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Author SHA1 Message Date
Ludovic Courtès e98c354d1a
gnu: guile-ssh: Use 'git-fetch'. 
* gnu/packages/ssh.scm (guile-ssh)[source]: Change to 'git-fetch'.
 2019-01-14 23:43:49 +01:00
Ludovic Courtès a8b0556ea1
gnu: libssh: Update to 0.8.6. 
* gnu/packages/patches/libssh-hostname-parser-bug.patch: Remove.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/ssh.scm (libssh): Update to 0.8.6.
[source](patches): Remove.
[arguments]: Add #:phases.
(guile-ssh)[source](modules, snippet]: New fields.
 2019-01-14 23:43:49 +01:00
Ludovic Courtès 152d4076a4
gnu: guile-json: Add 3.1.0. 
* gnu/packages/guile.scm (guile-json-3): New variable.
 2019-01-14 23:43:49 +01:00
Ricardo Wurmus 21b41a79fe
gnu: Move Perl compression packages to new module. 
* gnu/packages/compression.scm (perl-compress-raw-bzip2,
perl-compress-raw-zlib, perl-io-compress, perl-archive-zip,
perl-archive-extract): Move from here...
* gnu/packages/perl-compression.scm: ...to this new file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/ci.scm, gnu/packages/libreoffice.scm, gnu/packages/perl.scm:
Adjust references.
 2019-01-14 18:12:54 +01:00
Ricardo Wurmus b80ecc5a63
gnu: texlive-latex-fontspec: Propagate l3packages. 
* gnu/packages/tex.scm (texlive-latex-fontspec)[inputs]: Remove
texlive-latex-l3kernel.
[propagated-inputs]: Add texlive-latex-l3packages.
 2019-01-14 15:42:32 +01:00
Ricardo Wurmus 2fea7041a3
gnu: texlive-latex-l3packages: Propagate l3kernel. 
* gnu/packages/tex.scm (texlive-latex-l3packages)[inputs]: Move
texlive-latex-l3kernel from here...
[propagated-inputs]: ...to here.
 2019-01-14 15:39:22 +01:00
Ricardo Wurmus 73635e3f69
gnu: Add texlive-latex-changepage. 
* gnu/packages/tex.scm (texlive-latex-changepage): New variable.
 2019-01-14 14:13:21 +01:00
Ricardo Wurmus 6309d21579
gnu: Add texlive-generic-babel-german. 
* gnu/packages/tex.scm (texlive-generic-babel-german): New variable.
 2019-01-14 14:13:21 +01:00
Ricardo Wurmus d68c8017f1
gnu: texlive-latex-base: Install configuration files. 
* gnu/packages/tex.scm (texlive-latex-base)[arguments]: Install all
configuration files.
[native-inputs]: Move texlive-generic-hyph-utf8 from here...
[propagated-inputs]: ...to here.
 2019-01-14 14:13:21 +01:00
Efraim Flashner 6c56e9c493
gnu: opencv: Use 'git-fetch'. 
* gnu/packages/image-processing.scm (opencv)[source]: Use 'git-fetch'.
[native-inputs]: Use 'git-fetch' for opencv_extras and opencv_contrib.
Remove unzip.
[arguments]: Update custom 'unpack-submodule-sources accordingly. Update
paths in configure-flags, 'diable-broken-tests phase.
 2019-01-14 15:07:42 +02:00
Efraim Flashner 7b28210531
gnu: python-django-filter: Use 'invoke'. 
* gnu/packages/django.scm (python-django-filter)[arguments]: Use
'invoke'.
 2019-01-14 15:07:42 +02:00
Efraim Flashner 8e21fa0bd3
gnu: opencv: Loosen test suite failures. 
* gnu/packages/image-processing.scm (opencv)[native-inputs]: Add patch
to opencv-contrib.
[arguments]: Update 'unpack-submodule-sources phase.
* gnu/packages/patches/opencv-rgbd-aarch64-test-fix.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2019-01-14 15:07:42 +02:00
Efraim Flashner fdeb2def6a
gnu: opencv: Update configure flags. 
