186ed87337
gnu: r-genomeinfodb: Update to 1.8.1.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.1.
2016-05-20 15:18:23 +02:00
0fc4a8afba
gnu: btrfs-progs: Update to 4.5.3.
...
* gnu/packages/linux.scm (btrfs-progs): Update to 4.5.3.
2016-05-19 21:04:22 -04:00
0e40755d35
gnu: jemalloc: Update to 4.2.0.
...
* gnu/packages/jemalloc.scm (jemalloc): Update to 4.2.0.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2016-05-19 20:43:13 +03:00
119b83989d
gnu: expat: Fix CVE-2016-0718. Improve fix for CVE-2015-1283.
...
* gnu/packages/patches/expat-CVE-2015-1283-refix.patch,
gnu/packages/patches/expat-CVE-2016-0718.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/xml.scm (expat)[replacement]: New field.
(expat/fixed): New variable.
[source]: Use new patches.
2016-05-19 10:27:18 -04:00
9684e30b9b
gnu: flann: Do not install .a files.
...
* gnu/packages/maths.scm (flann)[arguments]: Add #:phases.
2016-05-19 14:51:21 +02:00
458480235b
gnu: python: Add 'python' variables for different major/minor versions.
...
* gnu/packages/python.scm (python-2): Rename variable to...
(python-2.7): ...this.
(python-2): Refer to "python-2.7".
(python): Rename variable to...
(python-3.4): ...this.
(python-3): Refer to "python-3.4".
(python): Refer to "python-3".
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-05-19 14:51:21 +02:00
39b3033731
gnu: flann: Strip .mex file.
...
* gnu/packages/maths.scm (flann)[arguments]: Add #:strip-directories.
2016-05-19 14:51:21 +02:00
0947698c42
gnu: Add r-biased-urn.
...
* gnu/packages/statistics.scm (r-biased-urn): New variable.
2016-05-19 22:13:43 +10:00
44c5f0258d
gnu: giflib: Use 'modify-phases'.
...
* gnu/packages/image.scm (giflib)[arguments]: Use 'modify-phases'.
2016-05-19 13:06:49 +03:00
3fdb2a84be
gnu: giflib: Update to 5.1.4 [fixes CVE-2015-7555, CVE-2016-3977].
...
* gnu/packages/image.scm (giflib): Update to 5.1.4.
2016-05-19 13:01:55 +03:00
5c447e280e
gnu: Add emacs-smartparens.
...
* gnu/packages/emacs.scm (emacs-smartparens): New variable.
Signed-off-by: Alex Kost <alezost@gmail.com>
2016-05-19 11:45:15 +03:00
21f05134fc
Update name for Kei Kebreau.
...
* .mailmap: Add Kei Kebreau.
* gnu/local.mk: Replace "Kei Yamashita" with "Kei Kebreau".
* gnu/packages/calendar.scm: Likewise.
* gnu/packages/dillo.scm: Likewise.
* gnu/packages/fltk.scm: Likewise.
* gnu/packages/game-development.scm: Likewise.
* gnu/packages/games.scm: Likewise.
* gnu/packages/gnome.scm: Likewise.
* gnu/packages/gtk.scm: Likewise.
* gnu/packages/music.scm: Likewise.
* gnu/packages/xfce.scm: Likewise.
Signed-off-by: Alex Kost <alezost@gmail.com>
2016-05-19 11:42:03 +03:00
b7b27a8f28
gnu: octave: Update to 4.0.2.
...
* gnu/packages/maths.scm (octave): Update to 4.0.2.
[inputs]: Added cyrus-sasl, openssl.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2016-05-19 04:32:23 +03:00
91231156ce
gnu: Add ntfs-3g.
...
* gnu/packages/linux.scm (ntfs-3g): New variable.
2016-05-18 23:41:03 +02:00
64851f4a23
gnu: wmbattery: Fix UPower-related memory leak.
...
