Commit graph

30988 commits

Author SHA1 Message Date
Ricardo Wurmus 95ae5acc89
gnu: r-category: Update to 2.48.0.
* gnu/packages/bioinformatics.scm (r-category): Update to 2.48.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus 6dfb0b25ae
gnu: r-gseabase: Update to 1.44.0.
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.44.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus 19a6149190
gnu: r-rbgl: Update to 1.58.0.
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.58.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus 2ff6604a53
gnu: r-annotationforge: Update to 1.24.0.
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.24.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus 856444a0a1
gnu: r-dexseq: Update to 1.28.0.
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus b5c552e654
gnu: r-deseq2: Update to 1.22.1.
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.22.1.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus 85fb33a051
gnu: r-genefilter: Update to 1.64.0.
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.64.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus f4a95a0d15
gnu: r-geneplotter: Update to 1.60.0.
* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.60.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus dadd682c53
gnu: r-copynumber: Update to 1.22.0.
* gnu/packages/bioinformatics.scm (r-copynumber): Update to 1.22.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus 090d4c0159
gnu: r-annotate: Update to 1.60.0.
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.60.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus 00281ea3cd
gnu: r-modelmetrics: Update to 1.2.2.
* gnu/packages/statistics.scm (r-modelmetrics): Update to 1.2.2.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus 9bd78484a2
gnu: r-preprocesscore: Update to 1.44.0.
* gnu/packages/statistics.scm (r-preprocesscore): Update to 1.44.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus 1b3552310d
gnu: r-tidyr: Update to 0.8.2.
* gnu/packages/statistics.scm (r-tidyr): Update to 0.8.2.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus 466397c35b
gnu: r-dt: Update to 0.5.
* gnu/packages/statistics.scm (r-dt): Update to 0.5.
[propagated-inputs]: Add r-promises.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus 9094eb892c
gnu: r-roxygen2: Update to 6.1.1.
* gnu/packages/statistics.scm (r-roxygen2): Update to 6.1.1.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus 0de3ebb099
gnu: r-survival: Update to 2.43-1.
* gnu/packages/statistics.scm (r-survival): Update to 2.43-1.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus 83ca17d8e8
gnu: r-matrix: Update to 1.2-15.
* gnu/packages/statistics.scm (r-matrix): Update to 1.2-15.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus 1966d8ffc7
gnu: r-lattice: Update to 0.20-38.
* gnu/packages/statistics.scm (r-lattice): Update to 0.20-38.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus 600a25eb04
gnu: r-mass: Update to 7.3-51.1.
* gnu/packages/statistics.scm (r-mass): Update to 7.3-51.1.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus a44f8b00fe
gnu: r-pander: Update to 0.6.3.
* gnu/packages/cran.scm (r-pander): Update to 0.6.3.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus 7466c3bb06
gnu: r-rcmdcheck: Update to 1.3.1.
* gnu/packages/cran.scm (r-rcmdcheck): Update to 1.3.1.
[propagated-inputs]: Add r-sessioninfo.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus fc532b452f
gnu: r-remotes: Update to 2.0.2.
* gnu/packages/cran.scm (r-remotes): Update to 2.0.2.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus 3d6fa1a3ad
gnu: r-sessioninfo: Update to 1.1.1.
* gnu/packages/cran.scm (r-sessioninfo): Update to 1.1.1.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus 244a5c43ec
gnu: r-flextable: Update to 0.4.6.
* gnu/packages/cran.scm (r-flextable): Update to 0.4.6.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus 84d0d860e1
gnu: r-sjmisc: Update to 2.7.6.
* gnu/packages/cran.scm (r-sjmisc): Update to 2.7.6.
[propagated-inputs]: Remove r-pillar, r-tibble, and r-tidyselect.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus cea8a60747
gnu: r-xts: Update to 0.11-2.
* gnu/packages/cran.scm (r-xts): Update to 0.11-2.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus 5d986a3b41
gnu: r-psych: Update to 1.8.10.
* gnu/packages/cran.scm (r-psych): Update to 1.8.10.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus 56af171ffd
gnu: r-ipred: Update to 0.9-8.
* gnu/packages/cran.scm (r-ipred): Update to 0.9-8.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus ec0ee08576
gnu: r-ffbase: Update to 0.12.7.
* gnu/packages/cran.scm (r-ffbase): Update to 0.12.7.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus 65dd0e6748
gnu: r-pkgload: Update to 1.0.2.
* gnu/packages/cran.scm (r-pkgload): Update to 1.0.2.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus 0dd84df121
gnu: r-ps: Update to 1.2.1.
* gnu/packages/cran.scm (r-ps): Update to 1.2.1.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus 269182b0f1
