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32990 Commits

Author SHA1 Message Date
Mark H Weaver 8b2aabd9d9
gnu: linux-libre@4.14: Update to 4.14.93. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.93.
(%linux-libre-4.14-hash): Update hash.
 2019-01-14 01:26:21 -05:00
Mark H Weaver e724e1543a
gnu: linux-libre@4.9: Update to 4.9.150. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.150.
 2019-01-14 01:25:28 -05:00
Mark H Weaver 0dd2a4f324
gnu: linux-libre@4.4: Update to 4.4.170. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.170.
 2019-01-14 01:24:40 -05:00
Gabriel Hondet 64d25f0be2
gnu: Add ocaml-merlin. 
* gnu/packages/ocaml.scm (ocaml-merlin): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-01-13 23:30:15 +01:00
Gabriel Hondet cc353cc067
gnu: Add emacs-tldr. 
* gnu/packages/emacs.scm (emacs-tldr): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-01-13 23:30:15 +01:00
Meiyo Peng 5144df2c6c
system: Add sudoedit to %setuid-programs. 
* gnu/system.scm (%setuid-programs): Add sudoedit.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-01-13 23:30:15 +01:00
Christopher Baines 24a23bea20
gnu: Add python-miniboa. 
python2-miniboa is required for the linkchecker testsuite.

* gnu/packages/python.scm (python-miniboa, python2-miniboa): New variable.
 2019-01-13 20:47:40 +00:00
Christopher Baines c4aa1ebc81
gnu: python-pillow: Update to 5.4.1. 
I'm looking at this, as this release fixes an issue with the Django testsuite:

https://github.com/python-pillow/Pillow/pull/3525

* gnu/packages/python.scm (python-pillow): Update to 5.4.1.
 2019-01-13 17:09:52 +00:00
Ricardo Wurmus 14bba460ab
gnu: r-biocgenerics: Move to bioconductor. 
* gnu/packages/bioinformatics.scm (r-biocgenerics): Move from here...
* gnu/packages/bioconductor.scm (r-biocgenerics): ...to here.
 2019-01-13 13:04:18 +01:00
Ricardo Wurmus 7097c7009d
gnu: r-annotate: Move to bioconductor. 
* gnu/packages/bioinformatics.scm (r-annotate): Move from here...
* gnu/packages/bioconductor.scm (r-annotate): ...to here.
 2019-01-13 13:04:18 +01:00
Ricardo Wurmus c80fb90f4a
gnu: r-vegan: Move from bioinformatics to cran. 
* gnu/packages/bioinformatics.scm (r-vegan): Move from here...
* gnu/packages/cran.scm (r-vegan): ...to here.
 2019-01-13 13:04:18 +01:00
Efraim Flashner d691e96657
gnu: conda: Use 'invoke'. 
* gnu/packages/package-management.scm (conda)[arguments]: Use 'invoke'.
 2019-01-13 12:44:03 +02:00
Efraim Flashner 675e7bba3e
gnu: python-conda: All phases return #t. 
* gnu/packages/package-management.scm (python-conda)[arguments]: Use
'invoke'.
 2019-01-13 12:44:03 +02:00
Efraim Flashner e227f248a6
gnu: python-conda: Fix test suite. 
* gnu/packages/package-management.scm (python-conda)[native-inputs]: Add
python-cytoolz.
 2019-01-13 12:44:00 +02:00
Ricardo Wurmus 82acd43cbd
gnu: Add r-raster. 
* gnu/packages/cran.scm (r-raster): New variable.
 2019-01-13 11:14:44 +01:00
Ricardo Wurmus 104e7c3c92
gnu: r-ggformula: Update to 0.9.1. 
* gnu/packages/cran.scm (r-ggformula): Update to 0.9.1.
 2019-01-13 11:14:43 +01:00
Ricardo Wurmus 3fe45dda0a
gnu: r-tibble: Update to 2.0.1. 
* gnu/packages/statistics.scm (r-tibble): Update to 2.0.1.
 2019-01-13 11:14:43 +01:00
Ricardo Wurmus 523762e332
gnu: r-psych: Update to 1.8.12. 
