99caa6f75f
gnu: python-plastid: Update to 1.4.6.
...
* gnu/packages/bioinformatics.scm (python-plastid, python2-plastid): Update to
1.4.6.
[propagated-inputs]: Add python-termcolor.
2016-09-27 20:07:12 +10:00
67f66812f5
gnu: Add python-termcolor.
...
* gnu/packages/python.scm (python-termcolor, python2-termcolor): New
variables.
2016-09-27 20:07:02 +10:00
f536dce522
gnu: python-pysam: Enable tests.
...
* gnu/packages/bioinformatics.scm (python-pysam)[source]: Change from
PyPi to source archive due to missing test data.
[arguments]: Add check phase after install.
[native-inputs]: Add python-nose, samtools and bcftools.
2016-09-27 20:06:00 +10:00
dff26b2363
gnu: python-pysam: Delete bundled htslib.
...
* gnu/packages/bioinformatics.scm (python-pysam)[source]: Add snippet
to delete htslib.
[arguments]: Add htslib flags in 'set-flags phase.
[propagated-inputs]: New field. Add htslib.
2016-09-27 20:06:00 +10:00
397d463a12
gnu: python-pysam: Use 'modify-phases'.
...
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Use
'modify-phases'.
2016-09-27 20:06:00 +10:00
bdc7be59eb
gnu: Add bcftools.
...
* gnu/packages/bioinformatics.scm (bcftools): New variable.
2016-09-27 20:06:00 +10:00
e301bfc886
gnu: python2-pbcore: Update to 1.2.10.
...
* gnu/packages/bioinformatics.scm (python2-pbcore): Update to 1.2.10.
[propagated-inputs]: New field. Add python2-pyxb.
2016-09-27 20:06:00 +10:00
c2efe1aea8
gnu: Add python-pyxb.
...
* gnu/packages/xml.scm (python-pyxb, python2-pyxb): New variables.
2016-09-27 20:06:00 +10:00
fd49eb213f
gnu: python-pysam: Update to 0.9.1.4.
...
* gnu/packages/bioinformatics.scm (python-pysam, python2-pysam): Update
to 0.9.1.4.
2016-09-27 20:05:57 +10:00
9ad0965228
gnu: openssl-next: Update to 1.1.0b [fixes CVE-2016-6309].
...
* gnu/packages/tls.scm (openssl-next): Update to 1.1.0b.
2016-09-26 17:09:08 -04:00
8be42e5daf
gnu: openssl: Update replacement to 1.0.2j [fixes CVE-2016-7052].
...
* gnu/packages/tls.scm (openssl): Update replacement to 1.0.2j.
(openssl-1.0.2i): Replace with...
(openssl-1.0.2j): ... new variable.
2016-09-26 17:09:05 -04:00
58478cc1cb
gnu: libftdi: Propagate the libusb input.
...
* gnu/packages/libftdi.scm (libftdi): Change libusb from an input to a
propagated-input.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-09-26 14:30:37 -04:00
675d7ae26f
gnu: ncbi-vdb: Only build on i686 and x86_64.
...
* gnu/packages/bioinformatics.scm (ncbi-vdb)[supported-systems]: Only
build on i686 and x86_64.
[arguments]: Add mandatory "-msse2" flag to CFLAGS.
2016-09-26 14:30:59 +02:00
bc600b80a2
gnu: ghc-pandoc: Update to 1.17.2.
...
* gnu/packages/haskell.scm (ghc-pandoc): Update to 1.17.2.
2016-09-26 14:30:59 +02:00
5a502d9abd
gnu: ghc-texmath: Update to 0.8.6.5.
...
* gnu/packages/haskell.scm (ghc-texmath): Update to 0.8.6.5.
2016-09-26 14:30:58 +02:00
2e9b1276b7
gnu: ghc-cmark: Update to 0.5.3.1.
...
* gnu/packages/haskell.scm (ghc-cmark): Update to 0.5.3.1.
2016-09-26 14:30:58 +02:00
8f1e2dca55
gnu: ghc-highlighting-kate: Update to 0.6.3.
...
* gnu/packages/haskell.scm (ghc-highlighting-kate): Update to 0.6.3.
