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* doc: Improve Info categories.Ludovic Courtès2016-03-03
| | | | | | * doc/guix.texi: Change main category to "System administration". Fix syntax of subnodes. Add entries for 'guix pull' and 'guix gc'. Add "Emacs" category.
* build: Use (guix grafts) as needed.Ludovic Courtès2016-03-03
| | | | | | | This is a followup to 7adf9b8. * build-aux/check-final-inputs-self-contained.scm: Use (guix grafts). * build-aux/check-available-binaries.scm: Likewise.
* gnu: youtube-dl: Update to 2016.03.01.Efraim Flashner2016-03-03
| | | | * gnu/packages/video.scm (youtube-dl): Update to 2016.03.01.
* gnu: mpv: Update to 0.16.0.Efraim Flashner2016-03-03
| | | | * gnu/packages/video.scm (mpv): Update to 0.16.0.
* gnu: perl: Replace with patched version [fixes CVE-2016-2381].Leo Famulari2016-03-03
| | | | | | | | * gnu/packages/patches/perl-CVE-2016-2381.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/perl.scm (perl)[replacement]: New field. (perl-fixed): New variable. * gnu/packages/commencement.scm (perl-boot0)[replacement]: New field.
* gnu: irssi: Support proxy, socks, bot.Efraim Flashner2016-03-03
| | | | | * gnu/packages/irc.scm (irssi)[arguments]: Add configure flags to support proxy, socks and bot.
* gnu: irssi: Update to 0.8.18.Efraim Flashner2016-03-03
| | | | | * gnu/packages/irc.scm (irssi): Update to 0.8.18. [source]: Update uri.
* build: Build (guix import github) only when Guile-JSON is available.Ludovic Courtès2016-03-03
| | | | | | | Reported by Justus Winter <justus@gnupg.org>. * Makefile.am (MODULES): Add guix/import/github.scm only when HAVE_GUILE_JSON.
* po: Drop removed file 'weechat.scm'.Justus Winter2016-03-03
| | | | | | | | | Fixes <http://bugs.gnu.org/22888>. weechat has been merged into 'irc.scm' in e288f007. * po/packages/POTFILES.in: Drop removed file 'weechat.scm'. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* system: GRUB menu entry says "beta" instead of "alpha"Petter2016-03-03
| | | | | | * gnu/system.scm (kernel->grub-label): Change "alpha" to "beta'. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* system: Add rfkill to '%base-packages'.Ludovic Courtès2016-03-03
| | | | * gnu/system.scm (%base-packages): Add RFKILL.
* gnu: python-pysam: Move cython and setuptools to native inputs.Ricardo Wurmus2016-03-03
| | | | | | * gnu/packages/bioinformatics.scm (python-pysam)[inputs]: Move "python-cython" and "python-setuptools" from here... [native-inputs]: ... to here.
* gnu: deeptools: Update to 2.1.1.Ricardo Wurmus2016-03-03
| | | | | * gnu/packages/bioinformatics.scm (deeptools): Update to 2.1.1. [inputs]: Add "python2-numpydoc" and "python2-pybigwig".
* gnu: deeptools: Change "propagated-inputs" to "inputs".Ricardo Wurmus2016-03-03
| | | | | | * gnu/packages/bioinformatics.scm (deeptools)[propagated-inputs]: Move all inputs from here... [inputs]: ...to here.
* gnu: Add python-pybigwig.Ricardo Wurmus2016-03-03
| | | | | * gnu/packages/bioinformatics.scm (python-pybigwig, python2-pybigwig): New variables.
* gnu: python-pysam: Update to 0.8.4.Ricardo Wurmus2016-03-03
| | | | * gnu/packages/bioinformatics.scm (python-pysam): Update to 0.8.4.
* gnu: python-pysam, python2-pysam: Move to bioinformatics.scm.Ricardo Wurmus2016-03-03
| | | | | | * gnu/packages/python.scm (python-pysam, python2-pysam): Move to... * gnu/packages/bioinformatics.scm (python-pysam, python2-pysam): ...here.
* lint: derivation: Disable grafts, but check replacements.Ludovic Courtès2016-03-03
| | | | | * guix/scripts/lint.scm (check-derivation): Pass #:graft? #f. When 'package-replacement' exists, compute its derivation.
* gnu: Add procmail.Lukas Gradl2016-03-02
| | | | | | | | * gnu/packages/patches/procmail-ambiguous-getline-debian.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/mail.scm (procmail): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
* guix build: -S returns the replacement's source.Ludovic Courtès2016-03-03
| | | | | | | | Reported by Mark H Weaver. * guix/scripts/build.scm (options->derivations): When SRC and GRAFT? are true, use the source of P's replacement. * tests/guix-build.sh: Add test.
