages/tex.scm (texlive-fonts-amsfonts)[source]: Declare a
source file-name.
---
 gnu/packages/tex.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index 10b48f13bd..1fedd2cb4a 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -742,6 +742,7 @@ symbol fonts.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/fonts/source/public/amsfonts"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "07h20rvpbdb4k72hzmjkyb29426zr9wxsfp6yd4ajbbpd3vx8grb"))))
-- 
cgit v1.2.3


From 9700a0d0a5670bc278b219847d0cd555f00314c2 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 22:29:32 +0200
Subject: gnu: texlive-latex-amsfonts: Declare a source file-name.

* gnu/packages/tex.scm (texlive-latex-amsfonts)[source]: Declare a
source file-name.
---
 gnu/packages/tex.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index 1fedd2cb4a..ef0abaf870 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -824,6 +824,7 @@ details can be found in the documentation.")
     (source (origin
               (method svn-fetch)
               (uri (texlive-ref "latex" "amsfonts"))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0slzfv5h2m03b2xvm2sasznz4azh6rgi069z161dja3l8rln79hm"))))
-- 
cgit v1.2.3


From b63aefe53ecaebfcb4088d1b3821f23e8a1b7e68 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 22:30:18 +0200
Subject: gnu: texlive-tex-plain: Declare a source file-name.

* gnu/packages/tex.scm (texlive-tex-plain)[source]: Declare a source
file-name.
---
 gnu/packages/tex.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index ef0abaf870..c6f39dfa59 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -854,6 +854,7 @@ individual symbols defined in @code{amssymb.sty}.")
                                         %texlive-tag "/Master/texmf-dist/"
                                         "/tex/plain"))
                     (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
                 "0mjgl3gscn3ps29yjambz1j9fg81ynnncb96vpprwx4xsijhsns0"))))
-- 
cgit v1.2.3


From 8d514ae7538d9b0a7afbea5a3bf249c61f0d66cc Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 22:39:41 +0200
Subject: gnu: texlive-latex-base: Declare a source file-name.

* gnu/packages/tex.scm (texlive-latex-base)[source]: Declare a source
file-name.
[native-inputs]: Add a source file-name.
---
 gnu/packages/tex.scm | 6 ++++++
 1 file changed, 6 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index c6f39dfa59..3a30777f20 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -887,6 +887,11 @@ book).")
                                        %texlive-tag "/Master/texmf-dist/"
                                        dir))
                    (revision %texlive-revision)))
+             (file-name (string-append "texlive-generic-"
+                                       (last (string-split
+                                               (string-drop-right dir 1) #\/))
+                                       "-" (number->string %texlive-revision)
+                                       "-checkout"))
              (sha256 (base32 hash))))))
     (package
       (name "texlive-latex-base")
@@ -894,6 +899,7 @@ book).")
       (source (origin
                 (method svn-fetch)
                 (uri (texlive-ref "latex" "base"))
+                (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
                   "1h9pir2hz6i9avc4lrl733p3zf4rpkg8537x1zdbhs91hvhikw9k"))))
-- 
cgit v1.2.3


From 8d32139df0bdea0b3ac3e68592d148d23b4e5a8e Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 22:52:05 +0200
Subject: gnu: texlive-latex-base: Use 'invoke'.

* gnu/packages/tex.scm (texlive-latex-base)[arguments]: Replace
'system*' with 'invoke'.
---
 gnu/packages/tex.scm | 30 ++++++++++++++----------------
 1 file changed, 14 insertions(+), 16 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index 3a30777f20..05a7cd834b 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -946,12 +946,10 @@ book).")
 
                (mkdir "build")
                (mkdir "web2c")
-               (and (zero? (system* "luatex" "-ini" "-interaction=batchmode"
-                                    "-output-directory=build"
-                                    "unpack.ins"))
-                    (zero? (system* "tex" "-ini" "-interaction=batchmode"
-                                    "-output-directory=web2c"
-                                    "tex.ini"))
+               (and (invoke "luatex" "-ini" "-interaction=batchmode"
+                            "-output-directory=build" "unpack.ins")
+                    (invoke "tex" "-ini" "-interaction=batchmode"
+                            "-output-directory=web2c" "tex.ini")
                     ;; LaTeX, pdfetex/pdftex, and XeTeX require e-TeX, which
                     ;; is enabled only in extended mode (activated with a
                     ;; leading asterisk).  We should not use luatex here,
@@ -959,25 +957,25 @@ book).")
                     ;; incompatible with any other TeX engine.
                     (every
                      (lambda (format)
-                       (zero? (system* "latex" "-ini" "-interaction=batchmode"
-                                       "-output-directory=web2c"
-                                       "-translate-file=cp227.tcx"
-                                       (string-append "*" format ".ini"))))
+                       (invoke "latex" "-ini" "-interaction=batchmode"
+                               "-output-directory=web2c"
+                               "-translate-file=cp227.tcx"
+                               (string-append "*" format ".ini")))
                      '("latex"
                        "pdflatex"
                        "pdfetex"))
                     (every
                      (lambda (format)
-                       (zero? (system* format "-ini" "-interaction=batchmode"
-                                       "-output-directory=web2c"
-                                       (string-append "*" format ".ini"))))
+                       (invoke format "-ini" "-interaction=batchmode"
+                               "-output-directory=web2c"
+                               (string-append "*" format ".ini")))
                      '("xetex"
                        "xelatex"))
                     (every
                      (lambda (format)
-                       (zero? (system* "luatex" "-ini" "-interaction=batchmode"
-                                       "-output-directory=web2c"
-                                       (string-append format ".ini"))))
+                       (invoke "luatex" "-ini" "-interaction=batchmode"
+                               "-output-directory=web2c"
+                               (string-append format ".ini")))
                      '("dviluatex" "dvilualatex" "luatex" "lualatex")))))
            (replace 'install
              (lambda* (#:key outputs #:allow-other-keys)
-- 
cgit v1.2.3


