Merge branch 'master' into core-updates

173 files changed, 8687 insertions, 3528 deletions

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)
diff --git a/gnu/packages/accessibility.scm b/gnu/packages/accessibility.scm
index 2ca4e27f81..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)))
@@ -109,7 +111,6 @@ 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")
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
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index cf9524eb5f..ad31bc498f 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)
@@ -610,14 +611,14 @@ 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
@@ -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
@@ -1993,12 +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
@@ -2006,7 +2003,7 @@ shortcut syntax and completion options.")
                     version ".tar.xz"))
               (sha256
                (base32
-                "0abf8cfpkprmhw5ca8iyqgrggh65lgqvmfllc1y6qz7zw1gas894"))))
+                "1qjp8i1s9bz7g6kiqrkzzkxn5pfspa4sy53b6z40fqmdf9przdfb"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -2032,8 +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")
@@ -2043,8 +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")
@@ -2067,7 +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)
@@ -2085,25 +2081,34 @@ 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)
@@ -2373,7 +2378,7 @@ 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 +2386,7 @@ 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 +2394,7 @@ 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 +2403,8 @@ 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="
@@ -2426,23 +2433,26 @@ 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"
                                   "/archive/" version ".tar.gz"))
+              (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"))
@@ -2455,8 +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
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))))
diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 8c42ac31cc..57f273cc7a 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, 2018 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))
@@ -599,6 +602,104 @@ 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 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 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")
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"))
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index d5c45e9479..eb7b79ee7a 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 \"\""))
@@ -1154,6 +1155,7 @@ PS, and DAB+.")
                                            (string-map (lambda (c)
                                                          (if (char=? c #\.) #\- c))
                                                        version)))))
+              (file-name (string-append "faust-" version "-checkout"))
               (sha256
                (base32
                 "06km0ygwxxwgw1lqldccqidxhmjfz8ck0wnbd95qk5sg8sbpc068"))))
@@ -1627,14 +1629,14 @@ 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
@@ -1644,7 +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
@@ -1782,6 +1784,7 @@ software.")
                 (uri (git-reference
                       (url "http://lv2plug.in/git/lv2.git")
                       (commit commit)))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
                   "1gp2rd99dfmpibvpixrqn115mrhybzf3if3h8bssf6siyi13f29r")))))))
@@ -1795,6 +1798,7 @@ 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"))))
@@ -2023,6 +2027,7 @@ 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"))))
@@ -2102,6 +2107,7 @@ 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"))))
@@ -2377,7 +2383,8 @@ 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
@@ -2530,7 +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)
@@ -2538,7 +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/")
diff --git a/gnu/packages/autotools.scm b/gnu/packages/autotools.scm
index fa291c556a..b7df530088 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>
@@ -125,8 +125,8 @@ 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."
@@ -192,7 +192,13 @@ 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
@@ -254,7 +260,7 @@ 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
@@ -317,6 +323,21 @@ 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 "1.16.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://gnu/automake/automake-"
+                                  version ".tar.xz"))
+              (sha256
+               (base32
+                "08g979ficj18i1w6w5219bgmns7czr03iadf20mk3lrzl8wbn1ax"))
+              (patches
+               (search-patches "automake-skip-amhello-tests.patch"))))))
+
 (define-public libtool
   (package
     (name "libtool")
@@ -335,7 +356,7 @@ 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/backup.scm b/gnu/packages/backup.scm
index 6e7bcc1479..5487157c86 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -544,7 +544,10 @@ 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/base.scm b/gnu/packages/base.scm
index 2a50080599..f630ccec2b 100644
--- a/gnu/packages/base.scm
+++ b/gnu/packages/base.scm
@@ -13,6 +13,7 @@
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -543,6 +544,7 @@ 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/"
@@ -845,6 +847,14 @@ 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)
+    (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/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)))
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b758c72dec..d0873c9676 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")
@@ -1854,38 +1828,22 @@ 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
@@ -3019,6 +2977,76 @@ 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 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
@@ -3097,6 +3125,90 @@ 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)
@@ -3211,10 +3323,89 @@ 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")
-    (version "1.6")
+    (version "1.7")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -3222,17 +3413,8 @@ VCF.")
                     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)
@@ -4629,6 +4811,7 @@ 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"))))
@@ -4687,7 +4870,7 @@ to the user's query of interest.")
 (define-public samtools
   (package
     (name "samtools")
-    (version "1.5")
+    (version "1.7")
     (source
      (origin
        (method url-fetch)
@@ -4696,7 +4879,7 @@ 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)
@@ -6017,14 +6200,14 @@ 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
@@ -6200,14 +6383,14 @@ 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
@@ -6968,13 +7151,13 @@ 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
@@ -7034,13 +7217,13 @@ 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")
@@ -7089,13 +7272,13 @@ 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)
@@ -7519,13 +7702,13 @@ 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)
@@ -8365,14 +8548,14 @@ 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
@@ -8542,6 +8725,16 @@ 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)))
@@ -8706,6 +8899,7 @@ 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"))))
@@ -10460,6 +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=.*")
@@ -10588,14 +10792,14 @@ 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)
@@ -10659,9 +10863,37 @@ 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 "cf0be5ae5302684bd03e78ab65b142900bbbb840")
-        (revision "1"))
+  (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
+        (revision "2"))
     (package
       (name "r-dropbead")
       (version (string-append "0-" revision "." (string-take commit 7)))
@@ -10671,9 +10903,10 @@ 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"))))
+           "0sbzma49aiiyw8b0jpr7fnhzys9nsqmp4hy4hdz1gzyg1lhnca26"))))
       (build-system r-build-system)
       (propagated-inputs
        `(("r-ggplot2" ,r-ggplot2)
@@ -11424,6 +11657,7 @@ 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"))))
@@ -11879,3 +12113,738 @@ 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)))
+
+;; 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-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")
+    (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+)))
+
+(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.")))
+
+(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")))
+
+(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"))))))
+
+(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.")))
+
+(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")))
+
+(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)))
+
+(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+)))
+
+(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+)))
+
+(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+)))
diff --git a/gnu/packages/boost.scm b/gnu/packages/boost.scm
index bf584fa6c3..69fbc2777a 100644
--- a/gnu/packages/boost.scm
+++ b/gnu/packages/boost.scm
@@ -111,6 +111,20 @@ 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")
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
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)))
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
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 8e1eb127b2..73d3efd9e1 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
@@ -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")
@@ -834,146 +834,231 @@ 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")
-    (version "0.4")
+    (name "python-testscenarios-bootstrap")
+    (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)))
+     `(("python-pbr" ,python-pbr-minimal)
+       ("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-pbr" ,python-pbr)
+       ("python-testtools" ,python-testtools)))
+    (description
+     "Testscenarios provides clean dependency injection for Python unittest
+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))
 
-(define-public python-subunit
+(define-public python-subunit-bootstrap
   (package
-    (name "python-subunit")
-    (version "0.0.21")
+    (name "python-subunit-bootstrap")
+    (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 "python-subunit" version))
        (sha256
         (base32
-         "1nkw9wfbvizmpajbj3in8ns07g7lwkiv8hip14jjlwk3cacls6jv"))))
+         "1yii2gx3z6323as3iraj1yphj76dy7i3h6kj63pnc5y0hwjs5sgx"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-extras" ,python-extras)
-       ("python-mimeparse" ,python-mimeparse)))
+       ("python-testtools" ,python-testtools-bootstrap)))
     (native-inputs
-     `(("python-testscenarios" ,python-testscenarios)))
+     `(("python-fixtures" ,python-fixtures-bootstrap)
+       ("python-hypothesis" ,python-hypothesis)
+       ("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))
 