* gnu/packages/gnustep.scm (wmbattery)[source](snippet): New field.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-05-18 23:41:03 +02:00
65e46ca0ed
gnu: qtkeychain: Update to 0.6.2.
...
* gnu/packages/qt.scm (qtkeychain): Update to 0.6.2.
2016-05-18 18:06:47 +03:00
bd9fe0f03b
gnu: Add krona-tools.
...
* gnu/packages/web.scm (krona-tools): New variable.
2016-05-18 22:21:52 +10:00
0affdfb805
gnu: hurd-headers: Update to 0.8.
...
* gnu/packages/hurd.scm (hurd-headers): Update to version 0.8.
2016-05-18 15:17:52 +03:00
eb3be3a791
gnu: mig: Update to 1.7.
...
* gnu/packages/hurd.scm (mig): Update to version 1.7.
2016-05-18 15:17:44 +03:00
614f39271e
gnu: gnumach-headers: Update to 1.7.
...
* gnu/packages/hurd.scm (gnumach-headers): Update to version 1.7.
2016-05-18 15:17:38 +03:00
7c544991dc
gnu: diamond: Do not specify target architecture.
...
* gnu/packages/bioinformatics.scm (diamond)[arguments]: Do not
specify target architecture.
2016-05-18 21:25:06 +10:00
e62ffce538
gnu: Add Piranha.
...
* gnu/packages/bioinformatics.scm (piranha): New variable.
2016-05-18 11:59:34 +02:00
dbd40ac19d
gnu: python2-pandas: Fix native-inputs.
...
* gnu/packages/python.scm (python2-pandas)[native-inputs]: Use python2-
versions of python-panda's native-inputs, not of inputs.
2016-05-18 10:52:41 +03:00
f1876bfc7a
gnu: Add signify.
...
* gnu/packages/crypto.scm (signify): New variable.
2016-05-17 17:52:59 -04:00
ad42be8388
gnu: libndp: Update to 1.6 [fixes CVE-2016-3698].
...
* gnu/packages/networking.scm (libndp): Update to 1.6.
2016-05-17 14:31:09 -04:00
9576cc72dc
gnu: Add emacs-zenburn-theme.
...
* gnu/packages/emacs.scm (emacs-zenburn-theme): New variable.
Signed-off-by: Alex Kost <alezost@gmail.com>
2016-05-17 21:06:36 +03:00
fb2b0f5c87
gnu: gd: Fix-CVE-2016-3074.
...
* gnu/packages/patches/gd-CVE-2016-3074.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gd.scm (gd)[source]: Use it.
2016-05-17 13:18:15 -04:00
bbb5d8aeea
gnu: gd: Specify 'cpe-name'.
...
* gnu/packages/gd.scm (gd)[properties]: New field.
2016-05-17 18:15:59 +02:00
99effc8faa
lint: Honor 'cpe-name' and 'cpe-version' package properties.
...
* guix/scripts/lint.scm (package-name->cpe-name): Remove.
(package-vulnerabilities): Honor 'cpe-name' and 'cpe-version'
properties.
* gnu/packages/grub.scm (grub)[properties]: New field.
* gnu/packages/gnuzilla.scm (icecat)[properties]: Add 'cpe-name' and
'cpe-version'.
* doc/guix.texi (Invoking guix lint): Mention 'cpe-name'.
2016-05-17 18:15:53 +02:00
1c29f3ef84
gnu: emacs-constants: Remove old patch.
...
* gnu/packages/patches/emacs-constants-lisp-like.patch: Remove it.
* gnu/local.mk (dist_patch_DATA): Remove entry for above patch.
2016-05-17 14:17:38 +02:00
aa8fff0ceb
store: Clarify 'query-path-hash' docstring.
...
* guix/store.scm (query-path-hash): Clarify docstring.
2016-05-17 14:02:48 +02:00
149590380a
import: Gracefully report import failures.
...
Previously, something like 'guix import gnu which' would spit out a
backtrace if, say, the 'which' tarball could not be authenticated.