gnu: r-rgraphviz: Update to 2.26.0.
* gnu/packages/graph.scm (r-rgraphviz): Update to 2.26.0.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus bb47aca5e7
gnu: Add hdf5-1.10.
* gnu/packages/maths.scm (hdf5-1.10): New variable.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus d639d8884c
gnu: r-regioner: Update to 1.14.0.
* gnu/packages/bioconductor.scm (r-regioner): Update to 1.14.0.
[propagated-inputs]: Add r-biostrings.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus ed35d7ca1f
gnu: r-ruvseq: Update to 1.16.0.
* gnu/packages/bioconductor.scm (r-ruvseq): Update to 1.16.0.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus 286157dc49
gnu: Add r-biocneighbors.
* gnu/packages/bioconductor.scm (r-biocneighbors): New variable.
2018-11-07 12:26:33 +01:00
Ricardo Wurmus 318bcbc451
gnu: r-dnabarcodes: Update to 1.12.0.
* gnu/packages/bioconductor.scm (r-dnabarcodes): Update to 1.12.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 6f1e1d0f88
gnu: r-inspect: Update to 1.12.0.
* gnu/packages/bioconductor.scm (r-inspect): Update to 1.12.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus c348cfed74
gnu: r-rots: Update to 1.10.0.
* gnu/packages/bioconductor.scm (r-rots): Update to 1.10.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 016afac30f
gnu: r-glimma: Update to 1.10.0.
* gnu/packages/bioconductor.scm (r-glimma): Update to 1.10.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 6ea9ae9c39
gnu: r-goseq: Update to 1.34.0.
* gnu/packages/bioconductor.scm (r-goseq): Update to 1.34.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus b858338c76
gnu: r-ctc: Update to 1.56.0.
* gnu/packages/bioconductor.scm (r-ctc): Update to 1.56.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 5f2d0e635e
gnu: r-genomicinteractions: Update to 1.16.0.
* gnu/packages/bioconductor.scm (r-genomicinteractions): Update to 1.16.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus bbc4787cf2
gnu: r-interactionset: Update to 1.10.0.
* gnu/packages/bioconductor.scm (r-interactionset): Update to 1.10.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus c4fed658a9
gnu: r-riboseqr: Update to 1.16.0.
* gnu/packages/bioconductor.scm (r-riboseqr): Update to 1.16.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus e22e462b33
gnu: r-riboprofiling: Update to 1.12.0.
* gnu/packages/bioconductor.scm (r-riboprofiling): Update to 1.12.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus e9427b2c78
gnu: r-ripseeker: Update to 1.22.0.
* gnu/packages/bioconductor.scm (r-ripseeker): Update to 1.22.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus aa802eafb6
gnu: r-chipcomp: Update to 1.12.0.
* gnu/packages/bioconductor.scm (r-chipcomp): Update to 1.12.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 4728e27511
gnu: r-bayseq: Update to 2.16.0.
* gnu/packages/bioconductor.scm (r-bayseq): Update to 2.16.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 57d2fcd9ee
gnu: r-chippeakanno: Update to 3.16.0.
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.16.0.
[propagated-inputs]: Remove r-biocinstaller; add r-biocmanager.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 14520b640e
gnu: r-graph: Update to 1.60.0.
* gnu/packages/bioconductor.scm (r-graph): Update to 1.60.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 95ee4a466b
gnu: r-multtest: Update to 2.38.0.
* gnu/packages/bioconductor.scm (r-multtest): Update to 2.38.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus a92f523026
gnu: r-qdnaseq: Update to 1.18.0.
* gnu/packages/bioconductor.scm (r-qdnaseq): Update to 1.18.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 9add0933d0
gnu: r-cghcall: Update to 2.44.0.
* gnu/packages/bioconductor.scm (r-cghcall): Update to 2.44.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 46cdceef4c
gnu: r-cghbase: Update to 1.42.0.
* gnu/packages/bioconductor.scm (r-cghbase): Update to 1.42.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus f1c606ce8c
gnu: r-marray: Update to 1.60.0.
* gnu/packages/bioconductor.scm (r-marray): Update to 1.60.0.
2018-11-07 12:26:32 +01:00
Ricardo Wurmus 98652568a4
gnu: r-diffbind: Update to 2.10.0.
* gnu/packages/bioconductor.scm (r-diffbind): Update to 2.10.0.
2018-11-07 12:26:31 +01:00
Ricardo Wurmus 6168692159
gnu: r-hpar: Update to 1.24.0.
* gnu/packages/bioconductor.scm (r-hpar): Update to 1.24.0.
2018-11-07 12:26:31 +01:00
Ricardo Wurmus 1e605c030f
gnu: Add r-biocmanager.
* gnu/packages/cran.scm (r-biocmanager): New variable.
2018-11-07 12:26:31 +01:00
Ricardo Wurmus b58940cb03
gnu: Add r-ncdf4.
* gnu/packages/cran.scm (r-ncdf4): New variable.
2018-11-07 12:26:31 +01:00
Ricardo Wurmus bfa5662e38
gnu: Add r-rcppannoy.
* gnu/packages/cran.scm (r-rcppannoy): New variable.
2018-11-07 12:26:31 +01:00
Mathieu Othacehe 8243f4e55a
gnu: slang: Use a correct location for terminfo dirs.
As termcap is disabled and no terminfo directory is given, slang is not able
to query terminal capabilities. Specifying a correct path for terminfo will
automatically disable termcap support in the configuration.