2016-09-26 14:30:58 +02:00
ae87e4fcde
gnu: ghc-pandoc-types: Update to 1.16.1.1.
...
* gnu/packages/haskell.scm (ghc-pandoc-types): Update to 1.16.1.1.
2016-09-26 14:30:58 +02:00
1da48e4302
gnu: ghc-tagsoup: Update to 0.14.
...
* gnu/packages/haskell.scm (ghc-tagsoup): Update to 0.14.
2016-09-26 14:30:58 +02:00
1a545a1e7c
gnu: tbb: Fail on test errors.
...
* gnu/packages/tbb.scm (tbb)[arguments]: Add phase
"fail-on-test-errors".
2016-09-26 14:30:58 +02:00
ba4529c4f7
gnu: ghc-tls: Update to 1.3.8.
...
* gnu/packages/haskell.scm (ghc-tls): Update to 1.3.8.
2016-09-26 14:30:57 +02:00
7f5ca399bf
gnu: tbb: Use modify-phases syntax.
...
* gnu/packages/tbb.scm (tbb)[arguments]: Use "modify-phases" syntax.
2016-09-26 14:30:57 +02:00
af8de20386
gnu: vsearch: Update to 2.1.1.
...
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.1.1.
2016-09-26 20:35:32 +10:00
204adc3017
gnu: azr3: Fix libsigc++ build errors.
...
* gnu/packages/audio.scm (azr3)[arguments]: Add "-std=gnu++11" flag.
[source]: Add patch.
* gnu/packages/patches/azr3.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
2016-09-26 10:47:58 +02:00
3ef08dceb3
gnu: qtractor: Update to 0.7.9.
...
* gnu/packages/music.scm (qtractor): Update to 0.7.9.
2016-09-26 08:16:13 +02:00
f3cfe4515a
gnu: Add r-txdb-hsapiens-ucsc-hg19-knowngene.
...
* gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene):
New variable.
2016-09-26 07:47:55 +02:00
684f29bd2e
gnu: Add r-grohmm.
...
* gnu/packages/bioinformatics.scm (r-grohmm): New variable.
2016-09-26 07:47:55 +02:00
7f903d7300
gnu: Add r-systempiper.
...
* gnu/packages/bioinformatics.scm (r-systempiper): New variable.
2016-09-26 07:47:55 +02:00
cb99d457f0
gnu: Add r-shortread.
...
* gnu/packages/bioinformatics.scm (r-shortread): New variable.
2016-09-26 07:47:54 +02:00
89f40c5e4e
gnu: Add r-gostats.
...
* gnu/packages/bioinformatics.scm (r-gostats): New variable.
2016-09-26 07:47:54 +02:00
1a1931f7e0
gnu: Add r-category.
...
* gnu/packages/bioinformatics.scm (r-category): New variable.
2016-09-26 07:47:54 +02:00
ad740ff818
gnu: Add r-gseabase.
...
* gnu/packages/bioinformatics.scm (r-gseabase): New variable.
2016-09-26 07:47:53 +02:00
cd9e7dc7ff
gnu: Add r-rbgl.
...
* gnu/packages/bioinformatics.scm (r-rbgl): New variable.
2016-09-26 03:25:23 +02:00
e816377374
gnu: Add r-annotationforge.
...
* gnu/packages/bioinformatics.scm (r-annotationforge): New variable.
2016-09-26 03:25:17 +02:00
9e330278ee
gnu: Add r-batchjobs.
...
* gnu/packages/statistics.scm (r-batchjobs): New variable.
2016-09-26 03:25:11 +02:00
dc4fb16d25
gnu: Add r-fail.
...
* gnu/packages/statistics.scm (r-fail): New variable.
2016-09-26 03:25:06 +02:00
cd26ec3bbf
gnu: Add r-bbmisc.
...
* gnu/packages/statistics.scm (r-bbmisc): New variable.
2016-09-26 03:25:02 +02:00
929d4aaea1
gnu: Add r-checkmate.
...
* gnu/packages/statistics.scm (r-checkmate): New variable.
2016-09-26 03:24:59 +02:00
0d90462fa3
gnu: Add r-backports.
...
