Commit Graph

32234 Commits

Author SHA1 Message Date
Thorsten Wilms 7a44e8752e
gnu: Add caps-plugins-lv2.
* gnu/packages/audio.scm (caps-plugins-lv2): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-16 23:09:00 +01:00
David Thompson a7b7d48cc7
gnu: tiled: Update to 1.2.1.
* gnu/packages/game-development.scm (tiled): Update to 1.2.1.
2018-11-16 10:34:29 -05:00
Mathieu Othacehe 2aee2a96b6
guile: newt: Update revision to 2.
* gnu/packages/guile.scm (guile-newt): Update revision to 2.
2018-11-16 17:42:07 +09:00
Andreas Enge eea7cd7519
gnu: Add cmh.
* gnu/packages/algebra.scm (cmh): New variable.
2018-11-16 09:06:31 +01:00
Andreas Enge 44ff80fc0e
gnu: gp2c: Update to 0.0.11pl1.
* gnu/packages/algebra.scm (gp2c): Update to 0.0.11pl1.
2018-11-16 08:48:47 +01:00
Maxim Cournoyer 03592a6f88
gnu: emacs-realgud: Patch configure.ac to repair the build.
This fixes https://bugs.gnu.org/33196, a build problem caused by a defective
Elisp snippet in a check in configure.ac.

* gnu/packages/patches/emacs-realgud-fix-configure-ac.patch: Add patch.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/emacs.scm (emacs-realgud)[source]: Use it.
2018-11-15 22:42:35 -05:00
pimi 30f0d21b40
gnu: Add nanopolish.
* gnu/packages/bioinformatics.scm (nanopolish): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2018-11-15 22:23:57 +01:00
Roel Janssen 2d86eaff5b
gnu: sambamba: Update to 0.6.8.
* gnu/packages/bioinformatics.scm (sambamba): Update to 0.6.8.
2018-11-15 13:09:01 +01:00
Mark H Weaver 2e0f69057a
gnu: bioinformatics: Return #t from all phases and snippets.
* gnu/packages/bioinformatics.scm (bamtools, ribotaper, bioawk)
(codingquarry, fraggenescan, minced, pplacer, star, subread, sailfish)
(salmon): Return #t from all phases and snippets, use 'invoke' where
appropriate, and remove vestigal plumbing.
2018-11-14 23:44:18 -05:00
Mark H Weaver 96272e2822
gnu: databases: Return #t from all phases.
* gnu/packages/databases.scm (4store, go-gopkg.in-mgo.v2, mongodb)
(sparql-query, tdb, sqlcipher, python-sqlparse, mongo-tools): Return #t from
all phases, use invoke where appropriate, and remove vestigial plumbing.
2018-11-14 23:44:16 -05:00
Mark H Weaver 9f6f726c7f
gnu: compression: Return #t from all phases.
* gnu/packages/compression.scm (perl-compress-raw-zlib, java-snappy)
(java-iq80-snappy, pzstd, java-tukaani-xz): Return #t from all phases.
2018-11-14 23:44:14 -05:00
Mark H Weaver 29594404a1
gnu: check: Return #t from all phases.
* gnu/packages/check.scm (cmdtest, python-pytest-cov, python-fixtures)
(python-pytest-localserver, python-pytest-flakes)
(python2-coverage-test-runner, python-pylint, python-behave-web-api):
Return #t from all phases, and use invoke where appropriate.
2018-11-14 23:44:12 -05:00
Mark H Weaver ee527187a6
gnu: audio: Return #t from all phases.
* gnu/packages/audio.scm (clalsadrv, jack-2, libsbsms, zita-convolver)
(zita-resampler, zita-alsa-pcmi, gsm, cava): Return #t from all phases.
(ladspa): Use 'modify-phases'.  Return #t from all phases.
2018-11-14 23:44:10 -05:00
Mark H Weaver c6bf07d14a
gnu: xorg: Return #t from all phases.
* gnu/packages/xorg.scm (xcompmgr)
* gnu/packages/xdisorg.scm (xdotool, scrot, unclutter, xscreensaver)
(tint2, nxbelld, xautolock): Return #t from all phases.
2018-11-14 23:44:08 -05:00
Mark H Weaver aa6f87a2b9
gnu: xml: Return #t from all phases.
* gnu/packages/xml.scm (python-libxml2, perl-xml-sax, xlsx2csv, libxls)
(java-kxml2): Return #t from all phases.
2018-11-14 23:44:06 -05:00
Mark H Weaver 9dcfd6aac9
gnu: video: Return #t from all phases.
* gnu/packages/video.scm (youtube-dl-gui, avidemux, xvid, twitchy, aegisub):
Return #t from all phases, use invoke where appropriate, and remove vestigial
plumbing.
2018-11-14 23:44:04 -05:00
Mark H Weaver 4851af9ebe
gnu: perl: Return #t from all phases.
* gnu/packages/gd.scm (perl-gd-securityimage)
* gnu/packages/libevent.scm (perl-ev)
* gnu/packages/markup.scm (perl-text-markdown-discount)
* gnu/packages/perl-check.scm (perl-test2-bundle-extended)
* gnu/packages/perl.scm (perl-digest-md5, perl-encode-hanextra)
(perl-ipc-run, perl-pathtools)
* gnu/packages/photo.scm (perl-image-exiftool): Return #t from all phases.
2018-11-14 23:44:02 -05:00
Mark H Weaver 366c1cbbc6
gnu: networking: Return #t from all phases.
* gnu/packages/networking.scm (miredo, tcp-wrappers, librdkafka, ifstatus)
(iodine, httpstat, perl-socket6, perl-netaddr-ip, libproxy, openvswitch)
(libnet, asio): Return #t from all phases.
2018-11-14 23:43:59 -05:00
Mark H Weaver 9922278b25
gnu: linux: Return #t from all phases.
* gnu/packages/linux.scm (iproute, ntfs-3g, cpupower, radeontop, tlp):
Return #t from all phases.
2018-11-14 23:43:57 -05:00
Mark H Weaver fccacffbf4
gnu: image: Return #t from all phases.
* gnu/packages/image.scm (libpng-apng, pngcrush, leptonica, zimg)
(perceptualdiff): Return #t from all phases.
2018-11-14 23:43:54 -05:00
Mark H Weaver cb8ba848d2
gnu: admin: Return #t from all phases.
* gnu/packages/admin.scm (daemon-tools, rottlog, wpa-supplicant-minimal)
(wakelan, cpulimit, nmap, sunxi-tools): Return #t from all phases.
2018-11-14 23:43:48 -05:00
Mark H Weaver 7413c31693
gnu: linux-libre: Update to 4.19.2.
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.19.2.
(%linux-libre-hash): Update hash.
2018-11-14 19:16:24 -05:00
Mark H Weaver 24ba798731
gnu: linux-libre@4.14: Update to 4.14.81.
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.81.
(%linux-libre-4.14-hash): Update hash.
2018-11-14 19:14:39 -05:00
Mark H Weaver 6a1cff70bc
gnu: linux-libre@4.9: Update to 4.9.137.
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.137.
2018-11-14 19:13:46 -05:00
Ludovic Courtès 21f7d88e7a
gnu: texlive-bin: Fix substitution regexp.
This is a followup to commit be200ef316.

* gnu/packages/tex.scm (texlive-bin)[arguments]: In
'disable-failing-test' phase, escape "|" characters.
2018-11-14 23:49:19 +01:00
Paul Garlick ae0f1dd1a4
gnu: Add fenics.