* gnu/packages/image-processing.scm (opencv)[arguments]: Don't use
precompiled headers. Enable all available CPU optimizations.
 2019-01-14 15:07:42 +02:00
Efraim Flashner b5baf9529e
gnu: opencv: Don't hardcode build directories. 
* gnu/packages/image-processing.scm (opencv)[arguments]: Change
OPENCV_EXTRA_MODULES_PATH and OPENCV_TEST_DATA_PATH to use 'getcwd'
instead of hardcoding the build path.
 2019-01-14 15:07:41 +02:00
Efraim Flashner 6949f45c10
gnu: opencv: Fix building on non-x86_64 systems. 
* gnu/packages/image-processing.scm (opencv)[arguments]: Add
configure-flag to disable carotene. Don't require x86_64 CPU
except on x86_64. Fix typo.
 2019-01-14 15:07:41 +02:00
Efraim Flashner c5c42f0a9c
gnu: gnurl: Update to 7.63.0. 
* gnu/packages/gnunet.scm (gnurl): Update to 7.63.0.
 2019-01-14 13:57:49 +02:00
Clément Lassieur 6e46be066a
gnu: emacs-pass: Update to 1.8. 
* gnu/packages/emacs.scm (emacs-pass): Update to 1.8.
 2019-01-14 12:33:46 +01:00
Rutger Helling 478040d4fb
gnu: dosbox: Update to 0.74-2. 
* gnu/packages/emulators.scm (dosbox): Update to 0.74-2.
[arguments]: Use invoke in 'autogen.sh phase.
 2019-01-14 09:08:04 +01:00
Mark H Weaver 72b308364f
gnu: linux-libre: Update to 4.20.2. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.20.2.
(%linux-libre-hash): Update hash.
 2019-01-14 01:29:47 -05:00
Mark H Weaver 8fa75a2266
gnu: linux-libre@4.19: Update to 4.19.15. 
* gnu/packages/linux.scm (%linux-libre-4.19-version): Update to 4.19.15.
(%linux-libre-4.19-hash): Update hash.
 2019-01-14 01:28:02 -05:00
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
Ricardo Wurmus 16d296bbd1
gnu: r-shades: Update to 1.3.1. 
* gnu/packages/cran.scm (r-shades): Update to 1.3.1.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus 6eab52e0dd
gnu: r-ggeffects: Update to 0.8.0. 
* gnu/packages/cran.scm (r-ggeffects): Update to 0.8.0.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus de7631b278
gnu: r-slam: Update to 0.1-44. 
* gnu/packages/cran.scm (r-slam): Update to 0.1-44.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus 2652e2534f
gnu: r-refgenome: Update to 1.7.3.1. 
* gnu/packages/cran.scm (r-refgenome): Update to 1.7.3.1.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus f0867a0e8b
gnu: r-findpython: Update to 1.0.4. 
* gnu/packages/cran.scm (r-findpython): Update to 1.0.4.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus 12502bf4e8
gnu: r-prediction: Update to 0.3.6.1. 
* gnu/packages/cran.scm (r-prediction): Update to 0.3.6.1.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus fbd263cd4a
gnu: r-abn: Update to 1.3. 
* gnu/packages/cran.scm (r-abn): Update to 1.3.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus 1b1444012b
gnu: r-sjstats: Update to 0.17.3. 
* gnu/packages/cran.scm (r-sjstats): Update to 0.17.3.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus 9df469a1d4
gnu: r-emmeans: Update to 1.3.1. 
* gnu/packages/cran.scm (r-emmeans): Update to 1.3.1.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus 1afe56444e
gnu: r-glmmtmb: Update to 0.2.3. 
* gnu/packages/cran.scm (r-glmmtmb): Update to 0.2.3.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus 1417d5f1d5
gnu: r-rio: Update to 0.5.16. 
* gnu/packages/cran.scm (r-rio): Update to 0.5.16.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus 962304c31c
gnu: r-arules: Update to 1.6-2. 
* gnu/packages/cran.scm (r-arules): Update to 1.6-2.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus f2fc34f241
gnu: r-fnn: Update to 1.1.2.2. 