* gnu/packages/statistics.scm (r-backports): New variable.
2016-09-26 03:24:55 +02:00
8e1bfc7e8c
gnu: Add r-sendmailr.
...
* gnu/packages/statistics.scm (r-sendmailr): New variable.
2016-09-26 03:24:50 +02:00
0c77fd50f8
gnu: Add r-pheatmap.
...
* gnu/packages/statistics.scm (r-pheatmap): New variable.
2016-09-26 03:24:44 +02:00
092197a548
gnu: Add r-matrix.
...
* gnu/packages/statistics.scm (r-matrix): New variable.
2016-09-26 03:21:32 +02:00
ad34f0ac96
gnu: Add r-deseq2.
...
* gnu/packages/bioinformatics.scm (r-deseq2): New variable.
2016-09-26 03:21:27 +02:00
2301fd3e4d
gnu: Add r-genefilter.
...
* gnu/packages/bioinformatics.scm (r-genefilter): New variable.
2016-09-26 03:21:19 +02:00
2d21d44dbd
gnu: Add r-hmisc.
...
* gnu/packages/statistics.scm (r-hmisc): New variable.
2016-09-26 03:21:13 +02:00
07a664cde0
gnu: Add r-geneplotter.
...
* gnu/packages/bioinformatics.scm (r-geneplotter): New variable.
2016-09-26 03:21:07 +02:00
8c6de58849
gnu: Add r-annotate.
...
* gnu/packages/bioinformatics.scm (r-annotate): New variable.
2016-09-26 03:20:59 +02:00
2213730c5b
gnu: Add r-rpart.
...
* gnu/packages/statistics.scm (r-rpart): New variable.
2016-09-26 03:20:52 +02:00
356c6d61a6
gnu: Add r-rjson.
...
* gnu/packages/web.scm (r-rjson): New variable.
2016-09-26 03:20:44 +02:00
bbed0ab6b4
gnu: Add r-hwriter.
...
* gnu/packages/web.scm (r-hwriter): New variable.
2016-09-26 03:20:19 +02:00
57a31efb4b
gnu: tcc: Disable build on MIPS.
...
* gnu/packages/c.scm (tcc)[supported-systems]: Disable build on
mips64el.
2016-09-26 03:01:06 +02:00
9311722703
gnu: Add optipng.
...
* gnu/packages/image.scm (optipng): New variable.
Signed-off-by: Kei Kebreau <kei@openmailbox.org>
2016-09-25 16:53:00 -04:00
217f3fdfe6
gnu: openldap: Use gnutls.
...
* gnu/packages/openldap.scm (openldap)[inputs]: Switch to gnutls.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2016-09-25 22:25:02 +03:00
7acd71d13d
gnu: epiphany: Drop NSS and libwnck.
...
These dependencies were dropped in Epiphany 3.21.x.
* gnu/packages/gnome.scm (epiphany)[inputs]: Remove "nss" and "libwnck".
2016-09-25 13:04:00 +02:00
9f58932ecc
gnu: epiphany: Update to 3.22.0.
...
* gnu/packages/gnome.scm (epiphany): Update to 3.22.0.
2016-09-25 13:04:00 +02:00
58d04dbaf0
gnu: python-virtualenv: Update to 15.0.3.
...
* gnu/packages/python.scm (python-virtualenv): Update to 15.0.3.
[arguments]: Disable failing test.
2016-09-25 13:04:00 +02:00
1535c0a6b6
gnu: linux-libre: Update to 4.7.5.
...
* gnu/packages/linux.scm (linux-libre): Update to 4.7.5.
2016-09-25 03:57:57 -04:00
dfcce0cc8d
gnu: linux-libre@4.4: Update to 4.4.22.
...
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.22.
2016-09-25 03:55:37 -04:00
94c5dc8c03
gnu: Add pam-krb5
...
* gnu/packages/admin.scm (pam-krb5): New variable.
2016-09-25 06:40:29 +02:00
9f2989b6cc
gnu: perl: Split configure phase.
...
* gnu/packages/perl.scm (perl)[arguments]: Split 'configure' phase into
'setup-configure' and 'configure' phases.