* gnu/packages/simulation.scm (fenics): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-14 21:34:09 +01:00
Paul Garlick 0ace6c0b84
gnu: Add fenics-dolfin.
* gnu/packages/simulation.scm (fenics-dolfin): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-14 21:34:09 +01:00
Paul Garlick 6b7f1f8afa
gnu: Add python-fenics-ffc.
* gnu/packages/simulation.scm (python-fenics-ffc): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-14 21:34:09 +01:00
Paul Garlick 0fc499834f
gnu: Add python-fenics-fiat.
* gnu/packages/simulation.scm (python-fenics-fiat): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-14 21:34:08 +01:00
Paul Garlick 3941cf5afa
gnu: Add python-fenics-ufl.
* gnu/packages/simulation.scm (python-fenics-ufl): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-14 21:34:08 +01:00
Paul Garlick f7a4757a4c
gnu: Add python-fenics-dijitso.
* gnu/packages/simulation.scm (python-fenics-dijitso): New varaible.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-14 21:34:08 +01:00
Paul Garlick 6b5687d053
gnu: Add python-slepc4py.
* gnu/packages/maths.scm (python-slepc4py): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-14 21:34:08 +01:00
Paul Garlick 90ff287401
gnu: Add python-petsc4py.
* gnu/packages/maths.scm (python-petsc4py): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-14 21:34:08 +01:00
Paul Garlick 54fcd547b3
gnu: Add python-mpi4py.
* gnu/packages/mpi.scm (python-mpi4py): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-14 21:34:08 +01:00
Ludovic Courtès 7a54b2281d
gnu: guix-daemon: Install 'guix-authenticate'.
Fixes <https://bugs.gnu.org/33368>.
Reported by Konrad Hinsen <konrad.hinsen@fastmail.net>.

* gnu/packages/package-management.scm (guix-daemon)[arguments]: In
'install' phase, build "install-nodist_libexecSCRIPTS" target to install
'guix-authenticate'.
2018-11-14 21:34:08 +01:00
Marius Bakke 79ee97a144
Merge branch 'master' into core-updates 2018-11-14 21:20:46 +01:00
Marius Bakke 7d9d521fbc
gnu: aide: Provide libpcre.a and libz.a.
* gnu/packages/admin.scm (aide)[inputs]: Add PCRE:STATIC and ZLIB:STATIC.
2018-11-14 21:07:01 +01:00
Marius Bakke e921993c25
gnu: xf86-video-r128: Update to 6.12.0.
* gnu/packages/xorg.scm (xf86-video-r128): Update to 6.12.0.
2018-11-14 21:05:30 +01:00
Marius Bakke 24dd6ec38a
gnu: mtools: Update to 4.0.20.
* gnu/packages/mtools.scm (mtools): Update to 4.0.20.
[source](uri): Change to 'bz2' compressed tarball.
2018-11-14 21:05:30 +01:00
Marius Bakke 7939387da8
gnu: nano: Update to 3.2.
* gnu/packages/nano.scm (nano): Update to 3.2.
2018-11-14 21:05:30 +01:00
Marius Bakke d63f588486
gnu: sudo: Update to 1.8.26.
* gnu/packages/admin.scm (sudo): Update to 1.8.26.
2018-11-14 21:05:30 +01:00
Marius Bakke bac2974e86
gnu: feh: Update to 3.0.
* gnu/packages/image-viewers.scm (feh): Update to 3.0.
2018-11-14 21:05:30 +01:00
Ricardo Wurmus ee66a13563
gnu: Add jamm.
* gnu/packages/bioinformatics.scm (jamm): New variable.
2018-11-14 15:13:20 +01:00
Ricardo Wurmus e4f4a04a51
gnu: Add r-ouch.
* gnu/packages/cran.scm (r-ouch): New variable.
2018-11-14 15:13:20 +01:00
Ricardo Wurmus 10483a64ee
gnu: Add r-activity.
* gnu/packages/cran.scm (r-activity): New variable.
2018-11-14 15:13:20 +01:00
Ricardo Wurmus 3cef715a46
gnu: Add r-circular.
* gnu/packages/cran.scm (r-circular): New variable.
2018-11-14 15:13:20 +01:00
Ricardo Wurmus 08bf097a0b
gnu: Add r-overlap.
* gnu/packages/cran.scm (r-overlap): New variable.
2018-11-14 15:13:20 +01:00
Ricardo Wurmus acbf23da44
gnu: Add r-acdm.
* gnu/packages/cran.scm (r-acdm): New variable.
2018-11-14 15:13:20 +01:00
Ricardo Wurmus ffdeda3ce0
gnu: Add r-acd.
* gnu/packages/cran.scm (r-acd): New variable.
2018-11-14 15:13:20 +01:00
Ricardo Wurmus 488dc4e1e2
gnu: Add r-abn.
* gnu/packages/cran.scm (r-abn): New variable.
2018-11-14 15:13:20 +01:00
Ricardo Wurmus 0c92f3734e
gnu: Add r-rjags.
* gnu/packages/cran.scm (r-rjags): New variable.
2018-11-14 15:13:20 +01:00
Ricardo Wurmus 0bca8643a2
gnu: Add jags.
* gnu/packages/statistics.scm (jags): New variable.
2018-11-14 15:13:17 +01:00
Ricardo Wurmus 51b262f310
gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Update to 3.4.4.
* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene):
Update to 3.4.4.
2018-11-13 23:34:40 +01:00
Ricardo Wurmus d34959b8d4
gnu: r-org-mm-eg-db: Update to 3.7.0.
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.7.0.
2018-11-13 23:34:40 +01:00
Ricardo Wurmus 314511b862
gnu: r-org-dm-eg-db: Update to 3.7.0.
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.7.0.
2018-11-13 23:34:39 +01:00
Ricardo Wurmus 76bd16bcf6
gnu: r-org-ce-eg-db: Update to 3.7.0.
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.7.0.
2018-11-13 23:34:39 +01:00
Ricardo Wurmus fc7683fa30
gnu: r-org-hs-eg-db: Update to 3.7.0.
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.7.0.
2018-11-13 23:34:39 +01:00
Ricardo Wurmus cb9e6ed702
gnu: r-genomationdata: Update to 1.14.0.
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.14.0.
2018-11-13 23:34:39 +01:00
Ricardo Wurmus 13e70f6304
gnu: r-go-db: Update to 3.7.0.
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.7.0.
2018-11-13 23:34:39 +01:00
Ricardo Wurmus 13a574652b
gnu: r-genomeinfodbdata: Update to 1.2.0.
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 1.2.0.
2018-11-13 23:34:39 +01:00
Taegil Bae 3f995aaf21
gnu: spice-vdagent: Fix typo in desktop file.
Fixes <https://bugs.gnu.org/33346>.

* gnu/packages/spice.scm (spice-vdagent)[arguments]: Fix typo in
'patch-spice-vdagent.desktop' phase.
2018-11-13 15:26:30 -05:00
Alex Vong c991806a7d
gnu: ImageMagick: Update to 6.9.10-14.
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.10-14.
2018-11-14 03:09:37 +08:00
Leo Famulari d540137509
gnu: libssh: Fetch source over HTTPS.
* gnu/packages/ssh.scm (libssh)[source]: Use HTTPS URL.
2018-11-13 11:43:35 -05:00
Leo Famulari 978d59737a
gnu: direnv: Build with Go 1.9.
* gnu/packages/shellutils.scm (direnv)[native-inputs]: Remove go.