* gnu/packages/cran.scm (r-fnn): Update to 1.1.2.2.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus f0fe1a5a45
gnu: r-shinyace: Update to 0.3.3. 
* gnu/packages/cran.scm (r-shinyace): Update to 0.3.3.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus 5f1f11049f
gnu: r-cubature: Update to 2.0.3. 
* gnu/packages/cran.scm (r-cubature): Update to 2.0.3.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus 7abb15f2bb
gnu: r-tseries: Update to 0.10-46. 
* gnu/packages/cran.scm (r-tseries): Update to 0.10-46.
 2019-01-12 23:35:15 +01:00
Ricardo Wurmus 9d83132757
gnu: r-statnet-common: Update to 4.2.0. 
* gnu/packages/cran.scm (r-statnet-common): Update to 4.2.0.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus 7e9e9c9c46
gnu: r-tinytex: Update to 0.10. 
* gnu/packages/cran.scm (r-tinytex): Update to 0.10.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus fc00a1f0fc
gnu: r-pillar: Update to 1.3.1. 
* gnu/packages/cran.scm (r-pillar): Update to 1.3.1.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus 111516f9d6
gnu: r-gclus: Update to 1.3.2. 
* gnu/packages/cran.scm (r-gclus): Update to 1.3.2.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus ed46a05c75
gnu: r-laeken: Update to 0.5.0. 
* gnu/packages/cran.scm (r-laeken): Update to 0.5.0.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus fc74de42da
gnu: r-ddalpha: Update to 1.3.8. 
* gnu/packages/cran.scm (r-ddalpha): Update to 1.3.8.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus 221b3b164d
gnu: r-rmysql: Update to 0.10.16. 
* gnu/packages/cran.scm (r-rmysql): Update to 0.10.16.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus 1c6d199ee8
gnu: r-mitml: Update to 0.3-7. 
* gnu/packages/cran.scm (r-mitml): Update to 0.3-7.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus 5703991841
gnu: r-recipes: Add missing input. 
* gnu/packages/cran.scm (r-recipes)[propagated-inputs]: Add r-withr.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus 77f97229c9
gnu: r-dimred: Add missing input. 
* gnu/packages/cran.scm (r-dimred)[propagated-inputs]: Add r-magrittr.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus 8f88701491
gnu: r-lava: Update to 1.6.4. 
* gnu/packages/cran.scm (r-lava): Update to 1.6.4.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus 397dba01c6
gnu: r-powerlaw: Update to 0.70.2. 
* gnu/packages/cran.scm (r-powerlaw): Update to 0.70.2.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus 72c4987506
gnu: r-circlize: Update to 0.4.5. 
* gnu/packages/cran.scm (r-circlize): Update to 0.4.5.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus 422dea1774
gnu: r-ps: Update to 1.3.0. 
* gnu/packages/cran.scm (r-ps): Update to 1.3.0.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus dcf89cc0cf
gnu: r-haven: Update to 2.0.0. 
* gnu/packages/cran.scm (r-haven): Update to 2.0.0.
 2019-01-12 23:35:14 +01:00
Ricardo Wurmus 69aad34ae0
gnu: r-feather: Update to 0.3.2. 
* gnu/packages/cran.scm (r-feather): Update to 0.3.2.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus 1add168ab5
gnu: r-htmltable: Update to 1.13.1. 
* gnu/packages/cran.scm (r-htmltable): Update to 1.13.1.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus 37349c717e
gnu: r-httpuv: Update to 1.4.5.1. 
* gnu/packages/cran.scm (r-httpuv): Update to 1.4.5.1.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus 0c025a7f79
gnu: r-clipr: Update to 0.5.0. 
* gnu/packages/cran.scm (r-clipr): Update to 0.5.0.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus 2e4fc4ac62
gnu: r-caret: Update to 6.0-81. 
* gnu/packages/statistics.scm (r-caret): Update to 6.0-81.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus aa72d7f7f5
gnu: r-quantreg: Update to 5.38. 
* gnu/packages/statistics.scm (r-quantreg): Update to 5.38.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus 9b7df80b9b
gnu: r-rcppeigen: Update to 0.3.3.5.0. 
