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2016-03-03gnu: Add python-pybigwig.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pybigwig, python2-pybigwig): New variables.
2016-03-03gnu: python-pysam: Update to 0.8.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.8.4.
2016-03-03gnu: python-pysam, python2-pysam: Move to bioinformatics.scm.Ricardo Wurmus
* gnu/packages/python.scm (python-pysam, python2-pysam): Move to... * gnu/packages/bioinformatics.scm (python-pysam, python2-pysam): ...here.
2016-03-03lint: derivation: Disable grafts, but check replacements.Ludovic Courtès
* guix/scripts/lint.scm (check-derivation): Pass #:graft? #f. When 'package-replacement' exists, compute its derivation.
2016-03-02gnu: Add procmail.Lukas Gradl
* 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>
2016-03-03guix build: -S returns the replacement's source.Ludovic Courtès
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.
2016-03-03hydra: Completely disable grafting.Ludovic Courtès
* build-aux/hydra/gnu-system.scm (hydra-jobs): Parameterize '%graft?'. Build package replacements when they are available.
2016-03-03hydra: Improve readability.Ludovic Courtès
* build-aux/hydra/gnu-system.scm (hydra-jobs): Use 'filter-map' instead of directly 'fold-packages'.
2016-03-02utils: Use '@' for separating package names and version numbers.Mathieu Lirzin
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.
2016-03-02packages: Factorize package specification search.Mathieu Lirzin
* gnu/packages.scm (%find-package): New procedure. (specification->package, specification->package+output): Use it.
2016-03-02gnu: icecat: Update bundled graphite2 to 1.3.6 [unspecified security fixes].Mark H Weaver
* 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.
2016-03-02gnu: nss: Update to 3.21.1.Mark H Weaver
* gnu/packages/gnuzilla.scm (nss): Update to 3.21.1.
2016-03-02gnu: graphite2: Replace with 1.3.6 [unspecified security fixes].Mark H Weaver
See <https://bodhi.fedoraproject.org/updates/FEDORA-2016-dec1faadc5> * gnu/packages/fontutils.scm (graphite2)[replacement]: New field. (graphite2-1.3.6): New variable.
2016-03-02gnu: Add password-store.Jessica Tallon
* 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>
2016-03-02gnu: Add cppcheck.Roel Janssen
* gnu/packages/check.scm (cppcheck): New variable.
2016-03-02tests: Disable grafts by default.Ludovic Courtès
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.
2016-03-02graph: Ignore 'GUIX_BUILD_OPTIONS'.Ludovic Courtès
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'.
2016-03-02guix build: Move '--no-grafts' to the common build options.Ludovic Courtès
* 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.
2016-03-02guix archive: Use 'with-store'.Ludovic Courtès
* guix/scripts/archive.scm (guix-archive): Use 'with-store' instead of an explicit 'open-connection'.
2016-03-02gnu: openssl: Enable ssl2 at build time to ensure ABI compatible graft.Mark H Weaver
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.
2016-03-01gnu: ilmbase: Fix typo in adding a patch.Leo Famulari
* gnu-system.am (dist_patch_DATA): Fix typo. 5e8276dcf4e3a05f69176dca816f00616e7f0593
2016-03-02gnu: xfce: Don't wrap 'startxfce4'.宋文武
The necessary environment variables are set by 'etc/profile' now. * gnu/packages/xfce.scm (xfce)[build-system]: Use 'trivial-build-system'. [arguments]: Simplify.
2016-03-01gnu: ilmbase: Add patch to fix build on i686.Leo Famulari
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.
2016-03-01gnu: openssh: Update to 7.2p1.Leo Famulari
* gnu/packages/ssh.scm (openssh): Update to 7.2p1.
2016-03-01gnu: libressl: Update to 2.2.6.Leo Famulari
* gnu/packages/tls.scm (libressl): Update to 2.2.6.
2016-03-01gnu: parallel: Update to 20160222.Leo Famulari
* gnu/packages/parallel.scm (parallel): Update to 20160222.
2016-03-01gnu: r-go-db: Bioconductor changed URL for data downloads.Pjotr Prins
* gnu/packages/bioinformatics.scm (r-go-db)[source]: Update data URL.