From 620ea2de26f9ef43e4b7a9dcc2f587a17764595a Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 13 Mar 2018 22:56:27 +0200
Subject: gnu: python2-quex: Parameterize the source uri.

* gnu/packages/python.scm (python2-quex)[source]: Replace hard-coded
version with parameterized one.  Remove unnecessary file-name field.
---
 gnu/packages/python.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 8db00dbf37..106c040bf8 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -13001,11 +13001,12 @@ filesystem events on Linux.")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "mirror://sourceforge/quex/HISTORY/0.67/quex-" version ".zip"))
+       (uri (string-append "mirror://sourceforge/quex/HISTORY/"
+                           (version-major+minor version)
+                           "/quex-" version ".zip"))
        (sha256
         (base32
-         "14gv8ll3ipqv4kyc2xiy891nrmjl4ic823zfyx8hassagyclyppw"))
-       (file-name (string-append name "-" version ".zip"))))
+         "14gv8ll3ipqv4kyc2xiy891nrmjl4ic823zfyx8hassagyclyppw"))))
     (build-system python-build-system)
     (native-inputs
      `(("unzip" ,unzip)))
-- 
cgit v1.2.3


From 23cdeaa97130ae908bfe9990cef85e4fe402aedf Mon Sep 17 00:00:00 2001
From: David Thompson <dthompson2@worcester.edu>
Date: Tue, 13 Mar 2018 20:32:44 -0400
Subject: gnu: tiled: Update to 1.1.3.

* gnu/packages/game-development.scm (tiled): Update to 1.1.3.
---
 gnu/packages/game-development.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index 3025a68ec1..03a70bea49 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -386,7 +386,7 @@ support.")
 (define-public tiled
   (package
     (name "tiled")
-    (version "1.1.2")
+    (version "1.1.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/bjorn/tiled/archive/v"
@@ -394,7 +394,7 @@ support.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0l4wc10d10fi0a5spbi318kjfzlizmycpr4wwlq04sk3b5kra0w0"))))
+                "08bxl6vc7ynnji4r6ij9ayr2jixvfhv4daplw5p96s0gkhdqd90k"))))
     (build-system gnu-build-system)
     (inputs
      `(("qtbase" ,qtbase)
-- 
cgit v1.2.3


From fdcbe78b14b8ef2f11b3ba8ff261d3972ca3ef90 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 14 Mar 2018 06:27:07 +0100
Subject: gnu: kurly: Update to 1.2.1.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/curl.scm (kurly): Update to 1.2.1.
[arguments]: Install the man page, and put README.md in its right place.
Rename ‘install-readme’ to ‘install-documentation’ to match this change.
---
 gnu/packages/curl.scm | 22 ++++++++++++++--------
 1 file changed, 14 insertions(+), 8 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/curl.scm b/gnu/packages/curl.scm
index 32509fc3fc..ccff18e632 100644
--- a/gnu/packages/curl.scm
+++ b/gnu/packages/curl.scm
@@ -6,6 +6,7 @@
 ;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -152,7 +153,7 @@ tunneling, and so on.")
 (define-public kurly
   (package
     (name "kurly")
-    (version "1.1.0")
+    (version "1.2.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -161,19 +162,24 @@ tunneling, and so on.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1q192f457sjypgvwq7grrf8gq8w272p3zf1d5ppc20mriqm0mbc3"))))
+                "01kp33gvzxmk6ipz7323wqwmbc90q2mwzsjig8rzpqsm4kji5hi6"))))
     (build-system go-build-system)
     (arguments
      `(#:import-path "github.com/davidjpeacock/kurly"
        #:install-source? #f
        #:phases
        (modify-phases %standard-phases
-         (add-after 'install 'install-readme
-           (lambda* (#:key outputs import-path #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (readme (string-append "src/" import-path "/README.md"))
-                    (misc (string-append out "/share/kurly/misc/")))
-               (install-file readme misc)
+         (add-after 'install 'install-documentation
+           (lambda* (#:key import-path outputs #:allow-other-keys)
+             (let* ((source (string-append "src/" import-path))
+                    (out (assoc-ref outputs "out"))
+                    (doc (string-append out "/share/doc/" ,name "-" ,version))
+                    (man (string-append out "/share/man/man1")))
+               (with-directory-excursion source
+                 (install-file "README.md" doc)
+                 (mkdir-p man)
+                 (copy-file "meta/kurly.man"
+                            (string-append man "/kurly.1")))
                #t))))))
     (inputs
      `(("go-github-com-alsm-ioprogress" ,go-github-com-alsm-ioprogress)
-- 
cgit v1.2.3


From d773fef1ce2d6f6386c8d388ce2b63ed9a264843 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 14 Mar 2018 06:43:02 +0100
Subject: gnu: inkscape: Update to 0.92.3.

