192e1ea8d1
gnu: r-summarizedexperiment: Update to 1.2.2.
...
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.2.
2016-05-20 15:18:23 +02:00
d7420566a9
gnu: r-biocparallel: Update to 1.6.2.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.2.
2016-05-20 15:18:23 +02:00
73af676feb
gnu: r-annotationdbi: Update to 1.34.2.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.2.
2016-05-20 15:18:23 +02:00
679e670b36
gnu: r-variantannotation: Update to 1.18.1.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.1.
2016-05-20 15:18:23 +02:00
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
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
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
0c56023557
gnu: r-graph: Update to 1.50.0.
...
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.50.0.
2016-05-16 20:58:08 +02:00
c12b0a5a30
gnu: r-genomicfeatures: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.0.
2016-05-16 20:57:55 +02:00
d23fbf1eb9
gnu: r-rtracklayer: Update to 1.32.0.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.0.
2016-05-16 20:57:43 +02:00
3cd551ea7b
gnu: r-genomicalignments: Update to 1.8.0.
...
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.0.
2016-05-16 20:57:30 +02:00
d848ed7cf2
gnu: r-summarizedexperiment: Update to 1.2.0.
...
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.0.
2016-05-16 20:57:21 +02:00
b4c5a0db22
gnu: r-rsamtools: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.24.0.
2016-05-16 20:57:10 +02:00
2477d9773a
gnu: r-biostrings: Update to 2.40.0.
...
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.0.
2016-05-16 20:56:58 +02:00
6a2a0de1ab
gnu: r-biocparallel: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.0.
2016-05-16 20:56:39 +02:00
63cea37234
gnu: r-biomart: Update to 2.28.0.
...
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.28.0.
2016-05-16 20:56:29 +02:00
c4a4e17938
gnu: r-annotationdbi: Update to 1.34.0.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.0.
2016-05-16 20:56:19 +02:00
4466a02c9f
gnu: r-biobase: Update to 2.32.0.
...
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.32.0.
2016-05-16 20:56:09 +02:00
828980cad6
gnu: r-genomicranges: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.0.
2016-05-16 20:55:58 +02:00
e782ca3e97
gnu: r-xvector: Update to 0.12.0.
...
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.0.
2016-05-16 20:55:46 +02:00
052ee32b24
gnu: r-variantannotation: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to
1.18.0.
2016-05-16 20:55:32 +02:00
d1ab3d8fa5
gnu: r-genomeinfodb: Update to 1.8.0.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.0.
2016-05-16 20:55:20 +02:00
952ff8c862
gnu: r-iranges: Update to 2.6.0.
...
* gnu/packages/bioinformatics (r-iranges): Update to 2.6.0.
2016-05-16 20:55:11 +02:00
3654a61146
gnu: r-s4vectors: Update to 0.10.0.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.0.
2016-05-16 20:54:59 +02:00
a936bf59ea
gnu: r-dnacopy: Update to 1.46.0.
...
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.46.0.
2016-05-16 20:54:37 +02:00
dbfeba5209
gnu: r-biocgenerics: Update to 0.18.0.
...
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.18.0.
2016-05-16 20:53:48 +02:00
af3ac1f5f7
gnu: imagemagick: Update to 6.9.4-1.
...
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.4-1.
2016-05-16 14:27:48 -04:00
b6c2f7dafd
gnu: libgit2: Update to 0.24.1.
...
* gnu/packages/version-control.scm (libgit2): Update to 0.24.1.
2016-05-16 19:34:49 +03:00
8a0ac5bd55
gnu: tmux: Update to 2.2.
...
* gnu/packages/tmux.scm (tmux): Update to 2.2.
2016-05-16 19:34:49 +03:00
d3699b311b
gnu: Add ledger.
...
* gnu/packages/finance.scm (ledger): New variable.
Co-authored-by: Alex Kost <alezost@gmail.com>
2016-05-16 18:01:18 +03:00
f17a544756
gnu: Add utfcpp.
...
* gnu/packages/textutils.scm (utfcpp): New variable.
Signed-off-by: Alex Kost <alezost@gmail.com>
2016-05-16 18:01:18 +03:00
80ed14d38f
gnu: asymptote: Install Emacs data.
...
* gnu/packages/plotutils.scm (asymptote)[arguments]: Add a phase to
install Emacs-Lisp files in an appropriate place.
Signed-off-by: Alex Kost <alezost@gmail.com>
2016-05-16 18:01:18 +03:00
47c96a577d
gnu: mu: Update to 0.9.16.
...
* gnu/packages/mail.scm (%mu-gtester-patch): Remove.
(mu): Update to 0.9.16.
[source]: Remove 'patches'.
2016-05-16 18:01:18 +03:00
704f219668
gnu: mu: Install emacs autoloads.
...
* gnu/packages/mail.scm (mu)[arguments]: Add 'install-emacs-autoloads'
phase. Use appropriate modules and imported-modules.
2016-05-16 18:01:18 +03:00
789bda83d2
gnu: mu: Install emacs files in a proper place.
...
* gnu/packages/mail.scm (mu)[arguments]: Add 'patch-configure.ac' phase
to avoid adding "mu4e" sub-directory to 'lispdir' variable.
2016-05-16 18:01:18 +03:00
99404fff9f
gnu: mu: Use 'modify-phases'.