[inputs]: Add go-1.9.
2018-11-13 11:28:23 -05:00
Leo Famulari 021bf6af18
gnu: Poppler: Fix CVE-2018-19149.
* gnu/packages/patches/poppler-CVE-2018-19149.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/pdf.scm (poppler)[replacement]: New field.
(poppler/fixed): New variable.
(poppler-qt4, poppler-qt5): Use package/inherit.
2018-11-13 11:28:23 -05:00
Leo Famulari 8263b9f71f
gnu: certbot, python-acme: Update to 0.28.0.
* gnu/packages/tls.scm (certbot, python-acme): Update to 0.28.0.
2018-11-13 10:10:42 -05:00
Ludovic Courtès 3483f82413
gnu: guix: Update to f5a2724.
* gnu/packages/package-management.scm (guix): Update to f5a2724.
2018-11-13 15:44:25 +01:00
Ludovic Courtès d3f75179e5
services: nscd: Add 'invalidate' and 'statistics' actions.
* gnu/services/base.scm (nscd-action-procedure, nscd-actions): New
procedures.
(nscd-shepherd-service): Add 'modules' and 'actions' fields.
* gnu/tests/base.scm (run-basic-test)["nscd invalidate action"]
["nscd invalidate action, wrong table"]: New tests.
* doc/guix.texi (Services): Mention 'herd doc nscd action'.
(Base Services): Document the actions.
2018-11-13 14:59:45 +01:00
Ludovic Courtès 190877748e
services: mcron: Fix typo in comment.
* gnu/services/mcron.scm (shepherd-schedule-action): Fix typo in comment.
2018-11-13 14:59:45 +01:00
Oleg Pykhalov 155956449a
gnu: restic: Fix build phase.
* gnu/packages/backup.scm (restic)[arguments]: Set "HOME" environment variable
in build phase.
2018-11-13 15:03:15 +03:00
Ricardo Wurmus 6018683683
gnu: c-toxcore: Fetch sources from git.
* gnu/packages/messaging.scm (c-toxcore)[source]: Fetch from git.
2018-11-13 10:51:41 +01:00
Rutger Helling 7fed5481fe
gnu: wine-staging: Update to 3.20.
* gnu/packages/wine.scm (wine-staging-patchset-data): Update to 3.20.
* gnu/packages/wine.scm (wine-staging): Update to 3.20.
2018-11-13 10:24:42 +01:00
Julien Lepiller 0dd60c1c9b
gnu: php: Update to 7.2.12.
* gnu/packages/php.scm (php): Update to 7.2.12.
2018-11-12 23:57:42 +01:00
Arun Isaac e740a90228
gnu: youtube-dl: Update to 2018.11.07.
* gnu/packages/video.scm (youtube-dl): Update to 2018.11.07.
2018-11-12 22:09:12 +05:30
Efraim Flashner 53bcee9ea7
gnu: vifm: Update to 0.10.
* gnu/packages/vim.scm (vifm): Update to 0.10.
2018-11-12 12:37:00 +02:00
Pierre Neidhardt 5c4758415d
gnu: go-github-com-aarzilli-golua: Fix for go-1.11.
* gnu/packages/golang.scm (go-github-com-aarzilli-golua)[arguments]: Fix for go-1.11.
[native-inputs]: Remove lua.
[propagated-inputs]: Add lua.
2018-11-12 10:31:23 +01:00
Pierre Neidhardt 46a4ae2212
gnu: go-github-com-wtolson-go-taglib: Fix tests and build for go-1.11.
* gnu/packages/golang.scm (go-github-com-wtolson-go-taglib)[arguments]: Fix tests for go-1.11.
[native-inputs]: Remove pkg-config and taglib.
[propagated-inputs]: Add pkg-config and taglib.
2018-11-12 10:30:10 +01:00
Pierre Neidhardt 66fa8f0f77
gnu: go-gopkg.in-asn1-ber.v1: Fix tests for go-1.11.
* gnu/packages/syncthing.scm (go-gopkg.in-asn1-ber.v1): Fix tests for go-1.11.
2018-11-12 10:29:43 +01:00
Pierre Neidhardt d4780c8238
gnu: go-github-com-audriusbutkevicius-cli: Fix tests for go-1.11.
* gnu/packages/syncthing.scm (go-github-com-audriusbutkevicius-cli): Fix tests for go-1.11.
2018-11-12 10:29:37 +01:00
Pierre Neidhardt 46a37b5966
gnu: go-github-com-prometheus-common-expfmt: Fix tests for go-1.11.
* gnu/packages/syncthing.scm (go-github-com-prometheus-common-expfmt): Fix tests for go-1.11.
2018-11-12 10:29:31 +01:00
Pierre Neidhardt 9a65a05201
gnu: go: Update default to 1.11.
* gnu/packages/golang.scm (go): Update default to 1.11.
2018-11-12 10:28:46 +01:00
Ricardo Wurmus 5f9b38ba34
gnu: r-s4vectors: Update to 0.20.1.
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.20.1.
2018-11-11 23:13:48 +01:00
Ricardo Wurmus 06910a8689
gnu: r-rcmdcheck: Update to 1.3.2.
* gnu/packages/cran.scm (r-rcmdcheck): Update to 1.3.2.
2018-11-11 23:13:48 +01:00
Ricardo Wurmus 2a4c5877a9
gnu: r-ggpubr: Update to 0.1.9.
* gnu/packages/cran.scm (r-ggpubr): Update to 0.1.9.
2018-11-11 23:13:48 +01:00
Ricardo Wurmus 441cf11de1
gnu: r-dplyr: Update to 0.7.8.
* gnu/packages/statistics.scm (r-dplyr): Update to 0.7.8.
2018-11-11 23:13:48 +01:00
Ricardo Wurmus 41d2c26e67
gnu: r-rcpparmadillo: Update to 0.9.200.4.0.
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.200.4.0.
2018-11-11 23:13:48 +01:00
Ricardo Wurmus 23dd886a95
gnu: r-rtsne: Update to 0.15.
* gnu/packages/statistics.scm (r-rtsne): Update to 0.15.
2018-11-11 23:13:48 +01:00
Ricardo Wurmus 7865c8c460
gnu: r-lme4: Update to 1.1-19.
* gnu/packages/statistics.scm (r-lme4): Update to 1.1-19.
2018-11-11 23:13:48 +01:00
Marius Bakke a509b18087
gnu: webkitgtk@2.22: Adjust to documentation output.
This is a follow-up to commit 0ead0b4d2c.

* gnu/packages/webkit.scm (webkitgtk)[arguments]: Remove hard coded file list.
(webkitgtk-2.22)[arguments]: Inherit phases using SUBSTITUTE-KEYWORD-ARGUMENTS.
2018-11-11 22:47:06 +01:00
Ricardo Wurmus aaf0e47f6d
gnu: libtoxcore: Update to 0.0.0-2.bf69b54.
* gnu/packages/messaging.scm (libtoxcore): Update to 0.0.0-2.bf69b54.
[native-inputs]: Add check.
2018-11-11 20:51:51 +01:00
Ricardo Wurmus e874f34d3f
gnu: mumi: Update to 0.0.0-2.bfd96ce7.
* gnu/packages/mail.scm (mumi): Update to 0.0.0-2.bfd96ce7.
2018-11-11 20:51:51 +01:00
Leo Famulari ec35067631
gnu: PostgreSQL: Update to 10.6 [fixes CVE-2018-16850].
* gnu/packages/databases.scm (postgresql): Update to 10.6.