* gnu/packages/slang.scm (slang)[source]: Remove the snippet disabling
termcap.
[arguments]: Set MISC_TERMINFO_DIRS to a correct location.
2018-11-07 18:39:19 +09:00
Mathieu Othacehe a7903ca150
gnu: terminals: Change libtsm and kmscon repositories.
Those two packages (from the same author) are no longer maintained and do not
even compile. Switch to a fork that is maintained even if it does not have any
release yet.

* gnu/packages/terminals.scm (libtsm)[origin]: Use
"https://github.com/Aetf/libtsm" as new origin and switch to git-fetch method.
(kmscon)[origin]: Use "https://github.com/Aetf/kmscon" as new origin and
switch to git-fetch method.
2018-11-07 18:27:01 +09:00
Mathieu Othacehe 2d9dace8c2
services: kmscon: Add an auto-login option.
Add an auto-login option that behaves as the one of mingetty-service.

* gnu/services/base.scm (kmscon-configuration)[auto-login]: New field.
(kmscon-service-type): Pass it to kmscon command.
* doc/guix.texi (Base Services): Document it.
2018-11-07 18:21:42 +09:00
Mathieu Othacehe f4e8bc5f25
services: kmscon: Do not switch to vt at start.
* gnu/services/base.scm (kmscon-service-type): Add "--no-switchvt" to kmscon
command.
2018-11-07 18:15:00 +09:00
Mathieu Othacehe 581720bc74
gnu: Add guile-newt.
* gnu/packages/guile.scm (guile-newt): New variable.
2018-11-07 18:09:30 +09:00
Efraim Flashner cbb5d2e145
gnu: kodi: Fix typo.
This is a follow-up to 2c17bd7b29.

* gnu/packages/kodi.scm (kodi)[arguments]: Remove unwanted symbols.
2018-11-07 10:38:13 +02:00
Leo Famulari 02e2133bd2
gnu: LibreOffice: Update to 6.1.3.2.
* gnu/packages/libreoffice.scm (libreoffice): Update to 6.1.3.2.
2018-11-06 23:13:50 -05:00
Leo Famulari b20aef98a0
gnu: GnuPG: Update to 2.2.11.
* gnu/packages/gnupg.scm (gnupg): Update to 2.2.11.
2018-11-06 17:26:45 -05:00
Ludovic Courtès c5ce2db569
install: Add 'install-database-and-gc-roots'.
* gnu/build/install.scm (%root-profile): New variable.
(install-database-and-gc-roots): New procedure.
(populate-single-profile-directory): Replace inline code with a call to
'install-database-and-gc-roots'.
2018-11-06 23:21:24 +01:00
Ludovic Courtès b27ef1d46c
pack: Import (guix store database) only when '--localstatedir' is passed.
This is another way to address <https://bugs.gnu.org/32184>, which was
previously addressed in commit 19c924af4f.

