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Author SHA1 Message Date
Nicolas Goaziou c777570b57
gnu: Add sshpass. 
* gnu/packages/ssh.scm (sshpass): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-29 00:04:39 +02:00
Leo Famulari cfbb3b0d00
gnu: python-beautifulsoup4: Update to 4.5.0. 
* gnu/packages/python.scm (python-beautifulsoup4, python2-beautifulsoup4):
Update to 4.5.0.
 2016-07-28 17:50:52 -04:00
ng0 adca268e97
gnu: perl-devel-symdump: Update to 2.17. 
* 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
David Craven 6144dff516
gnu: Add virt-viewer. 
* gnu/packages/spice.scm (virt-viewer): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-07-28 17:08:42 -04:00
David Craven 33b0f4a4b2
gnu: Add spice-vdagent. 
* gnu/packages/spice.scm (spice-vdagent): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-07-28 17:08:42 -04:00
David Craven 3cbd37e440
gnu: Add spice. 
* gnu/packages/spice.scm (spice): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-07-28 17:08:42 -04:00
David Craven bb28cf90e9
gnu: Add spice-gtk. 
* gnu/packages/spice.scm (spice-gtk): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-07-28 17:08:42 -04:00
David Craven 289e472f56
gnu: Add spice-protocol. 
* gnu/packages/spice.scm (spice-protocol): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-07-28 17:08:41 -04:00
David Craven 2ef2654de4
gnu: Add virglrenderer. 
* gnu/packages/spice.scm (virglrenderer): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-07-28 17:08:41 -04:00
David Craven 1d2c67c11e
gnu: Add usbredir. 
* 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
Leo Famulari a1dfa02233
Revert "gnu: gd: Update to 2.2.3 [fixes CVE-2016-6207]." 
This reverts commit ae46cd0e4c.
 2016-07-28 16:45:02 -04:00
Ludovic Courtès 4e3bfaf406
guix package: Suggest prefix search path settings. 
* guix/scripts/package.scm (build-and-use-profile): Pass #:kind 'prefix
to 'display-search-paths'.
 2016-07-28 20:07:59 +02:00
Mark H Weaver ae46cd0e4c
gnu: gd: Update to 2.2.3 [fixes CVE-2016-6207]. 
* 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
Ludovic Courtès 386b71d1b9
gnu: commencement: 'guile-final' is now "hidden". 
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
Ludovic Courtès 6980511b73
packages: Add 'hidden-package'. 
* 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
Alex Griffin cb55f9c652
gnu: Add asciinema. 
* gnu/packages/terminals.scm (asciinema): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-28 15:43:40 +02:00
Alex Griffin 71d9b98078
gnu: gnome: Propagate file-roller. 
* 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
Ludovic Courtès d222522edf
doc: Discourage software bundling. 
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
ng0 3a78fab83d
doc: Send changes in your patch which are related. 
* 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
Ludovic Courtès 189b1543cb
doc: Mention separate branch for packages with many dependents. 
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
Ben Woodcroft 6547708f71
gnu: r-genomicfeatures: Update to 1.24.5. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.5.
 2016-07-28 21:54:44 +10:00
Ben Woodcroft 2c9f6251fc
gnu: r-bsgenome: Update to 1.40.1. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.1.
 2016-07-28 21:45:17 +10:00
Ben Woodcroft b0f0778a7c
gnu: r-iranges: Update to 2.6.1. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.6.1.
 2016-07-28 21:45:17 +10:00
Ben Woodcroft f403941f81
gnu: r-limma: Update to 3.28.17. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.28.17.
 2016-07-28 21:45:16 +10:00
Ben Woodcroft 2b2ff0bd91
gnu: r-xvector: Update to 0.12.1. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.1.
 2016-07-28 21:45:16 +10:00
Ben Woodcroft a463055862
gnu: r-genomicranges: Update to 1.24.2. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.2.
 2016-07-28 21:45:16 +10:00
Ben Woodcroft bab15ccec4
gnu: r-annotationdbi: Update to 1.34.4. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.4.
