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2016-01-14gnu: r-go-db: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-go-db)[propagated-inputs]: Add "r-annotationdbi".
2016-01-14gnu: r-sparsem: Add missing "gfortran" input.Ricardo Wurmus
* gnu/packages/statistics.scm (r-sparsem)[inputs]: Add "gfortran".
2016-01-14gnu: bowtie: Update to 2.2.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bowtie): Update to 2.2.6. [source]: Remove patch; do not set CC and CPP variables. [inputs]: Add "tbb". [arguments]: Pass "prefix" and "WITH_TBB" make flags; remove custom "install" phase. * gnu/packages/patches/bowtie-fix-makefile.patch: Remove file. * gnu-system.am (dist_patch_DATA): Remove patch file.
2016-01-14gnu: gnupg: Add TOFU support.Efraim Flashner
* gnu/packages/gnupg.scm (gnupg)[inputs]: Add sqlite.
2016-01-14import: gem: Beautify description field.Ben Woodcroft
* guix/import/gem.scm (gem->guix-package): Use 'beautify-description'.
2016-01-14import: cran: Move beautify-description to utils module.Ben Woodcroft
* guix/import/cran.scm (beautify-description): Move from here... * guix/import/utils.scm: ... to here.
2016-01-14emacs: Fix heading face in "Package Info".Alex Kost
Reported by Ludovic Courtès <ludo@gnu.org> on #guix. This fixes a regression introduced in commit 7171d824. 'insert-text-button' procedure does not allow to override a button face, so a specialized button type should be used instead. * emacs/guix-ui-package.el (guix-package-heading): New button type. (guix-package-info-insert-heading): Use it.
2016-01-14gnu: orfm: Update to 0.5.3.Ben Woodcroft
* gnu/packages/bioinformatics.scm (orfm): Update to 0.5.3. [native-inputs]: Add inputs required for tests. [description]: Add commas.
2016-01-14gnu: Add ruby-bio-commandeer.Ben Woodcroft
* gnu/packages/ruby.scm (ruby-bio-commandeer): New variable.
2016-01-14gnu: Add ruby-systemu.Ben Woodcroft
* gnu/packages/ruby.scm (ruby-systemu): New variable.
2016-01-13hydra: Add missing phase and inputs for 'make dist' job.Ludovic Courtès
* build-aux/hydra/guix.scm (tarball-package): Inherit from 'guix-devel' rather than 'guix'. Pass #:phases to 'dist-package'.
2016-01-13build-system/gnu: 'dist-package' can be passed the phases.Ludovic Courtès
* guix/build-system/gnu.scm (dist-package): Add #:phases parameter and honor it.
2016-01-13monad-repl: Close connection when leaving the monad REPL.Ludovic Courtès
* guix/monad-repl.scm (store-monad-language): Add 'store' parameter and use it. Remove call to 'open-connection'. (enter-store-monad): Use 'with-store' and pass the store to 'store-monad-language.
2016-01-13gnu: julia: Update to 0.4.3.Ricardo Wurmus
* gnu/packages/julia.scm (julia): Update to 0.4.3. (libuv-julia): Update to 07730c4bd595.
2016-01-13emacs: Move loading packages to "guix-emacs.el".Alex Kost
* emacs/guix-init.el: Move the code for auto-loading Emacs packages to... (guix-package-enable-at-startup): Move to... * emacs/guix-emacs.el (guix-package-enable-at-startup): ... here.
2016-01-13emacs: Make "guix-emacs.el" independent.Alex Kost
"guix-emacs.el" may be used just for "instructing" Emacs where to find Emacs packages installed with Guix, so it should have as few dependencies as possible. See <http://lists.gnu.org/archive/html/guix-devel/2016-01/msg00022.html>. * emacs/guix-emacs.el: Require 'guix-profiles' optionally. (guix-emacs-load-autoloads): Use 'guix-profile-prompt' only if it is available.
2016-01-13emacs: Complete --file in 'guix build' popup.Alex Kost
* emacs/guix-command.el (guix-command-improve-build-argument): Use 'guix-read-file-name' to complete --file option.
2016-01-13emacs: Add missing shell completions.Alex Kost
* emacs/guix-pcomplete.el (guix-pcomplete-complete-option-arg): Complete file name for '--install-from-file' option of 'guix package' command, and for '--file' and '--with-source' options of 'guix build' command.
2016-01-13gnu: isc-dhcp: Update to 4.3.3-P1 [fixes CVE-2015-8605].Mark H Weaver
* gnu/packages/admin.scm (isc-dhcp): Update to 4.3.3-P1.
2016-01-13gnu: samtools: Update to 1.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (samtools): Update to 1.3. [arguments]: Enable tests for all architectures; set ncurses in configure-flags instead of make-flags; simplify "patch-tests" phase; restore "configure" phase.