2018-11-11 14:10:03 -05:00
Marius Bakke 8c5749f1b5
gnu: python-cffi: Fix test failure on i686.
* gnu/packages/patches/python-cffi-x87-stack-clean.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/libffi.scm (python-cffi)[source](patches): Add it.
2018-11-11 17:18:05 +01:00
Pierre Neidhardt 0ead0b4d2c
gnu: webkitgtk: Include documentation.
* gnu/packages/webkit.scm (webkitgtk): Include documentation.
2018-11-11 16:44:46 +01:00
Pierre Neidhardt 50ee7e93fc
gnu: gtk-doc: Use local docbook-xsl.
* gnu/packages/gtk.scm (gtk-doc): Use local docbook-xsl.
2018-11-11 16:41:45 +01:00
Ricardo Wurmus 89c7894805
gnu: faust-2: Update to 2.5.23.
* gnu/packages/audio.scm (faust-2): Update to 2.5.23.
[native-inputs]: Replace llvm-with-rtti with llvm-3.8-with-rtti.
* gnu/packages/llvm.scm (llvm-with-rtti): Rename this variable...
(llvm-3.8-with-rtti): ...to this variable; inherit from llvm-3.8.
2018-11-11 16:19:59 +01:00
Clément Lassieur 37a350ecce
gnu: gajim: Move python-docutils from inputs to native-inputs.
* gnu/packages/messaging.scm (gajim): Move python-docutils from inputs to
native-inputs.
2018-11-11 16:00:08 +01:00
Clément Lassieur 60c5b44489
gnu: gajim: Get the second 'wrap-program' phase to return #t.
* gnu/packages/messaging.scm (gajim)[arguments]: Get the second 'wrap-program'
phase to return #t.
2018-11-11 16:00:00 +01:00
Clément Lassieur 992a496503
gnu: gajim: Update to 1.1.0.
* gnu/packages/messaging.scm (gajim): Update to 1.1.0.
[arguments]: Set #:test-target to "test_nogui".  Remove the
'remove-test-resolver' and 'start-xserver' phases.
[inputs]: Remove python-pyasn1.  Add python-cssutils, python-keyring and
python-precis-i18n.
2018-11-11 15:59:07 +01:00
Clément Lassieur a311f42e1b
gnu: python-nbxmpp: Update to 0.6.8.
* gnu/packages/messaging.scm (python-nbxmpp): Update to 0.6.8.
2018-11-11 15:59:03 +01:00
Clément Lassieur 4ad3786b7b
gnu: Add python-precis-i18n.
* gnu/packages/messaging.scm (python-precis-i18n): New variable.
2018-11-11 15:58:50 +01:00
Ricardo Wurmus 902068b436
gnu: tiled: Fetch sources from git.
* gnu/packages/game-development.scm (tiled)[source]: Fetch from git.
2018-11-11 13:18:27 +01:00
Ricardo Wurmus 9066424778
gnu: privoxy: Remove custom bootstrap phase.
* gnu/packages/tor.scm (privoxy)[arguments]: Remove autoconf phase.
2018-11-11 13:10:56 +01:00
Ricardo Wurmus 2b61cd37b4
gnu: cifs-utils: Remove autoreconf phase.
* gnu/packages/samba.scm (cifs-utils)[arguments]: Remove autoreconf phase.
2018-11-11 13:08:56 +01:00
Ricardo Wurmus cd1f661e82
gnu: libiax2: Fetch sources from git.
* gnu/packages/telephony.scm (libiax2)[source]: Fetch from git.
2018-11-11 13:06:31 +01:00
Ricardo Wurmus 5a103bb84e
gnu: libiax2: Remove custom bootstrap phase.
* gnu/packages/telephony.scm (libiax2)[arguments]: Remove.
2018-11-11 13:04:08 +01:00
Ricardo Wurmus 6f3dd09f8d
gnu: libharu: Remove custom bootstrap phase.
* gnu/packages/pdf.scm (libharu)[arguments]: Remove autogen phase.
2018-11-11 13:00:53 +01:00
Ricardo Wurmus 2b2ab39cfc
gnu: libharu: Fetch sources from git.
* gnu/packages/pdf.scm (libharu)[source]: Fetch from git.
2018-11-11 13:00:35 +01:00
Ricardo Wurmus bc74e9e4cd
gnu: scsh: Remove custom bootstrap phase.
* gnu/packages/shells.scm (scsh)[arguments]: Remove autoreconf phase.
2018-11-11 12:56:22 +01:00
Ricardo Wurmus e5ff963a6d
gnu: xdelta: Remove custom bootstrap phase.
* gnu/packages/compression.scm (xdelta)[arguments]: Remove autoconf phase.
2018-11-11 12:52:46 +01:00
Ricardo Wurmus 0633c77b1b
gnu: xdelta: Fetch sources from git.
* gnu/packages/compression.scm (xdelta)[source]: Fetch from git.
2018-11-11 12:52:30 +01:00
Ricardo Wurmus 112fcafbae
gnu: libtar: Remove custom bootstrap phase.
* gnu/packages/compression.scm (libtar)[arguments]: Remove autoconf phase.
2018-11-11 12:47:51 +01:00
Ricardo Wurmus 3478945948
gnu: minizip: Remove custom bootstrap phase.
* gnu/packages/compression.scm (minizip)[arguments]: Remove autoreconf phase.
2018-11-11 12:45:52 +01:00
Ricardo Wurmus 4078beab93
gnu: inotify-tools: Remove custom bootstrap phase.
* gnu/packages/linux.scm (inotify-tools)[arguments]: Remove.
2018-11-11 12:36:35 +01:00
Ricardo Wurmus 88f9fea723
gnu: inotify-tools: Fetch sources from git.
* gnu/packages/linux.scm (inotify-tools)[source]: Fetch from git.
2018-11-11 12:36:15 +01:00
Ricardo Wurmus 2286107f60
gnu: par2cmdline: Remove custom bootstrap phase.
* gnu/packages/backup.scm (par2cmdline)[arguments]: Remove.
2018-11-11 12:31:35 +01:00
Ricardo Wurmus 5cdbdc2b13
gnu: par2cmdline: Fetch sources from git.
* gnu/packages/backup.scm (par2cmdline)[source]: Fetch from git.
2018-11-11 12:31:18 +01:00
Ricardo Wurmus 2fef54fd64
gnu: hpcguix-web: Do not re-bootstrap.
* gnu/packages/web.scm (hpcguix-web)[arguments]: Do not run autoreconf after
the bootstrap phase; remove "autoconf" phase to "set-variables"; end phase
with #T.
2018-11-11 12:27:01 +01:00
Ricardo Wurmus cbb6a15056
gnu: schismtracker: Remove custom bootstrap phase.
* gnu/packages/music.scm (schismtracker)[arguments]: Remove autoconf phase.
2018-11-11 12:19:23 +01:00
Ricardo Wurmus 8865973848
gnu: lilypond: Use INVOKE.
* gnu/packages/music.scm (lilypond)[arguments]: Use INVOKE and return #T
unconditionally.
2018-11-11 12:15:03 +01:00
Ricardo Wurmus 3b9e9415fa
gnu: schismtracker: Fetch sources from git.
* gnu/packages/music.scm (schismtracker)[source]: Fetch from git.
2018-11-11 12:07:21 +01:00
Ricardo Wurmus 234a1825b2
gnu: clyrics: Fetch sources from git.
* gnu/packages/music.scm (clyrics)[source]: Fetch from git.