* gnu/packages/inkscape.scm (inkscape): Update to 0.92.3.
[source]: Remove patch.
---
 gnu/packages/inkscape.scm | 14 ++------------
 1 file changed, 2 insertions(+), 12 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/inkscape.scm b/gnu/packages/inkscape.scm
index dc5a30b868..1e98369ea3 100644
--- a/gnu/packages/inkscape.scm
+++ b/gnu/packages/inkscape.scm
@@ -46,25 +46,15 @@
 (define-public inkscape
   (package
     (name "inkscape")
-    (version "0.92.2")
+    (version "0.92.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://media.inkscape.org/dl/"
                                   "resources/file/"
                                   "inkscape-" version ".tar.bz2"))
-              (patches
-               (list
-                ;; Fix compatibility with poppler >= 0.58.
-                (origin
-                  (method url-fetch)
-                  (uri (string-append "https://gitlab.com/inkscape/inkscape/commit/"
-                                      "9418824967eb4c53371ef8588243fed4cab496e0.patch"))
-                  (sha256
-                   (base32
-                    "0wwyhkqb1qyazz5f6wqrc223l6k8qnmadiw28q8gihlgvh38rvll")))))
               (sha256
                (base32
-                "1lyghk6yarcv9nwkh6k366p6hb7rfilqcvbyji09hki59khd0a56"))))
+                "1chng2yw8dsjxc9gf92aqv7plj11cav8ax321wmakmv5bb09cch6"))))
     (build-system cmake-build-system)
     (inputs
      `(("aspell" ,aspell)
-- 
cgit v1.2.3


From 5ecfa6f5659bebefabbc6ba3322faf3936358ed5 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 14 Mar 2018 06:44:28 +0100
Subject: gnu: r-stringi: Update to 1.1.7.

* gnu/packages/statistics.scm (r-stringi): Update to 1.1.7.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index b7a12d907a..78afb77a8b 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -939,14 +939,14 @@ solution for sending email, including attachments, from within R.")
 (define-public r-stringi
   (package
     (name "r-stringi")
-    (version "1.1.6")
+    (version "1.1.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "stringi" version))
        (sha256
         (base32
-         "122im5m8x9bqpahc0hbxmvdq6hnsmgnxwwyjpvbihyv2jq5kd44m"))))
+         "0nck1s2iglmkrn15ay2chrrwsy5lngcylz2sc87fxy5skxaahxdl"))))
     (build-system r-build-system)
     (inputs `(("icu4c" ,icu4c)))
     (native-inputs `(("pkg-config" ,pkg-config)))
-- 
cgit v1.2.3


From 186cef9e1c023a7d0afb8a5ce796332d2ad99215 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 14 Mar 2018 06:53:16 +0100
Subject: gnu: simplescreenrecorder: Update to 0.3.10.

* gnu/packages/video.scm (simplescreenrecorder): Update to 0.3.10.
---
 gnu/packages/video.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 984d2f183d..6c9769d9fa 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -2038,7 +2038,7 @@ making @dfn{screencasts}.")
 (define-public simplescreenrecorder
   (package
     (name "simplescreenrecorder")
-    (version "0.3.9")
+    (version "0.3.10")
     (source
      (origin
        (method url-fetch)
@@ -2047,7 +2047,7 @@ making @dfn{screencasts}.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1gnf9wbiq2fcbqcn1a5nfmp8r0nxrrlgh2wly2mfkkwymynhx0pk"))))
+         "02rl9yyx3hlz9fqvgzv7ipmvx2qahj7ws5wx2m7zs3lssq3qag3g"))))
     (build-system cmake-build-system)
     ;; Although libx11, libxfixes, libxext are listed as build dependencies in
     ;; README.md, the program builds and functions properly without them.
-- 
cgit v1.2.3


From b4bf95162777b9db3c681292942895ea308e701e Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 14 Mar 2018 07:00:29 +0100
Subject: gnu: masscan: Update to 1.0.5.