2016-01-13build: Use 127 as the Linux hash-bang limit.Ludovic Courtès
Reported by taylanbayirli@gmail.com (Taylan Ulrich Bayırlı/Kammer). * m4/guix.m4 (LINUX_HASH_BANG_LIMIT): Set to 127.
2016-01-13gnu: skribilo: Update to 0.9.3.Ludovic Courtès
* gnu/packages/skribilo.scm (skribilo): Update to 0.9.3. [native-inputs]: New field.
2016-01-12doc: Fix typo in "Build Systems".Leo Famulari
* doc/guix.texi (Build Systems): Remove extra 's'.
2016-01-12gnu: boost: Update to 1.60.0.Eric Bavier
* 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.
2016-01-12gnu: boost: Use modify-phases.Eric Bavier
* gnu/packages/boost.scm (boost)[arguments]: Use modify-phases.
2016-01-12build: 'make check' errors out if file name limits would be hit.Ludovic Courtès
* 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.
2016-01-12build: Warn against long hash bang lines for tests.Ludovic Courtès
* 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.
2016-01-12doc: Show bootstrapping at the package level.Ludovic Courtès
* 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.
2016-01-12gnu: sudo: Add fix for CVE-2015-5602.Mark H Weaver
* 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.
2016-01-12gnu: global: Use modify-phases syntax.Efraim Flashner
* gnu/packages/code.scm (global)[arguments]: Use modify-phases syntax.
2016-01-12gnu: global: Update to 6.5.2.Efraim Flashner
* gnu/packages/code.scm (global): Update to 6.5.2.
2016-01-12gnu: icedtea-6: Fix directory name in "unpack" phase.Ricardo Wurmus
* gnu/packages/java.scm (icedtea-6)[arguments]: Change the directory prefix in the "unpack" phase to "icedtea6-".
2016-01-11gnu: linux-libre: Update to 4.4.Mark H Weaver
* 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>.
2016-01-12gnu: Add fxtract.Ben Woodcroft
* gnu/packages/bioinformatics.scm (fxtract): New variable.
2016-01-11gnu: youtube-dl: Update to 2016.01.09.Efraim Flashner
* gnu/packages/video.scm (youtube-dl): Update to 2016.01.09.
2016-01-11gnu: gp2c: Update to 0.0.9pl5.Andreas Enge
* gnu/packages/algebra.scm (gp2c): Update to 0.0.9pl5.
2016-01-11gnu: texlive: Use modify-phases syntax.Andreas Enge
* gnu/packages/texlive.scm (texlive-bin, texlive-texmf): Use modify-phases syntax.
2016-01-11gnu: man-pages: Update to 4.04.Efraim Flashner
* gnu/packages/man.scm (man-pages): Update to 4.04. [source]: Add alternate location.
2016-01-10build: Fix out-of-tree building of documentation.Taylan Ulrich Bayırlı/Kammer
* doc.am (.dot.png, .dot.pdf, .dot.eps): Put the generated files into $(srcdir).
2016-01-11gnu: bedtools: Update to 2.25.0.Ben Woodcroft
* 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.
2016-01-11gnu: bedtools: Use modify-phases.Ben Woodcroft
* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use modify-phases.
2016-01-09gnu: r: Update to 3.2.3.Andreas Enge
* gnu/packages/statistics.scm (r): Update to 3.2.3.
2016-01-09gnu: icecat: Update to 38.5.2-gnu1.Andreas Enge
* gnu/packages/gnuzilla.scm (icecat): Update to 38.5.2-gnu1.
2016-01-09gnu: ruby-2.1: Update to 2.1.8.Ben Woodcroft
* gnu/packages/ruby.scm (ruby-2.1): Update to 2.1.8.
2016-01-08gnu: i2c-tools: Update source and home-page URLs.Leo Famulari
* gnu/packages/linux.scm (i2c-tools)[source]: Update URL. [home-page]: Update URL.
2016-01-08gnu: lm-sensors: Update source and home-page URLs.Leo Famulari
* gnu/packages/linux.scm (lm-sensors)[source]: Update URL. [home-page]: Update URL.
2016-01-08gnu: nss: Update to 3.21 [fixes CVE-2015-7575].Mark H Weaver
* 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.
2016-01-08build-system/python: 'pypi-uri' takes an optional file name extension.Ludovic Courtès
Suggested by swedebugia <swedebugia@riseup.net>. * guix/build-system/python.scm (pypi-uri): Add 'extension' parameter and use it.
2016-01-08gnu: Add missing (gnu packages gcc) import.Mathieu Lirzin
* gnu/packages/bioinformatics.scm: Use (gnu packages gcc). This is required by 'r-impute' for 'gfortran'.
2016-01-08gnu: xterm: Update to 322.Mathieu Lirzin
* gnu/packages/xorg.scm (xterm): Update to 322.
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