 2016-07-28 21:45:15 +10:00
Ben Woodcroft a22999f245
gnu: r-biocparallel: Update to 1.6.3. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.3.
 2016-07-28 21:45:15 +10:00
Ben Woodcroft d104fc607d
gnu: r-biostrings: Update to 2.40.2. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.2.
 2016-07-28 21:45:15 +10:00
Ben Woodcroft 1864e051c9
gnu: r-summarizedexperiment: Update to 1.2.3. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.3.
 2016-07-28 21:45:15 +10:00
Ben Woodcroft 29b0cc8ad5
gnu: r-genomicalignments: Update to 1.8.4. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.4.
 2016-07-28 21:45:14 +10:00
Ben Woodcroft 5131e21064
gnu: r-rtracklayer: Update to 1.32.2. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.2.
 2016-07-28 21:45:14 +10:00
Ben Woodcroft 2a3e325f5e
gnu: r-genomeinfodb: Update to 1.8.3. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.3.
 2016-07-28 21:45:14 +10:00
Ben Woodcroft f2e791750b
gnu: r-s4vectors: Update to 0.10.2. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.2.
 2016-07-28 20:13:42 +10:00
Leo Famulari e335b82c4e
gnu: mysql: Update to 5.7.13 [fixes CVE-2016-{3477,3521,3615,5440}]. 
* 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
Tomáš Čech 46e4e84ffc
gnu: the-silver-searcher: Update to 0.32.0. 
* gnu/packages/code.scm(the-silver-searcher): Update to 0.32.0.
 2016-07-28 08:05:04 +02:00
Leo Famulari 8e5d8b1880
gnu: imagemagick: Update to 6.9.5-3. 
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.5-3.
 2016-07-27 23:25:13 -04:00
Leo Famulari ff7172feae
gnu: mariadb: Update to 10.1.16. 
* gnu/packages/databases.scm (mariadb): Update to 10.1.16.
 2016-07-27 23:25:08 -04:00
Alex Griffin b111bdb667
gnu: calibre: Update to 2.63.0. 
* 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
Carlos Sánchez de La Lama cad7e6abaf
system: Source /etc/environment before $HOME/.guix-profile/etc/profile. 
* 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
Ben Woodcroft 9712ef8d42
gnu: krona-tools: Update to 2.7. 
* 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
Ben Woodcroft 12c8f210ee
gnu: diamond: Update to 0.8.16. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.16.
 2016-07-27 23:17:57 +10:00
Andreas Enge fd6830b3a6
gnu: guix: Update revision number in version. 
This is a follow-up to commit 95af24a2f1.
Reported by Alex Kost <alezost@gmail.com>.
 2016-07-27 15:16:17 +02:00
Ludovic Courtès 37402ecb43
tests: Use unbuffered input ports when decompressing from 'guix publish'. 
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
Ludovic Courtès 688ec13c45
zlib: Protect against non-empty port internal buffers. 
* 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
Ludovic Courtès d00240c36e
zlib: Clarify when 'gzread!' can return zero. 
* 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 46bd451520
gnu: magit: Fix rebase commands that require perl. 
* gnu/packages/emacs.scm (magit)[inputs]: Add 'perl'.
[arguments]: Adjust 'patch-exec-paths' phase to make some rebase
commands find 'perl'.

Signed-off-by: Alex Kost <alezost@gmail.com>
 2016-07-27 11:15:45 +03:00
Tobias Geerinckx-Rice 82ee141bab
gnu: Add httping. 
* gnu/packages/networking.scm (httping): New variable.
 2016-07-27 03:59:47 +02:00
Tobias Geerinckx-Rice 42ff54d5fa
gnu: Add missing copyright symbol. 
* gnu/packages/networking.scm: Add missing "©" to header comments.
 2016-07-27 03:59:47 +02:00
ng0 ae83dcf6ba
gnu: gmime: Remove 'gpg' to 'gpg2' substitution. 
* gnu/packages/mail.scm (gmime)[arguments]: Remove the substitution which
previously changed 'gpg' to 'gpg2' in 'patch-paths-in-tests' phase.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-07-26 19:43:54 -04:00