61201e46a7
gnu: password-store: Wrap PATH.
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* gnu/packages/password-utils.scm (password-store)
[arguments]: Wrap PATH more thoroughly.
[native-inputs]: Move getopt to inputs.
[inputs]: Add sed.
Signed-off-by: Mathieu Lirzin <mthl@gnu.org>
2016-07-29 11:00:31 +02:00
f33e71fca2
gnu: perl-dbd-pg: Add description.
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* gnu/packages/databases.scm (perl-dbd-pg)[description]: Add non-empty
description.
2016-07-29 10:22:31 +02:00
bd883da3e3
build: Bump version number.
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* configure.ac: Change version to 0.11.0.
2016-07-29 10:15:56 +02:00
a3947cb1b8
gnu: Sync GNU descriptions with upstream.
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From 'guix lint -c gnu-description'.
* gnu/packages/gnunet.scm (gnunet): Adjust description.
* gnu/packages/marst.scm (marst): Likewise.
* gnu/packages/maths.scm (c-graph): Likewise.
* gnu/packages/networking.scm (macchanger): Likewise.
2016-07-29 10:13:12 +02:00
c777570b57
gnu: Add sshpass.
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* gnu/packages/ssh.scm (sshpass): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-07-29 00:04:39 +02:00
cfbb3b0d00
gnu: python-beautifulsoup4: Update to 4.5.0.
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* gnu/packages/python.scm (python-beautifulsoup4, python2-beautifulsoup4):
Update to 4.5.0.
2016-07-28 17:50:52 -04:00
adca268e97
gnu: perl-devel-symdump: Update to 2.17.
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* gnu/packages/perl.scm (perl-devel-symdump): Update to 2.17.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-07-28 17:41:06 -04:00
6144dff516
gnu: Add virt-viewer.
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* gnu/packages/spice.scm (virt-viewer): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-07-28 17:08:42 -04:00
33b0f4a4b2
gnu: Add spice-vdagent.
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* gnu/packages/spice.scm (spice-vdagent): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-07-28 17:08:42 -04:00
3cbd37e440
gnu: Add spice.
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* gnu/packages/spice.scm (spice): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-07-28 17:08:42 -04:00
bb28cf90e9
gnu: Add spice-gtk.
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* gnu/packages/spice.scm (spice-gtk): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-07-28 17:08:42 -04:00
289e472f56
gnu: Add spice-protocol.
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* gnu/packages/spice.scm (spice-protocol): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-07-28 17:08:41 -04:00
2ef2654de4
gnu: Add virglrenderer.
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* gnu/packages/spice.scm (virglrenderer): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-07-28 17:08:41 -04:00
1d2c67c11e
gnu: Add usbredir.
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* gnu/packages/spice.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-07-28 17:08:41 -04:00
a1dfa02233
Revert "gnu: gd: Update to 2.2.3 [fixes CVE-2016-6207]."
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This reverts commit ae46cd0e4c
2016-07-28 16:45:02 -04:00
4e3bfaf406
guix package: Suggest prefix search path settings.
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* guix/scripts/package.scm (build-and-use-profile): Pass #:kind 'prefix
to 'display-search-paths'.
2016-07-28 20:07:59 +02:00
ae46cd0e4c
gnu: gd: Update to 2.2.3 [fixes CVE-2016-6207].
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* gnu/packages/patches/gd-CVE-2016-5766.patch,
gnu/packages/patches/gd-CVE-2016-6128.patch,
gnu/packages/patches/gd-CVE-2016-6132.patch,
gnu/packages/patches/gd-CVE-2016-6214.patch,
gnu/packages/patches/gd-fix-test-on-i686.patch: Delete files.
* gnu/packages/patches/gd-fix-tests-on-i686.patch: New file.
* gnu/local.mk (dist_patch_DATA): Update accordingly.
* gnu/packages/gd.scm (gd): Update to 2.2.3.
[source]: Update patches field accordingly.
2016-07-28 14:06:12 -04:00
386b71d1b9
gnu: commencement: 'guile-final' is now "hidden".
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This way, we no longer have this annoying warning:
$ guix build guile -n
guix build: warning: ambiguous package specification `guile'
guix build: warning: choosing guile-2.0.11 from gnu/packages/guile.scm:128:2
* gnu/packages/commencement.scm (guile-final): Use 'hidden-package'.
* tests/packages.scm ("fold-packages, hidden package"): New test.
2016-07-28 18:53:13 +02:00
6980511b73
packages: Add 'hidden-package'.
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* guix/packages.scm (hidden-package, hidden-package?): New procedures.
* gnu/packages.scm (fold-packages): Filter out 'hidden-package?'.
* tests/packages.scm ("hidden-package"): New test.
2016-07-28 18:50:43 +02:00
cb55f9c652
gnu: Add asciinema.
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* gnu/packages/terminals.scm (asciinema): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-07-28 15:43:40 +02:00
71d9b98078
gnu: gnome: Propagate file-roller.
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* gnu/packages/gnome.scm (gnome)[propagated-inputs]: Add file-roller.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-07-28 15:42:30 +02:00
d222522edf
doc: Discourage software bundling.
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Fixes <http://bugs.gnu.org/24008 >.
Suggested by ng0 <ng0@we.make.ritual.n0.is>.
* doc/contributing.texi (Submitting Patches): Add item about bundling.
2016-07-28 15:41:00 +02:00
3a78fab83d
doc: Send changes in your patch which are related.
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* doc/contributing.texi (Submitting Patches): New @item:
This gives information about sending related changes and examples on
what we view as related changes.
Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2016-07-28 15:38:14 +02:00
189b1543cb
doc: Mention separate branch for packages with many dependents.
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Suggested by ng0 <ng0@we.make.ritual.n0.is>.
* doc/contributing.texi (Submitting Patches): Add note on packages with
more than 100 dependents.
2016-07-28 15:24:37 +02:00
6547708f71
gnu: r-genomicfeatures: Update to 1.24.5.
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* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.5.
2016-07-28 21:54:44 +10:00
2c9f6251fc
gnu: r-bsgenome: Update to 1.40.1.
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* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.1.
2016-07-28 21:45:17 +10:00
b0f0778a7c
gnu: r-iranges: Update to 2.6.1.
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* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.6.1.
2016-07-28 21:45:17 +10:00
f403941f81
gnu: r-limma: Update to 3.28.17.
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* gnu/packages/bioinformatics.scm (r-limma): Update to 3.28.17.
2016-07-28 21:45:16 +10:00
2b2ff0bd91
gnu: r-xvector: Update to 0.12.1.
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* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.1.
2016-07-28 21:45:16 +10:00
a463055862
gnu: r-genomicranges: Update to 1.24.2.
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* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.2.
2016-07-28 21:45:16 +10:00
bab15ccec4
gnu: r-annotationdbi: Update to 1.34.4.
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* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.4.
2016-07-28 21:45:15 +10:00
a22999f245
gnu: r-biocparallel: Update to 1.6.3.
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* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.3.
2016-07-28 21:45:15 +10:00
d104fc607d
gnu: r-biostrings: Update to 2.40.2.
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* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.2.
2016-07-28 21:45:15 +10:00
1864e051c9
gnu: r-summarizedexperiment: Update to 1.2.3.
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* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.3.
2016-07-28 21:45:15 +10:00
29b0cc8ad5
gnu: r-genomicalignments: Update to 1.8.4.
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* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.4.
2016-07-28 21:45:14 +10:00
5131e21064
gnu: r-rtracklayer: Update to 1.32.2.
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* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.2.
2016-07-28 21:45:14 +10:00
2a3e325f5e
gnu: r-genomeinfodb: Update to 1.8.3.
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* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.3.
2016-07-28 21:45:14 +10:00
f2e791750b
gnu: r-s4vectors: Update to 0.10.2.
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* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.2.
2016-07-28 20:13:42 +10:00
e335b82c4e
gnu: mysql: Update to 5.7.13 [fixes CVE-2016-{3477,3521,3615,5440}].
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* gnu/packages/patches/mysql-fix-failing-test.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/databases.scm (mysql): Update to 5.7.13.
2016-07-28 02:08:49 -04:00
46e4e84ffc
gnu: the-silver-searcher: Update to 0.32.0.
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* gnu/packages/code.scm(the-silver-searcher): Update to 0.32.0.
2016-07-28 08:05:04 +02:00
8e5d8b1880
gnu: imagemagick: Update to 6.9.5-3.
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* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.5-3.
2016-07-27 23:25:13 -04:00
ff7172feae
gnu: mariadb: Update to 10.1.16.
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* gnu/packages/databases.scm (mariadb): Update to 10.1.16.
2016-07-27 23:25:08 -04:00
b111bdb667
gnu: calibre: Update to 2.63.0.
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* gnu/packages/ebook.scm (calibre): Update to 2.63.0.
[inputs]: Remove unnecessary imagemagick dependency.
[phases]: Use modify-phases.
* gnu/packages/patches/calibre-drop-unrar.patch: Update
for new version.
Signed-off-by: Roel Janssen <roel@gnu.org>
2016-07-27 23:45:16 +02:00
cad7e6abaf
system: Source /etc/environment before $HOME/.guix-profile/etc/profile.
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* gnu/system.scm (operating-system-etc-service) <profile>: Move sourcing
of /etc/environment before that of $HOME/.guix-profile/etc/profile.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-07-27 23:08:20 +02:00
9712ef8d42
gnu: krona-tools: Update to 2.7.
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* gnu/packages/web.scm (krona-tools): Update to 2.7.
[arguments]: Delete 'build' phase. Install new scripts.
2016-07-27 23:39:56 +10:00
12c8f210ee
gnu: diamond: Update to 0.8.16.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.16.
2016-07-27 23:17:57 +10:00
fd6830b3a6
gnu: guix: Update revision number in version.
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This is a follow-up to commit 95af24a2f1
2016-07-27 15:16:17 +02:00
37402ecb43
tests: Use unbuffered input ports when decompressing from 'guix publish'.
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Fixes <http://bugs.gnu.org/24060 >.
Reported by Chris Marusich <cmmarusich@gmail.com>.
* tests/publish.scm (http-get-port): Explicitly call
'open-socket-for-uri' and add calls to 'setvbuf'.
2016-07-27 12:45:01 +02:00
688ec13c45
zlib: Protect against non-empty port internal buffers.
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* guix/zlib.scm (make-gzip-input-port)[gzfile]: Error out
if (drain-input port) returns a non-empty string.
* guix/zlib.scm (make-gzip-output-port)[gzfile]: Call 'force-output'.
2016-07-27 12:45:01 +02:00
d00240c36e
zlib: Clarify when 'gzread!' can return zero.
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* guix/zlib.scm (gzread!): Augment docstring to clarify when zero is
returned (based on reading zlib code).
(make-gzip-input-port)[read!]: Remove scary comment.
2016-07-27 12:45:01 +02:00
Alex Griffin