* gnu/packages/admin.scm (masscan): Update to 1.0.5.
[arguments]: Set CC to a real compiler instead of the default clang.
---
 gnu/packages/admin.scm | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 7623693722..ad31bc498f 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -2433,7 +2433,7 @@ on systems running the Linux kernel.")
 (define-public masscan
   (package
     (name "masscan")
-    (version "1.0.4")
+    (version "1.0.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/robertdavidgraham/masscan"
@@ -2441,16 +2441,18 @@ on systems running the Linux kernel.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1y9af345g00z83rliv6bmlqg37xwc7xpnx5xqdgmjikzcxgk9pji"))))
+                "0wxddsgyx27z45906icdhdbfsvfj8ij805208qpqjx46i0lnjs50"))))
     (build-system gnu-build-system)
     (inputs
      `(("libpcap" ,libpcap)))
     (arguments
      '(#:test-target "regress"
-       #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out")))
+       #:make-flags
+       (list "CC=gcc"
+             (string-append "PREFIX=" (assoc-ref %outputs "out")))
        #:phases
        (modify-phases %standard-phases
-         (delete 'configure) ; There is no ./configure script
+         (delete 'configure)            ; no ./configure script
          (add-after 'unpack 'patch-path
            (lambda* (#:key outputs inputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
@@ -2463,8 +2465,8 @@ on systems running the Linux kernel.")
 open ports, and also complete the TCP connection and interact with the remote
 application, collecting the information received.")
     (home-page "https://github.com/robertdavidgraham/masscan")
-        ;; 'src/siphash24.c' is the SipHash reference implementation, which
-        ;; bears a CC0 Public Domain Dedication.
+    ;; 'src/siphash24.c' is the SipHash reference implementation, which
+    ;; bears a CC0 Public Domain Dedication.
     (license license:agpl3+)))
 
 (define-public hungrycat
-- 
cgit v1.2.3


From e4740d7a51177de6ca060411bde638574abf0227 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 14 Mar 2018 09:10:47 +0100
Subject: gnu: calcurse: Update to 4.3.0.

* gnu/packages/calcurse.scm (calcurse): Update to 4.3.0.
---
 gnu/packages/calcurse.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/calcurse.scm b/gnu/packages/calcurse.scm
index 93eeaf0ee6..8ee5d86e3c 100644
--- a/gnu/packages/calcurse.scm
+++ b/gnu/packages/calcurse.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014, 2015, 2017 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -29,7 +30,7 @@
 (define-public calcurse
   (package
     (name "calcurse")
-    (version "4.2.2")
+    (version "4.3.0")
     (source
      (origin
       (method url-fetch)
@@ -37,7 +38,7 @@
                           version ".tar.gz"))
       (sha256
        (base32
-        "0il0y06akdqgy0f9p40m4x6arn66nh7sr1w1i41bszycs7div266"))))
+        "16jzg0nasnxdlz23i121x41pq5kbxmjzk52c5d863rg117fc7v1i"))))
     (build-system gnu-build-system)
     (inputs `(("ncurses" ,ncurses)))
     (native-inputs `(("tzdata" ,tzdata-for-tests)))
-- 
cgit v1.2.3


From 295fbbd75d753ffbb84fb78edd2d92c0275c170f Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 14 Mar 2018 10:21:18 +0100
Subject: gnu: geomyidae: Update to 0.31.

* gnu/packages/web.scm (geomyidae): Update to 0.31.
---
 gnu/packages/web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 1cf426b5c0..ceb7d9b7c7 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -6274,7 +6274,7 @@ in Perl but is not nearly as capable as @code{HTML::Tidy}.")
 (define-public geomyidae
   (package
     (name "geomyidae")
-    (version "0.29")
+    (version "0.31")
     (source
      (origin
        (method url-fetch)
@@ -6282,7 +6282,7 @@ in Perl but is not nearly as capable as @code{HTML::Tidy}.")
                            "geomyidae-" version ".tar.bz2"))
        (sha256
         (base32
-         "0qxgxp6psfrgfqhndyq2z54nb1qrmvvljddnxdwp207jbz366bja"))))
+         "1ih7220c6mgq4r7blm4kx3pxbl53sph58lqgwci6cmi3c0sq5c3x"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags (list "CC=gcc"
-- 
cgit v1.2.3


From 42958b5e0feff1000ba17a353bb58fdf45f20716 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 13 Mar 2018 22:34:43 +0100
Subject: gnu: Use patched static bash in glibc replacement.

* gnu/packages/base.scm (glibc-2.26-patched): Rename...
(glibc-2.26-patched-boot): ...to this.
(patched-static-bash, glibc-2.26-patched): New variables.
---
 gnu/packages/base.scm | 27 ++++++++++++++++++++++++++-
 1 file changed, 26 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm
index e91f7d43ef..56f79f5801 100644
--- a/gnu/packages/base.scm
+++ b/gnu/packages/base.scm
@@ -841,7 +841,7 @@ GLIBC/HURD for a Hurd host"
 ;; Below are old libc versions, which we use mostly to build locale data in
 ;; the old format (which the new libc cannot cope with.)
 
-(define glibc-2.26-patched
+(define glibc-2.26-patched-boot
   (package
     (inherit glibc)
     (source (origin
@@ -849,6 +849,31 @@ GLIBC/HURD for a Hurd host"
               (patches (cons (search-patch "glibc-allow-kernel-2.6.32.patch")
                              (origin-patches (package-source glibc))))))))
 
