a2f6a3d502
gnu: Add vdirsyncer.
...
* gnu/packages/dav.scm (vdirsyncer): New variable.
2016-01-15 16:45:24 -05:00
f75bbb028a
gnu: Add radicale.
...
* gnu/packages/dav.scm (radicale): New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.
2016-01-15 16:45:24 -05:00
89b8a5516f
gnu: Add python-pytest-xprocess.
...
* gnu/packages/python.scm (python-pytest-xprocess): New variable.
2016-01-15 16:45:24 -05:00
28cecbb7cc
gnu: Add python-wsgi-intercept.
...
* gnu/packages/python.scm (python-wsgi-intercept): New variable.
2016-01-15 16:45:24 -05:00
d7e729fe08
gnu: Add python-pytest-localserver.
...
* gnu/packages/python.scm (python-pytest-localserver): New variable.
2016-01-15 16:45:24 -05:00
6720dbb49f
gnu: Add python-pytest-cache.
...
* gnu/packages/python.scm (python-pytest-cache): New variable.
2016-01-15 16:45:24 -05:00
848964fe11
gnu: Add python-execnet.
...
* gnu/packages/python.scm (python-execnet): New variable.
2016-01-15 16:45:24 -05:00
7b3a4ee4c3
gnu: Add python-apipkg.
...
* gnu/packages/python.scm (python-apipkg): New variable.
2016-01-15 16:45:24 -05:00
7b17cab902
gnu: Add python-click-log.
...
* gnu/packages/python.scm (python-click-log): New variable.
2016-01-15 16:45:24 -05:00
d1deb90b3f
gnu: Add python-click-threading.
...
* gnu/packages/python.scm (python-click-threading): New variable.
2016-01-15 16:45:24 -05:00
561bb3cb1a
gnu: Add python-requests-toolbelt.
...
* gnu/packages/python.scm (python-requests-toolbelt): New variable.
2016-01-15 16:45:24 -05:00
5c6eea2ad1
gnu: Add python-atomicwrites.
...
* gnu/packages/python.scm (python-atomicwrites): New variable.
2016-01-15 16:45:24 -05:00
f5ca44b86e
gnu: glade: Update to 3.18.5.
...
* gnu/packages/gnome.scm (glade): Update to 3.18.5.
[arguments]: Disable tests; add "fix-docbook" phase.
[inputs]: Replace "gtk+-2" with "gtk+".
[native-inputs]: Add "itstool", "libxslt", "docbook-xml", "docbook-xsl";
replace "python" with "python-2".
2016-01-15 22:29:37 +01:00
45f2ffb48c
gnu: openssh: Update to 7.1p2.
...
* gnu/packages/ssh.scm (openssh): Update to 7.1p2.
2016-01-15 02:46:12 -05:00
1beec63ac8
Revert "gnu: openssh: Update to 7.1p2 [fixes CVE-0216-0778]."
...
This reverts commit 6d139e53b5
2016-01-15 02:45:58 -05:00
6d139e53b5
gnu: openssh: Update to 7.1p2 [fixes CVE-0216-0778].
...
* gnu/packages/ssh.scm (openssh): Update to 7.1p2.
2016-01-14 10:39:00 -05:00
df1f1d6936
gnu: Add docker-compose.
...
* gnu/packages/docker.scm (docker-compose): New variable.
2016-01-14 09:17:12 -05:00
b42c9c8124
gnu: Add python-dockerpty.
...
* gnu/packages/docker.scm (python-dockerpty): New variable.
2016-01-14 09:16:22 -05:00
d020bfc2df
gnu: Add python-docker-py.
...
* gnu/packages/docker.scm: New file.
* Makefile.am (GNU_SYSTEM_MODULES): Add it.
2016-01-14 09:16:22 -05:00
67c52bb3e7
gnu: Add python-websocket-client.
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* gnu/packages/python.scm (python-websocket-client): New variable.
2016-01-14 09:12:23 -05:00
210bf49754
gnu: Add python-texttable.
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* gnu/packages/python.scm (python-texttable, python2-texttable): New
variables.
2016-01-14 09:12:23 -05:00
b3667afbd2
gnu: Update python-jsonschema to 2.5.1.
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* gnu/packages/python.scm (python-jsonschema): Update to 2.5.1.