* gnu/packages/cran.scm (r-psych): Update to 1.8.12.
 2019-01-13 11:14:43 +01:00
Efraim Flashner d5fa25a5a0
gnu: bitshuffle: Fix build on armhf-linux. 
* gnu/packages/compression.scm (bitshuffle)[arguments]: Add custom phase
to only use NEON on aarch64.
 2019-01-13 11:31:04 +02:00
Rutger Helling 15d2cebf45
gnu: wine-staging: Update to 4.0-rc6. 
* gnu/packages/wine.scm (wine-staging-patchset-data): Update to 4.0-rc6.
* gnu/packages/wine.scm (wine-staging): Update to 4.0-rc6.
 2019-01-13 10:14:49 +01:00
Ricardo Wurmus c8d8925647
gnu: Sort package module references in (gnu packages graphviz). 
* gnu/packages/graphviz.scm: Sort package module references; delete
duplicates.
 2019-01-13 10:07:06 +01:00
Ricardo Wurmus 8b1c0dab45
gnu: Add python-pygraphviz. 
* gnu/packages/graphviz.scm (python-pygraphviz): New variable.
 2019-01-13 10:07:06 +01:00
Ricardo Wurmus 9e7f55de45
gnu: Add python-doctest-ignore-unicode. 
* gnu/packages/python.scm (python-doctest-ignore-unicode): New variable.
 2019-01-13 10:07:06 +01:00
Ricardo Wurmus c016e390bf
gnu: Add graphviz-2.38. 
* gnu/packages/graphviz.scm (graphviz-2.38): New variable.
 2019-01-13 10:07:06 +01:00
Marius Bakke 1710ffa4c7
gnu: sudo: Update to 1.8.27. 
* gnu/packages/admin.scm (sudo): Update to 1.8.27.
 2019-01-13 01:25:18 +01:00
Marius Bakke cb3e055f86
gnu: libassuan: Update to 2.5.2. 
* gnu/packages/gnupg.scm (libassuan): Update to 2.5.2.
 2019-01-13 01:25:17 +01:00
Marius Bakke 66470a5ad0
gnu: libgxps: Update to 0.3.1. 
* gnu/packages/gnome.scm (libgxps): Update to 0.3.1.
 2019-01-13 01:25:17 +01:00
Marius Bakke ad55c19211
gnu: libqmi: Update to 1.22.0. 
* gnu/packages/freedesktop.scm (libqmi): Update to 1.22.0.
 2019-01-13 01:25:17 +01:00
Marius Bakke de261ace27
gnu: libmbim: Update to 1.18.0. 
* gnu/packages/freedesktop.scm (libmbim): Update to 1.18.0.
 2019-01-13 01:25:17 +01:00
Marius Bakke 8bcae1e60c
gnu: libsodium: Update to 1.0.17. 
* gnu/packages/crypto.scm (libsodium): Update to 1.0.17.
 2019-01-13 01:25:17 +01:00
Marius Bakke 0b014776c9
gnu: exempi: Update to 2.5.0. 
* gnu/packages/freedesktop.scm (exempi): Update to 2.5.0.
 2019-01-13 01:25:17 +01:00
Marius Bakke 00262db23a
gnu: seabios: Update to 1.12.0. 
* gnu/packages/firmware.scm (seabios): Update to 1.12.0.
 2019-01-13 01:25:17 +01:00
Marius Bakke b2e765de4c
gnu: httpd: Update to 2.4.37. 
* gnu/packages/web.scm (httpd): Update to 2.4.37.
 2019-01-13 01:25:17 +01:00
Marius Bakke 1d7fbe0947
gnu: nasm: Update license. 
* gnu/packages/assembly.scm (nasm)[license]: Change to BSD-2.
 2019-01-13 01:25:16 +01:00
Marius Bakke 80459f5a21
gnu: nasm: Update home page. 
* gnu/packages/assembly.scm (nasm)[home-page]: Use HTTPS.