+(define patched-static-bash
+  (package
+    (inherit static-bash)
+    (arguments
+     (substitute-keyword-arguments (package-arguments static-bash)
+       ((#:configure-flags flags '())
+        ;; Add a '-L' flag so that the pseudo-cross-ld of
+        ;; BINUTILS-BOOT0 can find libc.a.
+        `(append ,flags
+                 (list (string-append "LDFLAGS=-static -L"
+                                      (assoc-ref %build-inputs
+                                                 "libc-patched:static")
+                                      "/lib"))))))
+    (native-inputs
+     `(("libc-patched" ,glibc-2.26-patched-boot)
+       ("libc-patched:static" ,glibc-2.26-patched-boot "static")))))
+
+(define glibc-2.26-patched
+  (package
+    (inherit glibc-2.26-patched-boot)
+    (inputs `(("static-bash" ,patched-static-bash)
+              ,@(alist-delete
+                 "static-bash"
+                 (package-inputs glibc-2.26-patched-boot))))))
+
 (define-public glibc-2.25
   (package
     (inherit glibc)
-- 
cgit v1.2.3


From c4fb2b9f4e9ca1c5b586090b765b51b2a5042eff Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 14 Mar 2018 00:09:03 +0100
Subject: gnu: Add replacement for static-bash-for-glibc.

This is needed to replace the static bash used in glibc-final.

* gnu/packages/commencement.scm (patched-glibc-final-with-bootstrap-bash,
patched-static-bash-for-glibc): New variables.
(static-bash-for-glibc)[replacement]: Use patched-static-bash-for-glibc as a
replacement.
---
 gnu/packages/commencement.scm | 42 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/commencement.scm b/gnu/packages/commencement.scm
index fe9fbebcc2..94847b019a 100644
--- a/gnu/packages/commencement.scm
+++ b/gnu/packages/commencement.scm
@@ -556,6 +556,14 @@ the bootstrap environment."
         ;; because we don't want to depend on bootstrap tools.
         ("static-bash" ,@(assoc-ref %boot0-inputs "bash")))))))
 
+(define patched-glibc-final-with-bootstrap-bash
+  (package
+    (inherit glibc-final-with-bootstrap-bash)
+    (source (origin
+              (inherit (package-source glibc-final-with-bootstrap-bash))
+              (patches (cons (search-patch "glibc-allow-kernel-2.6.32.patch")
+                             (origin-patches (package-source glibc-final-with-bootstrap-bash))))))))
+
 (define (cross-gcc-wrapper gcc binutils glibc bash)
   "Return a wrapper for the pseudo-cross toolchain GCC/BINUTILS/GLIBC
 that makes it available under the native tool names."
@@ -632,6 +640,40 @@ exec ~a/bin/~a-~a -B~a/lib -Wl,-dynamic-linker -Wl,~a/~a \"$@\"~%"
                    ("libc:static" ,glibc-final-with-bootstrap-bash "static")
                    ,@(fold alist-delete %boot1-inputs
                            '("gcc" "libc")))))
+    (let ((p (package-with-bootstrap-guile
+              (package-with-explicit-inputs bash inputs
+                                            (current-source-location)
+                                            #:guile %bootstrap-guile))))
+      (package (inherit p)
+               (replacement patched-static-bash-for-glibc)))))
+
+;; Same as static-bash-for-glibc, except that it uses a patched glibc for the
+;; "gcc" and "bash" packages.
+(define patched-static-bash-for-glibc
+  ;; A statically-linked Bash to be used by GLIBC-FINAL in system(3) & co.
+  (let* ((gcc  (cross-gcc-wrapper gcc-boot0 binutils-boot0
+                                  patched-glibc-final-with-bootstrap-bash
+                                  (car (assoc-ref %boot1-inputs "bash"))))
+         (bash (package
+                 (inherit static-bash)
+                 (arguments
+                  (substitute-keyword-arguments
+                      (package-arguments static-bash)
+                    ((#:guile _ #f)
+                     '%bootstrap-guile)
+                    ((#:configure-flags flags '())
+                     ;; Add a '-L' flag so that the pseudo-cross-ld of
+                     ;; BINUTILS-BOOT0 can find libc.a.
+                     `(append ,flags
+                              (list (string-append "LDFLAGS=-static -L"
+                                                   (assoc-ref %build-inputs
+                                                              "libc:static")
+                                                   "/lib"))))))))
+         (inputs `(("gcc" ,gcc)
+                   ("libc" ,patched-glibc-final-with-bootstrap-bash)
+                   ("libc:static" ,patched-glibc-final-with-bootstrap-bash "static")
+                   ,@(fold alist-delete %boot1-inputs
+                           '("gcc" "libc")))))
     (package-with-bootstrap-guile
      (package-with-explicit-inputs bash inputs
                                    (current-source-location)
-- 
cgit v1.2.3


From 911e66f922f2316f061656a6edf5f243342735b7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 14 Mar 2018 12:46:57 +0100
Subject: gnu: Add missing module to (gnu packages base).

This is a follow-up to commit 42958b5e0feff1000ba17a353bb58fdf45f20716.

Reported by pmikkelsen on IRC.