[native-inputs]: Remove.
[arguments]: Adjust builder.
2018-11-11 12:01:25 +01:00
Ricardo Wurmus 3a0592ae31
gnu: lmms: Fetch sources from git.
* gnu/packages/music.scm (lmms)[source]: Fetch from git.
2018-11-11 12:00:55 +01:00
Ricardo Wurmus caa39e56f7
gnu: milkytracker: Fetch sources from git.
* gnu/packages/music.scm (milkytracker)[source]: Fetch from git.
2018-11-11 11:44:24 +01:00
Ricardo Wurmus 08bc7f2665
gnu: dotconf: Fetch sources from git.
* gnu/packages/textutils.scm (dotconf)[source]: Fetch from git.
2018-11-11 11:37:01 +01:00
Ricardo Wurmus 7a52d0e075
gnu: dotconf: Remove custom bootstrap phase.
* gnu/packages/textutils.scm (dotconf)[arguments]: Remove autoreconf phase.
2018-11-11 11:36:39 +01:00
Ricardo Wurmus d68a15806b
gnu: libgtextutils: Remove custom bootstrap phase.
* gnu/packages/textutils.scm (libgtextutils)[arguments]: Remove.
2018-11-11 11:34:55 +01:00
Ricardo Wurmus fab455840e
gnu: libtoxcore: Remove custom bootstrap phase.
* gnu/packages/messaging.scm (libtoxcore)[arguments]: Remove autoconf phase.
2018-11-11 11:33:39 +01:00
Ricardo Wurmus 867d9de690
gnu: openocd: Use INVOKE.
* gnu/packages/embedded.scm (openocd)[arguments]: Use INVOKE and return #T
unconditionally.
2018-11-11 11:32:12 +01:00
Ricardo Wurmus 4cd6ab1b1f
gnu: libjaylink: Remove custom bootstrap phase.
* gnu/packages/embedded.scm (libjaylink)[arguments]: Remove.
2018-11-11 11:23:39 +01:00
Ricardo Wurmus a69cc70dea
gnu: lrdf: Replace bootstrap phase.
* gnu/packages/rdf.scm (lrdf)[arguments]: Remove autoreconf phase; replace
bootstrap phase instead.
2018-11-11 11:22:22 +01:00
Ricardo Wurmus d212ed2f00
gnu: lrdf: Fetch sources from git.
* gnu/packages/rdf.scm (lrdf)[source]: Fetch from git.
2018-11-11 11:21:55 +01:00
Efraim Flashner 2bdca67351
gnu: python-yapf: Update to 0.24.0.
* gnu/packages/python.scm (python-yapf): Update to 0.24.0.
2018-11-11 11:54:32 +02:00
Efraim Flashner 22d04ceda0
gnu: python-rq: Update to 0.12.0.
* gnu/packages/databases.scm (python-rq): Update to 0.12.0.
2018-11-11 11:54:28 +02:00
Ricardo Wurmus 2cabd29323
gnu: guildhall: Remove custom bootstrap phase.
* gnu/packages/guile.scm (guildhall)[arguments]: Remove autogen phase.
2018-11-11 10:38:00 +01:00
Ricardo Wurmus 34da5c394b
gnu: guile-dsv: Remove custom bootstrap phase.
* gnu/packages/guile.scm (guile-dsv)[arguments]: Remove autoreconf phase.
2018-11-11 10:22:45 +01:00
Ricardo Wurmus 5ad728e04c
gnu: opendht: Remove custom bootstrap phase.
* gnu/packages/crypto.scm (opendht)[arguments]: Remove autoconf phase.
2018-11-11 10:21:02 +01:00
Ricardo Wurmus 974056c05e
gnu: opendht: Fetch sources from git.
* gnu/packages/crypto.scm (opendht)[source]: Fetch from git.
2018-11-11 10:20:36 +01:00
Ricardo Wurmus a49b5322c5
gnu: lxsession: Remove custom bootstrap phase.
* gnu/packages/lxde.scm (lxsession)[arguments]: Remove autoreconf phase and
end rm-stamp phase with #T.
2018-11-11 10:16:43 +01:00
Efraim Flashner 261e421459
gnu: python-pyclipper: Enable tests.
* gnu/packages/python.scm (python-pyclipper)[arguments]: Enable tests.
[native-inputs]: Add python-pytest, python-pytest-runner,
python-unittest2.
2018-11-11 11:13:56 +02:00
Efraim Flashner 8189ce6f05
gnu: python-pyclipper: Update to 1.1.0post1.
* gnu/packages/python.scm (python-pyclipper): Update to 1.1.0post1.
[source]: Add snippet to remove cythonized source files.
[arguments]: Add custom phase to generate cythonized files.
[native-inputs]: Add python-cython.
[description]: Update clipper library version.
2018-11-11 11:13:56 +02:00
Efraim Flashner 95176544d5
gnu: python-paste: Update to 3.0.4.
* gnu/packages/python-web.scm (python-paste): Update to 3.0.4.
[source]: Remove patch, add snippet to remove one test.
[native-inputs]: Add python-pytest, python-pytest-runner.
* gnu/packages/patches/python-paste-remove-website-test.patch: Remove
file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2018-11-11 11:13:56 +02:00
Efraim Flashner 5ac2b2717f
gnu: python-networkx2: Remove variable.
* gnu/packages/python.scm (python-networkx2): Remove variable.
* gnu/packages/patches/python-networkx2-reproducible-build.patch: Remove
file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2018-11-11 11:13:55 +02:00
Efraim Flashner c92d056a8b
gnu: python-alembic: Update to 1.0.2.
* gnu/packages/databases.scm (python-alembic, python2-alembic): Update
to 1.0.2.
2018-11-11 11:13:53 +02:00
Ricardo Wurmus f1f1cebdd3
gnu: mdbtools: Fetch sources from git.
* gnu/packages/databases.scm (mdbtools)[source]: Fetch from git.
2018-11-11 10:09:54 +01:00
Ricardo Wurmus f626b71923
gnu: mdbtools: Remove custom bootstrap phase.
* gnu/packages/databases.scm (mdbtools)[arguments]: Remove.
2018-11-11 10:05:56 +01:00
Ricardo Wurmus 1410e178bb
gnu: pianobar: Fetch sources from git.
* gnu/packages/music.scm (pianobar)[source]: Fetch from git.
2018-11-11 10:03:06 +01:00
Ricardo Wurmus 487e3f5a80
gnu: ibus-rime: Fetch sources from git.
* gnu/packages/ibus.scm (ibus-rime)[source]: Fetch from git.
2018-11-11 10:03:06 +01:00
Ricardo Wurmus 863742856c
gnu: librime: Fetch sources from git.
* gnu/packages/ibus.scm (librime)[source]: Fetch from git.
2018-11-11 10:03:06 +01:00
Efraim Flashner 28b24e9975
gnu: bitshuffle: Don't use '-march=native'.
* gnu/packages/compression.scm (bitshuffle)[arguments]: Add custom phase
to substitute out the '-march=native' compilation flag.
2018-11-11 08:57:16 +02:00
Efraim Flashner 01029e2043
gnu: bitshuffle: Update to 0.3.5.
* gnu/packages/compression.scm (bitshuffle): Update to 0.3.5.
[source]: Add snippet to remove cythonized source files.
2018-11-11 08:57:16 +02:00
Efraim Flashner 5528b8e788
gnu: tvtime: Fix building with glibc@2.28.
