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2016-01-25gnu: Add sortmerna.•••* gnu/packages/bioinformatics.scm (sortmerna): New variable. Ben Woodcroft
2016-01-24doc: Fix typo in section on offloading.•••* doc/guix.texi (Daemon Offload Setup): Fix quoting typo in command. Andreas Enge
2016-01-24gnu: calibre: Update to 2.49.0.•••* gnu/packages/ebook.scm (calibre): Update to 2.49.0. Andreas Enge
2016-01-24gnu: cross-gcc-arguments: Enable C++, disable building of libstdc++-v3.•••* gnu/packages/cross-base.scm (cross-gcc-arguments)[arguments]: Disable building libstdc++-v3 and enable building C++ compiler. Ricardo Wurmus
2016-01-24gnu: Add Qtractor.•••* gnu/packages/music.scm (qtractor): New variable. Ricardo Wurmus
2016-01-24gnu: yoshimi: Update to 1.3.8.2.•••* gnu/packages/music.scm (yoshimi): Update to 1.3.8.2. Ricardo Wurmus
2016-01-24gnu: privoxy: Update to 3.0.24.•••* gnu/packages/tor.scm (privoxy): Update to 3.0.24. Efraim Flashner
2016-01-24gnu: tor: Update to 0.2.7.6.•••* gnu/packages/tor.scm (tor): Update to 0.2.7.6. Efraim Flashner
2016-01-24gnu: myrepos: Update to 1.20160123.•••* gnu/packages/version-control.scm (myrepos): Update to 1.20160123. Efraim Flashner
2016-01-24gnu: nano: Update to 2.5.1.•••* gnu/packages/nano.scm (nano): Update to 2.5.1. Efraim Flashner
2016-01-23build: container: Make 'unprivileged-user-namespace-supported?' more robust.•••* gnu/build/linux-container.scm (unprivileged-user-namespace-supported?): Only read and check the first character, to cope with a possible newline in the (pseudo-)file. Mark H Weaver
2016-01-23gnu: letsencrypt and acme: Update to 0.2.0.•••These packages should be updated together. * gnu/packages/tls.scm (letsencrypt): Update to 0.2.0. (acme): Update to 0.2.0. Leo Famulari
2016-01-23gnu: claws-mail: Update to 3.13.2.•••* gnu/packages/mail.scm (claws-mail): Update to 3.13.2. Efraim Flashner
2016-01-23gnu: Add cufflinks.•••* gnu/packages/bioinformatics.scm (cufflinks): New variable. Ricardo Wurmus
2016-01-23gnu: Add TopHat.•••* gnu/packages/bioinformatics.scm (tophat): New variable. * gnu/packages/patches/tophat-build-with-later-seqan.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. Ricardo Wurmus
2016-01-23gnu: star: Update to 2.5.1b.•••* gnu/packages/bioinformatics.scm (star): Update to 2.5.1b. [source]: Remove bundled htslib sources and pre-built binaries. [arguments]: Add phase "do-not-use-bundled-htslib". [inputs]: Add "htslib". Ricardo Wurmus
2016-01-23gnu: star: Use "modify-phases" syntax.•••* gnu/packages/bioinformatics.scm (star)[arguments]: Use "modify-phases" syntax. Ricardo Wurmus
2016-01-22gnu: fuse: Update to 2.9.5 [fixes CVE-2016-1233].•••* gnu/packages/linux.scm (fuse): Update to 2.9.5. Efraim Flashner
2016-01-21gnu: american-fuzzy-lop: Update to 1.96b.•••* gnu/packages/debug.scm (american-fuzzy-lop): Update to 1.96b. [arguments]: Create symbolic link to custom qemu, rather than copying. Eric Bavier
2016-01-21gnu: american-fuzzy-lop: Fix qemu configure flags.•••Fixes regression introduced in 06da1a6. * gnu/packages/debug.scm (american-fuzzy-lop)[qemu]: Override inherited #:configure-flags. Eric Bavier
2016-01-21gnu: Add iftop.•••* gnu/packages/admin.scm (iftop): New variable. Leo Famulari
2016-01-21Revert "gnu: Add iftop."•••This reverts commit 45da8c6dd10c93280277d17463d09fce6a25afe9. Leo Famulari
2016-01-21gnu: Add iftop.•••* gnu/packages/admin.scm (iftop): New variable. Leo Famulari
2016-01-22tests: Prevent 'http_proxy' from breaking Web server tests.•••* tests/lint.scm: Add call to 'unsetenv' to remove 'http_proxy'. * tests/publish.scm: Likewise. Ludovic Courtès
2016-01-22doc: Fix typo in "Locales".•••* doc/guix.texi (Locales): Add missing 's'. Ludovic Courtès
2016-01-22system: grub: Search root device by label or UUID if possible.•••Fixes <http://bugs.gnu.org/22281>. Reported by Christopher Allan Webber <cwebber@dustycloud.org>. * gnu/system/grub.scm (eye-candy): Add 'root-fs' parameter. Replace 'search --file' command in the output with whatever 'grub-root-search' returns. (grub-root-search): New procedure. (grub-configuration-file): Add 'store-fs' parameter. Use 'grub-root-search' instead of hard-coded 'search --file' commands. * gnu/system.scm (store-file-system, operating-system-store-file-system): New procedures. (operating-system-grub.cfg): Use it, and adjust call to 'grub-configuration-file'. * tests/system.scm: New file. * Makefile.am (SCM_TESTS): Add it. Ludovic Courtès
2016-01-21gnu: ffmpeg: Update to 2.8.5.•••* gnu/packages/video.scm (ffmpeg): Update to 2.8.5. Mark H Weaver
