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Author SHA1 Message Date
Ricardo Wurmus
4714d521e3
gnu: Add r-bsgenome-mmusculus-ucsc-mm10. 
* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm10): New
  variable.
 2016-06-15 17:08:08 +02:00
Ricardo Wurmus
c4e48b68bd
guix: Add downloader for Mercurial repositories. 
* guix/build/hg.scm: New file.
* guix/hg-download.scm: New file.
* Makefile.am (MODULES): Add them.
 2016-06-15 17:02:18 +02:00
Leo Famulari
9c4a8514d6
gnu: openssl: Fix CVE-2016-2177 and CVE-2016-2178. 
* gnu/packages/patches/openssl-CVE-2016-2177.patch,
gnu/packages/patches/openssl-CVE-2016-2178.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/tls.scm (openssl/fixed): Use them.
 2016-06-15 10:48:13 -04:00
Danny Milosavljevic
a44fd439dc
gnu: Add python-wcwidth and python2-wcwidth. 
* gnu/packages/python.scm (python-wcwidth, python2-wcwidth): New variables.

Co-authored-by: Leo Famulari <leo@famulari.name>
 2016-06-15 10:44:52 -04:00
Ricardo Wurmus
ce9cf64b78
gnu: Add log4cpp. 
* gnu/packages/logging.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
 2016-06-15 15:35:02 +02:00
Ricardo Wurmus
ba6a996eac
gnu: Add gengetopt. 
* gnu/packages/popt.scm (gengetopt): New variable.
 2016-06-15 15:34:58 +02:00
Hartmut Goebel
d3a858cb32
gnu: Add teensy-loader-cli. 
* gnu/packages/flashing-tools.scm (teensy-loader-cli): New variable.
* gnu/packages/patches/teensy-loader-cli-help.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2016-06-15 15:27:48 +02:00
Ludovic Courtès
1ec32f4a9d
store: Add #:select? parameter to 'add-to-store'. 
* guix/store.scm (write-arg): Remove 'file' case.
(true): New procedure.
(add-to-store): Add #:select? parameter and honor it.  Use hand-coded
stub instead of 'operation'.
(interned-file): Add #:select? parameter and honor it.
* doc/guix.texi (The Store Monad): Adjust 'interned-file' documentation
accordingly.
 2016-06-15 15:26:30 +02:00
Ludovic Courtès
0fb9a15bb5
gnu: grue-hunter: Move to (gnu packages games). 
* gnu/packages/grue-hunter.scm: Remove.  Move contents to...
* gnu/packages/games.scm (grue-hunter): ... here.  New variable.
* gnu/local.mk (GNU_SYSTEM_MODULES): Adjust accordingly.
 2016-06-15 15:26:30 +02:00
Ludovic Courtès
da675305dd
packages: The 'source' can be any lowerable object. 
* guix/packages.scm (expand-input): Use 'struct?' instead of 'origin?'
when matching SOURCE.
(package-source-derivation): Use 'lower-object' instead of
'origin->derivation'.
* tests/packages.scm ("package-source-derivation, local-file"): New
test.
* doc/guix.texi (package Reference): Update 'source' documentation
accordingly.
 2016-06-15 15:26:30 +02:00
Ludovic Courtès
789510640d
packages: 'origin->derivation' expects an origin and nothing else. 
* guix/packages.scm (origin->derivation): Rename 'source' parameter to
'origin'.  Move cases where SOURCE is a string to...
(package-source-derivation): ... here.
 2016-06-15 15:26:30 +02:00
Ludovic Courtès
5257ab6de2
packages: Recognize the '.Z' extension. 
Reported by thomasd on #guix.

* guix/packages.scm (patch-and-repack)[decompression-type]: Add "Z".
 2016-06-15 15:26:30 +02:00
Efraim Flashner
6dc554fa2a
gnu: pumpa: Build with qtbase. 
* gnu/packages/pumpio.scm (pumpa)[inputs]: Remove qt, add qtbase.
 2016-06-15 11:39:53 +03:00
Efraim Flashner
e2788cef13
gnu: pinentry-qt: Build with qtbase. 
* gnu/packages/gnupg.scm (pinentry-qt)[inputs]: Remove qt, add qtbase.
 2016-06-15 11:26:10 +03:00
Efraim Flashner
d438c9683b
gnu: Add qttools. 
