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* gnu: ruby-nokogiri: Upgrade to 1.6.7.1.Ben Woodcroft2015-12-231-3/+3
| | | | * gnu/packages/ruby.scm (ruby-nokogiri): Upgrade to 1.6.7.1.
* gnu: Add ruby-mini-portile-2.Ben Woodcroft2015-12-231-0/+10
| | | | * gnu/packages/ruby.scm (ruby-mini-portile-2): New variable.
* gnu: icedtea7: Update to 2.6.3.Ricardo Wurmus2015-12-231-9/+9
| | | | * gnu/packages/java.scm (icedtea7): Update to 2.6.3.
* gnu: icedtea6: Update to 1.13.9.Ricardo Wurmus2015-12-231-4/+4
| | | | * gnu/packages/java.scm (icedtea6): Update to 1.13.9.
* gnu: libmicrohttpd: Update to 0.9.48.Efraim Flashner2015-12-221-2/+2
| | | | * gnu/packages/gnunet.scm (libmicrohttpd): Update to 0.9.48.
* gnu: parallel: Update to 20151222.Efraim Flashner2015-12-221-2/+2
| | | | * gnu/packages/parallel.scm (parallel): Update to 20151222.
* gnu: sipwitch: Update to 1.9.15.Efraim Flashner2015-12-221-2/+2
| | | | * gnu/packages/telephony.scm (sipwitch): Update to 1.9.15.
* gnu: ucommon: Update to 7.0.0.Efraim Flashner2015-12-221-2/+4
| | | | | * gnu/packages/telephony.scm (ucommon): Update to 7.0.0. [inputs]: Add gnutls.
* gnu: isc-dhcp: Disable parallel build.Mark H Weaver2015-12-221-1/+2
| | | | * gnu/packages/admin.scm (isc-dhcp)[arguments]: Disable parallel build.
* gnu: isc-dhcp: Update to 4.3.3; update bundled bind to 9.9.8-P2.Mark H Weaver2015-12-211-91/+133
| | | | | | | | | | Fixes CVE-2015-8000 and CVE-2015-8461. * gnu/packages/admin.scm (isc-dhcp): Update to 4.3.3. [inputs]: Add 'bind-source-tarball'. [arguments]: Use modify-phases. Add 'replace-bundled-bind' phase. In 'post-configure' phase, avoid hard-coding version numbers of bundled bind.
* gnu: bind-utils: Update to 9.10.3-P2.Mark H Weaver2015-12-211-3/+3
| | | | | * gnu/packages/dns.scm (bind-utils): Update to 9.10.3-P2. [source]: Use HTTP URI instead of FTP.
* file-systems: The 'device' field can be a UUID (bytevector).Ludovic Courtès2015-12-221-5/+8
| | | | | | | | Previously a wrong-type-arg error would be raised when a file system with a UUID (bytevector) field was encountered. * gnu/system.scm (other-file-system-services)[device-mappings]: Check whether FS's device is a string.
* file-systems: Add a 'mount?' field.Ludovic Courtès2015-12-223-53/+65
| | | | | | | | | | | | | Fixes <http://bugs.gnu.org/22176>. Reported by Florian Paul Schmidt <mista.tapas@gmx.net>. * gnu/system/file-systems.scm (<file-system>)[mount?]: New field. (file-system->spec): Adjust accordingly. * gnu/services/base.scm (file-system-dmd-service): Return the empty list when FILE-SYSTEM has 'mount?' set to false. (user-processes-service): Select the subset of FILE-SYSTEMS that matches 'file-system-mount?'. * doc/guix.texi (File Systems): Document it.
* services: Add 'fstab-service-type'.Ludovic Courtès2015-12-222-62/+112
| | | | | | | | | | * gnu/services/base.scm (file-system->fstab-entry) (file-systems->fstab): New procedures. (fstab-service-type): New variable. * gnu/services/base.scm (file-system-dmd-service): New procedure, taken from... (file-system-service-type): ... here. * gnu/system.scm (essential-services): Add FSTAB-SERVICE-TYPE instance.