2016-09-25 10:09:00 +10:00
a8f3d49280
gnu: privoxy: Update to 3.0.26.
...
* gnu/packages/tor.scm (privoxy): Update to 3.0.26.
[home-page]: Use https.
2016-09-24 23:09:14 +03:00
0ab57b0d04
gnu: tor: Update to 0.2.8.8.
...
* gnu/packages/tor.scm (tor): Update to 0.2.8.8.
[source]: Update source url.
[home-page]: Use https.
2016-09-24 22:27:16 +03:00
b5b5105c3d
gnu: xorg-server: Set default font path to empty.
...
* gnu/packages/xorg.scm (xorg-server)[arguments]: Pass
"--with-default-font-path=" to #:configure-flags.
2016-09-24 14:28:09 +08:00
6fc48c2ee2
gnu: Add gforth.
...
* gnu/packages/gforth.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
Co-authored-by: 宋文武 <iyzsong@gmail.com>
2016-09-24 14:07:12 +08:00
54021cd8c6
gnu: Add gnome-calculator.
...
* gnu/packages/gnome.scm (gnome-calculator): New variable.
Signed-off-by: Kei Kebreau <kei@openmailbox.org>
2016-09-24 00:51:52 -04:00
8058880017
gnu: Add cmark.
...
* gnu/packages/markdown.scm (cmark): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-09-23 20:56:51 -04:00
93666cf783
gnu: Add enet.
...
* gnu/packages/networking.scm (enet): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-09-23 19:18:10 -04:00
03ddad84ba
gnu: flashrom: Update to 0.9.9
...
* gnu/packages/flashing-tools.scm (flashrom): Update to 0.9.9.
[source]: Use HTTPS URL. Remove "flashrom-use-libftdi1.patch".
[aruments]: Add 'CONFIG_ENABLE_LIBUSB0_PROGRAMMERS=no' to #:make-flags.
* gnu/packages/patches/flashrom-use-libftdi1.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-09-23 19:03:19 -04:00
0f5de84e98
gnu: Add nickle.
...
* gnu/packages/nickle.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-09-23 18:54:24 -04:00
047cd01d11
gnu: orpheus: Use 'modify-phases'.
...
* gnu/packages/orpheus.scm (orpheus)[arguments]: Use the 'modify-phases'
syntax.
2016-09-23 17:38:25 +03:00
5bd6270211
gnu: orpheus: Fix build on mips64el.
...
* gnu/packages/orpheus.scm (orpheus)[arguments]: On mips64el, pass
"--host=mips64el-unknown-linux-gnu" to ./configure.
2016-09-23 17:38:24 +03:00
236d522b80
gnu: giac-xcas: Update to 1.2.2-81.
...
* gnu/packages/algebra.scm (giac-xcas): Update to 1.2.2-81.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-09-23 09:57:20 -04:00
8f309571d3
gnu: r-curl: Respect CURL_CA_BUNDLE variable.
...
* gnu/packages/web.scm (r-curl)[arguments]: Add phase
"allow-CURL_CA_BUNDLE".
2016-09-23 13:13:41 +02:00
646a84338d
gnu: sra-tools: Update to 2.7.0.
...
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.7.0.
2016-09-23 11:46:53 +02:00
40974c933e
gnu: ncbi-vdb: Update to 2.7.0.
...
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.7.0.
2016-09-23 11:46:26 +02:00
48b419ebd6
gnu: ngs-sdk: Update to 1.2.5.
...
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.5.
2016-09-23 11:45:24 +02:00
4781820147
gnu: randomjungle: Only build on x86_64 and i686.
...
* gnu/packages/machine-learning.scm (randomjungle)[supported-systems]:
Only build on x86_64 and i686.
2016-09-23 08:23:51 +02:00
fc3b2cbb04
gnu: retroarch: Update to 1.3.6.
...
* gnu/packages/games.scm (retroarch): Update to 1.3.6.
2016-09-23 09:02:03 +03:00
5989d4eaac
gnu: synfig: Fix isnan error.
...
* gnu/packages/animation.scm (synfig)[arguments]: Add build phase to
replace "::isnan" with "std::isnan".
