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* gnu: pigx-scrnaseq: Use only one variant of Picard.Ricardo Wurmus2018-06-05
| | | | | * gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace "java-picard" with "java-picard-2.10.3".
* gnu: java-picard: Delete failing build phase.Ricardo Wurmus2018-06-05
| | | | | * gnu/packages/bioinformatics.scm (java-picard)[arguments]: Delete "generate-jar-indices" phase.
* gnu: java-cisd-jhdf5: Delete failing build phase.Ricardo Wurmus2018-06-05
| | | | | * gnu/packages/java.scm (java-cisd-jhdf5)[arguments]: Delete build phase "generate-jar-indices".
* gnu: java-picard-1.113: Delete failing build phase.Ricardo Wurmus2018-06-05
| | | | | * gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Delete "generate-jar-indices" build phase.
* gnu: java-picard-2.10.3: Delete failing build phase.Ricardo Wurmus2018-06-05
| | | | | * gnu/packages/bioinformatics.scm (java-picard-2.10.3)[arguments]: Delete generate-jar-indices phase.
* Merge branch 'master' into core-updatesRicardo Wurmus2018-06-05
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| * gnu: r-rtracklayer: Update to 1.40.3.Ricardo Wurmus2018-06-05
| | | | | | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.3.
| * gnu: r-ranger: Update to 0.10.1.Ricardo Wurmus2018-06-05
| | | | | | | | * gnu/packages/statistics.scm (r-ranger): Update to 0.10.1.
| * gnu: r-np: Update to 0.60-8.Ricardo Wurmus2018-06-05
| | | | | | | | * gnu/packages/cran.scm (r-np): Update to 0.60-8.
| * gnu: t-series: Update to 0.10-45.Ricardo Wurmus2018-06-05
| | | | | | | | * gnu/packages/cran.scm (t-series): Update to 0.10-45.
| * gnu: r-ksamples: Update to 1.2-8.Ricardo Wurmus2018-06-05
| | | | | | | | * gnu/packages/cran.scm (r-ksamples): Update to 1.2-8.
| * gnu: r-methylkit: Update to 1.6.1.Ricardo Wurmus2018-06-05
| | | | | | | | * gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.6.1.
| * gnu: r-bamsignals: Update to 1.12.1.Ricardo Wurmus2018-06-05
| | | | | | | | * gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.12.1.
* | Merge branch 'master' into core-updatesRicardo Wurmus2018-06-05
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| * build-system/r: Update to Bioconductor 3.7.Ricardo Wurmus2018-06-05
| | | | | | | | | | | | This is a follow-up to 41f17554d88795bf35fbfc3e05301a6d2f64cca0. * guix/build-system/r.scm (bioconductor-uri): Update to version 3.7.
| * gnu: p11-kit: Update to 0.23.12.Tobias Geerinckx-Rice2018-06-05
| | | | | | | | * gnu/packages/tls.scm (p11-kit): Update to 0.23.12.
| * gnu: beets: Return #t from phases.Tobias Geerinckx-Rice2018-06-05
| | | | | | | | | | * gnu/packages/music.scm (beets)[arguments]: Substitute INVOKE for SYSTEM* and return #t from all phases.
| * gnu: nano: Update to 2.9.8.Tobias Geerinckx-Rice2018-06-05
| | | | | | | | * gnu/packages/nano.scm (nano): Update to 2.9.8.
| * gnu: python-pycurl: Update to 7.43.0.2.Tobias Geerinckx-Rice2018-06-05
| | | | | | | | * gnu/packages/python-web.scm (python-pycurl): Update to 7.43.0.2.
| * gnu: fvwm: Update to 2.6.8.Tobias Geerinckx-Rice2018-06-05
| | | | | | | | * gnu/packages/fvwm.scm (fvwm): Update to 2.6.8.
| * gnu: perl-parse-yapp: Update to 1.21.Tobias Geerinckx-Rice2018-06-05
| | | | | | | | * gnu/packages/perl.scm (perl-parse-yapp): Update to 1.21.
| * gnu: perl-text-balanced: Update to 2.03.Tobias Geerinckx-Rice2018-06-05
| | | | | | | | | | * gnu/packages/perl.scm (perl-text-balanced): Update to 2.03. [source]: Update URI.
| * gnu: perl-posix-strftime-compiler: Update to 0.42.Tobias Geerinckx-Rice2018-06-05
| | | | | | | | | | * gnu/packages/perl.scm (perl-posix-strftime-compiler): Update to 0.42.
| * gnu: perl-moosex-methodattributes: Update to 0.31.Tobias Geerinckx-Rice2018-06-05
| | | | | | | | | | * gnu/packages/perl.scm (perl-moosex-methodattributes): Update to 0.31.
| * gnu: perl-module-install: Update to 1.19.Tobias Geerinckx-Rice2018-06-05
| | | | | | | | | | * gnu/packages/perl.scm (perl-module-install): Update to 1.19. [source]: Update URI.
| * gnu: perl-memoize-expirelru: Update to 0.56.Tobias Geerinckx-Rice2018-06-05
| | | | | | | | | | * gnu/packages/perl.scm (perl-memoize-expirelru): Update to 0.56. [source]: Update URI.
| * gnu: ccid, pcsc-lite: Move away from alioth.debian.org.Tobias Geerinckx-Rice2018-06-04
| | | | | | | | | | * gnu/packages/security-token.scm (ccid, pcsc-lite)[source, home-page]: Update upstream URI.