* gnu/packages/base.scm: Use srfi-1 for alist-delete.
---
 gnu/packages/base.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm
index 56f79f5801..a242baf787 100644
--- a/gnu/packages/base.scm
+++ b/gnu/packages/base.scm
@@ -53,6 +53,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system trivial)
   #:use-module (ice-9 match)
+  #:use-module (srfi srfi-1)
   #:export (glibc
             libiconv-if-needed))
 
-- 
cgit v1.2.3


From 7c8dcd66a179c1ee89a4c821a9dc79ad264b7728 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Wed, 14 Mar 2018 11:01:58 -0400
Subject: gnu: linux-libre@4.4: Update to 4.4.121.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.121.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index e30453ba2f..3f4502c4d2 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -408,8 +408,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.4
-  (make-linux-libre "4.4.120"
-                    "17zk5dbpa3kilf8m8i6r2jifjgi4yjim42gyk9j6n4218jjcszv6"
+  (make-linux-libre "4.4.121"
+                    "1d7djrhiib0ds9ssjkali6b5w6rzap4zgj5hf9jq1jmqpp54jkm4"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
-- 
cgit v1.2.3


From b4c1930b2d16f9d0bebb755c4f4727723a6e513b Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Wed, 14 Mar 2018 11:02:36 -0400
Subject: gnu: linux-libre@4.9: Update to 4.9.87.

* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.87.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 3f4502c4d2..8bce967f18 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -402,8 +402,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.86"
-                    "0fqixx3yyvznianygk8bfxzfqj8zpnjcalifhpfyb7rm3dyvi3wd"
+  (make-linux-libre "4.9.87"
+                    "1p8phvmxp04npzqzqcfmv8k9l5l65s7vpjcakdm0fxfkzvnswsp6"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
-- 
cgit v1.2.3


From b5a6fb3c08f9fe126691c1a967618c9074a20c5b Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Wed, 14 Mar 2018 11:03:12 -0400
Subject: gnu: linux-libre@4.14: Update to 4.14.26.

* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.26.
(%linux-libre-4.14-hash): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 8bce967f18..21d18d4d06 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -392,8 +392,8 @@ It has been modified to remove all non-free binary blobs.")
                     %linux-compatible-systems
                     #:configuration-file kernel-config))
 
-(define %linux-libre-4.14-version "4.14.25")
-(define %linux-libre-4.14-hash "0lrzw51ajdkc8mj9bn0lc4yx6q9sf29lcviapapqixg5hds72b94")
+(define %linux-libre-4.14-version "4.14.26")
+(define %linux-libre-4.14-hash "1m2zr17wpasg5riysbaa4g5i492jzr93py2jm088ki818s4a9cm3")
 
 (define-public linux-libre-4.14
   (make-linux-libre %linux-libre-4.14-version
-- 
cgit v1.2.3


From 9a42d5ebf2b4d8b3f214f6ca80aaf1fbf649c32d Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Wed, 14 Mar 2018 11:04:00 -0400
Subject: gnu: linux-libre: Update to 4.15.9.

* gnu/packages/linux.scm (%linux-libre-version): Update to 4.15.9.
(%linux-libre-hash): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 21d18d4d06..b81cb55d6b 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -383,8 +383,8 @@ It has been modified to remove all non-free binary blobs.")
 ;; supports qemu "virt" machine and possibly a large number of ARM boards.
 ;; See : https://wiki.debian.org/DebianKernel/ARMMP.
 
-(define %linux-libre-version "4.15.8")
-(define %linux-libre-hash "0178yi8k72sfv73gss2a1v7w1rmhyza3ia31jwg86gixqw74vifm")
+(define %linux-libre-version "4.15.9")
+(define %linux-libre-hash "13lcard7i6w2c1cf9rfhvmq79xk4qp2p1c1920mfi69l20yvm572")
 
 (define-public linux-libre
   (make-linux-libre %linux-libre-version
-- 
cgit v1.2.3


From 9c9912cf5bffa9c7e2cb3e05ca7649ea295fa3ca Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 14 Mar 2018 16:26:22 +0100
Subject: Revert "gnu: Add missing module to (gnu packages base)."

This reverts commit 911e66f922f2316f061656a6edf5f243342735b7.
---
 gnu/packages/base.scm | 1 -
 1 file changed, 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm
index a242baf787..56f79f5801 100644
--- a/gnu/packages/base.scm
+++ b/gnu/packages/base.scm
@@ -53,7 +53,6 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system trivial)
   #:use-module (ice-9 match)
-  #:use-module (srfi srfi-1)
   #:export (glibc
             libiconv-if-needed))
 
-- 
cgit v1.2.3


From 48b97be90bbbdf3108e70d9e23bc8f296d4451b5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 14 Mar 2018 16:26:24 +0100
Subject: Revert "gnu: Add replacement for static-bash-for-glibc."

This reverts commit c4fb2b9f4e9ca1c5b586090b765b51b2a5042eff.
---
 gnu/packages/commencement.scm | 42 ------------------------------------------
 1 file changed, 42 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/commencement.scm b/gnu/packages/commencement.scm
index 94847b019a..fe9fbebcc2 100644
--- a/gnu/packages/commencement.scm
+++ b/gnu/packages/commencement.scm
@@ -556,14 +556,6 @@ the bootstrap environment."
         ;; because we don't want to depend on bootstrap tools.
         ("static-bash" ,@(assoc-ref %boot0-inputs "bash")))))))
 