2016-01-21gnu: gajim: Update to 0.16.5 [fixes CVE-2015-8688].•••* gnu/packages/messaging.scm (gajim): Update to 0.16.5. [arguments]: Disable tests. Mark H Weaver
2016-01-21gnu: bind-utils: Build and install "nsupdate".•••* gnu/packages/dns.scm (bind-utils)[arguments]: Build and install "nsupdate" executable. Ricardo Wurmus
2016-01-21gnu: bind-utils: Generalize "build" and "install" phases.•••* gnu/packages/dns.scm (bind-utils)[arguments]: Generalize "build" and "install" phases. Ricardo Wurmus
2016-01-21gnu: bind-utils: Use "modify-phases" syntax.•••* gnu/packages/dns.scm (bind-utils): Use "modify-phases" syntax. Ricardo Wurmus
2016-01-21gnu: r-qtl: Update to 1.38-4.•••* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.38-4. Pjotr Prins
2016-01-21gnu: libxmp: Update to 4.3.10.•••* gnu/packages/audio.scm (libxmp): Update to 4.3.10. Mark H Weaver
2016-01-20gnu: Add NQC.•••* gnu/packages/lego.scm: New file. * gnu-system.am (GNU_SYSTEM_MODULES): Add it. Eric Bavier
2016-01-20gnu: licenses: Add Mozilla Public License 1.0.•••* guix/licenses.scm (mpl1.0): New variable. Eric Bavier
2016-01-20gnu: Add transmission-remote-cli.•••* gnu/packages/bittorrent.scm (transmission-remote-cli): New variable. Leo Famulari
2016-01-21doc: Explain how to make the Info manual visible.•••Suggested by David Thompson <dthompson2@worcester.edu> at <http://bugs.gnu.org/22402>. * doc/guix.texi (Binary Installation): Explain how to make the Info manual visible. Ludovic Courtès
2016-01-21doc: Explain how to remove services from a list.•••Suggested by <swedebugia@riseup.net>. * doc/guix.texi (Using the Configuration System): Add @unnumberedsubsubsec. Explain how to remove services from a list. Mention (gnu system). Ludovic Courtès
2016-01-21services: avahi: Export service type.•••* gnu/services/avahi.scm: Export 'avahi-service-type'. Ludovic Courtès
2016-01-20gnu: isc-dhcp: Update bundled bind to 9.9.8-P3 [fixes CVE-2015-8704].•••* gnu/packages/admin.scm (isc-dhcp): Update bundled bind to 9.9.8-P3. Mark H Weaver
2016-01-20gnu: bind-utils: Update to 9.10.3-P3 [fixes CVE-2015-8704].•••* gnu/packages/dns.scm (bind-utils): Update to 9.10.3-P3. Mark H Weaver
2016-01-20gnu: linux-libre: Add fix for CVE-2016-0728.•••* gnu/packages/patches/linux-libre-CVE-2016-0728.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/linux.scm (linux-libre)[source]: Add patch. Mark H Weaver
2016-01-20gnu: obs: Add support for webcams.•••* gnu/packages/video.scm (obs)[inputs]: Add v4l-utils. David Thompson
2016-01-20gnu: Add v4l-utils.•••* gnu/packages/video.scm (v4l-utils): New variable. David Thompson
2016-01-20gnu: arb: Correct patch.•••* gnu/packages/patches/arb-ldconfig.patch: Correct erroneously committed file. This is a follow-up to commit ffc8f345111566e8336cbb5a77a96973826165d8. Andreas Enge
2016-01-20gnu: arb: Update to 2.8.1.•••* gnu/packages/algebra.scm (arb)[source]: Update to 2.8.1. Add patch. * gnu/packages/patches/arb-ldconfig.patch: New file. * gnu-system.am (dist_patch_DATA): Register patch. Andreas Enge
2016-01-20tests: Move beatify-description tests to import-tests.•••Fixes <http://bugs.gnu.org/22391>. * tests/cran.scm (beautify-description: use double spacing, beautify-description: transform fragment into sentence). Move from here ... * tests/import-utils.scm: ... to here. New file. * Makefile.am (SCM_TESTS): Add import-utils. Ben Woodcroft
2016-01-20import: gem: Beautify only the description, not the synopsis.•••* guix/import/gem.scm (make-gem-sexp): Add synopsis argument. (gem->guix-package): Pass unbeautified synopsis to make-gem-sexp. * tests/gem.scm: Adapt it. Ben Woodcroft
2016-01-20import: Add Bioconductor importer and updater.•••* guix/import/cran.scm (%bioconductor-updater, latest-bioconductor-release, bioconductor-package?): New procedures. (cran->guix-package): Support repositories other than CRAN. (%bioconductor-url, %bioconductor-svn-url): New variables. (description->package): Update signature to distinguish between packages from different repositories. (latest-release): Rename procedure ... (latest-cran-release): ... to this. (cran-package?): Do not assume all R packages are available on CRAN. * tests/cran.scm: Update tests. * guix/scripts/import/cran.scm: Add "--archive" option and default to CRAN. * guix/scripts/refresh.scm (%updaters): Add "%bioconductor-updater". * doc/guix.texi: Document Bioconductor importer and updater. Ricardo Wurmus
2016-01-20gnu: enlightenment: Update to 0.20.3.•••* gnu/packages/enlightenment.scm (enlightenment): Update to 0.20.3. Efraim Flashner
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