* gnu/build/install.scm (register-closure): Move to...
* gnu/build/vm.scm (register-closure): ... here.  New procedure.
* guix/scripts/pack.scm (self-contained-tarball)[build]: Remove
now unneeded 'with-extensions' form and custom (guix config) module.
* tests/guix-pack.sh: Revert the strategy from
commit 19c924af4f.
* tests/pack.scm ("self-contained-tarball"): Likewise.
2018-11-06 23:21:23 +01:00
Ludovic Courtès ec4c81fe32
pack: Move store database creation to a separate derivation.
* guix/scripts/pack.scm (store-database): New procedure.
(self-contained-tarball): Use it when LOCALSTATEDIR? is true.
Remove 'schema' and add 'database'.
[build]: Pass DATABASE to 'populate-single-profile-directory'.
(squashfs-image): Remove #:deduplicate? parameter.
[build]: Remove (gnu build install) and (guix config) from the imported
modules.  Remove 'with-extensions'.
* gnu/build/install.scm (populate-single-profile-directory): Remove
 #:deduplicate?, #:register?, and #:schema; add #:database.  Remove call
to 'register-closure' and simply copy DATABASE instead.
2018-11-06 23:21:23 +01:00
Marius Bakke c6b05bacc0
gnu: nginx: Update to 1.14.1 [security fixes].
This fixes CVE-2018-16843, CVE-2018-16844, and CVE-2018-16845.

* gnu/packages/web.scm (nginx): Update to 1.14.1.
2018-11-06 21:34:30 +01:00
Leo Famulari f25614229b
gnu: Syncthing: Update to 0.14.52.
* gnu/packages/syncthing.scm (syncthing): Update to 0.14.52.
2018-11-06 11:16:22 -05:00
Ludovic Courtès 4cceb1432a
gnu: libgit2: Work around test failures on 32-bit platforms.
* gnu/packages/patches/libgit2-oom-test.patch: New file.
* gnu/packages/version-control.scm (libgit2)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Add it.
2018-11-06 17:08:46 +01:00
Stefan Stefanović 158c02dffa
gnu: Add xcb-util-errors.
* gnu/packages/xorg.scm (xcb-util-errors): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-06 17:00:02 +01:00
Ludovic Courtès 3527f600b5
gnu: guile-sqlite3: Update home page.
* gnu/packages/guile.scm (guile-sqlite3)[home-page]: Update.
2018-11-06 17:00:01 +01:00
lakshmi cddc0300b7
gnu: Add r-weights.
* gnu/packages/cran.scm (r-weights): New variable.

Signed-off-by: Gábor Boskovits <boskovits@gmail.com>
2018-11-06 16:06:42 +01:00
Tobias Geerinckx-Rice fe4fb278b8
gnu: youtube-dl: Update to 2018.11.03.
* gnu/packages/video.scm (youtube-dl): Update to 2018.11.03.
2018-11-06 15:34:37 +01:00
Tobias Geerinckx-Rice b1eeeb8dd4
gnu: terraform-docs: Update to 0.5.0.
* gnu/packages/terraform.scm (terraform-docs): Update to 0.5.0.
[native-inputs]: Remove them all.
2018-11-06 15:34:36 +01:00
Tobias Geerinckx-Rice c3b8300af3
gnu: jq: Don't use NAME in source URI.
* gnu/packages/web.scm (jq)[source]: Code more hard.
2018-11-06 15:34:36 +01:00
Tobias Geerinckx-Rice 418dd6adb5
gnu: jq: Update to 1.6.
* gnu/packages/web.scm (jq): Update to 1.6.
[source]: Remove upstreamed patch.
* gnu/packages/patches/jq-CVE-2015-8863.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2018-11-06 15:34:36 +01:00
Rutger Helling c58f3ebaf8
gnu: ffmpeg: Update to 4.1.
* gnu/packages/video.scm (ffmpeg): Update to 4.1.
2018-11-06 12:02:59 +01:00
Efraim Flashner 730e5fbc66
Revert "gnu: c-ares: Update to 1.15.0."
c-ares has more than 3000 dependant packages.