| * gnu: ranger: Enable image support.Rutger Helling2018-06-04
| | | | | | | | | | * gnu/packages/disk.scm (ranger)[inputs]: Add 'w3m'. [arguments]: Add wrapper for W3MIMGDISPLAY_PATH environment variable.
| * gnu: lz4: Use HTTPS home page.Tobias Geerinckx-Rice2018-06-04
| | | | | | | | * gnu/packages/compression.scm (lz4)[home-page]: Use HTTPS.
| * gnu: thermald: Update to 1.7.2.Tobias Geerinckx-Rice2018-06-04
| | | | | | | | | | * gnu/packages/admin.scm (thermald): Update to 1.7.2. [arguments]: Remove Upstart kluge as promised.
| * gnu: pdfgrep: Update to 2.1.1.Tobias Geerinckx-Rice2018-06-04
| | | | | | | | * gnu/packages/pdf.scm (pdfgrep): Update to 2.1.1.
| * gnu: lxqt-build-tools: Update to 0.5.0.Tobias Geerinckx-Rice2018-06-04
| | | | | | | | * gnu/packages/lxqt.scm (lxqt-build-tools): Update to 0.5.0.
| * gnu: perl-libintl-perl: Update to 1.29.Tobias Geerinckx-Rice2018-06-04
| | | | | | | | * gnu/packages/perl.scm (perl-libintl-perl): Update to 1.29.
| * gnu: perl-hash-multivalue: Update to 0.16.Tobias Geerinckx-Rice2018-06-04
| | | | | | | | | | * gnu/packages/perl.scm (perl-hash-multivalue): Update to 0.16. [source]: Update URI.
| * gnu: perl-file-pushd: Update to 1.016.Tobias Geerinckx-Rice2018-06-04
| | | | | | | | * gnu/packages/perl.scm (perl-file-pushd): Update to 1.016.
| * gnu: perl-exception-class: Update to 1.44.Tobias Geerinckx-Rice2018-06-04
| | | | | | | | * gnu/packages/perl.scm (perl-exception-class): Update to 1.44.
| * gnu: perl-datetime-timezone: Update to 2.19.Tobias Geerinckx-Rice2018-06-04
| | | | | | | | * gnu/packages/perl.scm (perl-datetime-timezone): Update to 2.19.
| * gnu: perl-test-without-module: Update to 0.20.Tobias Geerinckx-Rice2018-06-04
| | | | | | | | * gnu/packages/perl-check.scm (perl-test-without-module): Update to 0.20.
| * gnu: perl-datetime: Update to 1.49.Tobias Geerinckx-Rice2018-06-04
| | | | | | | | * gnu/packages/perl.scm (perl-datetime): Update to 1.49.
| * gnu: perl-context-preserve: Update to 0.03.Tobias Geerinckx-Rice2018-06-04
| | | | | | | | * gnu/packages/perl.scm (perl-context-preserve): Update to 0.03.
| * gnu: perl-class-load-xs: Update to 0.10.Tobias Geerinckx-Rice2018-06-04
| | | | | | | | | | | | * gnu/packages/perl.scm (perl-class-load-xs): Update to 0.10. [native-inputs]: Replace perl-test-requires with perl-test-needs. Add perl-test-without-module.
| * gnu: perl-class-load: Update to 0.24.Tobias Geerinckx-Rice2018-06-04
| | | | | | | | | | | | * gnu/packages/perl.scm (perl-class-load): Update to 0.24. [native-inputs]: Replace perl-test-requires with perl-test-needs. Add perl-test-without-module.
| * gnu: sent: Say ‘plain text’.Tobias Geerinckx-Rice2018-06-04
| | | | | | | | | | | | ‘Plaintext’ is a crypto term. ‘Slideshow’ is apparently acceptable. * gnu/packages/suckless.scm (sent)[synopsis, description]: Add spaces.
| * gnu: snd: Version documentation directory.Tobias Geerinckx-Rice2018-06-04
| | | | | | | | | | * gnu/packages/audio.scm (snd)[arguments]: Install documentation to the conventional location. Remove redundant MKDIR-P. Align cosmetically.
| * gnu: acpica: Update to 20180531.Tobias Geerinckx-Rice2018-06-04
| | | | | | | | * gnu/packages/admin.scm (acpica): Update to 20180531.
| * gnu: isync: Add SASL support.Tobias Geerinckx-Rice2018-06-04
| | | | | | | | | | | | This adds ~5.5 MiB (7.5%) to isync's now-78.6 MiB closure. * gnu/packages/mail.scm (isync)[inputs]: Add CYRUS-SASL.
* | gnu: elfutils: Disable test suite on MIPS.Mark H Weaver2018-06-04
| | | | | | | | * gnu/packages/elf.scm (elfutils)[arguments]: Add (#:tests? #f) on MIPS.
* | gnu: perf: Work around GCC bug.Ludovic Courtès2018-06-04
| | | | | | | | | | | | | | | | Works around <https://bugs.gnu.org/31708>. * gnu/packages/patches/perf-gcc-ice.patch: New patch. * gnu/packages/linux.scm (perf)[source]: Use it. * gnu/local.mk (dist_patch_DATA): Add it.
* | gnu: signing-party: Update to commit d6f2296.Ludovic Courtès2018-06-04
| | | | | | | | | | | | | | | | * gnu/packages/gnupg.scm (signing-party): Update to commit d6f2296. [home-page]: Change to salsa.debian.org. [source]: Use git-fetch. [arguments]: Remove 'change-directory' phase. In 'configure' phase, modify 'gpgwrap/Makefile' instead of 'gpgwrap/src/Makefile'.
* | Merge branch 'master' into core-updatesRicardo Wurmus2018-06-04
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