* gnu/packages/statistics.scm (r-rcppeigen): Update to 0.3.3.5.0.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus bcc17f7f11
gnu: r-rrcov: Update to 1.4-7. 
* gnu/packages/statistics.scm (r-rrcov): Update to 1.4-7.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus 70ee5ab137
gnu: r-cowplot: Update to 0.9.4. 
* gnu/packages/statistics.scm (r-cowplot): Update to 0.9.4.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus 7213ef07c6
gnu: r-rann: Update to 2.6.1. 
* gnu/packages/statistics.scm (r-rann): Update to 2.6.1.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus 2c8594d963
gnu: r-sfsmisc: Update to 1.1-3. 
* gnu/packages/statistics.scm (r-sfsmisc): Update to 1.1-3.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus 54ebdf6f74
gnu: r-rmarkdown: Update to 1.11. 
* gnu/packages/statistics.scm (r-rmarkdown): Update to 1.11.
[propagated-inputs]: Remove r-rprojroot.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus fb45934202
gnu: r-rstudioapi: Update to 0.9.0. 
* gnu/packages/statistics.scm (r-rstudioapi): Update to 0.9.0.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus 8f49d99a84
gnu: r-git2r: Update to 0.24.0. 
* gnu/packages/statistics.scm (r-git2r): Update to 0.24.0.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus c12e429348
gnu: r-httr: Update to 1.4.0. 
* gnu/packages/statistics.scm (r-httr): Update to 1.4.0.
 2019-01-12 23:35:13 +01:00
Ricardo Wurmus 02c89c5812
gnu: r-commonmark: Update to 1.7. 
* gnu/packages/statistics.scm (r-commonmark): Update to 1.7.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus fe8c44502b
gnu: r-checkmate: Update to 1.9.0. 
* gnu/packages/statistics.scm (r-checkmate): Update to 1.9.0.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus ca4861c602
gnu: r-backports: Update to 1.1.3. 
* gnu/packages/statistics.scm (r-backports): Update to 1.1.3.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus 23347dc353
gnu: r-dbplyr: Update to 1.3.0. 
* gnu/packages/statistics.scm (r-dbplyr): Update to 1.3.0.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus f12ed3664d
gnu: r-tibble: Update to 2.0.0. 
* gnu/packages/statistics.scm (r-tibble): Update to 2.0.0.
[propagated-inputs]: Add r-fansi and r-pkgconfig.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus c668a95861
gnu: r-rlang: Update to 0.3.1. 
* gnu/packages/statistics.scm (r-rlang): Update to 0.3.1.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus 495866a9d7
gnu: r-knitr: Update to 1.21. 
* gnu/packages/statistics.scm (r-knitr): Update to 1.21.
[propagated-inputs]: Add r-xfun.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus bf3aded0cf
gnu: r-markdown: Update to 0.9. 
* gnu/packages/statistics.scm (r-markdown): Update to 0.9.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus eae93bd3f2
gnu: r-bh: Update to 1.69.0-1. 
* gnu/packages/statistics.scm (r-bh): Update to 1.69.0-1.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus b6e27673e6
gnu: r-pheatmap: Update to 1.0.12. 
* gnu/packages/statistics.scm (r-pheatmap): Update to 1.0.12.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus ca2bc7e037
gnu: r-mgcv: Update to 1.8-26. 
* gnu/packages/statistics.scm (r-mgcv): Update to 1.8-26.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus 60f1bce09f
gnu: r-codetools: Update to 0.2-16. 
* gnu/packages/statistics.scm (r-codetools): Update to 0.2-16.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus 3dbd87f504
gnu: r-class: Update to 7.3-15. 
* gnu/packages/statistics.scm (r-class): Update to 7.3-15.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus 35cf4874cc
gnu: r-survival: Update to 2.43-3. 
* gnu/packages/statistics.scm (r-survival): Update to 2.43-3.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus 11a36548d9
gnu: r-argparse: Update to 2.0.0. 
* gnu/packages/cran.scm (r-argparse): Update to 2.0.0.
[propagated-inputs]: Add r-r6; remove r-proto.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus 527c605598
gnu: r-callr: Update to 3.1.1. 