[inputs]: Add python-vcversioner.
2016-01-14 09:12:06 -05:00
ea521b42c2
gnu: Add python-vcversioner.
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* gnu/packages/python.scm (python-vcversioner, python2-vcversioner): New
variables.
2016-01-14 09:05:19 -05:00
e90051808b
gnu: Add version 2.7 variant of python-requests.
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* gnu/packages/python.scm (python-requests-2.7): New variable.
2016-01-14 09:05:19 -05:00
3141b83d4d
gnu: r-go-db: Add missing input.
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* gnu/packages/bioinformatics.scm (r-go-db)[propagated-inputs]: Add
"r-annotationdbi".
2016-01-14 14:43:59 +01:00
d7786ce9b0
gnu: r-sparsem: Add missing "gfortran" input.
...
* gnu/packages/statistics.scm (r-sparsem)[inputs]: Add "gfortran".
2016-01-14 14:43:59 +01:00
0047d26a22
gnu: bowtie: Update to 2.2.6.
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* gnu/packages/bioinformatics.scm (bowtie): Update to 2.2.6.
[source]: Remove patch; do not set CC and CPP variables.
[inputs]: Add "tbb".
[arguments]: Pass "prefix" and "WITH_TBB" make flags; remove custom
"install" phase.
* gnu/packages/patches/bowtie-fix-makefile.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove patch file.
2016-01-14 14:43:25 +01:00
2d12284d38
gnu: gnupg: Add TOFU support.
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* gnu/packages/gnupg.scm (gnupg)[inputs]: Add sqlite.
2016-01-14 15:05:36 +02:00
6b6f7d6a0e
gnu: orfm: Update to 0.5.3.
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* gnu/packages/bioinformatics.scm (orfm): Update to 0.5.3.
[native-inputs]: Add inputs required for tests.
[description]: Add commas.
2016-01-14 08:00:10 +10:00
3d84a99e73
gnu: Add ruby-bio-commandeer.
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* gnu/packages/ruby.scm (ruby-bio-commandeer): New variable.
2016-01-14 08:00:02 +10:00
7c033c4627
gnu: Add ruby-systemu.
...
* gnu/packages/ruby.scm (ruby-systemu): New variable.
2016-01-14 07:51:44 +10:00
e5a19fed19
gnu: julia: Update to 0.4.3.
...
* gnu/packages/julia.scm (julia): Update to 0.4.3.
(libuv-julia): Update to 07730c4bd595.
2016-01-13 17:05:38 +01:00
75418ae0fd
gnu: isc-dhcp: Update to 4.3.3-P1 [fixes CVE-2015-8605].
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* gnu/packages/admin.scm (isc-dhcp): Update to 4.3.3-P1.
2016-01-13 09:38:57 -05:00
c44734115a
gnu: samtools: Update to 1.3.
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* gnu/packages/bioinformatics.scm (samtools): Update to 1.3.
[arguments]: Enable tests for all architectures; set ncurses in
configure-flags instead of make-flags; simplify "patch-tests" phase;
restore "configure" phase.
2016-01-13 15:12:22 +01:00
98f2339189
gnu: skribilo: Update to 0.9.3.
...
* gnu/packages/skribilo.scm (skribilo): Update to 0.9.3.
[native-inputs]: New field.
2016-01-13 11:13:34 +01:00
c91d3fb7f4
gnu: boost: Update to 1.60.0.
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* gnu/packages/boost.scm (boost): Update to 1.60.0.
[source]: Remove patch.
* gnu/packages/patches/boost-mips-avoid-m32.patch: Delete patch
* gnu-system.am (dist_patch_DATA): Remove patch.
Also fix dependent packages:
* gnu/packages/patches/csound-header-ordering.patch: New patch.
* gnu/packages/audio.scm (csound)[source]: Use it.
[arguments]: Add 'set-flags phase.
* gnu/packages/patches/libcmis-fix-test-onedrive.patch: New patch.
* gnu/packages/libreoffice.scm (libcmis)[source]: Use it.
(libreoffice)[arguments]: Add LDFLAGS to #:configure-flags.
(librevenge)[inputs]: Move boost from here...
[propogated-inputs]: to here.
