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2016-01-12gnu: boost: Update to 1.60.0.•••* gnu/packages/boost.scm (boost): Update to 1.60.0. [source]: Remove patch. * gnu/packages/patches/boost-mips-avoid-m32.patch: Delete patch * gnu-system.am (dist_patch_DATA): Remove patch. Also fix dependent packages: * gnu/packages/patches/csound-header-ordering.patch: New patch. * gnu/packages/audio.scm (csound)[source]: Use it. [arguments]: Add 'set-flags phase. * gnu/packages/patches/libcmis-fix-test-onedrive.patch: New patch. * gnu/packages/libreoffice.scm (libcmis)[source]: Use it. (libreoffice)[arguments]: Add LDFLAGS to #:configure-flags. (librevenge)[inputs]: Move boost from here... [propogated-inputs]: to here. [arguments]: Add LDFLAGS to #:configure-flags. * gnu/packages/patches/openimageio-boost-1.60.patch: New patch. * gnu/packages/graphics.scm (openimageio): Use it. * gnu-system.am (dist_patch_DATA): Add patches. Eric Bavier
2016-01-12gnu: boost: Use modify-phases.•••* gnu/packages/boost.scm (boost)[arguments]: Use modify-phases. Eric Bavier
2016-01-12build: 'make check' errors out if file name limits would be hit.•••* Makefile.am (SCM_TESTS, SH_TESTS, TESTS, AM_TESTS_ENVIRONMENT) (SCM_LOG_COMPILER, SH_LOG_COMPILER, AM_SCM_LOG_FLAGS) (AM_SH_LOG_FLAGS): Move within 'if CAN_RUN_TESTS'. (check-local) [!CAN_RUN_TESTS]: New target. * daemon.am (AM_TESTS_ENVIRONMENT, TESTS): Ditto. * m4/guix.m4 (GUIX_CHECK_FILE_NAME_LIMITS): Add parameter and set it. Ludovic Courtès
2016-01-12build: Warn against long hash bang lines for tests.•••* m4/guix.m4 (GUIX_TEST_HASH_BANG_LENGTH): New macro. (GUIX_CHECK_FILE_NAME_LIMITS): Use it. Warn against long hash bang lines in tests. Ludovic Courtès
2016-01-12doc: Show bootstrapping at the package level.•••* doc/images/bootstrap-packages.dot: New file. * doc.am (DOT_FILES): Add it. * doc/guix.texi (Bootstrapping): Show 'guix graph' commands. Includes 'images/bootstrap-packages' and comment it. Ludovic Courtès
2016-01-12gnu: sudo: Add fix for CVE-2015-5602.•••* gnu/packages/patches/sudo-CVE-2015-5602.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/admin.scm (sudo)[source]: Add patch. Mark H Weaver
2016-01-12gnu: global: Use modify-phases syntax.•••* gnu/packages/code.scm (global)[arguments]: Use modify-phases syntax. Efraim Flashner
2016-01-12gnu: global: Update to 6.5.2.•••* gnu/packages/code.scm (global): Update to 6.5.2. Efraim Flashner
2016-01-12gnu: icedtea-6: Fix directory name in "unpack" phase.•••* gnu/packages/java.scm (icedtea-6)[arguments]: Change the directory prefix in the "unpack" phase to "icedtea6-". Ricardo Wurmus
2016-01-11gnu: linux-libre: Update to 4.4.•••* gnu/packages/linux.scm (linux-libre): Update to 4.4. * gnu/packages/linux-libre-i686.conf, gnu/packages/linux-libre-x86_64.conf: Update from <https://jxself.org/git/kernel-configs.git>. Mark H Weaver
2016-01-12gnu: Add fxtract.•••* gnu/packages/bioinformatics.scm (fxtract): New variable. Ben Woodcroft
2016-01-11gnu: youtube-dl: Update to 2016.01.09.•••* gnu/packages/video.scm (youtube-dl): Update to 2016.01.09. Efraim Flashner
2016-01-11gnu: gp2c: Update to 0.0.9pl5.•••* gnu/packages/algebra.scm (gp2c): Update to 0.0.9pl5. Andreas Enge
2016-01-11gnu: texlive: Use modify-phases syntax.•••* gnu/packages/texlive.scm (texlive-bin, texlive-texmf): Use modify-phases syntax. Andreas Enge
2016-01-11gnu: man-pages: Update to 4.04.•••* gnu/packages/man.scm (man-pages): Update to 4.04. [source]: Add alternate location. Efraim Flashner
2016-01-10build: Fix out-of-tree building of documentation.•••* doc.am (.dot.png, .dot.pdf, .dot.eps): Put the generated files into $(srcdir). Taylan Ulrich Bayırlı/Kammer
2016-01-11gnu: bedtools: Update to 2.25.0.•••* gnu/packages/bioinformatics.scm (bedtools): Update to 0.25.0. [source]: Remove patch merged upstream. [arguments]: Use 'modify-phases'. Remove 'patch-makefile-SHELL-definition' phase. * gnu/packages/patches/bedtools-32bit-compilation.patch: Remove file. * gnu-system.am (dist_patch_DATA): Remove it. Ben Woodcroft
2016-01-11gnu: bedtools: Use modify-phases.•••* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use modify-phases. Ben Woodcroft
2016-01-09gnu: r: Update to 3.2.3.•••* gnu/packages/statistics.scm (r): Update to 3.2.3. Andreas Enge
