Justus Winter
8a56a3d7a3
po: Drop removed file 'weechat.scm'.
...
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>
2016-03-03 17:42:47 +01:00
Petter
d0a65256a3
system: GRUB menu entry says "beta" instead of "alpha"
...
* gnu/system.scm (kernel->grub-label): Change "alpha" to "beta'.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-03-03 17:42:47 +01:00
Ludovic Courtès
16cc99610d
system: Add rfkill to '%base-packages'.
...
* gnu/system.scm (%base-packages): Add RFKILL.
2016-03-03 17:42:47 +01:00
Ricardo Wurmus
649e9b3b47
gnu: python-pysam: Move cython and setuptools to native inputs.
...
* gnu/packages/bioinformatics.scm (python-pysam)[inputs]: Move
"python-cython" and "python-setuptools" from here...
[native-inputs]: ... to here.
2016-03-03 13:47:19 +01:00
Ricardo Wurmus
3acb8c857c
gnu: deeptools: Update to 2.1.1.
...
* gnu/packages/bioinformatics.scm (deeptools): Update to 2.1.1.
[inputs]: Add "python2-numpydoc" and "python2-pybigwig".
2016-03-03 13:47:12 +01:00
Ricardo Wurmus
14bda1ff49
gnu: deeptools: Change "propagated-inputs" to "inputs".
...
* gnu/packages/bioinformatics.scm (deeptools)[propagated-inputs]: Move
all inputs from here...
[inputs]: ...to here.
2016-03-03 13:47:02 +01:00
Ricardo Wurmus
69e0e03c36
gnu: Add python-pybigwig.
...
* gnu/packages/bioinformatics.scm (python-pybigwig, python2-pybigwig):
New variables.
2016-03-03 13:46:52 +01:00
Ricardo Wurmus
d454640c38
gnu: python-pysam: Update to 0.8.4.
...
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.8.4.
2016-03-03 13:46:39 +01:00
Ricardo Wurmus
55a9a8c2b9
gnu: python-pysam, python2-pysam: Move to bioinformatics.scm.
...
* gnu/packages/python.scm (python-pysam, python2-pysam): Move to...
* gnu/packages/bioinformatics.scm (python-pysam, python2-pysam):
...here.
2016-03-03 13:46:26 +01:00
Ludovic Courtès
937690f909
lint: derivation: Disable grafts, but check replacements.
...
* guix/scripts/lint.scm (check-derivation): Pass #:graft? #f. When
'package-replacement' exists, compute its derivation.
2016-03-03 09:46:17 +01:00
Lukas Gradl
e90819c40a
gnu: Add procmail.
...
* 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>
2016-03-02 20:44:18 -05:00
Ludovic Courtès
94d609aba8
guix build: -S returns the replacement's source.
...
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.
2016-03-03 00:18:30 +01:00
Ludovic Courtès
49c4fd2aab
hydra: Completely disable grafting.
...
* build-aux/hydra/gnu-system.scm (hydra-jobs): Parameterize '%graft?'.
Build package replacements when they are available.
2016-03-03 00:18:30 +01:00
Ludovic Courtès
f8187bde7f
hydra: Improve readability.
...
* build-aux/hydra/gnu-system.scm (hydra-jobs): Use 'filter-map' instead
of directly 'fold-packages'.
2016-03-03 00:18:30 +01:00
Mathieu Lirzin
1b846da8c3
utils: Use '@' for separating package names and version numbers.
...
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.
2016-03-02 21:41:41 +01:00
Mathieu Lirzin
fad155d47e
packages: Factorize package specification search.
...
* gnu/packages.scm (%find-package): New procedure.
(specification->package, specification->package+output): Use it.
2016-03-02 21:41:41 +01:00
Mark H Weaver
b134a80c36
gnu: icecat: Update bundled graphite2 to 1.3.6 [unspecified security fixes].
...
* 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.
2016-03-02 15:13:15 -05:00
Mark H Weaver
bd009cd95d
gnu: nss: Update to 3.21.1.
...
* gnu/packages/gnuzilla.scm (nss): Update to 3.21.1.
2016-03-02 15:13:14 -05:00
Mark H Weaver
d47ad0890c
gnu: graphite2: Replace with 1.3.6 [unspecified security fixes].
...
See <https://bodhi.fedoraproject.org/updates/FEDORA-2016-dec1faadc5 >
* gnu/packages/fontutils.scm (graphite2)[replacement]: New field.
(graphite2-1.3.6): New variable.
2016-03-02 15:12:18 -05:00
Jessica Tallon
c285a400a2
gnu: Add password-store.
...
* 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>
2016-03-02 14:18:51 -05:00
Roel Janssen
dd6e70f920
gnu: Add cppcheck.
...
* gnu/packages/check.scm (cppcheck): New variable.
2016-03-02 15:17:56 +01:00
Ludovic Courtès
442a6ff5ea
tests: Disable grafts by default.
...
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.
2016-03-02 14:47:07 +01:00
Ludovic Courtès
637cd12543
graph: Ignore 'GUIX_BUILD_OPTIONS'.
...
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'.
2016-03-02 14:47:07 +01:00
Ludovic Courtès
7573d30ff8
guix build: Move '--no-grafts' to the common build options.