* gnu/packages/tvtime.scm (tvtime)[arguments]: Add custom phase to add
missing import.
2018-11-11 08:57:13 +02:00
Efraim Flashner cab70d4c2a
gnu: perl-autovivification: Update to 0.18.
* gnu/packages/perl.scm (perl-autovivification): Update to 0.18.
2018-11-11 08:21:59 +02:00
Mark H Weaver 717d29e25b
gnu: icecat: Add more fixes from mozilla-esr60.
* gnu/packages/gnuzilla.scm (icecat)[source]: Add selected fixes
from the upstream mozilla-esr60 source repository.
2018-11-10 20:29:19 -05:00
Mark H Weaver 3b14494616
gnu: icecat: Update to 60.3.0-gnu1.
* gnu/packages/gnuzilla.scm (icecat): Update to 60.3.0-gnu1.
[source]: Switch back to the normal source URI.  Remove patches that
are no longer applicable.
* gnu/packages/patches/icecat-CVE-2018-12383.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2018-11-10 20:28:32 -05:00
Mark H Weaver e22842f5ca
gnu: linux-libre@4.14: Update to 4.14.80.
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.80.
(%linux-libre-4.14-hash): Update hash.
2018-11-10 20:23:57 -05:00
Mark H Weaver 62168a5558
gnu: linux-libre@4.9: Update to 4.9.136.
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.136.
2018-11-10 20:23:15 -05:00
Mark H Weaver fc43d6d4d9
gnu: linux-libre@4.4: Update to 4.4.163.
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.163.
2018-11-10 20:22:30 -05:00
Ricardo Wurmus 4cbbb16045
gnu: nxbelld: Remove custom bootstrap phase.
* gnu/packages/xdisorg.scm (nxbelld)[arguments]: Remove autoreconf phase.
2018-11-10 23:42:54 +01:00
Ricardo Wurmus f116e1fcae
gnu: wmclock: Remove custom bootstrap phase.
* gnu/packages/gnustep.scm (wmclock)[arguments]: Remove.
2018-11-10 23:42:54 +01:00
Ricardo Wurmus e17f867c62
gnu: wmbattery: Remove custom bootstrap phase.
* gnu/packages/gnustep.scm (wmbattery)[arguments]: Remove autoconf phase.
2018-11-10 23:42:54 +01:00
Ricardo Wurmus 7db147ec45
gnu: rtmidi: Remove custom bootstrap phase.
* gnu/packages/audio.scm (rtmidi)[arguments]: Remove autoconf phase.
2018-11-10 23:42:54 +01:00
Ricardo Wurmus cdb4048d72
gnu: portaudio: Remove custom bootstrap phase.
* gnu/packages/audio.scm (portaudio)[arguments]: Remove autoreconf phase.
2018-11-10 23:42:54 +01:00
Pierre Langlois 78e3d554d1
gnu: Add emacs-ivy-rich.
* gnu/packages/emacs.scm (emacs-ivy-rich): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-10 23:33:47 +01:00
Meiyo Peng d5b23d2b7d
gnu: Add ibus-rime.
* gnu/packages/ibus.scm (ibus-rime): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-10 23:33:47 +01:00
Meiyo Peng 1329f095bb
gnu: Add rime-data.
* gnu/packages/ibus.scm (rime-data): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-10 23:33:47 +01:00
Meiyo Peng 78209a165b
gnu: Add librime.
* gnu/packages/ibus.scm (librime): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-10 23:33:47 +01:00
Meiyo Peng 2f968763c3
gnu: ibus: Indent code properly.
* gnu/packages/ibus.scm (ibus, ibus-libpinyin): Indent code properly.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-10 23:33:47 +01:00
Meiyo Peng 1a0363cf07
gnu: Add opencc.
* gnu/packages/textutils.scm (opencc): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-10 23:33:46 +01:00
Meiyo Peng 9d466489cd
gnu: Add marisa.
* gnu/packages/datastructures.scm (marisa): New variable.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2018-11-10 23:33:46 +01:00
Ludovic Courtès 30288ae57e
gnu: mdadm: Update to 4.1.
* gnu/packages/linux.scm (mdadm): Update to 4.1.
2018-11-10 23:33:46 +01:00
Ricardo Wurmus 37ebc19cfb
gnu: msgpack: Remove custom bootstrap phase.
* gnu/packages/serialization.scm (msgpack)[arguments]: Remove.
2018-11-10 23:30:52 +01:00
Ricardo Wurmus bed4eb373e
gnu: gxtuner: Fetch sources from git.
* gnu/packages/music.scm (gxtuner)[source]: Fetch from git.
2018-11-10 23:29:26 +01:00
Ricardo Wurmus a7fde1a86d
gnu: cava: Fetch sources from git.
* gnu/packages/audio.scm (cava)[source]: Fetch from git.
2018-11-10 23:29:26 +01:00
Ricardo Wurmus c2a2d364df
gnu: cli-visualizer: Fetch sources from git.
* gnu/packages/audio.scm (cli-visualizer)[source]: Fetch from git.
2018-11-10 23:29:26 +01:00
Ricardo Wurmus b249ff5d37
gnu: dcadec: Fetch sources from git.
* gnu/packages/audio.scm (dcadec)[source]: Fetch from git.
2018-11-10 23:29:26 +01:00
Ricardo Wurmus 4289a306b7
gnu: cuetools: Fetch sources from git.
* gnu/packages/audio.scm (cuetools)[source]: Fetch from git.
2018-11-10 23:29:26 +01:00
Ricardo Wurmus 8e5995e397
gnu: xjackfreak: Fetch sources from git.
* gnu/packages/audio.scm (xjackfreak)[source]: Fetch from git.
2018-11-10 23:29:26 +01:00
Ricardo Wurmus 458baefb40
gnu: rsound: Fetch sources from git.
* gnu/packages/audio.scm (rsound)[source]: Fetch from git.
2018-11-10 23:29:26 +01:00
Ricardo Wurmus eca7729301
gnu: rtmidi: Fetch sources from git.
* gnu/packages/audio.scm (rtmidi)[source]: Fetch from git.
2018-11-10 23:29:26 +01:00
Ricardo Wurmus 0b8db03504
gnu: infamous-plugins: Fetch sources from git.
* gnu/packages/audio.scm (infamous-plugins)[source]: Fetch from git.
2018-11-10 23:29:26 +01:00
Ricardo Wurmus 2ae2395422
gnu: swh-plugins-lv2: Fetch sources from git.
* gnu/packages/audio.scm (swh-plugins-lv2)[source]: Fetch from git.
2018-11-10 23:29:26 +01:00
Ricardo Wurmus 917dc89672
gnu: csound: Fetch sources from git.
* gnu/packages/audio.scm (csound)[source]: Fetch from git.
2018-11-10 23:29:26 +01:00
Ricardo Wurmus b255365cd1
gnu: lvtk: Fetch sources from git.
* gnu/packages/audio.scm (lvtk)[source]: Fetch from git.
2018-11-10 23:29:26 +01:00
Ricardo Wurmus 78eff85770
gnu: ams-lv2: Fetch sources from git.
* gnu/packages/music.scm (ams-lv2)[source]: Fetch from git.
2018-11-10 23:29:25 +01:00
Ricardo Wurmus 57906fad59
gnu: portmidi-for-extempore: Fetch sources from git.
* gnu/packages/music.scm (portmidi-for-extempore)[source]: Fetch from git.
2018-11-10 23:29:25 +01:00
Ricardo Wurmus ca364e7a3c
gnu: jalv-select: Fetch sources from git.