+;; 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-bootstrap")
+    (version "3.0.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "fixtures" version))
+              (sha256
+               (base32
+                "1vxj29bzz3rd4pcy51d05wng9q9dh4jq6wx92yklsm7i6h1ddw7w"))))
+    (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")
-    (version "1.4.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "fixtures" version))
-       (sha256
-        (base32
-         "0djxvdwm8s60dbfn7bhf40x6g818p3b3mlwijm1c3bqg7msn271y"))))
-    (build-system python-build-system)
     (arguments
      '(#:phases
        (modify-phases %standard-phases
@@ -982,25 +1067,23 @@ 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")
+       ("python-testtools" ,python-testtools-bootstrap)))
     (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 +1094,26 @@ Python tests.")
         (base32
          "1ssqb07c277010i6gzzkbdd46gd9mrj0bi0i8vn560n2k2y4j93m"))))
     (build-system python-build-system)
+    (arguments '(#:tests? #f))
+    (propagated-inputs
+     `(("python-fixtures" ,python-fixtures-bootstrap)
+       ("python-subunit" ,python-subunit-bootstrap)
+       ("python-testtools" ,python-testtools-bootstrap)))
+    (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 +1122,10 @@ 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))
@@ -1629,18 +1728,20 @@ 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)
diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm
index c9048ccb8e..9e5d42952f 100644
--- a/gnu/packages/ci.scm
+++ b/gnu/packages/ci.scm
@@ -184,8 +184,8 @@ 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)))
@@ -197,7 +197,7 @@ their dependencies.")
                 (file-name (string-append name "-" version))
                 (sha256
                  (base32
-                  "1r97z5lkzg6vx014rfmv1pp3x3bl1shb6wkcgnlncwqf56a9bzi1"))))
+                  "1827vgk47rcgm2x0cxzvg79ni6vazjzr8hr9pljlvbd9awzr7hxp"))))
       (build-system gnu-build-system)
       (arguments
        '(#:modules ((guix build utils)
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)))))
diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm
index 2067067f20..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)
@@ -139,10 +140,10 @@ 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
@@ -204,23 +205,24 @@ 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)
@@ -228,13 +230,13 @@ 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")))
@@ -496,3 +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)))
diff --git a/gnu/packages/commencement.scm b/gnu/packages/commencement.scm
index a475016876..33b957adfe 100644
--- a/gnu/packages/commencement.scm
+++ b/gnu/packages/commencement.scm
@@ -67,6 +67,15 @@
 ;;; 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
@@ -649,27 +658,32 @@ 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-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)))
-
-    ;; 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
diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index dfdebdb1b3..e95b2a3d27 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 --
@@ -598,6 +598,7 @@ 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"))))
@@ -841,14 +842,14 @@ 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
@@ -866,7 +867,7 @@ 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
@@ -1014,7 +1015,8 @@ 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
@@ -1068,21 +1070,23 @@ 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.")
@@ -1128,7 +1132,7 @@ 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/"
@@ -1136,7 +1140,7 @@ 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"
@@ -1176,7 +1180,9 @@ 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
@@ -1185,13 +1191,14 @@ 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
@@ -1202,6 +1209,8 @@ 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")
@@ -1531,6 +1540,7 @@ 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"))))
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
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index e1fb1b6215..b7126518c1 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")
@@ -1472,14 +1499,14 @@ 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")
@@ -1637,21 +1664,21 @@ 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
@@ -2139,14 +2166,14 @@ 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)
@@ -2225,3 +2252,965 @@ 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+)))
+
+(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)))
+
+(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+)))
+
+(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)))
+
+(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+)))
+
+(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)))
+
+(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)))
+
+(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)))
+
+(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)))
+
+(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)))
+
+(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)))
+
+(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+)))
+
+(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)))
+
+(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)))
+
+(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+)))
+
+(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+))))
+
+(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)))
+
+(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+)))
+
+(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)))
+
+(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)))
+
+(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+)))
+
+(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)))
+
+(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))))
+
+(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)))
+
+(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)))
+
+(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)))
+
+(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)))
+
+(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+)))
+
+(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)))
+
+(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+)))
+
+(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+)))
+
+(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)))
+
+(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+)))
+
+(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)))
+
+(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+)))
+
+(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.  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+)))
+
+(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)))
+
+(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+)))
diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm
index 4922c58753..1e447d4f3a 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\\)/")
@@ -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")))
@@ -411,8 +411,9 @@ 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"))))))))
-    (home-page "http://www.dyne.org/software/tomb")
+               (invoke tomb "dig" "-s" "10" "secrets.tomb")
+               #t))))))
+    (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
diff --git a/gnu/packages/curl.scm b/gnu/packages/curl.scm
index e51e014e99..fbf177d9da 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.
 ;;;
@@ -47,7 +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-"
@@ -136,10 +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)
@@ -147,32 +148,38 @@ tunneling, and so on.")
                             version ".tar.xz"))
         (sha256
          (base32
-          "1qz303lagxidmkyym90mxiaqnqddwi2219vzydsyn29n4iski0ba"))))))
+          "1z310hrjm2vmbcpkyp81dcmj9rk127zkjyawpy2pah0nz6yslkp4"))))))
 
 (define-public kurly
   (package
     (name "kurly")
-    (version "1.1.0")
+    (version "1.2.1")
     (source (origin
               (method git-fetch)
               (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"))))
+                "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)
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index e289a604f9..56531f50e3 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>
@@ -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)
@@ -699,14 +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")
@@ -744,14 +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
@@ -840,7 +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"
@@ -848,18 +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)
@@ -871,7 +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")
@@ -888,20 +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)
@@ -925,8 +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
@@ -2037,14 +2048,14 @@ 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
@@ -2235,17 +2246,21 @@ 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)))
+    (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
@@ -2256,10 +2271,15 @@ 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
@@ -2270,30 +2290,31 @@ 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"))))
     (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
diff --git a/gnu/packages/debian.scm b/gnu/packages/debian.scm
new file mode 100644
index 0000000000..3c3189e073
--- /dev/null
+++ b/gnu/packages/debian.scm
@@ -0,0 +1,170 @@
+;;; 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 (guix build-system trivial)
+  #:use-module (gnu packages base)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages gnupg)
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages wget))
+
+(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$")))
+             #t)))))
+    (native-inputs
+     `(("gnupg" ,gnupg)
+       ("jetring" ,jetring)))
+    (home-page "https://packages.qa.debian.org/d/debian-archive-keyring.html")
+    (synopsis "GnuPG archive keys of the Debian archive")
+    (description
+     "The Debian project digitally signs its Release files.  This package
+contains the archive keys used for that.")
+    (license (list license:public-domain ; the keys
+                   license:gpl2+)))) ; see debian/copyright
+
+(define-public ubuntu-keyring
+  (package
+    (name "ubuntu-keyring")
+    (version "2018.02.28")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "https://launchpad.net/ubuntu/+archive/primary/"
+                            "+files/" name "_" version ".tar.gz"))
+        (sha256
+         (base32
+          "1zj3012cz7rlx9pm39wnwa0lmi1h38n6bkgbz81vnmcsvqsc9a3a"))))
+    (build-system trivial-build-system)
+    (arguments
+     `(#:modules ((guix build utils))
+       #:builder (begin
+                   (use-modules (guix build utils))
+                   (let* ((out (assoc-ref %outputs "out"))
+                          (apt (string-append out "/etc/apt/trusted.gpg.d/"))
+                          (key (string-append out "/share/keyrings/")))
+                     (setenv "PATH" (string-append
+                                      (assoc-ref %build-inputs "gzip") "/bin:"
+                                      (assoc-ref %build-inputs "tar") "/bin"))
+                     (invoke "tar" "xvf" (assoc-ref %build-inputs "source"))
+                     (for-each (lambda (file)
+                                 (install-file file apt))
+                               (find-files "." "ubuntu-[^am].*\\.gpg$"))
+                     (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
+
+(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)))
diff --git a/gnu/packages/debug.scm b/gnu/packages/debug.scm
index 777018bfb2..1f238637a4 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.
 ;;;
@@ -66,8 +67,6 @@
                     (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 +74,7 @@
                              (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
@@ -87,10 +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)
@@ -99,12 +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)
@@ -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
diff --git a/gnu/packages/dictionaries.scm b/gnu/packages/dictionaries.scm
index 25e4613170..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.
@@ -211,7 +212,7 @@ 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 +220,8 @@ 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
diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index 0b447b5176..a901af6f14 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)
@@ -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")
@@ -265,15 +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")
@@ -755,3 +760,52 @@ 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)))
+
+(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)))
diff --git a/gnu/packages/docbook.scm b/gnu/packages/docbook.scm
index 03fc54450e..3034bc5493 100644
--- a/gnu/packages/docbook.scm
+++ b/gnu/packages/docbook.scm
@@ -177,7 +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/"
@@ -185,8 +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/emacs.scm b/gnu/packages/emacs.scm
index 81e6885f66..c2c162c75c 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>
@@ -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))
                 (_ "")))
 
