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
46bd451520
gnu: magit: Fix rebase commands that require perl.
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* 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
82ee141bab
gnu: Add httping.
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* gnu/packages/networking.scm (httping): New variable.
2016-07-27 03:59:47 +02:00
42ff54d5fa
gnu: Add missing copyright symbol.
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* gnu/packages/networking.scm: Add missing "©" to header comments.
2016-07-27 03:59:47 +02:00
ae83dcf6ba
gnu: gmime: Remove 'gpg' to 'gpg2' substitution.
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* 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
d3896fc4ce
gnu: dmd: Remove package, superseded by shepherd.
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* gnu/packages/admin.scm (dmd): Remove variable.
2016-07-26 22:50:26 +02:00
90c2ee889b
gnu: Add perl-db-file.
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* gnu/packages/databases.scm (perl-db_file): New variable.
Signed-off-by: Andreas Enge <andreas@enge.fr>
2016-07-26 22:43:48 +02:00
9e90fc7713
profiles: Output in 'package->manifest-entry' defaults to "out".
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Fixes <http://bugs.gnu.org/24029 >.
Reported by Dylan Jeffers <sapientech@openmailbox.org>.
* guix/profiles.scm (package->manifest-entry): Change #:output to
default to "out".
(packages->manifest): Add 'package?' in second 'match' clause.
* tests/profiles.scm ("package->manifest-entry defaults to \"out\""):
New test.
2016-07-26 18:18:53 +02:00
201855221f
environment: Set 'GUIX_ENVIRONMENT' to the profile.
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* guix/scripts/environment.scm (create-environment): Set
'GUIX_ENVIRONMENT' to PROFILE.
* tests/guix-environment.sh: Test it.
* doc/guix.texi (Invoking guix environment): Document it.
2016-07-26 17:59:25 +02:00
8173ceee1f
import: pypi: Correctly handle new-style URLs.
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Fixes <http://bugs.gnu.org/23997 >.
* guix/import/pypi.scm (guix-package->pypi-name): Rewrite using
'basename' and 'hyphen-package-name->name+version'.
* tests/pypi.scm ("guix-package->pypi-name, old URL style")
("guix-package->pypi-name, new URL style"): New tests.
2016-07-26 17:49:34 +02:00
debc6360e1
doc: Explain authentication in "System Installation".
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Suggested by Vincent Legoll <vincent.legoll@gmail.com>.
* doc/guix.texi (OPENPGP-SIGNING-KEY-ID): New constant.
(Binary Installation): Use it.
(USB Stick Installation): Copy and adjust the authentication bit from
"Binary Installation".
2016-07-26 15:07:29 +02:00
6e42660b12
doc: Better illustration use of package revision numbers.
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* doc/guix.texi (Version Numbers): Add the
revision to the example of the git package used in 7.6.3.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-07-26 14:55:47 +02:00
88a8ce87a4
gnu: icecat: Install icons.
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* gnu/packages/gnuzilla.scm (icecat)[arguments]: Add
'install-icons' phase.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-07-26 14:53:16 +02:00
2b76f13507
gnu: Add haveged.
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* gnu/packages/linux.scm (haveged): New variable.
2016-07-26 11:20:52 +02:00
af7aaaebab
gnu: Add perceptualdiff.
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* gnu/packages/image.scm (perceptualdiff): New variable.
2016-07-26 11:20:27 +02:00
ca80985c6c
gnu: linux-libre@4.1: Update to 4.1.28.
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* gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.28.
2016-07-26 01:36:12 -04:00
de348a0bb7
gnu: linux-libre: Update to 4.7.
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* gnu/packages/linux.scm (linux-libre): Update to 4.7.
* gnu/packages/linux-libre-4.7-x86_64.conf,
gnu/packages/linux-libre-4.7-i686.conf: New files.
* gnu/packages/linux-libre-4.6-x86_64.conf,
gnu/packages/linux-libre-4.6-i686.conf: Delete files.
* Makefile.am (KCONFIGS): Update accordingly.
2016-07-26 00:46:40 -04:00
0e5f606159
gnu: calibre: Build with non-modular Qt.
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* gnu/packages/ebook.scm (calibre)[native-inputs]: Replace QTBASE by QT.
[inputs]: Replace QTBASE by QT and PYTHON2-PYQT by PYTHON2-PYQT-5.5.
This essentially reverts commit 76806c54ed
2016-07-26 00:38:39 +02:00
4a8c35e143
gnu: pyqt: Add versions based on non-modular Qt 5.5.
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* gnu/packages/qt.scm (python-pyqt-5.5, python2-pyqt-5.5): New variables.
2016-07-26 00:38:20 +02:00
95af24a2f1
gnu: guix: Update development snapshot.
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* gnu/packages/package-management.scm (guix-devel): Update to 97c8aef
2016-07-25 22:53:27 +02:00
97c8aef15d
system: Add mapped devices for RAID.
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* gnu/system/mapped-devices.scm (raid-device-mapping, open-raid-device,
close-raid-device): New variables.
* doc/guix.texi (Mapped Devices): Add documentation for RAID devices,
reorganize documentation for LUKS devices.
Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2016-07-25 22:22:21 +02:00
424a323e92
doc: Explain when guix edit is read-only.
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* doc/guix.texi (Invoking guix edit): Explain when you can and can't
edit the recipe.
Signed-off-by: Alex Kost <alezost@gmail.com>
2016-07-25 17:18:53 +03:00
090bdb9e91
gnu: emacs-solarized-theme: Remove unneeded dependencies.
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* gnu/packages/emacs.scm (emacs-solarized-theme)[propagated-inputs]:
Remove 'emacs-f' and 'emacs-s'.
2016-07-25 17:18:53 +03:00
c48899eba2
gnu: emacs: Install site-start.el in non-versioned directory.
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Reported by Ricardo Wurmus on #guix.
* gnu/packages/emacs.scm (emacs)[arguments]: Put "site-start.el" in
"/share/emacs/site-lisp" instead of "/share/emacs/<version>/site-lisp"
to let inherited package with another version find it.
2016-07-25 17:18:53 +03:00
07f7cc03ce
gnu: Add guile-daemon.
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* gnu/packages/guile.scm (guile-daemon): New variable.
2016-07-25 17:18:53 +03:00
bd9af61035
gnu: Add guile-xosd.
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* gnu/packages/guile.scm (guile-xosd): New variable.
2016-07-25 17:18:53 +03:00
6cfd1a687a
gnu: Add xdpyprobe.
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* gnu/packages/xdisorg.scm (xdpyprobe): New variable.
2016-07-25 17:18:53 +03:00
1a3e6b15ba
doc: Describe how to make X server find TrueType fonts.
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* doc/guix.texi (Application Setup): Document how to add TrueType fonts
installed in a Guix profile to the X server font path.
2016-07-25 17:18:52 +03:00
9eb5a449ee
profiles: Add fonts-dir-file hook.
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* guix/profiles.scm (fonts-dir-file): New procedure.
(%default-profile-hooks): Add it.
2016-07-25 17:18:52 +03:00
Ben Woodcroft