...
* 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.
2016-03-02 14:47:07 +01:00
Ludovic Courtès
1cbdf82d3b
guix archive: Use 'with-store'.
...
* guix/scripts/archive.scm (guix-archive): Use 'with-store' instead of
an explicit 'open-connection'.
2016-03-02 14:47:07 +01:00
Mark H Weaver
ed742bc4b4
gnu: openssl: Enable ssl2 at build time to ensure ABI compatible graft.
...
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.
2016-03-02 01:58:42 -05:00
Leo Famulari
eb8065cd27
gnu: ilmbase: Fix typo in adding a patch.
...
* gnu-system.am (dist_patch_DATA): Fix typo.
5e8276dcf4
2016-03-01 20:47:11 -05:00
宋文武
6150b5c780
gnu: xfce: Don't wrap 'startxfce4'.
...
The necessary environment variables are set by 'etc/profile' now.
* gnu/packages/xfce.scm (xfce)[build-system]: Use 'trivial-build-system'.
[arguments]: Simplify.
2016-03-02 08:32:47 +08:00
Leo Famulari
5e8276dcf4
gnu: ilmbase: Add patch to fix build on i686.
...
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.
2016-03-01 19:08:31 -05:00
Leo Famulari
88ccca45f6
gnu: openssh: Update to 7.2p1.
...
* gnu/packages/ssh.scm (openssh): Update to 7.2p1.
2016-03-01 16:32:41 -05:00
Leo Famulari
599860d2b9
gnu: libressl: Update to 2.2.6.
...
* gnu/packages/tls.scm (libressl): Update to 2.2.6.
2016-03-01 16:30:13 -05:00
Leo Famulari
043c3f0bed
gnu: parallel: Update to 20160222.
...
* gnu/packages/parallel.scm (parallel): Update to 20160222.
2016-03-01 15:15:38 -05:00
Pjotr Prins
f82c8c3cba
gnu: r-go-db: Bioconductor changed URL for data downloads.
...
* gnu/packages/bioinformatics.scm (r-go-db)[source]: Update data URL.
2016-03-01 19:47:26 +02:00
Pjotr Prins
27acfaea4c
gnu: r-iranges: Update to 2.4.8.
...
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.4.8.
2016-03-01 19:47:26 +02:00
Pjotr Prins
8921841da8
gnu: r-s4vectors: Update to 0.8.11.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.8.11.
2016-03-01 19:47:25 +02:00
Pjotr Prins
b70fa3c7f7
gnu: r-ggplot2: Update to 2.0.0.
...
* gnu/packages/statistics.scm (r-ggplot2): Update to 2.0.0.
2016-03-01 19:47:24 +02:00
Ludovic Courtès
caeadfddb0
gnu: openssl: Replace with 1.0.2g [fixes 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.
2016-03-01 16:00:46 +01:00
Ludovic Courtès
c22a1324e6
grafts: Graft recursively.
...
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.
2016-03-01 16:00:46 +01:00
Efraim Flashner
d06fc008bd
gnu: tiled: Use 'modify-phases'.
...
* gnu/packages/game-development.scm (tiled)[arguments]: Use 'modify-phases'.
2016-03-01 14:55:55 +02:00
Efraim Flashner
e8ea01d902
gnu: tiled: Update to 0.15.1.
...
* gnu/packages/game-development.scm (tiled): Update to 0.15.1.
2016-03-01 14:55:55 +02:00
Ricardo Wurmus
d1e32822b4
gnu: Add PePr.
...
* gnu/packages/bioinformatics.scm (pepr): New variable.
2016-03-01 11:51:24 +01:00
Ricardo Wurmus
d29150b55d
gnu: Add bwa-pssm.
...
* gnu/packages/bioinformatics.scm (bwa-pssm): New variable.
2016-03-01 10:31:04 +01:00
Ricardo Wurmus
b4464d384c
gnu: Add gdsl.
...
* gnu/packages/datastructures.scm (gdsl): New variable.
2016-03-01 10:30:04 +01:00
Efraim Flashner
e288f0075c
gnu: weechat: Move to irc.scm.
...
* 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.
2016-03-01 11:09:32 +02:00
Efraim Flashner
a61bd6a5e3
gnu: irssi: Use 'modify-phases'.
...
* gnu/packages/irc.scm (irssi)[arguments]: Use 'modify-phases'.
2016-03-01 11:09:32 +02:00
Efraim Flashner
27930f853d
gnu: irssi: Move to irc.scm.
...
* 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.
2016-03-01 11:09:32 +02:00
Efraim Flashner
980f058d92
gnu: Add quassel.
...
* gnu/packages/irc.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Register it.
2016-03-01 11:09:32 +02:00
Efraim Flashner
550791b8f1
gnu: Add snorenotify.
...
* gnu/packages/kde.scm (snorenotify): New variable.
2016-03-01 11:09:32 +02:00
Efraim Flashner
d34c594aeb
gnu: Add qca.
...
* gnu/packages/kde.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Register it.
2016-03-01 11:09:32 +02:00
Efraim Flashner
d8ea278204
gnu: Add oxygen-icons.
...
* gnu/packages/kde-frameworks.scm (oxygen-icons): New variable.
2016-03-01 11:09:32 +02:00