2016-09-23 07:45:16 +02:00
56f33f3fd5
gnu: ccache: Upgrade to 3.3.1.
...
* gnu/packages/ccache.scm (ccache): Upgrade to 3.3.1.
[description]: Adjust supported languages.
2016-09-22 23:56:17 -05:00
bd368c7174
gnu: ccache: Use modify-phases.
...
* gnu/packages/ccache.scm (ccache)[arguments]: Use modify-phases.
2016-09-22 23:43:20 -05:00
1a0ae573c7
gnu: boost: Add -j for build.
...
* gnu/packages/boost.scm (boost)[arguments]: Add -j flag for build
phase.
2016-09-22 22:34:04 -05:00
6941965526
gnu: boost: Upgrade to 1.61.0.
...
* gnu/packages/boost.scm (boost): Upgrade to 1.61.0
* gnu/packages/databases.scm (mysql)[arguments]: Compute boost minor
version for substitution.
2016-09-22 22:33:37 -05:00
71b611bc34
gnu: Add ghc-transformers-0.4.2.0.
...
* gnu/packages/haskell.scm (ghc-transformers-0.4.2.0): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-09-22 20:10:01 -04:00
10a03d6665
gnu: Add ghc-system-fileio.
...
* gnu/packages/haskell.scm (ghc-system-fileio): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-09-22 20:10:00 -04:00
23feb6e4fb
gnu: Add ghc-system-filepath.
...
* gnu/packages/haskell.scm (ghc-system-filepath): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-09-22 20:10:00 -04:00
58c85b1f82
gnu: Add ghc-options.
...
* gnu/packages/haskell.scm (ghc-options): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-09-22 20:10:00 -04:00
c92d944c1e
gnu: Add ghc-chell-quickcheck.
...
* gnu/packages/haskell.scm (ghc-chell-quickcheck): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-09-22 20:10:00 -04:00
475d366866
gnu: Add ghc-chell-quickcheck-bootstrap.
...
* gnu/packages/haskell.scm (ghc-chell-quickcheck-bootstrap): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-09-22 20:09:59 -04:00
8ea94489fd
gnu: Add ghc-chell.
...
* gnu/packages/haskell.scm (ghc-chell): New variables.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-09-22 20:09:59 -04:00
7e06c4aa98
gnu: Add ghc-options-bootstrap.
...
* gnu/packages/haskell.scm (ghc-options-bootstrap): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-09-22 20:09:59 -04:00
25b3bdb5ff
gnu: Add ghc-shelly.
...
* gnu/packages/haskell.scm (ghc-shelly): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-09-22 20:09:59 -04:00
3f7aa1029b
gnu: Add ghc-system-fileio-bootstrap.
...
* gnu/packages/haskell.scm (ghc-system-fileio-bootstrap): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-09-22 20:09:58 -04:00
ddd5955b1e
gnu: Add ghc-system-filepath-bootstrap.
...
* gnu/packages/haskell.scm (ghc-system-filepath-bootstrap): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-09-22 20:09:58 -04:00
2b41f4afc1
gnu: Add ghc-lifted-async.
...
* gnu/packages/haskell.scm (ghc-lifted-async): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-09-22 20:09:58 -04:00
6aab9ba6d4
gnu: Add ghc-constraints.
...
* gnu/packages/haskell.scm (ghc-constraints): New variable.
2016-09-22 20:09:58 -04:00
e7e2f03c8f
gnu: Add ghc-array.
...
* gnu/packages/haskell.scm (ghc-array): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-09-22 20:09:57 -04:00
3db882776b
gnu: Add ghc-graphviz.
...
* gnu/packages/haskell.scm (ghc-graphviz): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-09-22 20:09:57 -04:00
d4cca6b0ae
gnu: Add ghc-fgl-arbitrary.
...
* gnu/packages/haskell.scm (ghc-fgl-arbitrary): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-09-22 20:09:57 -04:00
ce242fd05e
gnu: ghc-fgl: Update to 5.5.3.0.
...
* gnu/packages/haskell.scm (ghc-fgl): Update to 5.5.3.0.
[inputs]: Add ghc-hspec and ghc-quickcheck.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-09-22 20:09:57 -04:00
Ben J Woodcroft