...
* gnu/packages/mail.scm (mu): Use 'modify-phases'.
2016-05-16 18:01:18 +03:00
7d0c3c8d01
gnu: python-pandas: Update to 0.18.1.
...
* gnu/packages/python.scm (python-pandas): Update to 0.18.1.
[native-inputs]: Remove python-setuptools.
[properties]: Define python2-pandas.
(python2-pandas)[native-inputs]: Add python2-setuptools.
* gnu/packages/patches/python-pandas-fix-tslib-test-failure.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2016-05-16 17:39:42 +03:00
8226c2717c
gnu:: java-swt: Use ant-build-system.
...
* gnu/packages/java.scm (java-swt): Use ant-build-system.
[native-inputs]: Remove JDK.
2016-05-16 16:17:18 +02:00
81b98756a3
gnu: Add SBC.
...
* gnu/packages/linux.scm (sbc): New variable.
2016-05-16 16:16:21 +02:00
002528bca5
gnu: rapicorn: Fix tests.
...
* gnu/packages/graphics.scm (rapicorn)[arguments]: Add build phases
"fix-tests" and "pre-check". Generalize "replace-/bin/ls" phase to
"replace-fhs-paths".
[propagated-inputs]: Add python2-enum34.
[native-inputs]: Add xorg-server.
2016-05-16 16:16:15 +02:00
44877dcc66
gnu: hugs: Update urls.
...
* gnu/packages/hugs.scm (hugs)[source]: Update url.
[home-page]: Use https.
2016-05-16 14:47:59 +03:00
a83e604662
gnu: hmmer: Update urls.
...
* gnu/packages/bioinformatics.scm (hmmer)[source]: Project has moved to
eddylab, with their downloads.
[home-page]: Update to new homepage.
2016-05-16 14:28:53 +03:00
d03f944614
gnu: guile-irregex: Update to 0.9.4.
...
* gnu/packages/guile.scm (guile-irregex): Update to 0.9.4.
2016-05-16 14:18:21 +03:00
3a66217ff2
gnu: gkrellm: Update urls.
...
* gnu/packages/gkrellm.scm (gkrellm)[source]: Download from new site.
[home-page]: Update to new site.
2016-05-16 14:12:54 +03:00
bf512da1e4
gnu: giblib: Add mirror for source.
...
* gnu/packages/image.scm (giblib)[source]: Add a download mirror from
slackbuilds.
2016-05-16 14:07:47 +03:00
284539ce86
gnu: geeqie: Update source location.
...
* gnu/packages/geeqie.scm (geeqie)[source]: Download from Github.
[home-page]: Project has moved to new url.
2016-05-16 12:59:40 +03:00
fd02719c7b
gnu: fvwm: Update to 2.6.6.
...
* gnu/packages/fvwm.scm (fvwm): Update to 2.6.6.
[source]: Change download location to Github.
2016-05-16 12:31:25 +03:00
66395a6157
gnu: gmsh: Add missing inputs.
...
* gnu/packages/maths.scm (gmsh)[inputs]: Add fontconfig, libxft.
2016-05-16 10:18:43 +03:00
b4370be9de
gnu: python-cryptography, python-cryptography-vectors: Update to 1.3.2.
...
* gnu/packages/python.scm (python-cryptography): Update to 1.3.2.
(python-cryptography-vectors): Update to 1.3.2.
2016-05-16 02:13:18 -04:00
3fef0a2fa1
gnu: unixodbc: Update to 2.3.4.
...
* gnu/packages/databases.scm (unixodbc): Update to 2.3.4.
2016-05-16 06:10:06 +03:00
6747a852c5
gnu: tdb: Update to 1.3.9.
...
* gnu/packages/databases.scm (tdb): Update to 1.3.9.
2016-05-16 06:10:06 +03:00
ec374039e4
gnu: postgresql: Update to 9.5.3.
...
* gnu/packages/databases.scm (postgresql): Update to 9.5.3.
2016-05-16 06:10:06 +03:00
9a12ca7771
gnu: wireless-regdb: Update to 2016.05.02.
...
* gnu/packages/linux.scm (wireless-regdb): Update to 2016.05.02.
2016-05-16 06:10:06 +03:00
2f9e312a39
gnu: iw: Update to 4.3.
...
* gnu/packages/linux.scm (iw): Update to 4.3.
[source]: Use kernel mirror.
[home-page]: Update to new home-page.
2016-05-16 06:10:06 +03:00
30897c60a4
gnu: mdadm: Update to 3.4.
...
* gnu/packages/linux.scm (mdadm): Update to 3.4.
[source]: Remove patch.
* gnu/packages/patches/mdadm-gcc-4.9-fix.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2016-05-16 06:10:06 +03:00
e9eb24b1b2
gnu: bluez: Update to 5.39.
...
* gnu/packages/linux.scm (bluez): Update to 5.39.
[source]: Use kernel mirror.
2016-05-16 06:10:06 +03:00
2b193389d2
gnu: libical: Update to 2.0.0.
...
* gnu/packages/calendar.scm (libical): Update to 2.0.0.
[arguments]: Add configure-flag to add "/lib64" to the rpath.
2016-05-16 06:10:06 +03:00
Ricardo Wurmus