60739965da
gnu: python-pysam: Update to 0.11.2.2.
...
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.11.2.2.
2017-07-23 10:29:35 +10:00
bca2c57658
gnu: bamm: Use htslib-1.3.
...
* gnu/packages/bioinformatics (htslib-1.3): New variable.
(bamm)[inputs]: Replace htslib with htslib-1.3.
2017-07-23 10:29:35 +10:00
98593f9f51
gnu: bcftools: Update to 1.4.1.
...
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.4.1.
[arguments]: Move Makefile modifications from here ...
[source]: ... to added patch. Adjust patch for update to 1.4.
* gnu/packages/patches/bcftools-fix-makefile.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
2017-07-23 10:29:35 +10:00
4ab1644049
gnu: samtools: Update to 1.4.1.
...
* gnu/packages/bioinformatics.scm (samtools): Update to 1.4.1.
[arguments]: Add '--with-htslib=system' configure flag.
[inputs]: Add htslib.
2017-07-23 10:29:34 +10:00
a9e4a1e641
gnu: htslib: Update to 1.4.1.
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* gnu/packages/bioinformatics.scm (htslib): Update to 1.4.1.
[inputs]: Add curl, openssl.
2017-07-23 10:29:34 +10:00
c842d42593
gnu: samtools: Use "modify-phases" syntax.
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* gnu/packages/bioinformatics.scm (samtools)[arguments]: Use "modify-phases"
syntax.
2017-07-23 10:29:34 +10:00
c62d1a6e6c
gnu: bspwm: Update to 0.9.3.
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* gnu/packages/wm.scm (bspwm): Update to 0.9.3.
Signed-off-by: Leo Famulari <leo@famulari.name>
2017-07-22 20:17:46 -04:00
7e3c977da6
gnu: Add oksh.
...
* gnu/packages/shells.scm (oksh): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2017-07-22 20:15:21 -04:00
36378bd57e
gnu: quassel: Enable TLS.
...
* gnu/packages/patches/quassel-fix-tls-check.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/irc.scm (quassel)[source]: Use it.
Signed-off-by: Leo Famulari <leo@famulari.name>
2017-07-22 20:04:53 -04:00
e745221408
gnu: youtube-dl: Update to 2017.07.23.
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* gnu/packages/video.scm (youtube-dl): Update to 2017.07.23.
2017-07-23 01:59:32 +02:00
4b8b245b83
gnu: mosh: Update to 1.3.2.
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* gnu/packages/ssh.scm (mosh): Update to 1.3.2.
2017-07-23 01:27:29 +02:00
a68a83f015
gnu: Add openmolar.
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* gnu/packages/medical.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
Co-authored-by: Quiliro <quiliro@fsfla.org>
2017-07-22 23:48:58 +02:00
2456153adc
gnu: Add python-pyqt+qscintilla.
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* gnu/packages/qt.scm (python-pyqt+qscintilla): New variable.
2017-07-22 23:48:58 +02:00
06d04dbcfc
gnu: Add python-qscintilla.
...
* gnu/packages/qt.scm (python-qscintilla): New variable.
Co-authored-by: Quiliro <quiliro@fsfla.org>
2017-07-22 23:48:57 +02:00
3befd0a97c
gnu: Add qscintilla.
...
* gnu/packages/qt.scm (qscintilla): New variable.
Co-authored-by: Quiliro <quiliro@fsfla.org>
2017-07-22 23:48:57 +02:00
056468dc5f
gnu: Add cran module.
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* gnu/packages/cran.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/statistics.scm (r-colorspace): Move to cran.scm.
2017-07-22 23:48:57 +02:00
30f8349efb
gnu: linux-libre: Update to 4.12.3.
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* gnu/packages/linux.scm (%linux-libre-version): Update to 4.12.3.
(%linux-libre-hash): Update hash.
2017-07-22 14:46:00 -04:00
d422eac54e
gnu: linux-libre@4.9: Update to 4.9.39.
...
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.39.
2017-07-22 14:45:06 -04:00
f97c67a275
gnu: linux-libre@4.4: Update to 4.4.78.
...
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.78.
2017-07-22 14:44:24 -04:00
3a4b0b126b
gnu: r-s4vectors: Update to 0.14.3.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.14.3.
2017-07-22 17:31:19 +02:00
a35a1e9c13
gnu: r-genomicranges: Update to 1.28.4.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.28.4.
2017-07-22 17:22:07 +02:00
aa51da7eef
gnu: Remove python-fake-factory leftovers.
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This is a followup to c799eb2eb8
2017-07-22 15:07:45 +02:00
c799eb2eb8
gnu: Remove python-fake-factory.
...
Superseded by python-faker since ce7911ddae
2017-07-22 14:31:28 +02:00
2580c2f07f
gnu: python-pyopenssl: Update to 17.2.0.
...
* gnu/packages/patches/python-pyopenssl-17.1.0-test-overflow.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/python.scm (python-pyopenssl, python2-pyopenssl): Update to 17.2.0.
[native-inputs]: Add PYTHON-FLAKY.
[source](patches): Remove.
2017-07-22 14:31:28 +02:00
4e52739c61
gnu: Add python-flaky.
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* gnu/packages/python.scm (python-flaky, python2-flaky): New variables.
2017-07-22 14:31:27 +02:00
6027cb8a82
gnu: maim: Update to 5.4.64.
...
* gnu/packages/xdisorg.scm (maim): Update to 5.4.64.
2017-07-22 14:31:27 +02:00
eb2b5f9d03
gnu: slop: Update to 6.3.47.
...
* gnu/packages/xdisorg.scm (slop): Update to 6.3.47.