* gnu/packages/qt.scm (qttools): New variable.
 2016-06-15 11:11:56 +03:00
Efraim Flashner
d5ca54ce47
gnu: Add qtlocation. 
* gnu/packages/qt.scm (qtlocation): New variable.
 2016-06-15 11:11:56 +03:00
Efraim Flashner
f5377013d6
gnu: Add qtwebchannel. 
* gnu/packages/qt.scm (qtwebchannel): New variable.
 2016-06-15 11:11:56 +03:00
Efraim Flashner
00806f2bb9
gnu: Add qtserialport. 
* gnu/packages/qt.scm (qtserialport): New variable.
 2016-06-15 11:11:56 +03:00
Efraim Flashner
bc8ede0150
gnu: Add qtwayland. 
* gnu/packages/qt.scm (qtwayland): New variable.
 2016-06-15 11:11:56 +03:00
Efraim Flashner
15378f93b9
gnu: Add qtmultimedia. 
* gnu/packages/qt.scm (qtmultimedia): New variable.
 2016-06-15 11:11:56 +03:00
Efraim Flashner
3474767cbd
gnu: Add qtsensors. 
* gnu/packages/qt.scm (qtsensors): New variable.
 2016-06-15 11:11:56 +03:00
Efraim Flashner
cac893ec09
gnu: Add qtwebsockets. 
* gnu/packages/qt.scm (qtwebsockets): New variable.
 2016-06-15 11:11:56 +03:00
Efraim Flashner
e98cb96d69
gnu: Add qtconnectivity. 
* gnu/packages/qt.scm (qtconnectivity): New variable.
 2016-06-15 11:11:56 +03:00
Efraim Flashner
e3a2ed8151
gnu: Add qtdeclarative. 
* gnu/packages/qt.scm (qtdeclarative): New variable.
 2016-06-15 11:11:56 +03:00
Efraim Flashner
98eec71280
gnu: Add qtxmlpatterns. 
* gnu/packages/qt.scm (qtxmlpatterns): New variable.
 2016-06-15 11:11:56 +03:00
Efraim Flashner
f6c13613af
gnu: Add qtx11extras. 
* gnu/packages/qt.scm (qtx11extras): New variable.
 2016-06-15 11:11:56 +03:00
Efraim Flashner
9b69421021
gnu: Add qtimageformats. 
* gnu/packages/qt.scm (qtimageformats): New variable.
 2016-06-15 11:11:56 +03:00
Efraim Flashner
19c1763113
gnu: Add qtsvg. 
* gnu/packages/qt.scm (qtsvg): New variable.
 2016-06-15 11:11:56 +03:00
Cyril Roelandt
266785d21e import: pypi: read requirements from wheels. 
* doc/guix.tex (Invoking guix import): Mention that the pypi importer
works better with "unzip".
* guix/import/pypi.scm (latest-wheel-release,
wheel-url->extracted-directory): New procedures.
* tests/pypi.scm (("pypi->guix-package, wheels"): New test.
 2016-06-14 22:03:22 +02:00
Ricardo Wurmus
4f54a63e1e
gnu: julia: Use unbundled release tarball. 
* gnu/packages/julia.scm (julia)[source]: Use smaller tarball without
bundled sources.
[inputs]: Add inputs for rmath-julia, suitesparse, objconv, dsfmt, and
virtualenv.
[arguments]: Add phase "prepare-deps" to copy tarballs to their expected
locations.
 2016-06-14 16:27:19 +02:00
Efraim Flashner
6138dedec9
gnu: perl-dbi: Update to 1.636. 
* gnu/packages/databases.scm (perl-dbi): Update to 1.636.
[home-page]: Update it.
 2016-06-14 15:06:48 +03:00
Efraim Flashner
0e8186eb12
gnu: perl-exporter-lite: Update to 0.08. 
* gnu/packages/perl.scm (perl-exporter-lite): Update to 0.08.
[home-page]: Update it.
 2016-06-14 15:04:09 +03:00
Efraim Flashner
67abcc05ba
gnu: perl-image-exiftool: Update to 10.20. 
* gnu/packages/photo.scm (perl-image-exiftool): Update to 10.20.
[home-page]: Update it.