* hydra: Completely disable grafting.Ludovic Courtès2016-03-03
| | | | | * build-aux/hydra/gnu-system.scm (hydra-jobs): Parameterize '%graft?'. Build package replacements when they are available.
* hydra: Improve readability.Ludovic Courtès2016-03-03
| | | | | * build-aux/hydra/gnu-system.scm (hydra-jobs): Use 'filter-map' instead of directly 'fold-packages'.
* utils: Use '@' for separating package names and version numbers.Mathieu Lirzin2016-03-02
| | | | | | | | | | | | | | | | | | | | | This provides the ability to use numbers in package names. Fixes <http://bugs.gnu.org/19219>. * guix/utils.scm (package-name->name+version): New procedure. * gnu/packages.scm (%find-package): Add a FALLBACK? keyword argument. Use the previous method when no package is found. (specification->package+output, specification->package): Adapt documentation to new syntax. * doc/guix.texi (Invoking guix package, Invoking guix import): Likewise. * guix/ui.scm (package-specification->name+version+output): Likewise. * guix/scripts/import/hackage.scm (show-help): Likewise. * tests/guix-build.sh: Adapt to new syntax. * tests/guix-lint.sh: Likewise. * tests/guix-package.sh: Likewise. * tests/ui.scm ("package-specification->name+version+output"): Likewise. * tests/utils.scm ("package-name->name+version"): Likewise. * NEWS: Mention new syntax.
* packages: Factorize package specification search.Mathieu Lirzin2016-03-02
| | | | | * gnu/packages.scm (%find-package): New procedure. (specification->package, specification->package+output): Use it.
* gnu: icecat: Update bundled graphite2 to 1.3.6 [unspecified security fixes].Mark H Weaver2016-03-02
| | | | | | * gnu/packages/patches/icecat-update-graphite2-pt2.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/gnuzilla.scm (icecat)[source]: Add patch.
* gnu: nss: Update to 3.21.1.Mark H Weaver2016-03-02
| | | | * gnu/packages/gnuzilla.scm (nss): Update to 3.21.1.
* gnu: graphite2: Replace with 1.3.6 [unspecified security fixes].Mark H Weaver2016-03-02
| | | | | | | See <https://bodhi.fedoraproject.org/updates/FEDORA-2016-dec1faadc5> * gnu/packages/fontutils.scm (graphite2)[replacement]: New field. (graphite2-1.3.6): New variable.
* gnu: Add password-store.Jessica Tallon2016-03-02
| | | | | | | * gnu/packages/password-utils.scm (password-store): New variable. Co-authored-by: Andreas Enge <andreas@enge.fr> Co-authored-by: Leo Famulari <leo@famulari.name>
* gnu: Add cppcheck.Roel Janssen2016-03-02
| | | | * gnu/packages/check.scm (cppcheck): New variable.
* tests: Disable grafts by default.Ludovic Courtès2016-03-02
| | | | | | | | | | | Fixes <http://bugs.gnu.org/22872>. Reported by myglc2 <myglc2@gmail.com>. * test-env.in: Define and export 'GUIX_BUILD_OPTIONS'. * tests/guix-build.sh: When setting 'GUIX_BUILD_OPTIONS', make sure it contains '--no-grafts'. * tests/guix-package.sh: Likewise. * tests/guix-daemon.sh: Add (%graft? #f) in Scheme snippets.
* graph: Ignore 'GUIX_BUILD_OPTIONS'.Ludovic Courtès2016-03-02
| | | | | | | | Previously 'GUIX_BUILD_OPTIONS' would be honored, but 'guix graph' does not support the common build options. * guix/scripts/graph.scm (guix-graph): Use 'args-fold*' instead of 'parse-command-line'.
* guix build: Move '--no-grafts' to the common build options.Ludovic Courtès2016-03-02
| | | | | | | | | | | | | | | | * guix/scripts/build.scm (%options): Move --no-grafts to... (%standard-build-options): ... here. (show-help, show-build-options-help): Adjust accordingly. * guix/scripts/archive.scm (%default-options): Add 'graft?'. (guix-archive): Parametrize '%graft?'. * guix/scripts/environment.scm (%default-options): Add 'graft?'. (guix-environment): Parametrize '%graft?'. * guix/scripts/package.scm (%default-options): Add 'graft?'. (guix-package): Parametrize '%graft?'. * guix/scripts/system.scm (%default-options): Add 'graft?'. (guix-system): Parametrize 'graft?'. * doc/guix.texi (Additional Build Options): Move --no-grafts to... (Common Build Options): ... here.
* guix archive: Use 'with-store'.Ludovic Courtès2016-03-02
| | | | | * guix/scripts/archive.scm (guix-archive): Use 'with-store' instead of an explicit 'open-connection'.