[inputs]: Add GLEW.
2017-07-22 14:31:27 +02:00
0cd95cefe0
gnu: parallel: Update to 20170722.
...
* gnu/packages/parallel.scm (parallel): Update to 20170722.
2017-07-22 13:47:26 +02:00
bc35c9d318
gnu: font-gnu-unifont: Update to 10.0.05.
...
* gnu/packages/fonts.scm (font-gnu-unifont): Update to 10.0.05.
2017-07-22 13:47:26 +02:00
f7975a3bde
gnu: nano: Update to 2.8.6.
...
* gnu/packages/nano.scm (nano): Update to 2.8.6.
2017-07-22 13:47:25 +02:00
f03d8d67a5
gnu: acct: Update to 6.6.4.
...
* gnu/packages/acct.scm (acct): Update to 6.6.4.
2017-07-22 13:47:25 +02:00
84fcb58050
gnu: Add conda.
...
* gnu/packages/package-management.scm (conda): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2017-07-22 12:26:30 +02:00
4bc08b6e79
gnu: Add python-conda.
...
* gnu/packages/package-management.scm (python-conda, python2-conda): New
variables.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2017-07-22 12:26:29 +02:00
513d35f191
gnu: Add python-anaconda-client.
...
* gnu/packages/package-management.scm (python-anaconda-client,
python2-anaconda-client): New variables.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2017-07-22 12:26:29 +02:00
1f84ff5135
gnu: Add python-clyent.
...
* gnu/packages/python.scm (python-clyent, python2-clyent): New variables.
2017-07-22 12:26:29 +02:00
3fee003950
gnu: Update python-pytz to 2017.2.
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* gnu/packages/python.scm (python-pytz, python2-pytz): Update to 2017.2.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2017-07-22 12:26:29 +02:00
de469015c4
gnu: man-pages: Update to 4.12.
...
* gnu/packages/man.scm (man-pages): Update to 4.12.
2017-07-22 12:18:58 +02:00
1ffe41711b
gnu: tint2: Update to 0.14.6.
...
* gnu/packages/xdisorg.scm (tint2): Update to 0.14.6.
2017-07-21 22:41:24 -05:00
e9185cbac6
gnu: icedtea@3: Update to 3.5.0 [security fixes].
...
Fixes CVE-2017-{10053,10067,10074,10074,10078,10081,10087,10089,10090,10096,
10101,10102,10107,10108,10109,10110,10111,10115,10116,10118,10135,10176,10193,
10198}.
* gnu/packages/java.scm (icedtea-8): Update to 3.5.0.
2017-07-21 17:30:08 -04:00
c800fd564b
services: cuirass: Add fallback parameter.
...
* gnu/services/cuirass.scm (<cuirass-configuration>)[fallback?]: New field.
(cuirass-shepherd-service): Take it into account.
* doc/guix.texi (Continuous Integration): Document it.
2017-07-21 21:46:47 +02:00
3c14378381
gnu: vim: Update to 8.0.0727 [fixes CVE-2017-11109].
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* gnu/packages/vim.scm (vim): Update to 8.0.0727.
(vim-full)[source]: Add field and hold back at version 8.0.0600.
2017-07-21 15:20:23 -04:00
6f226c078c
gnu: mysql: Update to 5.7.19.
...
* gnu/packages/databases.scm (mysql): Update to 5.7.19.
2017-07-21 14:50:24 -04:00
c95644f017
publish: Make the cache eviction policy less aggressive.
...
Suggested by Mark H Weaver <mhw@netris.org>.
* guix/scripts/publish.scm (nar-expiration-time): New procedure.
(render-narinfo/cached): Use it as the #:entry-expiration passed to
'maybe-remove-expired-cache-entries'.
2017-07-21 17:03:25 +02:00
deac674ab4
publish: Avoid 'valid-path?' RPC for non-existent items.
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* guix/scripts/publish.scm (render-narinfo/cached): Call 'file-exists?'
before calling 'valid-path?'. This makes the 404 path slightly faster.
2017-07-21 17:03:25 +02:00
35eb77b09d
store: Rewrite 'store-path-hash-part' to not use regexps.
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* guix/store.scm (store-path-hash-part): Rewrite without using a
regexp. This speeds up 'guix substitute'.
2017-07-21 17:03:25 +02:00
33463986ba
publish: Remove 'regexp-exec' call from the hot path.
...
* guix/scripts/publish.scm (extract-narinfo-hash): Rewrite without
resorting to regexps.
2017-07-21 17:03:24 +02:00
0a94dc6396
base32: Export the base32 charsets.
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* guix/base32.scm (%nix-base32-charset, %rfc4648-base32-charset): New
variables.
2017-07-21 17:03:24 +02:00
75a4d86f50
substitute: Avoid repeated calls to 'length'.
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* guix/scripts/substitute.scm (fetch-narinfos)[update-progress!]: Move
'length' call outside of lambda.
2017-07-21 17:03:24 +02:00
3d3e93b3f9
substitute: Optimize hash-part-to-path conversion on non-200 responses.
...
Previously this operation was linear in the number of requests and
involved costly calls to 'string-contains'.
* guix/scripts/substitute.scm (fetch-narinfos)[hash-part->path]: New
procedure.
[handle-narinfo-response]: Use it for caching when CODE is not 200.
2017-07-21 17:03:24 +02:00
0cf9f9b1e3
gnu: libpsl: Update to 0.18.0.
...
* gnu/packages/web.scm (libpsl): Update to 0.18.0.
[native-inputs]: Add pkg-config.
[inputs]: Replace icu4c with libidn2; add libunistring.
2017-07-21 12:24:47 +02:00
Ben Woodcroft