Ricardo Wurmus
2309ed6862
gnu: samtools-0.1: Adapt to changes in "samtools" variable.
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* gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Add
"LIBCURSES" make flag; delete "configure" phase; disable tests outside
of "substitute-keyword-arguments".
2016-01-16 15:50:51 +01:00
宋文武
c3e919d7a0
gnu: Add python-hy.
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* gnu/packages/python.scm (python-hy, python2-hy): New variables.
2016-01-16 08:18:37 +08:00
宋文武
e224b7d0bd
gnu: Add python-rply.
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* gnu/packages/python.scm (python-rply, python2-rply): New variables.
2016-01-16 08:18:37 +08:00
宋文武
4ecdeef8ae
gnu: Add python-astor.
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* gnu/packages/python.scm (python-astor, python2-astor): New variables.
2016-01-16 08:18:37 +08:00
宋文武
c06a3de93a
gnu: Add python-clint.
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* gnu/packages/python.scm (python-clint, python2-clint): New variables.
2016-01-16 08:17:04 +08:00
宋文武
2216e15cc3
gnu: Add python-args.
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* gnu/packages.scm (python-args, python2-args): New variables.
2016-01-16 08:16:51 +08:00
Leo Famulari
78e6c4a862
gnu: Add khal.
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* gnu/packages/calendar.scm (khal): New variable.
2016-01-15 16:45:24 -05:00
Leo Famulari
b97c1bfd56
gnu: python-urwid: Disable failing test test_remove_watch_file.
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* gnu/packages/python.scm (python-urwid)[arguments]: Add
'disable-failing-test' phase.
[source]: Use pypi-uri.
2016-01-15 16:45:24 -05:00
Leo Famulari
226d333103
gnu: Update python-tzlocal to 1.2.
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* gnu/packages/python.scm (python-tzlocal): Update to 1.2.
[source]: Use pypi-uri.
[arguments]: Remove the custom 'unpack phase.
[native-inputs]: Remove unzip, python-setuptools.
[propagated-inputs]: Add python-pytz.
2016-01-15 16:45:24 -05:00
Leo Famulari
6bbbb53eeb
gnu: Add python-sphinxcontrib-newsfeed.
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* gnu/packages/python.scm (python-sphinxcontrib-newsfeed): New variable.
2016-01-15 16:45:24 -05:00
Leo Famulari
5c299bf016
gnu: Add python-icalendar.
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* gnu/packages/python.scm (python-icalendar): New variable.
2016-01-15 16:45:24 -05:00
Leo Famulari
a2f6a3d502
gnu: Add vdirsyncer.
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* gnu/packages/dav.scm (vdirsyncer): New variable.
2016-01-15 16:45:24 -05:00
Leo Famulari
f75bbb028a
gnu: Add radicale.
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* gnu/packages/dav.scm (radicale): New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.
2016-01-15 16:45:24 -05:00
Leo Famulari
89b8a5516f
gnu: Add python-pytest-xprocess.
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* gnu/packages/python.scm (python-pytest-xprocess): New variable.
2016-01-15 16:45:24 -05:00
Leo Famulari
28cecbb7cc
gnu: Add python-wsgi-intercept.
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* gnu/packages/python.scm (python-wsgi-intercept): New variable.
2016-01-15 16:45:24 -05:00
Leo Famulari
d7e729fe08
gnu: Add python-pytest-localserver.
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* gnu/packages/python.scm (python-pytest-localserver): New variable.
2016-01-15 16:45:24 -05:00
Leo Famulari
6720dbb49f
gnu: Add python-pytest-cache.
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* gnu/packages/python.scm (python-pytest-cache): New variable.
2016-01-15 16:45:24 -05:00
Leo Famulari
848964fe11
gnu: Add python-execnet.
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* gnu/packages/python.scm (python-execnet): New variable.
2016-01-15 16:45:24 -05:00
Leo Famulari
7b3a4ee4c3
gnu: Add python-apipkg.
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* gnu/packages/python.scm (python-apipkg): New variable.
2016-01-15 16:45:24 -05:00
Leo Famulari
7b17cab902
gnu: Add python-click-log.
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* gnu/packages/python.scm (python-click-log): New variable.
2016-01-15 16:45:24 -05:00
Leo Famulari
d1deb90b3f
gnu: Add python-click-threading.
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* gnu/packages/python.scm (python-click-threading): New variable.
2016-01-15 16:45:24 -05:00
Leo Famulari
561bb3cb1a
gnu: Add python-requests-toolbelt.
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* gnu/packages/python.scm (python-requests-toolbelt): New variable.
2016-01-15 16:45:24 -05:00
Leo Famulari
5c6eea2ad1
gnu: Add python-atomicwrites.
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* gnu/packages/python.scm (python-atomicwrites): New variable.
2016-01-15 16:45:24 -05:00
Ricardo Wurmus
f5ca44b86e
gnu: glade: Update to 3.18.5.
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* 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
Mark H Weaver
45f2ffb48c
gnu: openssh: Update to 7.1p2.
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* gnu/packages/ssh.scm (openssh): Update to 7.1p2.
2016-01-15 02:46:12 -05:00
Mark H Weaver
1beec63ac8
Revert "gnu: openssh: Update to 7.1p2 [fixes CVE-0216-0778]."
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This reverts commit 6d139e53b5
.
2016-01-15 02:45:58 -05:00
Mark H Weaver
6d139e53b5
gnu: openssh: Update to 7.1p2 [fixes CVE-0216-0778].
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* gnu/packages/ssh.scm (openssh): Update to 7.1p2.
2016-01-14 10:39:00 -05:00
David Thompson
df1f1d6936
gnu: Add docker-compose.
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* gnu/packages/docker.scm (docker-compose): New variable.
2016-01-14 09:17:12 -05:00
David Thompson
b42c9c8124
gnu: Add python-dockerpty.
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* gnu/packages/docker.scm (python-dockerpty): New variable.
2016-01-14 09:16:22 -05:00
David Thompson
d020bfc2df
gnu: Add python-docker-py.
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* gnu/packages/docker.scm: New file.
* Makefile.am (GNU_SYSTEM_MODULES): Add it.
2016-01-14 09:16:22 -05:00
David Thompson
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
David Thompson
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
David Thompson
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
David Thompson
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
David Thompson
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
Ricardo Wurmus
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
Ricardo Wurmus
d7786ce9b0
gnu: r-sparsem: Add missing "gfortran" input.
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* gnu/packages/statistics.scm (r-sparsem)[inputs]: Add "gfortran".
2016-01-14 14:43:59 +01:00
Ricardo Wurmus
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
Efraim Flashner
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
Ben Woodcroft
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
Ben Woodcroft
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
Ben Woodcroft
7c033c4627
gnu: Add ruby-systemu.
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* gnu/packages/ruby.scm (ruby-systemu): New variable.
2016-01-14 07:51:44 +10:00
Ricardo Wurmus
e5a19fed19
gnu: julia: Update to 0.4.3.
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* gnu/packages/julia.scm (julia): Update to 0.4.3.
(libuv-julia): Update to 07730c4bd595.
2016-01-13 17:05:38 +01:00
Mark H Weaver
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
Ricardo Wurmus
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
Ludovic Courtès
98f2339189
gnu: skribilo: Update to 0.9.3.
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* gnu/packages/skribilo.scm (skribilo): Update to 0.9.3.
[native-inputs]: New field.
2016-01-13 11:13:34 +01:00
Eric Bavier
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
Eric Bavier
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
Mark H Weaver
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
Efraim Flashner
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