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* gnu: icecat: Update to 38.5.0-gnu1.•••* gnu/packages/patches/icecat-CVE-2015-7201-pt1.patch, gnu/packages/patches/icecat-CVE-2015-7201-pt2.patch, gnu/packages/patches/icecat-CVE-2015-7201-pt3.patch, gnu/packages/patches/icecat-CVE-2015-7205.patch, gnu/packages/patches/icecat-CVE-2015-7210.patch, gnu/packages/patches/icecat-CVE-2015-7212.patch, gnu/packages/patches/icecat-CVE-2015-7213-pt1.patch, gnu/packages/patches/icecat-CVE-2015-7213-pt2.patch, gnu/packages/patches/icecat-CVE-2015-7214.patch, gnu/packages/patches/icecat-CVE-2015-7222-pt1.patch, gnu/packages/patches/icecat-CVE-2015-7222-pt2.patch, gnu/packages/patches/icecat-CVE-2015-7222-pt3.patch, gnu/packages/patches/icecat-freetype-2.6.patch: Delete files. * gnu-system.am (dist_patch_DATA): Remove them. * gnu/packages/gnuzilla.scm (icecat): Update to 38.5.0-gnu1. [source]: Remove patches. Mark H Weaver2015-12-2315-1014/+3
* gnu: nss: Update to 3.20.2.•••* gnu/packages/gnuzilla.scm (nss): Update to 3.20.2. Mark H Weaver2015-12-231-2/+2
* gnu: ruby-nokogiri: Upgrade to 1.6.7.1.•••* gnu/packages/ruby.scm (ruby-nokogiri): Upgrade to 1.6.7.1. Ben Woodcroft2015-12-231-3/+3
* gnu: Add ruby-mini-portile-2.•••* gnu/packages/ruby.scm (ruby-mini-portile-2): New variable. Ben Woodcroft2015-12-231-0/+10
* gnu: icedtea7: Update to 2.6.3.•••* gnu/packages/java.scm (icedtea7): Update to 2.6.3. Ricardo Wurmus2015-12-231-9/+9
* gnu: icedtea6: Update to 1.13.9.•••* gnu/packages/java.scm (icedtea6): Update to 1.13.9. Ricardo Wurmus2015-12-231-4/+4
* gnu: libmicrohttpd: Update to 0.9.48.•••* gnu/packages/gnunet.scm (libmicrohttpd): Update to 0.9.48. Efraim Flashner2015-12-221-2/+2
* gnu: parallel: Update to 20151222.•••* gnu/packages/parallel.scm (parallel): Update to 20151222. Efraim Flashner2015-12-221-2/+2
* gnu: sipwitch: Update to 1.9.15.•••* gnu/packages/telephony.scm (sipwitch): Update to 1.9.15. Efraim Flashner2015-12-221-2/+2
* gnu: ucommon: Update to 7.0.0.•••* gnu/packages/telephony.scm (ucommon): Update to 7.0.0. [inputs]: Add gnutls. Efraim Flashner2015-12-221-2/+4
* gnu: isc-dhcp: Disable parallel build.•••* gnu/packages/admin.scm (isc-dhcp)[arguments]: Disable parallel build. Mark H Weaver2015-12-221-1/+2
* gnu: isc-dhcp: Update to 4.3.3; update bundled bind to 9.9.8-P2.•••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. Mark H Weaver2015-12-211-91/+133
* gnu: bind-utils: Update to 9.10.3-P2.•••* gnu/packages/dns.scm (bind-utils): Update to 9.10.3-P2. [source]: Use HTTP URI instead of FTP. Mark H Weaver2015-12-211-3/+3
* file-systems: The 'device' field can be a UUID (bytevector).•••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. Ludovic Courtès2015-12-221-5/+8
* file-systems: Add a 'mount?' field.•••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. Ludovic Courtès2015-12-223-53/+65
* services: Add 'fstab-service-type'.•••* 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. Ludovic Courtès2015-12-222-62/+112
* build: Add bioconductor-uri procedure.•••* guix/build-system/r.scm (bioconductor-uri): New procedure. Ricardo Wurmus2015-12-211-1/+8
* gnu: Add vmpk.•••* gnu/packages/music.scm (vmpk): New variable. Ricardo Wurmus2015-12-211-0/+43
* gnu: Add drumstick.•••* gnu/packages/music.scm (drumstick): New variable. Ricardo Wurmus2015-12-211-0/+47
* gnu: letsencrypt and acme: Update to 0.1.1.•••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. Leo Famulari2015-12-211-8/+6
* gnu: ffmpeg: Update to 2.8.4.•••* gnu/packages/video.scm (ffmpeg): Update to 2.8.4. Efraim Flashner2015-12-211-2/+2
* doc: Be more explicit in example of file-systems configuration.•••* gnu/system/examples/bare-bones.tmpl (file-systems): Change device label. * gnu/system/examples/desktop.tmpl (file-systems): Likewise. Leo Famulari2015-12-212-5/+5