* gnu/packages/cran.scm (r-callr): Update to 3.1.1.
[propagated-inputs]: Remove r-base64enc.
 2019-01-12 23:35:12 +01:00
Ricardo Wurmus b140569e18
gnu: r-readxl: Update to 1.2.0. 
* gnu/packages/cran.scm (r-readxl): Update to 1.2.0.
[propagated-inputs]: Add r-progress.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 0aad198e2b
gnu: r-pracma: Update to 2.2.2. 
* gnu/packages/maths.scm (r-pracma): Update to 2.2.2.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 44c69a536e
gnu: r-rcpparmadillo: Update to 0.9.200.5.0. 
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.200.5.0.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 0e87bf0177
gnu: r-processx: Update to 3.2.1. 
* gnu/packages/cran.scm (r-processx): Update to 3.2.1.
[propagated-inputs]: Remove r-assertthat, r-crayon, and r-testthat.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 2766d3436a
gnu: r-sjlabelled: Update to 1.0.16. 
* gnu/packages/cran.scm (r-sjlabelled): Update to 1.0.16.
[propagated-inputs]: Remove r-tibble and r-tidyselect.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 813d9c51e3
gnu: r-broom: Update to 0.5.1. 
* gnu/packages/cran.scm (r-broom): Update to 0.5.1.
[propagated-inputs]: Add r-generics.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 25c67ecfc6
gnu: Add r-generics. 
* gnu/packages/cran.scm (r-generics): New variable.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 646e1ef059
gnu: r-curl: Update to 3.3. 
* gnu/packages/cran.scm (r-curl): Update to 3.3.
[inputs]: Add zlib.
[native-inputs]: Add pkg-config.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus ef91530362
gnu: r-readr: Update to 1.3.1. 
* gnu/packages/statistics.scm (r-readr): Update to 1.3.1.
[propagated-inputs]: Add r-clipr and r-crayon.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 48102ce123
gnu: r-mvabund: Update to 4.0.1. 
* gnu/packages/cran.scm (r-mvabund): Update to 4.0.1.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus 04a18a81ae
gnu: r-writexl: Update to 1.1. 
* gnu/packages/cran.scm (r-writexl): Update to 1.1.
 2019-01-12 23:35:11 +01:00
Ricardo Wurmus a2315c6702
gnu: r-jsonlite: Update to 1.6. 
* gnu/packages/cran.scm (r-jsonlite): Update to 1.6.
 2019-01-12 23:35:11 +01:00
Kei Kebreau ea600ff709
gnu: python-pillow: Update homepage. 
* gnu/packages/python.scm (python-pillow)[homepage]: Update URL.
 2019-01-12 16:39:26 -05:00
Kei Kebreau acbf312573
gnu: python-pillow: Update to 5.4.0 
* gnu/packages/python.scm (python-pillow): Update to 5.4.0.
[arguments]: Add 'patch-ldconfig' phase.
 2019-01-12 16:38:36 -05:00
Ricardo Wurmus 146c6b62bf
gnu: Sort package modules in (gnu packages guile). 
* gnu/packages/guile.scm: Sort list of gnu/packages modules.
 2019-01-12 12:14:31 +01:00
Ricardo Wurmus 7d8baff97b
gnu: impressive: Update to 0.12.0. 
* gnu/packages/pdf.scm (impressive): Update to 0.12.0.
 2019-01-12 12:14:31 +01:00
Ricardo Wurmus 24155bf40d
gnu: Move Java compression packages to new module. 
* gnu/packages/compression.scm (bitshuffle-for-snappy): Export variable.
(java-snappy, java-snappy-1, java-iq80-snappy, java-jbzip2, java-tukaani-xz):
Move these variables from here...
* gnu/packages/java-compression.scm: ...to this new file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/java.scm, gnu/packages/bioinformatics.scm: Adjust module
references.
 2019-01-12 12:14:28 +01:00
guy fleury iteriteka 1704367719
gnu: Add Bochs. 
* gnu/packages/virtualization.scm (bochs): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2019-01-11 17:09:20 -05:00