* gnu: openssl: Enable ssl2 at build time to ensure ABI compatible graft.Mark H Weaver2016-03-02
| | | | | | | | Fixes <https://debbugs.gnu.org/22876> Reported by Christopher Allan Webber <cwebber@dustycloud.org>. * gnu/packages/tls.scm (openssl-1.0.2g)[arguments]: Override the inherited 'configure' phase to add "enable-ssl2" as an argument to ./config.
* gnu: ilmbase: Fix typo in adding a patch.Leo Famulari2016-03-01
| | | | | * gnu-system.am (dist_patch_DATA): Fix typo. 5e8276dcf4e3a05f69176dca816f00616e7f0593
* gnu: xfce: Don't wrap 'startxfce4'.宋文武2016-03-02
| | | | | | | The necessary environment variables are set by 'etc/profile' now. * gnu/packages/xfce.scm (xfce)[build-system]: Use 'trivial-build-system'. [arguments]: Simplify.
* gnu: ilmbase: Add patch to fix build on i686.Leo Famulari2016-03-01
| | | | | | | | Fixes <http://bugs.gnu.org/22049>. * gnu/packages/patches/ilmbase-fix-tests.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/graphics.scm (ilmbase)[source]: Add patch.
* gnu: openssh: Update to 7.2p1.Leo Famulari2016-03-01
| | | | * gnu/packages/ssh.scm (openssh): Update to 7.2p1.
* gnu: libressl: Update to 2.2.6.Leo Famulari2016-03-01
| | | | * gnu/packages/tls.scm (libressl): Update to 2.2.6.
* gnu: parallel: Update to 20160222.Leo Famulari2016-03-01
| | | | * gnu/packages/parallel.scm (parallel): Update to 20160222.
* gnu: r-go-db: Bioconductor changed URL for data downloads.Pjotr Prins2016-03-01
| | | | * gnu/packages/bioinformatics.scm (r-go-db)[source]: Update data URL.
* gnu: r-iranges: Update to 2.4.8.Pjotr Prins2016-03-01
| | | | * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.4.8.
* gnu: r-s4vectors: Update to 0.8.11.Pjotr Prins2016-03-01
| | | | * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.8.11.
* gnu: r-ggplot2: Update to 2.0.0.Pjotr Prins2016-03-01
| | | | * gnu/packages/statistics.scm (r-ggplot2): Update to 2.0.0.
* gnu: openssl: Replace with 1.0.2g [fixes ↵Ludovic Courtès2016-03-01
| | | | | | | | | | | CVE-2016-{0800,0705,0798,0797,0799,0702,0703,0704}]. See <http://openssl.org/news/secadv/20160301.txt>. Also fixes <http://bugs.gnu.org/22831>. * gnu/packages/patches/openssl-c-rehash-in.patch: New file. * gnu/packages/tls.scm (openssl)[replacement]: New field. (openssl-1.0.2g): New variable.
* grafts: Graft recursively.Ludovic Courtès2016-03-01
| | | | | | | | | | | | | | | | | | | | | | Fixes <http://bugs.gnu.org/22139>. * guix/grafts.scm (graft-derivation): Rename to... (graft-derivation/shallow): ... this. (graft-origin-file-name, item->deriver, non-self-references) (cumulative-grafts, graft-derivation): New procedures * tests/grafts.scm ("graft-derivation, grafted item is a direct dependency"): Clarify title. Use 'grafted' instead of 'graft' to refer to the grafted derivation. ("graft-derivation, grafted item is an indirect dependency") ("graft-derivation, no dependencies on grafted output"): New tests. * guix/packages.scm (input-graft): Change to take a package instead of an input. (input-cross-graft): Likewise. (fold-bag-dependencies): New procedure. (bag-grafts): Rewrite in terms of 'fold-bag-dependencies'. * tests/packages.scm ("package-derivation, indirect grafts"): Comment out. * doc/guix.texi (Security Updates): Mention run-time dependencies and recursive grafting.
* gnu: tiled: Use 'modify-phases'.Efraim Flashner2016-03-01
| | | | * gnu/packages/game-development.scm (tiled)[arguments]: Use 'modify-phases'.
* gnu: tiled: Update to 0.15.1.Efraim Flashner2016-03-01
| | | | * gnu/packages/game-development.scm (tiled): Update to 0.15.1.
* gnu: Add PePr.Ricardo Wurmus2016-03-01
| | | | * gnu/packages/bioinformatics.scm (pepr): New variable.
* gnu: Add bwa-pssm.Ricardo Wurmus2016-03-01
| | | | * gnu/packages/bioinformatics.scm (bwa-pssm): New variable.
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