 2019-01-13 01:25:16 +01:00
Marius Bakke 9f1448b74a
gnu: libgphoto2: Update to 2.5.22. 
* gnu/packages/photo.scm (libgphoto2): Update to 2.5.22.
 2019-01-13 01:25:16 +01:00
Marius Bakke ef61969c52
gnu: re2: Update to 2019-01-01. 
* gnu/packages/regex.scm (re2): Update to 2019-01-01.
 2019-01-13 01:25:16 +01:00
Marius Bakke c06ef010e3
gnu: libsecret: Update to 0.18.7. 
* gnu/packages/gnome.scm (libsecret): Update to 0.18.7.
[native-inputs]: Remove INTLTOOL.  Add GETTEXT-MINIMAL.
 2019-01-13 01:25:16 +01:00
Marius Bakke 48d5818a0e
gnu: fluidsynth: Update to 2.0.3. 
* gnu/packages/audio.scm (fluidsynth): Update to 2.0.3.
 2019-01-13 01:25:16 +01:00
Marius Bakke bf135622bd
gnu: rofi: Update to 1.5.2. 
* gnu/packages/xdisorg.scm (rofi): Update to 1.5.2.
 2019-01-13 01:25:16 +01:00
Marius Bakke 2bb187c484
gnu: xscreensaver: Update to 5.42. 
* gnu/packages/xdisorg.scm (xscreensaver): Update to 5.42.
[arguments]: Add "CFLAGS=-std=c99" to #:make-flags.
 2019-01-13 01:25:16 +01:00
Marius Bakke 0c4cee13b2
gnu: libcmis: Update to 0.5.2. 
* gnu/packages/libreoffice.scm (libcmis): Update to 0.5.2.
[source](uri): Use XZ-compressed tarball.
[arguments]: Remove #:phases.  Don't pass "--disable-werror" in #:configure-flags.
 2019-01-13 01:25:15 +01:00
Marius Bakke 48a51af9d2
gnu: http-parser: Update to 2.9.0. 
* gnu/packages/web.scm (http-parser): Update to 2.9.0.
 2019-01-13 01:25:15 +01:00
Marius Bakke 304db09257
gnu: http-parser: Download from git. 
* gnu/packages/web.scm (http-parser)[source]: Change to GIT-FETCH.
 2019-01-13 01:25:15 +01:00
Marius Bakke 9c2094785d
gnu: libetonyek: Adjust inputs. 
* gnu/packages/libreoffice.scm (libetonyek)[native-inputs]: Remove LIBLANGTAG.
Move GLM and MDDS to ...
[inputs]: ... here.
[propagated-inputs]: Add LIBLANGTAG and ZLIB.
 2019-01-13 01:25:15 +01:00
Marius Bakke 7c3acfcb69
gnu: libetonyek: Update to 0.1.9. 
* gnu/packages/libreoffice.scm (libetonyek): Update to 0.1.9.
[arguments]: Remove #:phases.
 2019-01-13 01:25:15 +01:00
Marius Bakke b1d2e0b4e0
gnu: libcdr: Update to 0.1.5. 
* gnu/packages/libreoffice.scm (libcdr): Update to 0.1.5.
[source](uri): Download over HTTPS.
[arguments]: Remove.
 2019-01-13 01:25:15 +01:00
Kei Kebreau 5b9c2690af
gnu: tintin++: Update to 2.01.5. 
* gnu/packages/games.scm (tintin++): Update to 2.01.5.
 2019-01-12 18:37:38 -05:00
Ricardo Wurmus c6e9b494e8
gnu: r-ruvseq: Update to 1.16.1. 
* gnu/packages/bioconductor.scm (r-ruvseq): Update to 1.16.1.
 2019-01-12 23:35:19 +01:00
Ricardo Wurmus c86fc96987
gnu: r-inspect: Update to 1.12.1. 
* gnu/packages/bioconductor.scm (r-inspect): Update to 1.12.1.
[propagated-inputs]: Add r-deseq2, r-plgem, r-shiny, r-summarizedexperiment,
and r-txdb-mmusculus-ucsc-mm9-knowngene.