* guix/upstream.scm (download-tarball): Mention failure modes in
docstring.
* guix/import/gnu.scm (gnu-package->sexp): Return #f when
'download-tarball' returns #f.
* guix/scripts/import.scm (guix-import): Call 'leave' when IMPORTER does
not return a (package ...) sexp.
2016-05-17 14:02:48 +02:00
787afdd0f1
import: Exit with non-zero when an unknown importer is asked.
...
* guix/scripts/import.scm (guix-import): Use 'leave' instead of 'format'
when IMPORTER is unknown.
2016-05-17 14:02:48 +02:00
f99f3f24ef
gnu: emacs-constants: Update to 2.6.
...
* gnu/packages/emacs.scm (emacs-constants): Change to versioned repository and
update to 2.6.
2016-05-17 14:01:20 +02:00
849485f5a0
gnu: sortmerna: Update to 2.1b.
...
* gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1b.
[inputs]: New field.
2016-05-17 21:45:49 +10:00
daaeed765a
gnu: vsearch: Update to 1.11.1.
...
* gnu/packages/bioinformatics.scm (vsearch): Update to 1.11.1.
2016-05-17 21:36:46 +10:00
122395f9fc
gnu: diamond: Update to 0.8.1.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.1.
[source]: Remove 'snippet'.
[build-system]: Use cmake-build-system.
[arguments]: Remove modifications to phases.
[native-inputs]: Remove field.
[inputs]: Remove 'boost'.
2016-05-17 21:07:00 +10:00
a9e41d2faf
gnu: emacs-constants: Factorize home-page in source URL.
...
* gnu/packages/emacs.scm (emacs-constants): Move 'home-page' above. Use
it in 'uri'.
2016-05-17 09:41:40 +02:00
4f04243405
gnu: 'uncompressed-file-fetch' no longer depends on gzip.
...
* gnu/packages/emacs.scm (uncompressed-file-fetch): Remove dependency on
GZIP.
2016-05-17 09:41:40 +02:00
cb307c0833
gnu: cflow: Update to 1.5.
...
* gnu/packages/code.scm (cflow): Update to 1.5.
2016-05-17 09:04:38 +03:00
11e4c1fd10
gnu: Add geiser-next.
...
Also, I previously committed to this repository in 2015; add self to copyright
headers for that year too.
* gnu/packages/emacs.scm (geiser-next): New variable.
2016-05-16 14:48:57 -05:00
9916ae15bb
import cran: latest-bioconductor-release: Wrap Bioconductor URL in list.
...
* guix/import/cran.scm (latest-bioconductor-release): Wrap Bioconductor
URL in list in the "urls" field of the "upstream-source" value.
2016-05-16 21:00:41 +02:00
96101b6718
gnu: r-zlibbioc: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.18.0.
2016-05-16 20:59:50 +02:00
a0fe3aeecf
gnu: r-motifrg: Update to 1.16.0.
...
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.16.0.
2016-05-16 20:59:38 +02:00
1f5786a918
gnu: r-seqlogo: Update to 1.38.0.
...
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.38.0.
2016-05-16 20:59:27 +02:00
8adc3b628d
gnu: r-genomation: Update to 1.4.0.
...
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.4.0.
2016-05-16 20:59:14 +02:00
7555817c2b
gnu: r-seqpattern: Update to 1.4.0.
...
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.4.0.
2016-05-16 20:59:04 +02:00
d1bff89d26
gnu: r-impute: Update to 1.46.0.
...
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.46.0.
2016-05-16 20:58:49 +02:00
5190ed1751
gnu: r-bsgenome: Update to 1.40.0.
...
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.0.
2016-05-16 20:58:35 +02:00
e48e88c217
gnu: r-topgo: Update to 2.24.0.
...
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.24.0.
[propagated-inputs]: Add r-matrixstats.
2016-05-16 20:58:24 +02:00
Ricardo Wurmus