* build: Add bioconductor-uri procedure.Ricardo Wurmus2015-12-211-1/+8
| | | | * guix/build-system/r.scm (bioconductor-uri): New procedure.
* gnu: Add vmpk.Ricardo Wurmus2015-12-211-0/+43
| | | | * gnu/packages/music.scm (vmpk): New variable.
* gnu: Add drumstick.Ricardo Wurmus2015-12-211-0/+47
| | | | * gnu/packages/music.scm (drumstick): New variable.
* gnu: letsencrypt and acme: Update to 0.1.1.Leo Famulari2015-12-211-8/+6
| | | | | | | | | These packages should be updated together. * gnu/packages/tls.scm (letsencrypt): Update to 0.1.1. [source]: Use pypi-uri. * gnu/packages/tls.scm (acme): Update to 0.1.1. [source]: Use pypi-uri.
* gnu: ffmpeg: Update to 2.8.4.Efraim Flashner2015-12-211-2/+2
| | | | * gnu/packages/video.scm (ffmpeg): Update to 2.8.4.
* doc: Be more explicit in example of file-systems configuration.Leo Famulari2015-12-212-5/+5
| | | | | | * gnu/system/examples/bare-bones.tmpl (file-systems): Change device label. * gnu/system/examples/desktop.tmpl (file-systems): Likewise.
* doc: Explain significance of partition labels.Leo Famulari2015-12-211-0/+8
| | | | | * doc/guix.texi (Preparing for Installation): Point out relationship between partition labels and the file-system configuration.
* gnu: grub: Add fix for CVE-2015-8730.Leo Famulari2015-12-213-1/+49
| | | | | | * gnu/packages/patches/grub-CVE-2015-8370.patch: New file. * gnu-system.am (dist_patch_DATA): Register patch. * gnu/packages/grub.scm: Apply patch.
* gnu: Add GenomicRanges.Ricardo Wurmus2015-12-211-0/+28
| | | | * gnu/packages/bioinformatics.scm (r-genomicranges): New variable.
* gnu: Add XVector.Ricardo Wurmus2015-12-211-0/+37
| | | | * gnu/packages/bioinformatics.scm (r-xvector): New variable.
* gnu: Add GenomeInfoDb.Ricardo Wurmus2015-12-211-0/+27
| | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): New variable.
* gnu: Add IRanges.Ricardo Wurmus2015-12-211-0/+30
| | | | * gnu/packages/bioinformatics.scm (r-iranges): New variable.
* gnu: Add S4Vectors.Ricardo Wurmus2015-12-211-0/+28
| | | | * gnu/packages/bioinformatics.scm (r-s4vectors): New variable.
* gnu: Add BiocGenerics.Ricardo Wurmus2015-12-211-0/+21
| | | | * gnu/packages/bioinformatics.scm (r-biocgenerics): New variable.
* gnu: Add r-acsnminer.Ricardo Wurmus2015-12-211-0/+26
| | | | * gnu/packages/bioinformatics.scm (r-acsnminer): New variable.
* gnu: Add r-gridextra.Ricardo Wurmus2015-12-211-0/+25
| | | | * gnu/packages/statistics.scm (r-gridextra): New variable.
* gnu: Add r-gtable.Ricardo Wurmus2015-12-211-0/+19
| | | | * gnu/packages/statistics.scm (r-gtable): New variable.
* gnu: Add r-rmarkdown.Ricardo Wurmus2015-12-211-0/+27
| | | | | | * gnu/packages/statistics.scm (r-rmarkdown): New variable. * gnu/packages/haskell.scm: Do not select libxml2 from the xml module to prevent circular package module imports.
* gnu: Add r-catools.Ricardo Wurmus2015-12-211-0/+23
| | | | * gnu/packages/statistics.scm (r-catools): New variable.
* gnu: Add r-bitops.Ricardo Wurmus2015-12-211-0/+18
| | | | * gnu/packages/statistics.scm (r-bitops): New variable.
