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
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
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
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
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
73635e3f69
gnu: Add texlive-latex-changepage.
...
* gnu/packages/tex.scm (texlive-latex-changepage): New variable.
2019-01-14 14:13:21 +01:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
d691e96657
gnu: conda: Use 'invoke'.
...
* gnu/packages/package-management.scm (conda)[arguments]: Use 'invoke'.
2019-01-13 12:44:03 +02:00
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
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
82acd43cbd
gnu: Add r-raster.
...
* gnu/packages/cran.scm (r-raster): New variable.
2019-01-13 11:14:44 +01:00
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
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
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
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
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
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
8b1c0dab45
gnu: Add python-pygraphviz.
...
* gnu/packages/graphviz.scm (python-pygraphviz): New variable.
2019-01-13 10:07:06 +01:00
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
c016e390bf
gnu: Add graphviz-2.38.
...
* gnu/packages/graphviz.scm (graphviz-2.38): New variable.
2019-01-13 10:07:06 +01:00
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
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
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
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
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
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
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
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
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
1d7fbe0947
gnu: nasm: Update license.
...
* gnu/packages/assembly.scm (nasm)[license]: Change to BSD-2.
2019-01-13 01:25:16 +01:00
80459f5a21
gnu: nasm: Update home page.
...
* gnu/packages/assembly.scm (nasm)[home-page]: Use HTTPS.
2019-01-13 01:25:16 +01:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
cad6fb2dec
gnu: Add r-plgem.
...
* gnu/packages/bioconductor.scm (r-plgem): New variable.
2019-01-12 23:35:19 +01:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Ludovic Courtès