* doc: Explain significance of partition labels.•••* doc/guix.texi (Preparing for Installation): Point out relationship between partition labels and the file-system configuration. Leo Famulari2015-12-211-0/+8
* gnu: grub: Add fix for CVE-2015-8730.•••* gnu/packages/patches/grub-CVE-2015-8370.patch: New file. * gnu-system.am (dist_patch_DATA): Register patch. * gnu/packages/grub.scm: Apply patch. Leo Famulari2015-12-213-1/+49
* gnu: Add GenomicRanges.•••* gnu/packages/bioinformatics.scm (r-genomicranges): New variable. Ricardo Wurmus2015-12-211-0/+28
* gnu: Add XVector.•••* gnu/packages/bioinformatics.scm (r-xvector): New variable. Ricardo Wurmus2015-12-211-0/+37
* gnu: Add GenomeInfoDb.•••* gnu/packages/bioinformatics.scm (r-genomeinfodb): New variable. Ricardo Wurmus2015-12-211-0/+27
* gnu: Add IRanges.•••* gnu/packages/bioinformatics.scm (r-iranges): New variable. Ricardo Wurmus2015-12-211-0/+30
* gnu: Add S4Vectors.•••* gnu/packages/bioinformatics.scm (r-s4vectors): New variable. Ricardo Wurmus2015-12-211-0/+28
* gnu: Add BiocGenerics.•••* gnu/packages/bioinformatics.scm (r-biocgenerics): New variable. Ricardo Wurmus2015-12-211-0/+21
* gnu: Add r-acsnminer.•••* gnu/packages/bioinformatics.scm (r-acsnminer): New variable. Ricardo Wurmus2015-12-211-0/+26
* gnu: Add r-gridextra.•••* gnu/packages/statistics.scm (r-gridextra): New variable. Ricardo Wurmus2015-12-211-0/+25
* gnu: Add r-gtable.•••* gnu/packages/statistics.scm (r-gtable): New variable. Ricardo Wurmus2015-12-211-0/+19
* gnu: Add r-rmarkdown.•••* 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. Ricardo Wurmus2015-12-211-0/+27
* gnu: Add r-catools.•••* gnu/packages/statistics.scm (r-catools): New variable. Ricardo Wurmus2015-12-211-0/+23
* gnu: Add r-bitops.•••* gnu/packages/statistics.scm (r-bitops): New variable. Ricardo Wurmus2015-12-211-0/+18
* gnu: Add AdaptiveSparsity.•••* gnu/packages/machine-learning.scm (r-adaptivesparsity): New variable. Ricardo Wurmus2015-12-211-0/+33
* gnu: Add r-rcpparmadillo.•••* gnu/packages/maths.scm (armadillo-for-rcpparmadillo): New variable. * gnu/packages/statistics.scm (r-rcpparmadillo): New variable. Ricardo Wurmus2015-12-212-0/+54
* gnu: Add armadillo.•••* gnu/packages/maths.scm (armadillo): New variable. Ricardo Wurmus2015-12-211-0/+29
* doc: Fix outdated claim about CRAN importer.•••* doc/guix.texi: The CRAN importer no longer extracts information from the HTML package description but from the package's DESCRIPTION file. Ricardo Wurmus2015-12-211-1/+1
* import: Drop empty list items.•••* guix/import/cran.scm (listify): Remove empty strings from result list. Ricardo Wurmus2015-12-211-3/+6
* http-client: Support basic authentication.•••* guix/http-client.scm (http-fetch): Add Authorization header to request when the URI contains userinfo. Ricardo Wurmus2015-12-211-3/+12
* gnu: Add libgit2.•••* gnu/packages/version-control.scm (libgit2): New variable. Ricardo Wurmus2015-12-211-0/+45
* gnu: mafft: Update to 7.267.•••* 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. Ben Woodcroft2015-12-211-3/+20
* gnu: rxvt-unicode: Install the terminal capability data.•••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. Mathieu Lirzin2015-12-211-12/+23
* gnu: msmtp: Update to 1.6.3.•••* gnu/packages/mail.scm (msmtp): Update to 1.6.3. [inputs]: Add libsecret. Efraim Flashner2015-12-211-2/+3
* gnu: claws-mail: Update to 3.13.1.•••* gnu/packages/mail.scm (claws-mail): Update to 3.13.1. Efraim Flashner2015-12-211-2/+3
* gnu: python-cython: Update to 0.23.4.•••* gnu/packages/python.scm (python-cython): Update to 0.23.4. Efraim Flashner2015-12-211-4/+3
* gnu: ruby: Update to 2.2.4.•••This version fixes CVE-2015-7551. * gnu/packages/ruby.scm (ruby): Update to 2.2.4. David Thompson2015-12-201-2/+2
* lint: The CPE name of GRUB is "grub2".•••Reported by Leo Famulari. * guix/scripts/lint.scm (package-name->cpe-name): Add "grub". Ludovic Courtès2015-12-201-0/+1
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