 2016-06-14 15:01:35 +03:00
Efraim Flashner
cf4a71322b
gnu: perl-test-deep: Update to 1.120. 
* gnu/packages/perl.scm (perl-test-deep): Update to 1.120.
[home-page]: Update it.
 2016-06-14 14:31:58 +03:00
Efraim Flashner
54c3c140ce
gnu: perl-xml-libxml: Update to 2.0125. 
* gnu/packages/xml.scm (perl-xml-libxml): Update to 2.0125.
 2016-06-14 14:29:03 +03:00
Efraim Flashner
e831256ff5
gnu: perl-xml-simple: Update to 2.22. 
* gnu/packages/xml.scm (perl-xml-simple): Update to 2.22.
[propagated-inputs]: Add perl-xml-sax.
[home-page]: Update it.
 2016-06-14 14:08:07 +03:00
Efraim Flashner
d0d2b0f9cd
gnu: parallel: Update to 20160522. 
* gnu/packages/parallel.scm (parallel): Update to 20160522.
 2016-06-14 10:08:14 +03:00
Alex Vong
feb5c55403
gnu: youtube-dl: Update to 2016.06.14. 
* gnu/packages/video.scm (youtube-dl): Update to 2016.06.14.
[source]: Use https.
[home-page]: Use https.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2016-06-14 09:07:02 +03:00
David Thompson
32ac717c5f gnu: Add gnome-shell-extensions. 
* gnu/packages/gnome.scm (gnome-shell-extensions): New variable.
 2016-06-13 19:22:54 -04:00
Ben Woodcroft
e4a44a6aa5
gnu: Add ruby-bio-kseq. 
* gnu/packages/bioinformatics.scm (ruby-bio-kseq): New variable.
 2016-06-14 07:57:09 +10:00
Ludovic Courtès
d3ef652aa1
gnu: wget: Update to 1.18. 
* gnu/packages/wget.scm (wget): Update to 1.18.
 2016-06-13 23:13:16 +02:00
Efraim Flashner
65089213c8
gnu: wayland: Update to 1.11.0. 
* gnu/packages/freedesktop.scm (wayland): Update to 1.11.0.
 2016-06-13 22:37:35 +03:00
Efraim Flashner
c6bccf713b
gnu: python-pykafka: Change uri. 
* gnu/packages/python.scm (python-pykafka)[source]: Update pypi uri.
 2016-06-13 21:31:13 +03:00
Nicolas Goaziou
2fb3dddabf
gnu: giac-xcas: Update to 1.2.2-59 
* gnu/packages/algebra.scm (giac-xcas): Update to 1.2.2-59.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-06-13 18:05:54 +02:00
Nicolas Goaziou
2e2c6e9655
gnu: asymptote: Update to 2.38 
* gnu/packages/plotutils.scm (asymptote): Update to 2.38.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-06-13 18:05:54 +02:00
Ludovic Courtès
c25637dfe8
utils: 'with-atomic-file-output' closes the port upon exception. 
Previously it could have left the file descriptor open.

* guix/utils.scm (with-atomic-file-output): Call 'close-port' in handler.
 2016-06-13 18:05:54 +02:00
Ludovic Courtès
d1f33ba44b
syscalls: Use 'syscall->procedure' everywhere. 
* guix/build/syscalls.scm (mkdtemp!, setns, %ioctl, network-interfaces):
(free-ifaddrs): Use 'syscall->procedure'.
 2016-06-13 18:05:54 +02:00
Ludovic Courtès
1752a17a1e
utils: 'with-atomic-file-output' calls 'fdatasync'. 
Suggested by Danny Milosavljevic <dannym@scratchpost.org>
at <https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00456.html>.

* guix/build/syscalls.scm (fdatasync): New procedure.
* guix/utils.scm (with-atomic-file-output): Use it.  Use 'close-port'
instead of 'close'.
 2016-06-13 18:05:54 +02:00
Ricardo Wurmus
9f8ee3fe0e
gnu: Add python-tables. 
* gnu/packages/python.scm (python-tables, python2-tables): New
  variables.
 2016-06-13 18:01:02 +02:00
Ricardo Wurmus
883302daf2
gnu: piranha: Update to 1.2.1. 
* gnu/packages/bioinformatics.scm (piranha): Update to 1.2.1.
 2016-06-13 11:53:38 +02:00