-(define patched-glibc-final-with-bootstrap-bash
-  (package
-    (inherit glibc-final-with-bootstrap-bash)
-    (source (origin
-              (inherit (package-source glibc-final-with-bootstrap-bash))
-              (patches (cons (search-patch "glibc-allow-kernel-2.6.32.patch")
-                             (origin-patches (package-source glibc-final-with-bootstrap-bash))))))))
-
 (define (cross-gcc-wrapper gcc binutils glibc bash)
   "Return a wrapper for the pseudo-cross toolchain GCC/BINUTILS/GLIBC
 that makes it available under the native tool names."
@@ -640,40 +632,6 @@ exec ~a/bin/~a-~a -B~a/lib -Wl,-dynamic-linker -Wl,~a/~a \"$@\"~%"
                    ("libc:static" ,glibc-final-with-bootstrap-bash "static")
                    ,@(fold alist-delete %boot1-inputs
                            '("gcc" "libc")))))
-    (let ((p (package-with-bootstrap-guile
-              (package-with-explicit-inputs bash inputs
-                                            (current-source-location)
-                                            #:guile %bootstrap-guile))))
-      (package (inherit p)
-               (replacement patched-static-bash-for-glibc)))))
-
-;; Same as static-bash-for-glibc, except that it uses a patched glibc for the
-;; "gcc" and "bash" packages.
-(define patched-static-bash-for-glibc
-  ;; A statically-linked Bash to be used by GLIBC-FINAL in system(3) & co.
-  (let* ((gcc  (cross-gcc-wrapper gcc-boot0 binutils-boot0
-                                  patched-glibc-final-with-bootstrap-bash
-                                  (car (assoc-ref %boot1-inputs "bash"))))
-         (bash (package
-                 (inherit static-bash)
-                 (arguments
-                  (substitute-keyword-arguments
-                      (package-arguments static-bash)
-                    ((#:guile _ #f)
-                     '%bootstrap-guile)
-                    ((#:configure-flags flags '())
-                     ;; Add a '-L' flag so that the pseudo-cross-ld of
-                     ;; BINUTILS-BOOT0 can find libc.a.
-                     `(append ,flags
-                              (list (string-append "LDFLAGS=-static -L"
-                                                   (assoc-ref %build-inputs
-                                                              "libc:static")
-                                                   "/lib"))))))))
-         (inputs `(("gcc" ,gcc)
-                   ("libc" ,patched-glibc-final-with-bootstrap-bash)
-                   ("libc:static" ,patched-glibc-final-with-bootstrap-bash "static")
-                   ,@(fold alist-delete %boot1-inputs
-                           '("gcc" "libc")))))
     (package-with-bootstrap-guile
      (package-with-explicit-inputs bash inputs
                                    (current-source-location)
-- 
cgit v1.2.3


From 441010a2d1f77b15f9becfac622e9b1d76b7b1fd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 14 Mar 2018 16:26:24 +0100
Subject: Revert "gnu: Use patched static bash in glibc replacement."

This reverts commit 42958b5e0feff1000ba17a353bb58fdf45f20716.
---
 gnu/packages/base.scm | 27 +--------------------------
 1 file changed, 1 insertion(+), 26 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm
index 56f79f5801..e91f7d43ef 100644
--- a/gnu/packages/base.scm
+++ b/gnu/packages/base.scm
@@ -841,7 +841,7 @@ GLIBC/HURD for a Hurd host"
 ;; Below are old libc versions, which we use mostly to build locale data in
 ;; the old format (which the new libc cannot cope with.)
 
-(define glibc-2.26-patched-boot
+(define glibc-2.26-patched
   (package
     (inherit glibc)
     (source (origin
@@ -849,31 +849,6 @@ GLIBC/HURD for a Hurd host"
               (patches (cons (search-patch "glibc-allow-kernel-2.6.32.patch")
                              (origin-patches (package-source glibc))))))))
 
-(define patched-static-bash
-  (package
-    (inherit static-bash)
-    (arguments
-     (substitute-keyword-arguments (package-arguments static-bash)
-       ((#:configure-flags flags '())
-        ;; Add a '-L' flag so that the pseudo-cross-ld of
-        ;; BINUTILS-BOOT0 can find libc.a.
-        `(append ,flags
-                 (list (string-append "LDFLAGS=-static -L"
-                                      (assoc-ref %build-inputs
-                                                 "libc-patched:static")
-                                      "/lib"))))))
-    (native-inputs
-     `(("libc-patched" ,glibc-2.26-patched-boot)
-       ("libc-patched:static" ,glibc-2.26-patched-boot "static")))))
-
-(define glibc-2.26-patched
-  (package
-    (inherit glibc-2.26-patched-boot)
-    (inputs `(("static-bash" ,patched-static-bash)
-              ,@(alist-delete
-                 "static-bash"
-                 (package-inputs glibc-2.26-patched-boot))))))
-
 (define-public glibc-2.25
   (package
     (inherit glibc)
-- 
cgit v1.2.3


From cb18d21e74d86411c04577cde4f2c1b81ae8701d Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 14 Mar 2018 16:08:20 +0100
Subject: gnu: libsoup: Update to 2.62.0.