@@ -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")
@@ -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"))))
@@ -4300,6 +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"))))
@@ -4492,14 +4494,14 @@ 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")
@@ -4519,7 +4521,7 @@ reproducible research.")
                                   (package-version emacs-org) ".tar"))
               (sha256
                (base32
-                "164i2asqh34p1g3iqsn7rziyxbi1ys8fwdmn7nsw5xph8qszv9zj"))))
+                "034wp70hcqnpidji5k1k80mj35iyyy098nbvc2sl7i2aca4m03zc"))))
     (arguments
      `(#:modules ((guix build emacs-build-system)
                   (guix build utils)
@@ -6785,8 +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)))
@@ -6798,7 +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)
@@ -6889,7 +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
@@ -6898,7 +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")
@@ -7311,3 +7313,51 @@ 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+)))
+
+(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+)))
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.
diff --git a/gnu/packages/enlightenment.scm b/gnu/packages/enlightenment.scm
index 413bc5f102..a0bf841415 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 +68,9 @@
                     version ".tar.xz"))
               (sha256
                (base32
-                "1h9jkb1pkp2g6ld7ra9mxgblx3x5id4162ja697klx9mfjkpxijn"))))
+                "1zkn5ix81xck3n84dxvkjh4alwc6zj8x989d0zqi5c6ppijvgadh"))))
+    (outputs '("out"       ; 49 MB
+               "include")) ; 17 MB
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -284,9 +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)
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"))))
diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm
index 12595dc31c..714af3df72 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.
 ;;;
@@ -70,11 +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))
@@ -94,11 +92,11 @@ 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 +106,7 @@ Linux-libre.")
          (file-name (string-append name "-" version "-checkout"))
          (sha256
           (base32
-           "08k7sdr9jagm43r2zv4h03j86klhkblpk73p12444a3vzg1gy1lv"))))
+           "1wgmj4d65izbhprwb5bcwimc2ryv19b9066lqzy4sa5m6wncm9cn"))))
       (build-system gnu-build-system)
       (native-inputs
        `(("flex" ,flex)
@@ -117,11 +115,11 @@ 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")
@@ -129,21 +127,22 @@ 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")
+       "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,
@@ -259,6 +258,8 @@ coreboot.")
                (setenv "WORKSPACE" cwd)
                (setenv "EDK_TOOLS_PATH" tools)
                (setenv "PATH" (string-append (getenv "PATH") ":" bin))
+               ; 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[ ]*=.*$") "TARGET = RELEASE\n")
@@ -268,14 +269,16 @@ coreboot.")
                           (number->string (parallel-job-count)))))
                ;; Build build support.
                (setenv "BUILD_CC" "gcc")
-               (zero? (system* "make" "-C" (string-append tools "/Source/C"))))))
+               (invoke "make" "-C" (string-append tools "/Source/C"))
+               #t)))
          (add-after 'build 'build-ia32
            (lambda _
              (substitute* "Conf/target.txt"
                (("^TARGET_ARCH[ ]*=.*$") "TARGET_ARCH = IA32\n")
                (("^ACTIVE_PLATFORM[ ]*=.*$")
                 "ACTIVE_PLATFORM = OvmfPkg/OvmfPkgIa32.dsc\n"))
-             (zero? (system* "build"))))
+             (invoke "build")
+             #t))
          ,@(if (string=? "x86_64-linux" (%current-system))
              '((add-after 'build 'build-x64
                 (lambda _
@@ -283,7 +286,8 @@ coreboot.")
                     (("^TARGET_ARCH[ ]*=.*$") "TARGET_ARCH = X64\n")
                     (("^ACTIVE_PLATFORM[ ]*=.*$")
                      "ACTIVE_PLATFORM = OvmfPkg/OvmfPkgX64.dsc\n"))
-                  (zero? (system* "build")))))
+                  (invoke "build")
+                  #t)))
              '())
          (delete 'build)
          (replace 'install
@@ -299,7 +303,7 @@ 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.")
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"))))
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")
diff --git a/gnu/packages/fontutils.scm b/gnu/packages/fontutils.scm
index 383243b13f..22382f745a 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/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+)))
diff --git a/gnu/packages/ftp.scm b/gnu/packages/ftp.scm
index 395e38d3ae..5a79edf245 100644
--- a/gnu/packages/ftp.scm
+++ b/gnu/packages/ftp.scm
@@ -168,7 +168,7 @@ as required.")
 (define-public libfilezilla
   (package
     (name "libfilezilla")
-    (version "0.12.0")
+    (version "0.12.1")
     (source
      (origin
        (method url-fetch)
@@ -176,7 +176,7 @@ as required.")
                            name "/" name "-" version ".tar.bz2"))
        (sha256
         (base32
-         "14zag4mhwp5mbir63j1k01jys973kmrivznmm78v6qa92l64jn0a"))))
+         "1gbqm42dd0m3fvqz3bk53889479dvn8679zp6ba8a9q2br2wkvv0"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("cppunit" ,cppunit)
diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index 2a5bc63294..db13ac0eff 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>
@@ -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)
@@ -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)))
@@ -1051,7 +1059,7 @@ games.")
 (define-public godot
   (package
     (name "godot")
-    (version "3.0")
+    (version "3.0.1")
     (source (origin
               (method url-fetch)
               (uri
@@ -1060,7 +1068,7 @@ games.")
               (file-name (string-append name "-" version))
               (sha256
                (base32
-                "1jhp269n1a7c663v2555444icbjwzscj4r8cq4rrrap7r7dr4hyc"))))
+                "0k8c12nzhl98i9il9s3awbwdamkrwxk0s47jr7n8a3z93rpszd2p"))))
     (build-system scons-build-system)
     (arguments
      `(#:scons ,scons-python2
@@ -1103,16 +1111,16 @@ 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 _
diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index eb98197a06..6d44d8d91e 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
@@ -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"))
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/ghostscript.scm b/gnu/packages/ghostscript.scm
index 6cad2ba93b..345ac76317 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 e802d6ce1a..34968f9d91 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.
 ;;;
@@ -124,7 +125,7 @@
        ;; '--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
@@ -462,7 +463,7 @@ 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
@@ -499,7 +500,7 @@ 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 +508,13 @@ 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 _
@@ -532,7 +536,7 @@ 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
@@ -544,7 +548,7 @@ 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)
@@ -553,7 +557,7 @@ 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)
@@ -623,6 +627,33 @@ 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")
@@ -663,7 +694,7 @@ 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 19cc4d2e34..a4ace442e8 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>
@@ -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
@@ -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+)))
@@ -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
@@ -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
@@ -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)
@@ -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,
@@ -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
@@ -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+")
@@ -5727,7 +5728,7 @@ 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 +5736,17 @@ 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 +5756,8 @@ 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
        ;;
diff --git a/gnu/packages/gnunet.scm b/gnu/packages/gnunet.scm
index 0569395d48..ac7f8ab85f 100644
--- a/gnu/packages/gnunet.scm
+++ b/gnu/packages/gnunet.scm
@@ -322,7 +322,7 @@ kinds of basic applications for the foundation of a GNU internet.")
                   "0k6mn28isjlxrnvbnblab3nh2xqx1b7san8k98kc35ap9lq0iz8w"))))
       (build-system gnu-build-system)
       (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 77f5771298..cb0651d626 100644
--- a/gnu/packages/gnupg.scm
+++ b/gnu/packages/gnupg.scm
@@ -1,10 +1,10 @@
 ;;; 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>
 ;;; 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>
@@ -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)
@@ -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+)))
diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm
index 8d9573fb81..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)))
@@ -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")
@@ -418,125 +418,26 @@ 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")
         (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
diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index f11cc76d9c..20a8c538be 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
@@ -385,6 +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"))))
@@ -410,6 +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"))))
@@ -434,6 +553,7 @@ 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"))))
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"))))
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))))
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
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/gtk.scm b/gnu/packages/gtk.scm
index 8b4925f950..aeca806ee6 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)
@@ -323,6 +325,7 @@ diagrams.")
                 (uri (git-reference
                       (url "http://git.drobilla.net/ganv.git")
                       (commit commit)))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
                   "1cr8w02lr6bk9mkxa12j3imq721b2an2yn4bj5wnwmpm91ddn2gi")))))))
@@ -1039,7 +1042,7 @@ 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
@@ -1049,7 +1052,7 @@ 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 "/"
@@ -1057,11 +1060,11 @@ 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'
-                     ("xorg-server" ,xorg-server)))
+                     ("xorg-server" ,xorg-server-1.19.3)))
     (propagated-inputs
      `(("pangomm" ,pangomm)
        ("cairomm" ,cairomm)
@@ -1069,7 +1072,11 @@ 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")
+       #:disallowed-references (,xorg-server-1.19.3)
+       #:phases (modify-phases %standard-phases
                   (add-before 'check 'run-xvfb
                     (lambda* (#:key inputs #:allow-other-keys)
                       (let ((xorg-server (assoc-ref inputs "xorg-server")))
@@ -1080,7 +1087,7 @@ 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
@@ -1114,6 +1121,38 @@ 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")
@@ -1236,6 +1275,95 @@ 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 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")
+    (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")
diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index a4685ec7e4..7f01441b0e 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -282,6 +282,21 @@ 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))
 
@@ -752,7 +767,7 @@ 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'.
@@ -1242,14 +1257,14 @@ 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)
@@ -1266,12 +1281,15 @@ 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)
@@ -1834,7 +1852,7 @@ 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'.
@@ -1982,35 +2000,30 @@ 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)
-      (native-inputs
-       `(("autoconf" ,autoconf)
-         ("automake" ,automake)
-         ("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
+  (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
diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index a24ee4b7c0..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")
@@ -866,3 +878,26 @@ 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)))
diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index e62c405ab7..c5408f8627 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")
@@ -1072,7 +1073,7 @@ 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)))
 
@@ -4980,6 +4981,22 @@ 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")
@@ -5013,6 +5030,27 @@ 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")
@@ -5562,6 +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")
@@ -5666,6 +5710,27 @@ 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")
@@ -5755,6 +5820,8 @@ 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)
@@ -5890,6 +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")
@@ -5921,6 +6039,29 @@ 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")
@@ -5997,6 +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")
@@ -7358,6 +7560,8 @@ 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)
@@ -8177,12 +8381,12 @@ 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
@@ -8528,6 +8732,8 @@ 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)
diff --git a/gnu/packages/image-viewers.scm b/gnu/packages/image-viewers.scm
index ff34da9f4a..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 "2.23.2")
+    (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
-                "1hw9xhhmm404ircmd7aw9n51n23wzjxzmav272ldk1pxb2jk3hcn"))))
+                "197sm78bm33dvahr5nxqkbmpmdn4b13ahc9mrgn1l7n104bg4phc"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases (delete 'configure))
diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm
index 5943457f94..b576c508ec 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>
@@ -59,6 +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)
@@ -1230,3 +1230,66 @@ 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+)))
+
+(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+)))
diff --git a/gnu/packages/imagemagick.scm b/gnu/packages/imagemagick.scm
index 97b3225a77..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 "6.9.9-35")
+    (version "6.9.9-37")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://imagemagick/ImageMagick-"
                                  version ".tar.xz"))
              (sha256
               (base32
-               "09c8298v7112y579mfp0bgsa3gsmcx2l5zbgfkwply4ihszprh0i"))))
+               "1hmfw0jcpc3s3gz9zrzjy9amyrfz6gzzjdsyaw3xw994aq9qf4lq"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags '("--with-frozenpaths" "--without-gcc-arch")
diff --git a/gnu/packages/inkscape.scm b/gnu/packages/inkscape.scm
index f1a3cb23f4..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)
@@ -87,7 +77,10 @@
        ("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
diff --git a/gnu/packages/irc.scm b/gnu/packages/irc.scm
index b00fd6cc19..e59b34417b 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.
 ;;;
@@ -272,23 +272,23 @@ 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
-    (home-page "http://tools.suckless.org/ii/")
+         (delete 'configure))))         ; no configure
+    (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.")
diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index d3fa88adbd..b4f64e2c2e 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)
@@ -1587,7 +1588,8 @@ 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"))
@@ -1596,65 +1598,90 @@ 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"
@@ -2015,6 +2042,510 @@ 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)))
+
+;; 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-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-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-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")
@@ -2480,7 +3011,7 @@ 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")
@@ -2657,6 +3188,418 @@ 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-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-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-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-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")
+    (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-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-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-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-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-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")
@@ -2940,39 +3883,30 @@ 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
@@ -5103,7 +6037,9 @@ 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"
@@ -5185,7 +6121,6 @@ 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)
@@ -5194,9 +6129,11 @@ 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 ,name "-" ,version ".jar")
+     `(#:jar-name (string-append "antlr3-" ,version ".jar")
        #:source-dir "src:runtime/Java/src"
        #:tests? #f
        #:phases
@@ -5228,12 +6165,13 @@ 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"
@@ -6056,7 +6994,8 @@ 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)
@@ -6365,6 +7304,7 @@ 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"))))
@@ -6956,7 +7896,7 @@ 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
@@ -6965,7 +7905,7 @@ 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
@@ -7030,54 +7970,56 @@ 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"
-               (("assertions.Assertions") "assertions.api.Assertions"))
-             (substitute* "src/test/java/com/neilalexander/jnacl/NaclSecretBoxTest.java"
-               (("assertions.Assertions") "assertions.api.Assertions"))
-             #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"))))))))
-    (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)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1d6g6xhn83byv5943n7935wwjsk0ibk0qdvqgr699qqgqqmwisbb"))))
+      (build-system ant-build-system)
+      (arguments
+       `(#:jar-name "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:mpl2.0)))
+      (license license:bsd-2))))
 