[arguments]: Add LDFLAGS to #:configure-flags.
* gnu/packages/patches/openimageio-boost-1.60.patch: New patch.
* gnu/packages/graphics.scm (openimageio): Use it.
* gnu-system.am (dist_patch_DATA): Add patches.
2016-01-12 21:07:53 +01:00
3abe8136fd
gnu: boost: Use modify-phases.
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* gnu/packages/boost.scm (boost)[arguments]: Use modify-phases.
2016-01-12 20:53:14 +01:00
16aa649117
gnu: sudo: Add fix for CVE-2015-5602.
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* gnu/packages/patches/sudo-CVE-2015-5602.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/admin.scm (sudo)[source]: Add patch.
2016-01-12 11:23:06 -05:00
9d9951d6a6
gnu: global: Use modify-phases syntax.
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* gnu/packages/code.scm (global)[arguments]: Use modify-phases syntax.
2016-01-12 14:47:10 +02:00
94c3a6f1a6
gnu: global: Update to 6.5.2.
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* gnu/packages/code.scm (global): Update to 6.5.2.
2016-01-12 14:39:15 +02:00
9f40b1171b
gnu: icedtea-6: Fix directory name in "unpack" phase.
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* gnu/packages/java.scm (icedtea-6)[arguments]: Change the directory
prefix in the "unpack" phase to "icedtea6-".
2016-01-12 11:39:21 +01:00
6b0d24b17c
gnu: linux-libre: Update to 4.4.
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* gnu/packages/linux.scm (linux-libre): Update to 4.4.
* gnu/packages/linux-libre-i686.conf,
gnu/packages/linux-libre-x86_64.conf: Update from
<https://jxself.org/git/kernel-configs.git >.
2016-01-11 19:13:37 -05:00
81f3e0c1f3
gnu: Add fxtract.
...
* gnu/packages/bioinformatics.scm (fxtract): New variable.
2016-01-12 07:49:19 +10:00
ec70fec559
gnu: youtube-dl: Update to 2016.01.09.
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* gnu/packages/video.scm (youtube-dl): Update to 2016.01.09.
2016-01-11 13:30:50 +02:00
4879d2ff66
gnu: gp2c: Update to 0.0.9pl5.
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* gnu/packages/algebra.scm (gp2c): Update to 0.0.9pl5.
2016-01-11 11:24:52 +01:00
4a6635f353
gnu: texlive: Use modify-phases syntax.
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* gnu/packages/texlive.scm (texlive-bin, texlive-texmf): Use modify-phases
syntax.
2016-01-11 10:59:29 +01:00
a916c82649
gnu: man-pages: Update to 4.04.
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* gnu/packages/man.scm (man-pages): Update to 4.04.
[source]: Add alternate location.
2016-01-11 09:37:50 +02:00
9b9b7ffd8e
gnu: bedtools: Update to 2.25.0.
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* gnu/packages/bioinformatics.scm (bedtools): Update to 0.25.0.
[source]: Remove patch merged upstream.
[arguments]: Use 'modify-phases'. Remove
'patch-makefile-SHELL-definition' phase.
* gnu/packages/patches/bedtools-32bit-compilation.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove it.
2016-01-11 00:36:13 +10:00
6573ac82ad
gnu: bedtools: Use modify-phases.
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* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use modify-phases.
2016-01-11 00:36:13 +10:00
695bea9803
gnu: r: Update to 3.2.3.
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* gnu/packages/statistics.scm (r): Update to 3.2.3.
2016-01-09 23:18:28 +01:00
13035f5a03
gnu: icecat: Update to 38.5.2-gnu1.
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* gnu/packages/gnuzilla.scm (icecat): Update to 38.5.2-gnu1.
2016-01-09 22:51:28 +01:00
4c40fa0229
gnu: ruby-2.1: Update to 2.1.8.
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* gnu/packages/ruby.scm (ruby-2.1): Update to 2.1.8.
2016-01-09 14:53:58 +10:00
f32274a71e
gnu: i2c-tools: Update source and home-page URLs.
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* gnu/packages/linux.scm (i2c-tools)[source]: Update URL.
[home-page]: Update URL.
2016-01-08 16:42:27 -05:00
3a04d5d4e4
gnu: lm-sensors: Update source and home-page URLs.