* gnu/packages/gnome.scm (libsoup): Update to 2.62.0.
---
 gnu/packages/gnome.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 4eb52066c5..56ee1aa885 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -2448,7 +2448,7 @@ libxml to ease remote use of the RESTful API.")
 (define-public libsoup
   (package
     (name "libsoup")
-    (version "2.60.3")
+    (version "2.62.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/libsoup/"
@@ -2456,7 +2456,7 @@ libxml to ease remote use of the RESTful API.")
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "08lawrdkkzycvpb1h0wfiqfz6dgx77jp0wxp546lxgisy9icf38v"))))
+                "1b5aff1igbsx1h4v3wmkffvzgiy8rscibqka7fmjf2lxs7l7lz5b"))))
     (build-system gnu-build-system)
     (outputs '("out" "doc"))
     (arguments
-- 
cgit v1.2.3


From 9a02dcf35a137cfd0f0591ca91c4a918735e8f1a Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 14 Mar 2018 16:26:09 +0100
Subject: gnu: curl: Update replacement to 7.59.0 [security fixes].

This fixes CVE-2018-1000120, CVE-2018-1000121, and CVE-2018-1000122.

* gnu/packages/curl.scm (curl-7.58.0): Rename to ...
(curl-7.59.0): ... this.  Update source hash.
(curl)[replacement]: Adjust accordingly.
---
 gnu/packages/curl.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/curl.scm b/gnu/packages/curl.scm
index ccff18e632..fbf177d9da 100644
--- a/gnu/packages/curl.scm
+++ b/gnu/packages/curl.scm
@@ -48,7 +48,7 @@
   (package
    (name "curl")
    (version "7.57.0")
-   (replacement curl-7.58.0)
+   (replacement curl-7.59.0)
    (source (origin
             (method url-fetch)
             (uri (string-append "https://curl.haxx.se/download/curl-"
@@ -137,10 +137,10 @@ tunneling, and so on.")
                                   "See COPYING in the distribution."))
    (home-page "https://curl.haxx.se/")))
 
-(define-public curl-7.58.0
+(define-public curl-7.59.0
   (package
     (inherit curl)
-    (version "7.58.0")
+    (version "7.59.0")
     (source
       (origin
         (method url-fetch)
@@ -148,7 +148,7 @@ tunneling, and so on.")
                             version ".tar.xz"))
         (sha256
          (base32
-          "1qz303lagxidmkyym90mxiaqnqddwi2219vzydsyn29n4iski0ba"))))))
+          "1z310hrjm2vmbcpkyp81dcmj9rk127zkjyawpy2pah0nz6yslkp4"))))))
 
 (define-public kurly
   (package
-- 
cgit v1.2.3


From 880e2170b7ef53399d9989d9895e6ea102a0c7ed Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 14 Mar 2018 16:36:05 +0100
Subject: gnu: man-db: Update to 2.8.2.

* gnu/packages/man.scm (man-db): Update to 2.8.2.
---
 gnu/packages/man.scm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/man.scm b/gnu/packages/man.scm
index 6d1efcee01..257cabbbb6 100644
--- a/gnu/packages/man.scm
+++ b/gnu/packages/man.scm
@@ -58,14 +58,14 @@ a flexible and convenient way.")
 (define-public man-db
   (package
     (name "man-db")
-    (version "2.7.6.1")
+    (version "2.8.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://savannah/man-db/man-db-"
                                   version ".tar.xz"))
               (sha256
                (base32
-                "0gqgs4zc3r87apns0k5qp689p2ylxx2596s2mkmkxjjay99brv88"))))
+                "0p0cvv5ykvyzq33qyfik11p2s0d2j75ans1avj9xv3c8vy3zzga5"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -131,6 +131,9 @@ a flexible and convenient way.")
        ("groff-minimal" ,groff-minimal)
        ("less" ,less)
        ("libpipeline" ,libpipeline)
+       ;; FIXME: 4.8 and later can use libseccomp, but it causes test
+       ;; failures in the build chroot.
+       ;;("libseccomp" ,libseccomp)
        ("util-linux" ,util-linux)))
     (native-search-paths
      (list (search-path-specification
-- 
cgit v1.2.3


From aac6cbbfede0bbfafdbbeeb460f00a244333895d Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 14 Mar 2018 16:43:01 +0100
Subject: gnu: samba: Update to 4.7.6 [fixes CVE-2018-1050 and CVE-2018-1057].

* gnu/packages/samba.scm (samba): Update to 4.7.6.
---
 gnu/packages/samba.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/samba.scm b/gnu/packages/samba.scm
index 10b26c0ce9..d7ae5715ff 100644
--- a/gnu/packages/samba.scm
+++ b/gnu/packages/samba.scm
@@ -148,14 +148,14 @@ anywhere.")
 (define-public samba
   (package
     (name "samba")
-    (version "4.7.5")
+    (version "4.7.6")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://download.samba.org/pub/samba/stable/"
                                  "samba-" version ".tar.gz"))
              (sha256
               (base32
-               "13gyr0sk9vx6mccr2h35ca3g92kp50cqxrlzfgrddfmskzx08v9i"))))
+               "0vkxqp3wh7bpn1fd45lznmrpn2ma1fq75yq28vi08rggr07y7v8y"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
-- 
cgit v1.2.3