2016-01-09gnu: icecat: Update to 38.5.2-gnu1.•••* gnu/packages/gnuzilla.scm (icecat): Update to 38.5.2-gnu1. Andreas Enge
2016-01-09gnu: ruby-2.1: Update to 2.1.8.•••* gnu/packages/ruby.scm (ruby-2.1): Update to 2.1.8. Ben Woodcroft
2016-01-08gnu: i2c-tools: Update source and home-page URLs.•••* gnu/packages/linux.scm (i2c-tools)[source]: Update URL. [home-page]: Update URL. Leo Famulari
2016-01-08gnu: lm-sensors: Update source and home-page URLs.•••* gnu/packages/linux.scm (lm-sensors)[source]: Update URL. [home-page]: Update URL. Leo Famulari
2016-01-08gnu: nss: Update to 3.21 [fixes CVE-2015-7575].•••* gnu/packages/gnuzilla.scm (nss): Update to 3.21. [arguments]: In configure phase, setenv CC=gcc. * gnu/packages/patches/nss-pkgconfig.patch: Adapt to NSS 3.21. Mark H Weaver
2016-01-08build-system/python: 'pypi-uri' takes an optional file name extension.•••Suggested by swedebugia <swedebugia@riseup.net>. * guix/build-system/python.scm (pypi-uri): Add 'extension' parameter and use it. Ludovic Courtès
2016-01-08gnu: Add missing (gnu packages gcc) import.•••* gnu/packages/bioinformatics.scm: Use (gnu packages gcc). This is required by 'r-impute' for 'gfortran'. Mathieu Lirzin
2016-01-08gnu: xterm: Update to 322.•••* gnu/packages/xorg.scm (xterm): Update to 322. Mathieu Lirzin
2016-01-08gnu: epiphany: Update to 3.18.2.•••* gnu/packages/gnome.scm (epiphany): Update to 3.18.2. 宋文武
2016-01-08gnu: webkitgtk: Update to 2.10.4.•••* gnu/packages/webkit.scm (webkitgtk): Update to 2.10.4. 宋文武
2016-01-08doc: Document network-manager-service.•••* doc/guix.texi (Networking Services): Document network-manager-service. 宋文武
2016-01-08doc: Add elaborate package search example.•••* doc/guix.texi (Invoking guix package): Add elaborate --search example using recsel and sexes. Ludovic Courtès
2016-01-07gnu: Add Pfff.•••* gnu/packages/textutils.scm (pfff): New variable. Pjotr Prins
2016-01-07gnu: mpv: Remove 'samba' input.•••This is a heavy-weight and uncommon feature. See <http://lists.gnu.org/archive/html/guix-devel/2015-12/msg00701.html>. * gnu/packages/video.scm (mpv)[inputs]: Remove 'samba'. Alex Kost
2016-01-07emacs: Display supported systems in "Package Info".•••* emacs/guix-main.scm (%package-param-alist): Add 'systems'. * emacs/guix-ui-package.el (guix-package-info-insert-systems): New procedure. (guix-package-info-format): Add it. (guix-output-info-format): Likewise. (guix-package-info-titles): Add "Supported systems" title. Alex Kost
2016-01-07gnu: Add genomation.•••* gnu/packages/bioinformatics.scm (r-genomation): New variable. Ricardo Wurmus
2016-01-07gnu: Add seqPattern.•••* gnu/packages/bioinformatics.scm (r-seqpattern): New variable. Ricardo Wurmus
2016-01-07gnu: Add impute.•••* gnu/packages/bioinformatics.scm (r-impute): New variable. Ricardo Wurmus
2016-01-07gnu: Add BSgenome.•••* gnu/packages/bioinformatics.scm (r-bsgenome): New variable. Ricardo Wurmus
2016-01-07gnu: Add plotly.•••* gnu/packages/statistics.scm (r-plotly): New variable. Ricardo Wurmus
2016-01-07gnu: Add viridis.•••* gnu/packages/statistics.scm (r-viridis): New variable. Ricardo Wurmus
2016-01-07gnu: Add topGO.•••* gnu/packages/bioinformatics.scm (r-topgo): New variable. Ricardo Wurmus
2016-01-07gnu: Add matrixStats.•••* gnu/packages/statistics.scm (r-matrixstats): New variable. Ricardo Wurmus
2016-01-07gnu: Add R.rsp.•••* gnu/packages/statistics.scm (r-r-rsp): New variable. Ricardo Wurmus
2016-01-07gnu: Add R.cache.•••* gnu/packages/statistics.scm (r-r-cache): New variable. Ricardo Wurmus
2016-01-07gnu: Add R.utils.•••* gnu/packages/statistics.scm (r-r-utils): New variable. Ricardo Wurmus
2016-01-07gnu: Add R.oo.•••* gnu/packages/statistics.scm (r-r-oo): New variable. Ricardo Wurmus
2016-01-07gnu: Add R.methodsS3.•••* gnu/packages/statistics.scm (r-r-methodss3): New variable. Ricardo Wurmus
2016-01-07gnu: Add base64enc.•••* gnu/packages/statistics.scm (r-base64enc): New variable. Ricardo Wurmus
2016-01-07gnu: Add DT.•••* gnu/packages/statistics.scm (r-dt): New variable. Ricardo Wurmus
2016-01-07gnu: Add SparseM.•••* gnu/packages/statistics.scm (r-sparsem): New variable. Ricardo Wurmus
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