 (define-public java-mvel2
   (package
@@ -7172,8 +8114,9 @@ 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
@@ -7213,7 +8156,8 @@ 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")
@@ -7243,7 +8187,8 @@ 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)))
@@ -7274,7 +8219,8 @@ 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)))
@@ -7631,7 +8577,8 @@ 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"
@@ -7645,7 +8592,13 @@ 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
@@ -7901,26 +8854,23 @@ 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)
@@ -7957,14 +8907,14 @@ 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/"
@@ -7977,7 +8927,6 @@ 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)))))
@@ -7985,8 +8934,9 @@ 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
@@ -8370,3 +9320,44 @@ 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+)))
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/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?
diff --git a/gnu/packages/kodi.scm b/gnu/packages/kodi.scm
index bb17edf2f5..6f8571d22a 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
@@ -163,7 +163,7 @@ 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)
@@ -175,7 +175,7 @@ generator library for C++.")
                 (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
-                  "1gr5aq1cjr3as9mnwrw29cxn4m6f6pfrxdahkdcjy70q3ldg90sl"))))
+                  "1c3g18n2vwhgcfz3dka1pmw58bnv2ram7xjvizfiykb3sgi9zfwp"))))
       (build-system gnu-build-system)
       (arguments
        '(#:tests? #f
@@ -198,7 +198,7 @@ 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)
@@ -210,7 +210,7 @@ generator library for C++.")
                 (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
-                  "198r0q73i55ga1dvyqq9nfcri0zq08b94hy8671lg14i3izx44dd"))))
+                  "0adafwsawxssj3nilkql447v0l4a2584rdpmy5rfjmznh91lykgh"))))
       (build-system gnu-build-system)
       (arguments
        '(#:tests? #f
@@ -235,20 +235,20 @@ 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))
@@ -261,7 +261,6 @@ generator library for C++.")
                               ;; "tools/depend/native/TexturePacker"
                               ;; "lib/gtest"
                               ;; "lib/cpluff"
-                              ;; "lib/libexif"
                               ;; "lib/libUPnP"
                               "lib/libUPnP/Neptune/ThirdParty"
                               "project/Win32BuildSetup/tools/7z"))
@@ -312,7 +311,7 @@ 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")))
@@ -414,7 +413,7 @@ 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+
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/libevent.scm b/gnu/packages/libevent.scm
index cdd331acf4..983c8625e4 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/libffi.scm b/gnu/packages/libffi.scm
index d55e7aec3d..8515edf925 100644
--- a/gnu/packages/libffi.scm
+++ b/gnu/packages/libffi.scm
@@ -79,13 +79,13 @@ 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
@@ -121,7 +121,8 @@ 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
@@ -130,15 +131,14 @@ 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")
@@ -152,13 +152,13 @@ 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.
diff --git a/gnu/packages/libftdi.scm b/gnu/packages/libftdi.scm
index 208e13546e..bbb98ff1f4 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
@@ -35,11 +36,11 @@
                     version ".tar.bz2"))
               (sha256
                (base32
-                "088yh8pxd6q53ssqndydcw1dkq51cjqyahc03lm6iip22cdazcf0"))))
+                "0x0vncf6i92slgrn0h7ghkskqbglbs534220qa84d0qg114zndpc"))))
     (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,
diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm
index aed90c500f..7a1a1433fd 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
@@ -295,14 +296,14 @@ 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)
@@ -428,7 +429,7 @@ 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.")
@@ -468,14 +469,14 @@ 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)
@@ -495,14 +496,14 @@ 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)
diff --git a/gnu/packages/libusb.scm b/gnu/packages/libusb.scm
index 904ab98cc0..7981a4f5cc 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"))))
diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 4085332eb3..c3bd73023d 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 "4.15.9")
+(define %linux-libre-hash "13lcard7i6w2c1cf9rfhvmq79xk4qp2p1c1920mfi69l20yvm572")
 
 (define-public linux-libre
   (make-linux-libre %linux-libre-version
@@ -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 "4.14.26")
+(define %linux-libre-4.14-hash "1m2zr17wpasg5riysbaa4g5i492jzr93py2jm088ki818s4a9cm3")
 
 (define-public linux-libre-4.14
   (make-linux-libre %linux-libre-4.14-version
@@ -402,20 +402,20 @@ 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 "4.9.87"
+                    "1p8phvmxp04npzqzqcfmv8k9l5l65s7vpjcakdm0fxfkzvnswsp6"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.4
-  (make-linux-libre "4.4.117"
-                    "1mlq9npyriwj0wpj24zah55bkxil31l182ypbn6b3x4yvmr8lhz0"
+  (make-linux-libre "4.4.121"
+                    "1d7djrhiib0ds9ssjkali6b5w6rzap4zgj5hf9jq1jmqpp54jkm4"
                     %intel-compatible-systems
                     #: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))
 
@@ -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
@@ -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)))
@@ -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")))
@@ -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
@@ -3706,7 +3706,7 @@ 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/"
@@ -3714,7 +3714,7 @@ of flash storage.")
                                   "/libseccomp-" version ".tar.gz"))
               (sha256
                (base32
-                "18dwfxzsw3agiy2dxbflrkhmjgvlji0wwkk636nabh2ng41qrp1x"))))
+                "0mdiyfljrkfl50q1m3ws8yfcyfjwf1zgkvcva8ffcwncji18zhkz"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("which" ,which)))
diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 020abc7494..1cda606c20 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)
@@ -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))
@@ -726,27 +728,29 @@ 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))
@@ -1366,6 +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"))))
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 6e8f9a74ae..7986671e97 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.
@@ -943,7 +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)))
@@ -1192,16 +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)))
@@ -1388,7 +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)
@@ -1396,7 +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")
diff --git a/gnu/packages/make-bootstrap.scm b/gnu/packages/make-bootstrap.scm
index e56ac937cb..e779376df9 100644
--- a/gnu/packages/make-bootstrap.scm
+++ b/gnu/packages/make-bootstrap.scm
@@ -198,6 +198,18 @@ 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
@@ -210,17 +222,7 @@ 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))))
 