This reverts commit b588adc96f.
2018-11-06 12:22:02 +02:00
Efraim Flashner b588adc96f
gnu: c-ares: Update to 1.15.0.
* gnu/packages/adns.scm (c-ares): Update to 1.15.0.
2018-11-06 08:32:56 +02:00
Oleg Pykhalov 7f860a8be1
gnu: services: dns: Fix 'ddclient-activation'.
* gnu/services/dns.scm (ddclient-activation): Fix procedure.
2018-11-06 07:16:44 +03:00
Marius Bakke adde15186d
gnu: xf86-video-intel: Update to commit 0932a6b37ba6d5c9e916a1cb6ab89c3205b81a0c.
* gnu/packages/xorg.scm (xf86-video-intel): Update to 2.99.917-11.0932a6b.
2018-11-05 23:53:30 +01:00
Marius Bakke 208e82297c
gnu: xapian: Update to 1.4.9.
* gnu/packages/patches/xapian-revert-5489fb2f8.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/search.scm (xapian): Update to 1.4.9.
[source](patches): Remove.
(python-xapian-bindings): Update to 1.4.9.
2018-11-05 23:46:38 +01:00
Marius Bakke d79c8148cc
gnu: libssh: Update to 0.7.7.
* gnu/packages/ssh.scm (libssh): Update to 0.7.7.
2018-11-05 23:46:38 +01:00
Marius Bakke b5a887637c
gnu: strace: Update to 4.25.
* gnu/packages/linux.scm (strace): Update to 4.25.
2018-11-05 23:46:38 +01:00
Marius Bakke 876428dd98
gnu: libmtp: Update to 1.1.16.
* gnu/packages/libusb.scm (libmtp): Update to 1.1.16.
2018-11-05 23:46:38 +01:00
Marius Bakke 039241bc96
gnu: libgit2: Update to 0.26.8.
* gnu/packages/version-control.scm (libgit2): Update to 0.26.8.
2018-11-05 23:46:38 +01:00
Marius Bakke c98a7e6b91
gnu: i3-wm: Update to 4.16.
* gnu/packages/wm.scm (i3-wm): Update to 4.16.
2018-11-05 23:46:38 +01:00
Marius Bakke 9c415f96ec
gnu: libgphoto2: Update to 2.5.20.
* gnu/packages/photo.scm (libgphoto2): Update to 2.5.20.
2018-11-05 23:46:38 +01:00
Marius Bakke 66044a3698
gnu: glm: Update to 0.9.9.3.
* gnu/packages/maths.scm (glm): Update to 0.9.9.3.
2018-11-05 23:46:38 +01:00
Marius Bakke 64b60f38e7
gnu: ffmpeg: Update to 4.0.3.
* gnu/packages/video.scm (ffmpeg): Update to 4.0.3.
2018-11-05 23:46:38 +01:00
Marius Bakke c5e5711002
gnu: ffmpeg@3.4: Update to 3.4.5.
* gnu/packages/video.scm (ffmpeg-3.4): Update to 3.4.5.
2018-11-05 23:46:37 +01:00
Marius Bakke 196653145a
gnu: feh: Update to 2.28.1.
* gnu/packages/image-viewers.scm (feh): Update to 2.28.1.
2018-11-05 23:46:37 +01:00
Marius Bakke 00815eea38
gnu: libsoup: Update to 2.64.2.
* gnu/packages/gnome.scm (libsoup): Update to 2.64.2.
2018-11-05 23:46:37 +01:00
Marius Bakke 0a56ffdf1f
gnu: mono: Update home page.
* gnu/packages/mono.scm (mono)[home-page]: Use HTTPS.
2018-11-05 23:46:37 +01:00