Age | Commit message (Collapse) | Author |
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* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.1.
[source]: Add patch to fix compilation.
[arguments]: Adjust regular expressions modifying 'SConstruct'.
* gnu/packages/patches/metabat-fix-compilation.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
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* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.4.8.
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* gnu/packages/bioinformatics.scm (bcftools): Update to 1.5.
[origin]: Remove fix-makefile patch.
[arguments]: Add configure flags, add LIBS make flag. Do not delete
configure phase.
* gnu/packages/patches/bcftools-fix-makefile.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
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* gnu/packages/bioinformatics.scm (samtools): Update to 1.5.
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* gnu/packages/bioinformatics.scm (htslib): Update to 1.5.
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* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.11.2.2.
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* gnu/packages/bioinformatics (htslib-1.3): New variable.
(bamm)[inputs]: Replace htslib with htslib-1.3.
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* 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.
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* gnu/packages/bioinformatics.scm (samtools): Update to 1.4.1.
[arguments]: Add '--with-htslib=system' configure flag.
[inputs]: Add htslib.
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* gnu/packages/bioinformatics.scm (htslib): Update to 1.4.1.
[inputs]: Add curl, openssl.
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* gnu/packages/bioinformatics.scm (samtools)[arguments]: Use "modify-phases"
syntax.
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* gnu/packages/wm.scm (bspwm): Update to 0.9.3.
Signed-off-by: Leo Famulari <leo@famulari.name>
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* gnu/packages/shells.scm (oksh): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
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* 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>
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* gnu/packages/video.scm (youtube-dl): Update to 2017.07.23.
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* gnu/packages/ssh.scm (mosh): Update to 1.3.2.
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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>
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* gnu/packages/qt.scm (python-pyqt+qscintilla): New variable.
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* gnu/packages/qt.scm (python-qscintilla): New variable.
Co-authored-by: Quiliro <quiliro@fsfla.org>
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* gnu/packages/qt.scm (qscintilla): New variable.
Co-authored-by: Quiliro <quiliro@fsfla.org>
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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.
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* gnu/packages/linux.scm (%linux-libre-version): Update to 4.12.3.
(%linux-libre-hash): Update hash.
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* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.39.
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* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.78.
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* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.14.3.
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* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.28.4.
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This is a followup to c799eb2eb8b1a820147af96988eddaa9f752994b.
* gnu/packages/patches/python-fake-factory-fix-build-32bit.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
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Superseded by python-faker since ce7911ddae5d30ba73c8c9552b7d4e71268e5db3.
* gnu/packages/python.scm (python-fake-factory, python2-fake-factory):
Remove variables.
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* 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.
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* gnu/packages/python.scm (python-flaky, python2-flaky): New variables.
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* gnu/packages/xdisorg.scm (maim): Update to 5.4.64.
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* gnu/packages/xdisorg.scm (slop): Update to 6.3.47.
[inputs]: Add GLEW.
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* gnu/packages/parallel.scm (parallel): Update to 20170722.
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* gnu/packages/fonts.scm (font-gnu-unifont): Update to 10.0.05.
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* gnu/packages/nano.scm (nano): Update to 2.8.6.
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* gnu/packages/acct.scm (acct): Update to 6.6.4.
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* gnu/packages/package-management.scm (conda): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
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* gnu/packages/package-management.scm (python-conda, python2-conda): New
variables.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
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* gnu/packages/package-management.scm (python-anaconda-client,
python2-anaconda-client): New variables.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
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* gnu/packages/python.scm (python-clyent, python2-clyent): New variables.
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* gnu/packages/python.scm (python-pytz, python2-pytz): Update to 2017.2.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
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* gnu/packages/man.scm (man-pages): Update to 4.12.
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* gnu/packages/xdisorg.scm (tint2): Update to 0.14.6.
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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.
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* gnu/services/cuirass.scm (<cuirass-configuration>)[fallback?]: New field.
(cuirass-shepherd-service): Take it into account.
* doc/guix.texi (Continuous Integration): Document it.
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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.
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* gnu/packages/databases.scm (mysql): Update to 5.7.19.
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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'.
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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.
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* guix/store.scm (store-path-hash-part): Rewrite without using a
regexp. This speeds up 'guix substitute'.
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