@@ -531,6 +533,13 @@ 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"
@@ -556,7 +565,9 @@ 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))
diff --git a/gnu/packages/man.scm b/gnu/packages/man.scm
index b3a688759a..644738f717 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
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/maths.scm b/gnu/packages/maths.scm
index 25e1d5a312..f9e5d2c3a2 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -8,11 +8,11 @@
 ;;; 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>
-;;; 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>
@@ -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")
@@ -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")
@@ -724,7 +747,11 @@ 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)
@@ -2489,7 +2516,7 @@ point numbers.")
 (define-public wxmaxima
   (package
     (name "wxmaxima")
-    (version "17.10.1")
+    (version "18.02.0")
     (source
      (origin
        (method url-fetch)
@@ -2498,12 +2525,12 @@ 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 +2539,9 @@ 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/maven.scm b/gnu/packages/maven.scm
new file mode 100644
index 0000000000..81021f6461
--- /dev/null
+++ b/gnu/packages/maven.scm
@@ -0,0 +1,130 @@
+;;; 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)))
+
+(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.")))
+
+(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.")))
+
+(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.")))
+
+(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.")))
diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index c97c48e0e0..d0e0431130 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
diff --git a/gnu/packages/mingw.scm b/gnu/packages/mingw.scm
index c7bc5c025d..f7f34e9dc3 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.
 ;;;
@@ -36,14 +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))))
@@ -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+)))
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.
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 63b82900c0..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"))))
@@ -2609,7 +2610,9 @@ 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)
@@ -3726,6 +3729,34 @@ 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")
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)
diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm
index 0fa8cea523..167d1af777 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>
@@ -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")
@@ -498,7 +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)
@@ -506,7 +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)
@@ -1031,7 +1067,7 @@ 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 +1075,7 @@ 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.
@@ -1403,14 +1439,14 @@ 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)
diff --git a/gnu/packages/node.scm b/gnu/packages/node.scm
index 982d3f905c..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))
@@ -41,23 +43,43 @@
 (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"))
+              (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
@@ -77,29 +99,13 @@
                (("'/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 +141,6 @@
                              (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")
@@ -155,6 +153,7 @@
     (native-inputs
      `(("python" ,python-2)
        ("perl" ,perl)
+       ("pkg-config" ,pkg-config)
        ("procps" ,procps)
        ("util-linux" ,util-linux)
        ("which" ,which)))
@@ -165,7 +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")
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/packages/ocaml.scm b/gnu/packages/ocaml.scm
index 2ec67ba7be..24f402128c 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>
@@ -1123,14 +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)))
@@ -1144,7 +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
@@ -1163,6 +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"))))
@@ -1242,6 +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"))
@@ -1307,6 +1310,7 @@ 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"))))
@@ -1644,6 +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)
@@ -1678,6 +1683,7 @@ 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)
@@ -3448,6 +3454,7 @@ 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"))))
diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index 2a55a80842..f0147bab59 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.
 ;;;
@@ -20,6 +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)
@@ -39,27 +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)))
@@ -70,50 +82,50 @@
 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
     (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
@@ -155,36 +167,66 @@ 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
   (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")
@@ -257,27 +299,22 @@ tested on Python versions 3.2, 2.7, and 2.6.")
 (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
@@ -289,16 +326,10 @@ 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
@@ -349,31 +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
@@ -387,28 +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)
-    (arguments
-     '(#:tests? #f)) ; FIXME: Requires python-mock >= 1.2.
+    (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
@@ -423,17 +452,15 @@ 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)))
@@ -458,34 +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
@@ -500,27 +526,23 @@ 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)
@@ -530,21 +552,28 @@ 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
     (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 +583,27 @@ 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
@@ -623,65 +646,49 @@ 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
     (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)
@@ -689,18 +696,21 @@ 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
@@ -827,25 +837,16 @@ 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
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 0bc9dd6dd7..376c7d4fdb 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)
@@ -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
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
diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm
index f83c05a25b..46b6e795ab 100644
--- a/gnu/packages/password-utils.scm
+++ b/gnu/packages/password-utils.scm
@@ -9,13 +9,14 @@
 ;;; 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>
 ;;; 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.
 ;;;
@@ -44,6 +45,8 @@
   #: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)
@@ -89,7 +92,7 @@ human.")
 (define-public keepassxc
   (package
     (name "keepassxc")
-    (version "2.2.4")
+    (version "2.3.1")
     (source
      (origin
        (method url-fetch)
@@ -98,10 +101,17 @@ human.")
                            version "-src.tar.xz"))
        (sha256
         (base32
-         "1pfkq1m5vb90kx67vyw70s1hc4ivjsvq2535vm6wdwwsncna6bz5"))))
+         "1gdrbpzwbs56anc3k5vklvcackcn214pc8gm5xh5zcymsi8q4zff"))))
     (build-system cmake-build-system)
+    (arguments
+     '(#:configure-flags '("-DWITH_XC_NETWORKING=YES"
+                           "-DWITH_XC_BROWSER=YES"
+                           "-DWITH_XC_SSHAGENT=YES")))
     (inputs
-     `(("libgcrypt" ,libgcrypt)
+     `(("argon2" ,argon2)
+       ("curl" ,curl) ; XC_NETWORKING
+       ("libgcrypt" ,libgcrypt)
+       ("libsodium" ,libsodium) ; XC_BROWSER
        ("libxi" ,libxi)
        ("libxtst" ,libxtst)
        ("qtbase" ,qtbase)
@@ -190,7 +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-"
@@ -198,7 +208,7 @@ applications, there is xclip integration." )
                                   ".tar.bz2"))
               (sha256
                (base32
-                "0ydbnqw6icdh07pnv2w6dhvq501bdfvrklv4xmyr8znca9d753if"))))
+                "1lq46mpxdsbl6qw4cj58hp9q7jckmyvbsi08p5zr77rjgqadxyyy"))))
     (build-system gnu-build-system)
     (inputs
      `(("ncurses" ,ncurses)
@@ -271,7 +281,7 @@ 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 +290,7 @@ 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
@@ -603,3 +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)))
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
+
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
+
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/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%
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)
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/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..c03807323f
--- /dev/null
+++ b/gnu/packages/patches/glibc-allow-kernel-2.6.32.patch
@@ -0,0 +1,46 @@
+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
++++ 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");				      \
+       }									      \
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>
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.");
-
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);
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;
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'){
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
+
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/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
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)) {
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))
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/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
diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index cef42847c6..cf9f21dbc9 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)))
@@ -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)))
@@ -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")
@@ -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)
@@ -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)
@@ -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)
@@ -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)
@@ -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)
@@ -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)))
@@ -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)))
@@ -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)
@@ -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)))
@@ -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")
@@ -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")
@@ -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)))
@@ -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)
@@ -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")
@@ -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/")
@@ -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
@@ -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")
@@ -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")
@@ -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)))
@@ -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
@@ -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)))
@@ -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)))
@@ -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")
@@ -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)))
@@ -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/")
@@ -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")
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+)))
diff --git a/gnu/packages/php.scm b/gnu/packages/php.scm
index b9a5eb4bf2..f3f279a533 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.
 ;;;
@@ -49,10 +50,19 @@
   #: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")
-    (version "7.2.1")
+    (version "7.2.3")
     (home-page "https://secure.php.net/")
     (source (origin
               (method url-fetch)
@@ -60,7 +70,7 @@
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "08l8zmp8wbavq6wlgx19irz59csb44jhbsr172bfsq36v8pzhv3c"))
+                "07v5bq5b97zdqwmig6sxqsdb50vdf04w6jzmjq5kqh9gaqdlzadk"))
               (modules '((guix build utils)))
               (snippet
                '(with-directory-excursion "ext"
@@ -277,11 +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")
@@ -298,7 +304,7 @@
        ("curl" ,curl)
        ("cyrus-sasl" ,cyrus-sasl)
        ("freetype" ,freetype)
-       ("gd" ,gd)
+       ("gd" ,gd-for-php)
        ("gdbm" ,gdbm)
        ("glibc" ,glibc)
        ("gmp" ,gmp)
diff --git a/gnu/packages/polkit.scm b/gnu/packages/polkit.scm
index 0e38dd61ee..a3dbc4ff79 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)
@@ -113,13 +116,13 @@
             ;; 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"
+             (apply invoke "make" "install"
                            (string-append "sysconfdir=" out "/etc")
                            (string-append "polkit_actiondir="
                                           out "/share/polkit-1/actions")
-                           make-flags))))))))
-    (home-page "http://www.freedesktop.org/wiki/Software/polkit/")
+                           make-flags)
+             #t))))))
+    (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
@@ -183,5 +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/pretty-print.scm b/gnu/packages/pretty-print.scm
index 2f61de8994..6edfba95cc 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.
 ;;;
@@ -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)
@@ -242,7 +243,7 @@ seen in a terminal.")
 (define-public highlight
   (package
     (name "highlight")
-    (version "3.33")
+    (version "3.42")
     (source
      (origin
        (method url-fetch)
@@ -250,10 +251,10 @@ 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)
@@ -261,12 +262,13 @@ 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"
                (("(pkg-config.*)lua" _ prefix)
-                (string-append prefix "lua-5.3")))
+                (string-append prefix "lua-" ,(version-major+minor
+                                               (package-version lua)))))
              #t)))))
     (inputs
      `(("lua" ,lua)
diff --git a/gnu/packages/profiling.scm b/gnu/packages/profiling.scm
index 4fdf260c67..d6f3aede28 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.
 ;;;
@@ -65,7 +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
@@ -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 _
@@ -95,28 +97,26 @@ 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)
+                                       "/share/doc/" ,name "-" ,version)))
                (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/")
+    (home-page "https://icl.utk.edu/papi/")
     (synopsis "Performance Application Programming Interface")
     (description
      "PAPI provides the tool designer and application engineer with a consistent
diff --git a/gnu/packages/pulseaudio.scm b/gnu/packages/pulseaudio.scm
index 249afd3f68..8a45137a7f 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+
@@ -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"))))
diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm
index b898f088be..3734b6ba10 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")
@@ -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"))))
@@ -720,14 +721,14 @@ 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")
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 219b7f9fe2..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:)
@@ -138,14 +141,14 @@ 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)
@@ -165,14 +168,14 @@ 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)
@@ -238,23 +241,58 @@ 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")
-    (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
        (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")
@@ -264,7 +302,7 @@ 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
@@ -295,7 +333,8 @@ 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)))
@@ -332,19 +371,19 @@ 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")
@@ -451,7 +490,8 @@ 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 +562,8 @@ 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
@@ -956,13 +997,13 @@ 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.
@@ -1306,14 +1347,14 @@ 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!
@@ -1519,7 +1560,8 @@ 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 +1671,8 @@ 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)
@@ -1700,13 +1743,13 @@ 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
@@ -1715,7 +1758,8 @@ 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 +1875,8 @@ transfers.")
        ;; (modify-phases %standard-phases
        ;;   (replace 'check
        ;;     (lambda _
-       ;;       (zero? (system* "nosetests")))))))
+       ;;       (invoke "nosetests")
+       ;;       #t)))))
     (propagated-inputs
       `(("python-aniso8601" ,python-aniso8601)
         ("python-flask" ,python-flask)
@@ -1877,16 +1922,16 @@ 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")
@@ -2081,14 +2126,14 @@ 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)
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 3c816cda53..106c040bf8 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>
@@ -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
@@ -1386,26 +1392,15 @@ 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)))
@@ -1431,21 +1426,20 @@ 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
@@ -1512,19 +1506,17 @@ 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")
@@ -1701,15 +1693,15 @@ 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-testresources" ,python-testresources)
-        ("python-testscenarios" ,python-testscenarios)
-        ("python-testtools" ,python-testtools)
+        ("python-testrepository" ,python-testrepository-bootstrap)
+        ("python-testresources" ,python-testresources-bootstrap)
+        ("python-testscenarios" ,python-testscenarios-bootstrap)
+        ("python-testtools" ,python-testtools-bootstrap)
         ("python-virtualenv" ,python-virtualenv)))
     (synopsis "Enhance the default behavior of Python’s setuptools")
     (description
@@ -1943,14 +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)))
@@ -2426,7 +2418,17 @@ 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
@@ -4282,15 +4284,14 @@ 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)))
@@ -4301,22 +4302,24 @@ 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
@@ -4507,13 +4510,13 @@ 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
@@ -4773,7 +4776,7 @@ 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
@@ -4859,20 +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
@@ -5067,6 +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/")
@@ -5078,7 +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
@@ -5558,14 +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
@@ -5744,7 +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)
@@ -5753,7 +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.
@@ -5835,21 +5857,60 @@ 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)
+    (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
 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)))
 
+;; 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)
+    (name "python-msgpack-transitional")
+    (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))
 
@@ -5879,14 +5940,14 @@ 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
@@ -6071,13 +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")
@@ -7170,13 +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)))
@@ -7346,14 +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
@@ -7449,14 +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)))
@@ -8072,21 +8133,22 @@ 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
     ;; standard library.
     (arguments
      `(#:python ,python-2))
-    (native-inputs
-     `(("python2-six" ,python2-six)))
+    (propagated-inputs
+     `(("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")
@@ -8547,12 +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
@@ -9314,21 +9376,29 @@ 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 _
-             (zero? (system* "./run_tests.py" "--unit")))))))
+             (invoke "./run_tests.py" "--unit")
+             #t)))))
     (native-inputs
      `(("python-mock" ,python-mock)
        ("python-pep8" ,python-pep8)
@@ -10127,14 +10197,14 @@ 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/")
@@ -10362,14 +10432,14 @@ 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)
@@ -10380,8 +10450,9 @@ 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
@@ -10944,6 +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"))))
@@ -11093,14 +11165,19 @@ 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)
+    (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
@@ -11108,7 +11185,9 @@ 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
@@ -11495,6 +11574,48 @@ 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")
@@ -11960,14 +12081,14 @@ 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)
@@ -12143,6 +12264,7 @@ 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"))))
@@ -12638,7 +12760,6 @@ 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")
@@ -12849,3 +12970,81 @@ 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))
+
+;; 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/"
+                           (version-major+minor version)
+                           "/quex-" version ".zip"))
+       (sha256
+        (base32
+         "14gv8ll3ipqv4kyc2xiy891nrmjl4ic823zfyx8hassagyclyppw"))))
+    (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
+
+(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"))))))
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
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)
diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index b15e1a2717..ee5d20955c 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)
@@ -280,6 +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.
@@ -635,6 +692,84 @@ 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-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")
@@ -1094,6 +1229,30 @@ 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")
@@ -1337,6 +1496,34 @@ 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")
@@ -1502,6 +1689,30 @@ 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")
@@ -1810,6 +2021,26 @@ 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")
@@ -3328,6 +3559,33 @@ 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")
diff --git a/gnu/packages/samba.scm b/gnu/packages/samba.scm
index 5ea7858a89..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
@@ -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
diff --git a/gnu/packages/sawfish.scm b/gnu/packages/sawfish.scm
index a3b3d3d857..4eced74f22 100644
--- a/gnu/packages/sawfish.scm
+++ b/gnu/packages/sawfish.scm
@@ -51,7 +51,7 @@
      `(("makeinfo"   ,texinfo)
        ("pkg-config" ,pkg-config)
 