 2019-01-12 23:35:19 +01:00
Ricardo Wurmus d220babf34
gnu: Add r-txdb-mmusculus-ucsc-mm9-knowngene. 
* gnu/packages/bioconductor.scm (r-txdb-mmusculus-ucsc-mm9-knowngene): New
variable.
 2019-01-12 23:35:19 +01:00
Ricardo Wurmus cad6fb2dec
gnu: Add r-plgem. 
* gnu/packages/bioconductor.scm (r-plgem): New variable.
 2019-01-12 23:35:19 +01:00
Ricardo Wurmus 45dcd7dcfd
gnu: r-rots: Update to 1.10.1. 
* gnu/packages/bioconductor.scm (r-rots): Update to 1.10.1.
 2019-01-12 23:35:19 +01:00
Ricardo Wurmus 0b469ee225
gnu: r-glimma: Update to 1.10.1. 
* gnu/packages/bioconductor.scm (r-glimma): Update to 1.10.1.
 2019-01-12 23:35:19 +01:00
Ricardo Wurmus 7f2b1c4af0
gnu: r-goseq: Update to 1.34.1. 
* gnu/packages/bioconductor.scm (r-goseq): Update to 1.34.1.
 2019-01-12 23:35:18 +01:00
Ricardo Wurmus add2b19561
gnu: r-chippeakanno: Update to 3.16.1. 
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.16.1.
 2019-01-12 23:35:18 +01:00
Ricardo Wurmus c476edc2cd
gnu: r-rtracklayer: Update to 1.42.1. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.42.1.
 2019-01-12 23:35:18 +01:00
Ricardo Wurmus 1e107b0960
gnu: r-scater: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.10.1.
 2019-01-12 23:35:18 +01:00
Ricardo Wurmus 0f268bb275
gnu: r-singlecellexperiment: Update to 1.4.1. 
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.4.1.
 2019-01-12 23:35:18 +01:00
Ricardo Wurmus a0224bd4f6
gnu: r-rhdf5lib: Update to 1.4.2. 
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.2.
 2019-01-12 23:35:18 +01:00
Ricardo Wurmus 40561d0249
gnu: r-hdf5array: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.10.1.
 2019-01-12 23:35:18 +01:00
Ricardo Wurmus ad10b3979d
gnu: r-qvalue: Update to 2.14.1. 
* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.14.1.
 2019-01-12 23:35:18 +01:00
Ricardo Wurmus 19cacb5a2d
gnu: r-gviz: Update to 1.26.4. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.4.
 2019-01-12 23:35:18 +01:00
Ricardo Wurmus c80595935d
gnu: r-biovizbase: Update to 1.30.1. 
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.30.1.
 2019-01-12 23:35:18 +01:00
Ricardo Wurmus 27194effd7
gnu: r-ensembldb: Update to 2.6.3. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.3.
 2019-01-12 23:35:18 +01:00
Ricardo Wurmus 43931ff72f
gnu: r-dirichletmultinomial: Update to 1.24.1. 
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.24.1.
 2019-01-12 23:35:18 +01:00
Ricardo Wurmus 15d89fe9f8
gnu: r-gage: Update to 2.32.1. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.32.1.
 2019-01-12 23:35:18 +01:00
Ricardo Wurmus 4615cf9f1a
gnu: r-annotationhub: Update to 2.14.2. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.2.
 2019-01-12 23:35:18 +01:00
Ricardo Wurmus ab4a862ab8
gnu: r-edaseq: Update to 2.16.3. 
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.16.3.
[propagated-inputs]: Add r-biocmanager.
 2019-01-12 23:35:18 +01:00
Ricardo Wurmus 3bdc41b352
gnu: r-deseq: Update to 1.34.1. 
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.34.1.
 2019-01-12 23:35:18 +01:00
Ricardo Wurmus 9abf344f8b
gnu: r-msnid: Update to 1.16.1. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.16.1.
 2019-01-12 23:35:17 +01:00
Ricardo Wurmus 880ed11e9f
gnu: r-msnbase: Update to 2.8.3. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.8.3.