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* gnu/packages/linux.scm (lm-sensors)[source]: Update URL.
[home-page]: Update URL.
2016-01-08 16:42:27 -05:00
bea25ae83c
gnu: nss: Update to 3.21 [fixes CVE-2015-7575].
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* gnu/packages/gnuzilla.scm (nss): Update to 3.21.
[arguments]: In configure phase, setenv CC=gcc.
* gnu/packages/patches/nss-pkgconfig.patch: Adapt to NSS 3.21.
2016-01-08 15:29:50 -05:00
2409f37f28
gnu: Add missing (gnu packages gcc) import.
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* gnu/packages/bioinformatics.scm: Use (gnu packages gcc). This is
required by 'r-impute' for 'gfortran'.
2016-01-08 14:18:46 +01:00
9ef824c10e
gnu: xterm: Update to 322.
...
* gnu/packages/xorg.scm (xterm): Update to 322.
2016-01-08 14:12:29 +01:00
a65e26f091
gnu: epiphany: Update to 3.18.2.
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* gnu/packages/gnome.scm (epiphany): Update to 3.18.2.
2016-01-08 17:34:08 +08:00
19e5258d84
gnu: webkitgtk: Update to 2.10.4.
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* gnu/packages/webkit.scm (webkitgtk): Update to 2.10.4.
2016-01-08 17:34:08 +08:00
c8d969b58f
gnu: Add Pfff.
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* gnu/packages/textutils.scm (pfff): New variable.
2016-01-07 21:13:35 +01:00
fbbaa4dde8
gnu: mpv: Remove 'samba' input.
...
This is a heavy-weight and uncommon feature. See
<http://lists.gnu.org/archive/html/guix-devel/2015-12/msg00701.html >.
* gnu/packages/video.scm (mpv)[inputs]: Remove 'samba'.
2016-01-07 22:30:18 +03:00
cb933df6da
gnu: Add genomation.
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* gnu/packages/bioinformatics.scm (r-genomation): New variable.
2016-01-07 17:18:17 +01:00
03ea5a357e
gnu: Add seqPattern.
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* gnu/packages/bioinformatics.scm (r-seqpattern): New variable.
2016-01-07 17:18:17 +01:00
c43a011de3
gnu: Add impute.
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* gnu/packages/bioinformatics.scm (r-impute): New variable.
2016-01-07 17:18:17 +01:00
c63cef6699
gnu: Add BSgenome.
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* gnu/packages/bioinformatics.scm (r-bsgenome): New variable.
2016-01-07 17:18:17 +01:00
fbf6045e33
gnu: Add plotly.
...
* gnu/packages/statistics.scm (r-plotly): New variable.
2016-01-07 17:18:17 +01:00
a28d646b63
gnu: Add viridis.
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* gnu/packages/statistics.scm (r-viridis): New variable.
2016-01-07 17:18:17 +01:00
d547ce5e70
gnu: Add topGO.
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* gnu/packages/bioinformatics.scm (r-topgo): New variable.
2016-01-07 17:18:17 +01:00
e05c37da4a
gnu: Add matrixStats.
...
* gnu/packages/statistics.scm (r-matrixstats): New variable.
2016-01-07 17:18:17 +01:00
3703ffb41f
gnu: Add R.rsp.
...
* gnu/packages/statistics.scm (r-r-rsp): New variable.
2016-01-07 17:18:17 +01:00
a63efbb453
gnu: Add R.cache.
...
* gnu/packages/statistics.scm (r-r-cache): New variable.
2016-01-07 17:18:17 +01:00
9c94b53b5b
gnu: Add R.utils.
...
* gnu/packages/statistics.scm (r-r-utils): New variable.
2016-01-07 17:18:17 +01:00
c8c75a8d88
gnu: Add R.oo.
...
* gnu/packages/statistics.scm (r-r-oo): New variable.
2016-01-07 17:18:17 +01:00
8bfe007c9c
gnu: Add R.methodsS3.
...
* gnu/packages/statistics.scm (r-r-methodss3): New variable.
2016-01-07 17:18:16 +01:00
a69a593595
gnu: Add base64enc.
...
* gnu/packages/statistics.scm (r-base64enc): New variable.