-       ("autoconf" ,(autoconf-wrapper))
+       ("autoconf" ,autoconf-wrapper)
        ("automake" ,automake)
        ("libtool"  ,libtool)))
     (inputs
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
diff --git a/gnu/packages/sdcc.scm b/gnu/packages/sdcc.scm
index 331425d98f..6d05470101 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)
@@ -59,10 +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.")
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)
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
diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm
index 8df4841eae..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
@@ -131,8 +132,9 @@ such as compact binary encodings, XML, or JSON.")
        (modify-phases %standard-phases
          (add-after 'unpack 'autoconf
            (lambda _
-             (system* "autoreconf" "-vfi"))))))
-    (home-page "http://www.msgpack.org")
+             (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
 serialization.")
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"))))
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"))))
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
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
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index c1012a635b..78afb77a8b 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -32,11 +32,14 @@
   #: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 bash)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cran)
@@ -170,21 +173,15 @@ 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.
@@ -265,6 +262,9 @@ be output in text, PostScript, PDF or HTML.")
        ("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
@@ -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/")
@@ -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")
@@ -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)))
@@ -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")
@@ -1187,13 +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")
@@ -1330,13 +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")
@@ -2232,14 +2233,14 @@ 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)))
@@ -2481,13 +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
@@ -2575,14 +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
@@ -2595,7 +2596,11 @@ 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
@@ -2811,6 +2816,19 @@ 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
@@ -3315,20 +3333,20 @@ 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)
@@ -3577,14 +3595,14 @@ 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)
@@ -4011,14 +4029,14 @@ 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")
@@ -4039,6 +4057,14 @@ 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
@@ -4882,27 +4908,6 @@ 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")
@@ -5356,14 +5361,14 @@ 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)
@@ -5445,6 +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"))))
@@ -5479,6 +5485,7 @@ tools.")
          (uri (hg-reference
                (url "https://bitbucket.org/tanaylab/tgconfig")
                (changeset changeset)))
+         (file-name (string-append name "-" version "-checkout"))
          (sha256
           (base32
            "0xy6c7s7mn1yx191154bwbv1bl424bnvc80syqpl1vdl28ba46rj"))))
@@ -5539,3 +5546,72 @@ 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 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")
+    (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+)))
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)
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
diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm
index f5e5bb85be..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))
@@ -1526,31 +1522,6 @@ 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"))
@@ -1577,97 +1548,6 @@ 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")
-    (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-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"))
@@ -1792,56 +1672,6 @@ 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-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"))
@@ -1868,56 +1698,6 @@ 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"))
-  (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"))
diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index 4e8efc8faf..05a7cd834b 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>
@@ -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"))))
@@ -255,10 +257,11 @@ 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"))))))
-    (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.")
@@ -278,6 +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"))))
@@ -292,7 +296,7 @@ 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
@@ -316,6 +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"))))
@@ -351,6 +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"))))
@@ -365,7 +371,7 @@ 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
@@ -385,6 +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"))))
@@ -399,7 +406,7 @@ 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
@@ -441,6 +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"))))
@@ -475,7 +483,7 @@ 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.")
@@ -492,7 +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"))))
@@ -526,6 +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"))))
@@ -575,7 +584,7 @@ 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,
@@ -594,6 +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"))))
@@ -657,6 +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"))))
@@ -712,7 +723,7 @@ 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
@@ -731,6 +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"))))
@@ -790,7 +802,7 @@ 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,
@@ -812,6 +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"))))
@@ -820,7 +833,7 @@ 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
@@ -841,6 +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"))))
@@ -873,6 +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")
@@ -880,6 +899,7 @@ book).")
       (source (origin
                 (method svn-fetch)
                 (uri (texlive-ref "latex" "base"))
+                (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
                   "1h9pir2hz6i9avc4lrl733p3zf4rpkg8537x1zdbhs91hvhikw9k"))))
@@ -926,12 +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,
@@ -939,25 +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)
@@ -1003,7 +1021,7 @@ 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
@@ -1024,7 +1042,7 @@ 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
@@ -1052,7 +1070,7 @@ 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,
@@ -1085,7 +1103,7 @@ 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
@@ -1112,7 +1130,7 @@ 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
@@ -1176,7 +1194,7 @@ 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
@@ -1199,7 +1217,7 @@ 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,
@@ -1227,7 +1245,7 @@ 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
@@ -1262,7 +1280,7 @@ 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:
@@ -1284,7 +1302,7 @@ 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
@@ -1347,7 +1365,7 @@ 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
@@ -1386,7 +1404,7 @@ 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
@@ -1420,7 +1438,7 @@ 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
@@ -1478,7 +1496,7 @@ 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
@@ -1507,7 +1525,7 @@ 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
@@ -1539,7 +1557,7 @@ 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)
@@ -1564,7 +1582,7 @@ 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
@@ -1586,7 +1604,7 @@ 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
@@ -1607,7 +1625,7 @@ 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
@@ -1727,7 +1745,7 @@ 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
@@ -1756,7 +1774,7 @@ 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
@@ -1784,7 +1802,7 @@ 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
@@ -1816,7 +1834,7 @@ 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
@@ -1842,7 +1860,7 @@ 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
@@ -1866,7 +1884,7 @@ 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
@@ -1888,7 +1906,7 @@ 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
@@ -1924,7 +1942,7 @@ 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
@@ -1959,7 +1977,7 @@ 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
@@ -1985,7 +2003,7 @@ 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
@@ -2009,7 +2027,7 @@ 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
@@ -2033,7 +2051,7 @@ 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
@@ -2071,7 +2089,7 @@ 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}
@@ -2096,7 +2114,7 @@ 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
@@ -2131,7 +2149,7 @@ 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
@@ -2166,7 +2184,7 @@ 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
@@ -2199,7 +2217,7 @@ 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
@@ -2237,7 +2255,7 @@ 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
@@ -2272,7 +2290,7 @@ 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
@@ -2306,7 +2324,7 @@ 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
@@ -2328,7 +2346,7 @@ 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
@@ -2348,7 +2366,7 @@ 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
@@ -2372,7 +2390,7 @@ 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
@@ -2397,7 +2415,7 @@ 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
@@ -2421,7 +2439,7 @@ 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
@@ -2441,7 +2459,7 @@ 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
@@ -2475,7 +2493,7 @@ 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;
@@ -2498,7 +2516,7 @@ 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
@@ -2538,7 +2556,7 @@ 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
@@ -2558,7 +2576,7 @@ 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
@@ -2580,7 +2598,7 @@ 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
@@ -2636,7 +2654,7 @@ 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
@@ -2668,7 +2686,7 @@ 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},
@@ -2702,7 +2720,7 @@ 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
@@ -2722,7 +2740,7 @@ 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
@@ -2745,7 +2763,7 @@ 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.
@@ -2770,7 +2788,7 @@ 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)
@@ -2804,7 +2822,7 @@ 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:
@@ -2879,7 +2897,7 @@ 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
@@ -2960,7 +2978,7 @@ 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
@@ -2983,7 +3001,7 @@ 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}
@@ -3016,7 +3034,7 @@ 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,
@@ -3053,7 +3071,7 @@ 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
@@ -3075,7 +3093,7 @@ 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
@@ -3108,7 +3126,7 @@ 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
@@ -3144,7 +3162,7 @@ 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
@@ -3164,7 +3182,7 @@ 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
@@ -3197,7 +3215,7 @@ 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
@@ -3219,7 +3237,7 @@ 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
@@ -3246,7 +3264,7 @@ 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},
@@ -3283,7 +3301,7 @@ 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
@@ -3406,7 +3424,7 @@ 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
@@ -3424,6 +3442,47 @@ 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")
@@ -3449,7 +3508,7 @@ TeX metrics (VF and TFM files) and macros for use with LaTeX.")
            (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
@@ -3472,7 +3531,7 @@ 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
@@ -3500,7 +3559,7 @@ 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
@@ -3539,7 +3598,7 @@ 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
@@ -3560,7 +3619,7 @@ 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
@@ -3593,7 +3652,7 @@ 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
@@ -3613,7 +3672,7 @@ 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
@@ -3648,7 +3707,7 @@ 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.
@@ -3682,7 +3741,7 @@ 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},
@@ -3716,7 +3775,7 @@ 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
@@ -3741,7 +3800,7 @@ 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
@@ -3776,7 +3835,7 @@ 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
diff --git a/gnu/packages/text-editors.scm b/gnu/packages/text-editors.scm
index 0207ca36ab..f1ccab9af9 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
@@ -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\"
diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm
index 3284be243e..2d8a104d54 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
@@ -116,27 +109,23 @@ 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
     (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,
@@ -519,10 +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"))
@@ -543,7 +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
@@ -641,6 +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"))))
@@ -652,7 +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")
diff --git a/gnu/packages/time.scm b/gnu/packages/time.scm
index a54524087f..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")
@@ -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
diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm
index e79065ae78..a7944c2ce7 100644
--- a/gnu/packages/tls.scm
+++ b/gnu/packages/tls.scm
@@ -115,7 +115,7 @@ 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)
@@ -123,7 +123,7 @@ 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)))
@@ -787,7 +787,15 @@ 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
diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm
index 4a39100511..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"
@@ -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)
@@ -230,7 +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
diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index 83b11ddd97..2907999fca 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)
@@ -472,7 +473,7 @@ to lock down your entire repository.")
 (define-public git-remote-gcrypt
   (package
    (name "git-remote-gcrypt")
-   (version "1.0.1")
+   (version "1.0.3")
    (source (origin
              (method git-fetch)
              (uri (git-reference
@@ -481,7 +482,7 @@ to lock down your entire repository.")
              (file-name (string-append name "-" version "-checkout"))
              (sha256
               (base32
-               "0znrx77vpm4a8l7yiybsxk5vrawijqqfxmp1p2yhaaw8cbgrj7az"))))
+               "1vay3204729c7wajgn3nxf0s0hzwpdrw14pl6kd8w2ss25gvw2k1"))))
    (build-system trivial-build-system)
    (arguments
     `(#:modules ((guix build utils))
@@ -633,6 +634,107 @@ 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 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")
@@ -683,6 +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"))))
@@ -800,6 +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"))))
@@ -826,7 +930,7 @@ 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
@@ -835,7 +939,7 @@ 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
@@ -856,7 +960,8 @@ 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"))
@@ -864,7 +969,7 @@ 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)
@@ -1389,7 +1494,7 @@ 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 +1502,7 @@ 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 +1515,7 @@ 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/")
@@ -1536,14 +1641,15 @@ 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")
@@ -1763,7 +1869,7 @@ 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
@@ -1771,7 +1877,7 @@ 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
diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index b45e96d1e9..bf5999177e 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)
@@ -1089,7 +1090,7 @@ projects while introducing many more.")
 (define-public gnome-mpv
   (package
     (name "gnome-mpv")
-    (version "0.13")
+    (version "0.14")
     (source
      (origin
        (method url-fetch)
@@ -1098,7 +1099,7 @@ projects while introducing many more.")
                            ".tar.xz"))
        (sha256
         (base32
-         "1w944ymyssgfcjiczrq4saig90crw9b9hhdsnchfbjsw173qi8n5"))))
+         "03kjwd5jq0i5ajnvhjwf5019bjjaa16xkdrhdkiz1k58ipjvvj93"))))
     (native-inputs
      `(("intltool" ,intltool)
        ("pkg-config" ,pkg-config)))
@@ -1156,7 +1157,7 @@ access to mpv's powerful playback capabilities.")
 (define-public youtube-dl
   (package
     (name "youtube-dl")
-    (version "2018.02.11")
+    (version "2018.03.10")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://yt-dl.org/downloads/"
@@ -1164,7 +1165,7 @@ access to mpv's powerful playback capabilities.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0zg34spkfiwjq55jrk417ifdcyvrj80gdbc338rdpfw2s6ibggv8"))))
+                "1ibmz91anli1vzkgw2i3h4wf1i8arzd74730ylwcwyg3375xryjb"))))
     (build-system python-build-system)
     (arguments
      ;; The problem here is that the directory for the man page and completion
@@ -1310,6 +1311,61 @@ 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* ((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
+     "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")
@@ -1981,7 +2037,7 @@ making @dfn{screencasts}.")
 (define-public simplescreenrecorder
   (package
     (name "simplescreenrecorder")
-    (version "0.3.9")
+    (version "0.3.10")
     (source
      (origin
        (method url-fetch)
@@ -1990,7 +2046,7 @@ 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.
@@ -2474,7 +2530,7 @@ 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
@@ -2482,7 +2538,7 @@ 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
@@ -2704,7 +2760,7 @@ 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/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"
diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm
index d7f5dc6597..0fc3197077 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.
@@ -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"))))
@@ -241,7 +242,7 @@ 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 +250,7 @@ and probably others.")
                     version ".tar.xz"))
               (sha256
                (base32
-                "102an395nv8l7qfx3syydzhmd9xfbycd6gvwy0h2kjz8w67ipkcn"))))
+                "17njq59hsraqyxrbhkrxr7dvx0p066s3pn8w1mi0yd9jldis7h23"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags '("--enable-iproute2=yes")))
@@ -262,24 +263,25 @@ 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
   (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
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".
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"))
 
diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 7dc4fdacaa..6db59daa2c 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)
@@ -156,6 +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"))))
@@ -791,7 +795,7 @@ for efficient socket-like bidirectional reliable communication channels.")
 (define-public libpsl
   (package
     (name "libpsl")
-    (version "0.19.1")
+    (version "0.20.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/rockdaboot/libpsl/"
@@ -799,7 +803,7 @@ for efficient socket-like bidirectional reliable communication channels.")
                                   "/libpsl-" version ".tar.gz"))
               (sha256
                (base32
-                "0ydwi9m39qv6k7zagqx2kzxzf59ipxj9r0c71xmwngdx3fslclbk"))))
+                "17r18y25ka2ck2ykfidbg4a7jpyzmkqwrzplgqjp7mwd2l9rc6cm"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -837,6 +841,7 @@ 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"))
@@ -2843,7 +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)
@@ -2851,7 +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)))
@@ -2925,7 +2930,7 @@ 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)
@@ -2933,7 +2938,7 @@ 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")
@@ -3203,7 +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)
@@ -3211,7 +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)))
@@ -3649,7 +3654,7 @@ library.")
 (define-public perl-www-mechanize
   (package
     (name "perl-www-mechanize")
-    (version "1.86")
+    (version "1.87")
     (source
      (origin
        (method url-fetch)
@@ -3657,7 +3662,7 @@ library.")
                            "WWW-Mechanize-" version ".tar.gz"))
        (sha256
         (base32
-         "0sfl6b7mx8nannnh3ys5jk44d1s1b2d1mffrnrphkzzykaw6hm0f"))))
+         "1kxrydhl7nxlyjv0xvyiyj4igdv4fwnggv0ihlp79bysbjjl54w1"))))
     (build-system perl-build-system)
     (native-inputs                      ;only for tests
      `(("perl-cgi" ,perl-cgi)
@@ -3772,13 +3777,13 @@ CDF, Atom 0.3, and Atom 1.0 feeds.")
 (define-public r-httpuv
   (package
     (name "r-httpuv")
-    (version "1.3.5")
+    (version "1.3.6.2")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "httpuv" version))
               (sha256
                (base32
-                "1sg4f223zfyd265b28rlhsn3b6mqflcpnmya98cjmjncmy9vjdj3"))))
+                "0h3hkw575b211bxma23inbq1565wkhiapgasd539h219apqs534f"))))
     (build-system r-build-system)
     (native-inputs `(("r-rcpp" ,r-rcpp)))
     (home-page "https://github.com/rstudio/httpuv")
@@ -6260,7 +6265,7 @@ 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)
@@ -6268,7 +6273,7 @@ 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"
@@ -6334,3 +6339,84 @@ 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 "1.31.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/nghttp2/nghttp2/"
+                           "releases/download/v" version "/"
+                           name "-" version ".tar.xz"))
+       (sha256
+        (base32
+         "1ivs74v9sa2sds3dq0s7vn9bkmhr2hgwyg1an1rah3agqwnkqmrn"))))
+    (build-system gnu-build-system)
+    (outputs (list "out"
+                   "lib"))              ; only libnghttp2
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+
+       ;; Required by tests.
+       ("cunit" ,cunit)
+       ("tzdata" ,tzdata-for-tests)))
+    (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)))
diff --git a/gnu/packages/wine.scm b/gnu/packages/wine.scm
index e71538f1b0..0327deaf24 100644
--- a/gnu/packages/wine.scm
+++ b/gnu/packages/wine.scm
@@ -26,9 +26,13 @@
   #: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 autotools)
+  #: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)
@@ -47,11 +51,13 @@
   #: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)
   #: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)
@@ -212,34 +218,83 @@ 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)
     (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)
+              ("sdl2" ,sdl2)
+              ("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.
@@ -261,7 +316,7 @@ 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
@@ -281,13 +336,13 @@ 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)
diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm
index 235aec36cb..f12eedab43 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
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+)))
diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm
index 3beaa97c90..87d14e20a4 100644
--- a/gnu/packages/xdisorg.scm
+++ b/gnu/packages/xdisorg.scm
@@ -401,7 +401,7 @@ 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
@@ -1096,7 +1096,7 @@ 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/"
@@ -1104,7 +1104,7 @@ 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)
@@ -1121,6 +1121,7 @@ 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.
@@ -1131,8 +1132,30 @@ connectivity of the X server running on a particular @code{DISPLAY}.")
              (substitute* '("test/helper-expand.c")
                (("~root") "/root")
                (("~") "")
-               (("g_get_home_dir \\(\\)") "\"/\"")))))))
-    (home-page "https://davedavenport.github.io/rofi/")
+               (("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://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
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)
diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm
index 565d27e78f..293b47a653 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>
@@ -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)))
@@ -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)
@@ -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")
@@ -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)
@@ -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"))
@@ -1006,12 +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"))
@@ -1060,9 +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
@@ -1109,7 +1111,7 @@ 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 +1120,7 @@ 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")
@@ -1249,14 +1251,14 @@ 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")
diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index f1ef480c42..d167269c24 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
@@ -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)))
@@ -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)
@@ -2001,7 +2001,7 @@ 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)
@@ -2011,7 +2011,7 @@ information used in connecting to the X server.")
                ".tar.bz2"))
         (sha256
           (base32
-            "0arnd1j8vzhzmw72mqhjjcb2qwcbs9qphsy3ps593ajyld8wzxhp"))))
+            "0pmzaz4kp38qv2lqiw5rnqhwzmwrq65m1x5j001mmv99wh9isnk1"))))
     (build-system gnu-build-system)
     (inputs
      `(("libxcb" ,libxcb)
@@ -2031,7 +2031,7 @@ the same way.")
 (define-public xbitmaps
   (package
     (name "xbitmaps")
-    (version "1.1.1")
+    (version "1.1.2")
     (source
       (origin
         (method url-fetch)
@@ -2041,7 +2041,7 @@ 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/")
@@ -2175,7 +2175,7 @@ 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)
@@ -2185,7 +2185,7 @@ X11 Inter-Client Communication Conventions Manual (ICCCM).")
                ".tar.bz2"))
         (sha256
           (base32
-            "11mv661nj1p22sqkv87ryj2lcx4m68a04b0rs6iqh3fzp42jrzg3"))))
+            "0whjiq6d5z4z75zh37pji6llfcyrg6q3mg9zx5zqyncnj39q30xf"))))
     (build-system gnu-build-system)
     (inputs
       `(("libxcursor" ,libxcursor)
@@ -2274,7 +2274,7 @@ available.")
 (define-public xdriinfo
   (package
     (name "xdriinfo")
-    (version "1.0.5")