* gnu/packages/music.scm (jalv-select)[source]: Fetch from git.
[arguments]: Add phase make-manpages-writable.
2018-11-10 23:29:25 +01:00
Nicolas Goaziou 79b8341292
gnu: emacs-circe: Update to 2.10.
* gnu/packages/emacs.scm (emacs-circe): Update to 2.10.
2018-11-10 23:27:05 +01:00
Ricardo Wurmus 74c903edab
Add missing license import.
* gnu/packages/mail.scm: Import agpl3+.
2018-11-10 22:37:07 +01:00
Ricardo Wurmus e3a4703174
gnu: Add mumi.
* gnu/packages/mail.scm (mumi): New variable.
2018-11-10 22:36:13 +01:00
Ricardo Wurmus 2d900b0464
gnu: Add guile-debbugs-next.
* gnu/packages/guile.scm (guile-debbugs-next): New variable.
2018-11-10 22:36:13 +01:00
Ricardo Wurmus 7453785624
gnu: Add guile-email.
* gnu/packages/guile.scm (guile-email): New variable.
2018-11-10 22:36:13 +01:00
Ricardo Wurmus 95906eee18
gnu: guile-ics: Remove custom bootstrap phase.
* gnu/packages/guile.scm (guile-ics)[arguments]: Remove.
2018-11-10 22:36:13 +01:00
Efraim Flashner 1a392ee7ae
gnu: nfs-utils: Fix building with glibc@2.28.
* gnu/packages/nfs.scm (nfs-utils)[arguments]: Add custom phase to fix
building with glibc@2.28.
2018-11-10 22:36:33 +02:00
Efraim Flashner c1ab159085
gnu: perl-autovivification: Update to 0.18.
* gnu/packages/perl.scm (perl-autovivification): Update to 0.18.
2018-11-10 22:36:33 +02:00
Efraim Flashner e8b9aaf0b1
mtd-utils: Update to 2.0.2.
* gnu/packages/linux.scm (mtd-utils): Update to 2.0.2.
[arguments]: Remove 'test-target, 'make-flags. Re-enable 'configure
phase. Add 'configure-flag for the unit-tests.
[native-inputs]: Add cmocka, pkg-config.
2018-11-10 20:54:34 +02:00
Efraim Flashner 1de2937283
gnu: idutils: Fix building with glibc@2.28.
* gnu/packages/idutils.scm (idutils)[source]: Add snippet to patch
bundled gnulib for glibc@2.28.
2018-11-10 20:18:37 +02:00
Efraim Flashner 211db9caf7
gnu: sharutils: Remove false comment.
This is a follow-up to b50d58b344.

* gnu/packages/compression.scm (sharutils)[source]: This snippet is, in
fact, a snippet.
2018-11-10 20:18:37 +02:00
Efraim Flashner 9829e0699b
gnu: lbzip2: Remove false comment.
This is a follow-up to f268b744b8.

* gnu/packages/compression.scm (lbzip2)[source]: This snippet is, in
fact, a snippet.
2018-11-10 20:18:34 +02:00
Clément Lassieur a7553a7360
services: dovecot: Set correct default value for the "auth" service.
* gnu/services/mail.scm (dovecot-configuration): Set 'service-count' to 0 for
the "auth" service.
2018-11-10 19:12:21 +01:00
Clément Lassieur be8dd4a5fe
services: dovecot: Allow to set 'process-limit'.
* doc/guix.texi (Mail Services): Update accordingly.
* gnu/services/mail.scm (service-configuration)[process-limit]: New field.
(dovecot-configuration)[services]: Set 'process-limit' to its correct default
value.
2018-11-10 19:12:18 +01:00
Clément Lassieur 8d9bb4b4d0
services: dovecot: Allow to set 'client-limit'.
* doc/guix.texi (Mail Services): Update accordingly.
* gnu/services/mail.scm (service-configuration)[client-limit]: New field.
(dovecot-configuration)[services]: Set 'client-limit' to its correct default
value.
2018-11-10 19:12:14 +01:00
Efraim Flashner f268b744b8
gnu: lbzip2: Fix building with glibc@2.28.
* gnu/packages/compression.scm (lbzip2)[source]: Add snippet to patch
bundled gnulib for glibc@2.28.
2018-11-10 20:07:56 +02:00
Efraim Flashner efe0a4a2a7
gnu: dvd+rw-tools: Use invoke.
* gnu/packages/cdrom.scm (dvd+rw-tools): Use 'invoke'.
2018-11-10 19:59:30 +02:00
Efraim Flashner 2529c8381f
gnu: dvd+rw-tools: Fix building with glibc@2.28.
* gnu/packages/cdrom.scm (dvd+rw-tools)[arguments]: Add custom phase to
add missing import.
2018-11-10 19:59:27 +02:00
Efraim Flashner 8754ea483d
gnu: f2fs-tools: Update to 1.11.0.
* gnu/packages/linux.scm (f2fs-tools): Update to 1.11.0.
2018-11-10 19:29:17 +02:00
Efraim Flashner 005ec8d09c
gnu: f2fs-tools: Update to 1.11.0.
* gnu/packages/linux.scm (f2fs-tools): Update to 1.11.0.
2018-11-10 19:29:05 +02:00
Ricardo Wurmus 03a415365a
gnu: r-ensembldb: Update to 2.6.1.
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.1.
2018-11-09 19:41:54 +01:00
Ricardo Wurmus 88514b9124
gnu: r-biostrings: Update to 2.50.1.
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.1.
2018-11-09 19:41:53 +01:00
Ricardo Wurmus 77bea84ba1
gnu: r-biocviews: Update to 1.50.5.
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.5.
2018-11-09 19:41:53 +01:00
Ricardo Wurmus 317f5a5a91
gnu: r-sn: Update to 1.5-3.
* gnu/packages/statistics.scm (r-sn): Update to 1.5-3.
2018-11-09 19:41:53 +01:00
Ricardo Wurmus 5174f06b0c
gnu: r-rgooglemaps: Update to 1.4.3.
* gnu/packages/geo.scm (r-rgooglemaps): Update to 1.4.3.
2018-11-09 19:41:53 +01:00
Ricardo Wurmus 492ec49890
gnu: r-tmb: Update to 1.7.15.
* gnu/packages/cran.scm (r-tmb): Update to 1.7.15.
2018-11-09 19:41:53 +01:00
Ricardo Wurmus fccb24501a
gnu: r-jomo: Update to 2.6-5.
* gnu/packages/cran.scm (r-jomo): Update to 2.6-5.
[propagated-inputs]: Add r-mass.
2018-11-09 19:41:50 +01:00
Ricardo Wurmus f87a18e660
gnu: r-rcpp: Update to 1.0.0.
* gnu/packages/cran.scm (r-rcpp): Update to 1.0.0.
[native-inputs]: Add r-knitr.
2018-11-09 19:01:42 +01:00
Ricardo Wurmus 06bc7b82f7
gnu: Add r-arm.
* gnu/packages/cran.scm (r-arm): New variable.
2018-11-09 18:04:37 +01:00
Ricardo Wurmus cf383cf08f
gnu: Add r-feature.
* gnu/packages/cran.scm (r-feature): New variable.
2018-11-09 18:04:37 +01:00
Ricardo Wurmus da256afb9e
gnu: Add r-ks.
* gnu/packages/cran.scm (r-ks): New variable.
2018-11-09 18:04:37 +01:00
Ricardo Wurmus 4106e6ad87
gnu: Add r-misc3d.