* gnu: Add AdaptiveSparsity.Ricardo Wurmus2015-12-211-0/+33
| | | | * gnu/packages/machine-learning.scm (r-adaptivesparsity): New variable.
* gnu: Add r-rcpparmadillo.Ricardo Wurmus2015-12-212-0/+54
| | | | | * gnu/packages/maths.scm (armadillo-for-rcpparmadillo): New variable. * gnu/packages/statistics.scm (r-rcpparmadillo): New variable.
* gnu: Add armadillo.Ricardo Wurmus2015-12-211-0/+29
| | | | * gnu/packages/maths.scm (armadillo): New variable.
* doc: Fix outdated claim about CRAN importer.Ricardo Wurmus2015-12-211-1/+1
| | | | | * doc/guix.texi: The CRAN importer no longer extracts information from the HTML package description but from the package's DESCRIPTION file.
* import: Drop empty list items.Ricardo Wurmus2015-12-211-3/+6
| | | | * guix/import/cran.scm (listify): Remove empty strings from result list.
* http-client: Support basic authentication.Ricardo Wurmus2015-12-211-3/+12
| | | | | * guix/http-client.scm (http-fetch): Add Authorization header to request when the URI contains userinfo.
* gnu: Add libgit2.Ricardo Wurmus2015-12-211-0/+45
| | | | * gnu/packages/version-control.scm (libgit2): New variable.
* gnu: mafft: Update to 7.267.Ben Woodcroft2015-12-211-3/+20
| | | | | | | * gnu/packages/bioinformatics.scm (mafft): Update to 7.267. [arguments]: Don't include mafft-homologs manpage. [inputs]: Add gawk and grep. [propagated-inputs]: Add coreutils.
* gnu: rxvt-unicode: Install the terminal capability data.Mathieu Lirzin2015-12-211-12/+23
| | | | | | | | | | This provides the necessary terminal capability data, which are required by ncurses-based applications. * gnu/packages/xdisorg.scm (rxvt-unicode)[native-inputs]: Add ncurses. [arguments]: Set the destination of the terminfo files. [native-search-path]: New field. Make them automatically available to the user.
* gnu: msmtp: Update to 1.6.3.Efraim Flashner2015-12-211-2/+3
| | | | | * gnu/packages/mail.scm (msmtp): Update to 1.6.3. [inputs]: Add libsecret.
* gnu: claws-mail: Update to 3.13.1.Efraim Flashner2015-12-211-2/+3
| | | | * gnu/packages/mail.scm (claws-mail): Update to 3.13.1.
* gnu: python-cython: Update to 0.23.4.Efraim Flashner2015-12-211-4/+3
| | | | * gnu/packages/python.scm (python-cython): Update to 0.23.4.
* gnu: ruby: Update to 2.2.4.David Thompson2015-12-201-2/+2
| | | | | | This version fixes CVE-2015-7551. * gnu/packages/ruby.scm (ruby): Update to 2.2.4.
* lint: The CPE name of GRUB is "grub2".Ludovic Courtès2015-12-201-0/+1
| | | | | | Reported by Leo Famulari. * guix/scripts/lint.scm (package-name->cpe-name): Add "grub".
* packages: Remove now redundant graph procedures.Ludovic Courtès2015-12-201-61/+0
| | | | | | | | | These procedures are now redundant with those in (guix graph) and are no longer used since commit a51cbecb. * gnu/packages.scm (vhash-refq, package-dependencies) (package-direct-dependents, package-transitive-dependents) (package-covering-dependents): Remove.
* profiles: Honor search paths of propagated inputs.Ludovic Courtès2015-12-202-1/+10
| | | | | | | | | | Fixes <http://bugs.gnu.org/22073>. Reported by Federico Beffa <beffa@ieee.org>. * guix/profiles.scm (package->manifest-entry): Use 'package-transitive-native-search-paths' when computing 'search-paths' field. * tests/profiles.scm ("package->manifest-entry, search paths"): New test.
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