+    (version "1.0.6")
     (source
       (origin
         (method url-fetch)
@@ -2284,7 +2284,7 @@ available.")
                ".tar.bz2"))
         (sha256
           (base32
-            "0681d0y8liqakkpz7mmsf689jcxrvs5291r20qi78mc9xxk3gfjc"))))
+            "0lcx8h3zd11m4w8wf7dyp89826d437iz78cyrix436bqx31x5k6r"))))
     (build-system gnu-build-system)
     (inputs
       `(("mesa" ,mesa)
@@ -3843,7 +3843,7 @@ 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)
@@ -3853,7 +3853,7 @@ 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)
@@ -3898,7 +3898,7 @@ 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)
@@ -3908,7 +3908,7 @@ 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)))
@@ -3925,7 +3925,7 @@ running on X server.")
 (define-public xlsfonts
   (package
     (name "xlsfonts")
-    (version "1.0.5")
+    (version "1.0.6")
     (source
      (origin
        (method url-fetch)
@@ -3935,7 +3935,7 @@ running on X server.")
              ".tar.bz2"))
        (sha256
         (base32
-         "1yi774g6r1kafsbnxbkrwyndd3i60362ck1fps9ywz076pn5naa0"))))
+         "0s6kxgv78chkwsqmhw929f4pf91gq63f4yvixxnan1h00cx0pf49"))))
     (build-system gnu-build-system)
     (inputs
      `(("xproto" ,xproto)
@@ -3952,7 +3952,7 @@ protocol.")
 (define-public xfontsel
   (package
     (name "xfontsel")
-    (version "1.0.5")
+    (version "1.0.6")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -3960,7 +3960,7 @@ protocol.")
                     version ".tar.bz2"))
               (sha256
                (base32
-                "1grir464hy52a71r3mpm9mzvkf7nwr3vk0b1vc27pd3gp588a38p"))))
+                "0700lf6hx7dg88wq1yll7zjvf9gbwh06xff20yffkxb289y0pai5"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -4084,7 +4084,7 @@ 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)
@@ -4094,7 +4094,7 @@ refers to the included common xorg.css stylesheet.")
                ".tar.bz2"))
         (sha256
           (base32
-            "1dbcv26w2yand2qy7b3h5rbvw1mdmdd57jw88v53sgdr3vrqvngy"))))
+            "07qy9lwjvxighcmg6qvjkgagad3wwvidrfx0jz85lgynz3qy0dmr"))))
     (build-system gnu-build-system)
     (inputs
       `(("xproto" ,xproto)
@@ -4113,7 +4113,7 @@ 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)
@@ -4123,7 +4123,7 @@ it for output on various types of printers.")
                ".tar.bz2"))
         (sha256
           (base32
-            "1ilvhqfjcg6f1hqahjkp8qaay9rhvmv2blvj3w9asraq0aqqivlv"))))
+            "06sjgahjiz85v0k0pmv5x05chc591xynl5ah1bqzz1bdr0lgnanj"))))
     (build-system gnu-build-system)
     (inputs
       `(("xproto" ,xproto)
@@ -4170,7 +4170,7 @@ and Reflect (RandR) extension.")
 (define-public xrdb
   (package
     (name "xrdb")
-    (version "1.1.0")
+    (version "1.1.1")
     (source
       (origin
         (method url-fetch)
@@ -4180,7 +4180,7 @@ and Reflect (RandR) extension.")
                ".tar.bz2"))
         (sha256
           (base32
-            "0nsnr90wazcdd50nc5dqswy0bmq6qcj14nnrhyi7rln9pxmpp0kk"))))
+            "1dqp486nd5sagbg572kl0k839nwvpqnb7jvppyb7jj5vrpkss8rd"))))
     (build-system gnu-build-system)
     (inputs
       `(("libxmu" ,libxmu)
@@ -4201,7 +4201,7 @@ file.")
 (define-public xrefresh
   (package
     (name "xrefresh")
-    (version "1.0.5")
+    (version "1.0.6")
     (source
       (origin
         (method url-fetch)
@@ -4211,7 +4211,7 @@ file.")
                ".tar.bz2"))
         (sha256
           (base32
-            "1mlinwgvql6s1rbf46yckbfr9j22d3c3z7jx3n6ix7ca18dnf4rj"))))
+            "0lv3rlshh7s0z3aqx5ahnnf8cl082m934bk7gv881mz8nydznz98"))))
     (build-system gnu-build-system)
     (inputs
       `(("libx11" ,libx11)))
@@ -4229,7 +4229,7 @@ up your screen.")
 (define-public xset
   (package
     (name "xset")
-    (version "1.2.3")
+    (version "1.2.4")
     (source
       (origin
         (method url-fetch)
@@ -4239,7 +4239,7 @@ up your screen.")
                ".tar.bz2"))
         (sha256
           (base32
-            "0qw0iic27bz3yz2wynf1gxs70hhkcf9c4jrv7zhlg1mq57xz90j3"))))
+            "0my987wjvra7l92ry6q44ky383yg3phzxhdbn3lqhapm1ll9bzg4"))))
     (build-system gnu-build-system)
     (inputs
       `(("xproto" ,xproto)
@@ -4258,7 +4258,7 @@ up your screen.")
 (define-public xsetroot
   (package
     (name "xsetroot")
-    (version "1.1.1")
+    (version "1.1.2")
     (source
       (origin
         (method url-fetch)
@@ -4268,7 +4268,7 @@ up your screen.")
                ".tar.bz2"))
         (sha256
           (base32
-            "1nf3ii31m1knimbidaaym8p61fq3blv8rrdr2775yhcclym5s8ds"))))
+            "0z21mqvmdl6rl63q77479wgkfygnll57liza1i3va7sr4fx45i0h"))))
     (build-system gnu-build-system)
     (inputs
       `(("libxmu" ,libxmu)
@@ -4343,7 +4343,7 @@ extension.")
 (define-public xwd
   (package
     (name "xwd")
-    (version "1.0.6")
+    (version "1.0.7")
     (source
       (origin
         (method url-fetch)
@@ -4353,7 +4353,7 @@ extension.")
                ".tar.bz2"))
         (sha256
           (base32
-            "0ybx48agdvjp9lgwvcw79r1x6jbqbyl3fliy3i5xwy4d4si9dcrv"))))
+            "1537i8q8pgf0sjklakzfvjwrq5b246qjywrx9ll8xfg0p6w1as6d"))))
     (build-system gnu-build-system)
     (inputs
       `(("libxt" ,libxt)
@@ -4376,7 +4376,7 @@ 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)
@@ -4386,7 +4386,7 @@ dump and twice whenthe dump is completed.")
                ".tar.bz2"))
         (sha256
           (base32
-            "1y1zn8ijqslb5lfpbq4bb78kllhch8in98ps7n8fg3dxjpmb13i1"))))
+            "00avrpw4h5mr1klp41lv2j4dmq465v6l5kb5bhm4k5ml8sm9i543"))))
     (build-system gnu-build-system)
     (inputs
       `(("libx11" ,libx11)
@@ -4404,7 +4404,7 @@ 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)
@@ -4414,7 +4414,7 @@ Various information is displayed depending on which options are selected.")
                ".tar.bz2"))
         (sha256
           (base32
-            "1ggql6maivah58kwsh3z9x1hvzxm1a8888xx4s78cl77ryfa1cyn"))))
+            "1a8hdgy40smvblnh3s9f0vkqckl68nmivx7d48zk34m8z18p16cr"))))
     (build-system gnu-build-system)
     (inputs
       `(("xproto" ,xproto)
@@ -4761,14 +4761,14 @@ 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.
@@ -5409,17 +5409,17 @@ 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)
@@ -5638,14 +5638,14 @@ 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)
@@ -5727,7 +5727,7 @@ of an X11 screen.")
 (define-public xmessage
   (package
     (name "xmessage")
-    (version "1.0.4")
+    (version "1.0.5")
     (source
      (origin
        (method url-fetch)
@@ -5737,7 +5737,7 @@ of an X11 screen.")
              ".tar.gz"))
        (sha256
         (base32
-         "1jmcac1xbwplbxfl75sr6w3zqhx1khpdzlqippjsr31cjp1rjc48"))))
+         "0sw0b0cbrjl44brw7qi1jkm61xd7a1lpj04418c6iqk6mf83llwr"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -5801,7 +5801,7 @@ 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
@@ -5809,7 +5809,7 @@ 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.
@@ -5932,7 +5932,7 @@ basic eye-candy effects.")
 (define-public xpra
   (package
     (name "xpra")
-    (version "2.2.4")
+    (version "2.2.5")
     (source
      (origin
        (method url-fetch)
@@ -5940,7 +5940,7 @@ basic eye-candy effects.")
                            version ".tar.xz"))
        (sha256
         (base32
-         "0v8yflvisk94bfj0zg4ggdfwrig0f3ss9kjnws3zflsr33cb2hxy"))))
+         "1q2l00nc3bgwlhjzkbk4a8x2l8z9w1799yn31icsx5hrgh98a1js"))))
     (build-system python-build-system)
     (inputs `(("ffmpeg" ,ffmpeg)
               ("flac" ,flac)
diff --git a/gnu/packages/zile.scm b/gnu/packages/zile.scm
index 97c964e94c..858117de28 100644
--- a/gnu/packages/zile.scm
+++ b/gnu/packages/zile.scm
@@ -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.