 2019-01-12 23:35:17 +01:00
Ricardo Wurmus 6451af78e1
gnu: r-mzid: Update to 1.20.1. 
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.20.1.
 2019-01-12 23:35:17 +01:00
Ricardo Wurmus a4f038dc97
gnu: r-mzr: Update to 2.16.1. 
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.1.
 2019-01-12 23:35:17 +01:00
Ricardo Wurmus 46508c3a92
gnu: r-sva: Update to 3.30.1. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.30.1.
 2019-01-12 23:35:17 +01:00
Ricardo Wurmus c20426ec5c
gnu: r-methylkit: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.8.1.
 2019-01-12 23:35:17 +01:00
Ricardo Wurmus 5c72ebafeb
gnu: r-copywriter: Update to 2.14.1. 
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.14.1.
 2019-01-12 23:35:17 +01:00
Ricardo Wurmus 86162c767e
gnu: r-rhdf5: Update to 2.26.2. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.26.2.
 2019-01-12 23:35:17 +01:00
Ricardo Wurmus 4c7b9222dd
gnu: r-tximport: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.10.1.
 2019-01-12 23:35:17 +01:00
Ricardo Wurmus 4bfde52178
gnu: r-genomicalignments: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.18.1.
 2019-01-12 23:35:17 +01:00
Ricardo Wurmus 1fa12b2f06
gnu: r-biostrings: Update to 2.50.2. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.2.
 2019-01-12 23:35:17 +01:00
Ricardo Wurmus d4fc834cf7
gnu: r-biocparallel: Update to 1.16.5. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.16.5.
 2019-01-12 23:35:17 +01:00
Ricardo Wurmus 52c977a05b
gnu: r-limma: Update to 3.38.3. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.38.3.
 2019-01-12 23:35:17 +01:00
Ricardo Wurmus 3fd48846eb
gnu: r-variantannotation: Update to 1.28.8. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.8.
 2019-01-12 23:35:17 +01:00
Ricardo Wurmus a619850930
gnu: r-edger: Update to 3.24.3. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.24.3.
 2019-01-12 23:35:17 +01:00
Ricardo Wurmus 00f105fe20
gnu: r-biocviews: Update to 1.50.10. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.10.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus 9c1b2b2ae0
gnu: r-systempiper: Update to 1.16.1. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.16.1.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus 3b8c884285
gnu: r-rbgl: Update to 1.58.1. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.58.1.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus ffe16ef33c
gnu: r-dexseq: Update to 1.28.1. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.1.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus f7e95c50b8
gnu: r-deseq2: Update to 1.22.2. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.22.2.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus feb561f721
gnu: r-scran: Update to 1.10.2. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.10.2.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus fd7301676e
gnu: r-sjplot: Update to 2.6.2. 
* gnu/packages/cran.scm (r-sjplot): Update to 2.6.2.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus e45f4a4dab
gnu: r-sjmisc: Update to 2.7.7. 
* gnu/packages/cran.scm (r-sjmisc): Update to 2.7.7.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus 5e8282a4a0
gnu: r-rmpi: Update to 0.6-9. 
* gnu/packages/cran.scm (r-rmpi): Update to 0.6-9.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus 80c4e75b87
gnu: r-seqminer: Update to 7.1. 
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 7.1.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus 3bc0667f3c
gnu: r-bookdown: Update to 0.9. 
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.9.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus c3e5b456be
gnu: r-protviz: Update to 0.4.0. 
* gnu/packages/cran.scm (r-protviz): Update to 0.4.0.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus 209e504bb1
gnu: r-ontologyindex: Update to 2.5. 
* gnu/packages/cran.scm (r-ontologyindex): Update to 2.5.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus e041740289
gnu: r-chemometricswithr: Update to 0.1.13. 
* gnu/packages/cran.scm (r-chemometricswithr): Update to 0.1.13.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus 9ad5f4ba19
gnu: r-grimport: Update to 0.9-1.1. 
* gnu/packages/cran.scm (r-grimport): Update to 0.9-1.1.
 2019-01-12 23:35:16 +01:00