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11077 Commits

Author SHA1 Message Date
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
Manolis Ragkousis fea1f275bc gnu: Add desmume. 
* gnu/packages/games.scm (desmume): New variable.
 2016-02-29 22:04:53 -05:00
Mark H Weaver 8d5ceb120d gnu: curl: Use updated libssh2 [fixes CVE-2016-7087]. 
* gnu/packages/curl.scm (curl)[inputs]: Use libssh2.
* gnu/packages/ssh.scm (libssh2-1.4): Remove variable.
 2016-02-29 20:09:29 -05:00
Christopher Allan Webber aa5946edb2 gnu: Remove python2-pil. 
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.
 2016-02-29 15:01:20 -08:00