2016-03-01gnu: r-iranges: Update to 2.4.8.Pjotr Prins
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.4.8.
2016-03-01gnu: r-s4vectors: Update to 0.8.11.Pjotr Prins
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.8.11.
2016-03-01gnu: r-ggplot2: Update to 2.0.0.Pjotr Prins
* gnu/packages/statistics.scm (r-ggplot2): Update to 2.0.0.
2016-03-01gnu: openssl: Replace with 1.0.2g [fixes ↵Ludovic Courtès
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.
2016-03-01grafts: Graft recursively.Ludovic Courtès
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.
2016-03-01gnu: tiled: Use 'modify-phases'.Efraim Flashner
* gnu/packages/game-development.scm (tiled)[arguments]: Use 'modify-phases'.
2016-03-01gnu: tiled: Update to 0.15.1.Efraim Flashner
* gnu/packages/game-development.scm (tiled): Update to 0.15.1.
2016-03-01gnu: Add PePr.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pepr): New variable.
2016-03-01gnu: Add bwa-pssm.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bwa-pssm): New variable.
2016-03-01gnu: Add gdsl.Ricardo Wurmus
* gnu/packages/datastructures.scm (gdsl): New variable.
2016-03-01gnu: weechat: Move to irc.scm.Efraim Flashner
* gnu/packages/weechat.scm (weechat): Move from here ... * gnu/packages/irc.scm (weechat): ... to here. * gnu/packages/weechat.scm: Delete file. * gnu-system.am (GNU_SYSTEM_MODULES): Remove weechat.scm.
2016-03-01gnu: irssi: Use 'modify-phases'.Efraim Flashner
* gnu/packages/irc.scm (irssi)[arguments]: Use 'modify-phases'.
2016-03-01gnu: irssi: Move to irc.scm.Efraim Flashner
* gnu/packages/irssi.scm (irssi): Move from here ... * gnu/packages/irc.scm (irssi): ... to here. * gnu/packages/irssi.scm: Delete file. * gnu-system.am (GNU_SYSTEM_MODULES): Remove irssi.scm.
2016-03-01gnu: Add quassel.Efraim Flashner
* gnu/packages/irc.scm: New file. * gnu-system.am (GNU_SYSTEM_MODULES): Register it.
2016-03-01gnu: Add snorenotify.Efraim Flashner
* gnu/packages/kde.scm (snorenotify): New variable.
2016-03-01gnu: Add qca.Efraim Flashner
* gnu/packages/kde.scm: New file. * gnu-system.am (GNU_SYSTEM_MODULES): Register it.
2016-03-01gnu: Add oxygen-icons.Efraim Flashner
* gnu/packages/kde-frameworks.scm (oxygen-icons): New variable.
2016-02-29gnu: Add desmume.Manolis Ragkousis
* gnu/packages/games.scm (desmume): New variable.
2016-02-29gnu: curl: Use updated libssh2 [fixes CVE-2016-7087].Mark H Weaver
* gnu/packages/curl.scm (curl)[inputs]: Use libssh2. * gnu/packages/ssh.scm (libssh2-1.4): Remove variable.
2016-02-29gnu: Remove python2-pil.Christopher Allan Webber
python2-pil is vulnerable to several security issues (CVE-2016-0740, CVE-2016-0775, and CVE-2016-2533). Fortunately, python2-pillow provides equivalent functionality, so this package can be cleanly removed. * gnu/packages/python.scm (python2-pil): Remove variable.
2016-02-29gnu: guile-for-guile-emacs: Use guile-2.0 search paths.Ricardo Wurmus
* gnu/packages/guile.scm (guile-for-guile-emacs)[native-search-paths]: Use the same search paths as guile-2.0.
2016-02-28gnu: msmtp: Install msmtpq.Leo Famulari
* gnu/packages/mail.scm (msmtp)[arguments]: Install msmtpq scripts.
2016-02-28gnu: git: Install symlinks instead of hard links.Ludovic Courtès
This reduces nar size by a factor of 10. Fixes <http://bugs.gnu.org/21949>. * gnu/packages/version-control.scm (git)[arguments]: Pass NO_INSTALL_HARDLINKS as #:make-flags.
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