2016-01-07 17:18:16 +01:00
a8227e4ae9
gnu: Add DT.
...
* gnu/packages/statistics.scm (r-dt): New variable.
2016-01-07 17:18:16 +01:00
d706257b5b
gnu: Add SparseM.
...
* gnu/packages/statistics.scm (r-sparsem): New variable.
2016-01-07 17:18:16 +01:00
fb25d8803f
gnu: Add GO.db.
...
* gnu/packages/bioinformatics.scm (r-go-db): New variable.
2016-01-07 17:18:16 +01:00
2fd7c04984
gnu: Add GenomicFeatures.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): New variable.
2016-01-07 17:18:16 +01:00
317755ff0f
gnu: Add rtracklayer.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): New variable.
2016-01-07 17:18:16 +01:00
d8a828af78
gnu: Add GenomicAlignments.
...
* gnu/packages/bioinformatics.scm (r-genomicalignments): New variable.
2016-01-07 17:18:16 +01:00
6e76dda2d0
gnu: Add SummarizedExperiment.
...
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): New variable.
2016-01-07 17:18:16 +01:00
f8d74f7018
gnu: Add Rsamtools.
...
* gnu/packages/bioinformatics.scm (r-rsamtools): New variable.
2016-01-07 17:18:16 +01:00
bf15935337
gnu: Add Biostrings.
...
* gnu/packages/bioinformatics.scm (r-biostrings): New variable.
2016-01-07 17:18:16 +01:00
e91d362e48
gnu: Add BiocParallel.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): New variable.
2016-01-07 17:18:16 +01:00
c465fa72ed
gnu: Add biomaRt.
...
* gnu/packages/bioinformatics.scm (r-biomart): New variable.
2016-01-07 17:18:16 +01:00
8b7bce740d
gnu: Add AnnotationDbi.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): New variable.
2016-01-07 17:18:16 +01:00
555e3399dc
gnu: Add Biobase.
...
* gnu/packages/bioinformatics.scm (r-biobase): New variable.
2016-01-07 17:18:16 +01:00
bc899123e7
gnu: Add snow.
...
* gnu/packages/statistics.scm (r-snow): New variable.
2016-01-07 17:18:16 +01:00
6b82f56cf9
gnu: Add futile.logger.
...
* gnu/packages/statistics.scm (r-futile-logger): New variable.
2016-01-07 17:18:16 +01:00
b9ff33b50e
gnu: Add futile.options.
...
* gnu/packages/statistics.scm (r-futile-options): New variable.
2016-01-07 17:18:16 +01:00
ca65d387fd
gnu: Add lambda.r.
...
* gnu/packages/statistics.scm (r-lambda-r): New variable.
2016-01-07 17:18:16 +01:00
543ded3619
gnu: Add r-xml.
...
* gnu/packages/statistics.scm (r-xml): New variable.
2016-01-07 17:18:16 +01:00
cefaa79c9e
gnu: Add RCurl.
...
* gnu/packages/statistics.scm (r-rcurl): New variable.
2016-01-07 17:18:16 +01:00
21e4d6a9cf
gnu: Add RSQLite.
...
* gnu/packages/statistics.scm (r-rsqlite): New variable.
2016-01-07 17:18:15 +01:00
fe9451c50a
gnu: Add xmlstarlet.
...
* gnu/packages/xml.scm (xmlstarlet): New variable.
2016-01-07 16:00:00 +01:00
29e255ca83
gnu: zita-convolver: Drop the '-march=native' optimization.
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* gnu/packages/audio.scm (zita-convolver)[source]: Add snippet.
2016-01-07 22:47:32 +08:00
6dff495580
gnu: zita-resampler: Drop the '-march=native' optimization.
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* gnu/packages/audio.scm (zita-resampler)[source]: Add snippet.
2016-01-07 22:47:32 +08:00
7d3a1a2dd2
gnu: Add ruby-ansi.
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* gnu/packages/ruby.scm (ruby-ansi): New variable.
2016-01-07 15:36:05 +01:00
5dfd276602
gnu: edirect: Update to 3.50.
...
* gnu/packages/bioinformatics.scm (edirect): Update to 3.50.
[native-inputs]: Remove "unzip".
2016-01-07 11:25:24 +01:00
Leo Famulari