* gnu/packages/cran.scm (r-misc3d): New variable.
2018-11-09 18:04:36 +01:00
Ricardo Wurmus 213e72a18d
gnu: Add r-multicool.
* gnu/packages/cran.scm (r-multicool): New variable.
2018-11-09 18:04:36 +01:00
Ricardo Wurmus f338e4807f
gnu: Add r-rgl.
* gnu/packages/cran.scm (r-rgl): New variable.
2018-11-09 18:04:36 +01:00
Ricardo Wurmus a961ae469c
gnu: Add r-destiny.
* gnu/packages/bioconductor.scm (r-destiny): New variable.
2018-11-09 17:15:31 +01:00
Marius Bakke 64461ba20a
Merge branch 'master' into core-updates 2018-11-09 17:02:08 +01:00
Ricardo Wurmus ff939ef4d5
gnu: Add r-h5.
* gnu/packages/cran.scm (r-h5): New variable.
2018-11-09 16:57:13 +01:00
Ricardo Wurmus 3a4c6288c8
gnu: Add r-aggregation.
* gnu/packages/cran.scm (r-aggregation): New variable.
2018-11-09 16:57:13 +01:00
Ricardo Wurmus 8a587c89af
gnu: Add r-savr.
* gnu/packages/bioconductor.scm (r-savr): New variable.
2018-11-09 16:45:21 +01:00
Ricardo Wurmus cee9ab244f
gnu: r-with-tests: Update to 3.5.1.
* gnu/packages/statistics.scm (r-with-tests): Update to 3.5.1.
2018-11-09 14:07:26 +01:00
Ricardo Wurmus 2eaaadb4d6
gnu: r-with-tests: Use INVOKE.
* gnu/packages/statistics.scm (r-with-tests)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-09 14:07:22 +01:00
Pierre Neidhardt ddd925f608
gnu: Add emacs-gtk-look.
* gnu/packages/emacs.scm (emacs-gtk-look): New variable.
2018-11-09 11:55:08 +01:00
Pierre Neidhardt 2cce23bfb8
gnu: Add xmlrpc-c.
* gnu/packages/xml.scm (xmlrpc-c): New variable.
2018-11-09 11:55:08 +01:00
Mathieu Othacehe 97f33b05ec
gnu: guile-newt: Update to revision 1.
* gnu/packages/guile.scm (guile-newt): Update to revision 1.
2018-11-09 19:39:14 +09:00
Ricardo Wurmus 1b12b572a5
gnu: powertabeditor: Fetch sources from git.
* gnu/packages/music.scm (powertabeditor)[source]: Fetch from git.
2018-11-09 08:37:53 +01:00
Ricardo Wurmus b1b82aed5d
gnu: powertabeditor: Use INVOKE.
* gnu/packages/music.scm (powertabeditor)[arguments]: Use INVOKE and return #T
unconditionally.
2018-11-09 08:37:53 +01:00
Kei Kebreau e4b62e229e
gnu: wxmaxima: Update to 18.10.1.
* gnu/packages/maths.scm (wxmaxima): Update to 18.10.1.
[source]: Update URL and remove patch.
* gnu/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch: Remove
file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
2018-11-09 01:09:06 -05:00
Leo Famulari 41d2b7f50b
gnu: PostgreSQL 9: Update to 9.6.11 [fixes CVE-2018-16850].
* gnu/packages/databases.scm (postgresql-9.6): Update to 9.6.11.
2018-11-08 13:42:56 -05:00
Pierre Neidhardt 2705780f3f
gnu: Add emacs-clang-format.
* gnu/packages/emacs.scm (emacs-clang-format): New variable.
2018-11-08 13:08:26 +01:00
Efraim Flashner e3407254d5
gnu: kodi: Update to 18.0b5.
* gnu/packages/kodi.scm (kodi): Update to 18.0b5.
[source]: Update snippet.
[inputs]: Add flatbuffers, fstrcmp.
(crossguid): Update to commit fef89a4174a7bf8cd99fa9154864ce9e8e3bf989.
(libdvdnav/kodi, libdvdread/kodi): Update to 6.0.0-Leia-Alpha-3.
(libdvdcss/kodi): Update to 1.4.2-Leia-Beta-5.
2018-11-08 12:01:24 +02:00
Efraim Flashner 988b78ba28
gnu: Add fstrcmp.
* gnu/packages/kodi.scm (fstrcmp): New variable.
2018-11-08 12:01:20 +02:00
Stefan Stefanović ec86863113
services: elogind: Fix spelling errors of left value fields in elogind config file.
* gnu/services/desktop.scm (elogind-configuration-file)[ini-file]:
    Fix spelling of left value fields:
    InhibitDelayMaxSecs, HoldoffTimeoutSecs, IdleActionSeconds, RemoveIpc.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-08 10:24:35 +01:00
Luther Thompson 9870b9f7f8
gnu: python-ilinkedlist: Update to 0.3.1.
* gnu/packages/python.scm (python-ilinkedlist): Update to 0.3.1.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-08 10:24:26 +01:00
Vagrant Cascadian 195e081b43
gnu: Add python-pyelftools.
* gnu/packages/python.scm (python-pyelftools):
  New public variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-08 10:24:22 +01:00
Ricardo Wurmus 69cb939ee7
gnu: libmusicbrainz: Use INVOKE.
* gnu/packages/music.scm (libmusicbrainz)[arguments]: Use INVOKE and return #T
unconditionally.
2018-11-08 10:17:15 +01:00
Ricardo Wurmus 9ab90ead36
gnu: pd: Remove custom autoconf phase.
* gnu/packages/music.scm (pd)[arguments]: Remove custom autoconf phase.
2018-11-08 10:14:08 +01:00
Ricardo Wurmus 4e82946888
gnu: cmus: Fetch sources from git.
* gnu/packages/music.scm (cmus)[source]: Fetch from git.
2018-11-08 10:10:06 +01:00
Ricardo Wurmus ec618c2005
gnu: cmus: Use INVOKE.
* gnu/packages/music.scm (cmus)[arguments]: Use INVOKE and return #T
unconditionally.
2018-11-08 10:09:32 +01:00
Ricardo Wurmus 9c30cba431
gnu: pcc: Use INVOKE.
* gnu/packages/c.scm (pcc)[arguments]: Use INVOKE and return #T
unconditionally.
2018-11-08 10:08:09 +01:00
Ricardo Wurmus a1e83a9856
gnu: pplacer-scripts: Use INVOKE.
* gnu/packages/bioinformatics.scm (pplacer-scripts)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-08 10:06:35 +01:00
Ricardo Wurmus ce49fdcce9
gnu: roary: Use INVOKE.
* gnu/packages/bioinformatics.scm (roary)[arguments]: Use INVOKE and return #T
unconditionally.
2018-11-08 09:58:05 +01:00
Ricardo Wurmus a9542937c8
gnu: seek: Use INVOKE.
* gnu/packages/bioinformatics.scm (seek)[arguments]: Use INVOKE and return #T
unconditionally; patch "gen_tools_am" shebang in "bootstrap" phase.
2018-11-08 09:54:22 +01:00
Ricardo Wurmus 9f527c9199
gnu: sailfish: Use INVOKE.
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use INVOKE instead of
SYSTEM*.
2018-11-08 09:52:46 +01:00
Ricardo Wurmus 86c6928ea3
gnu: vsearch: Update to 2.9.1.
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.9.1.
* gnu/packages/patches/vsearch-unbundle-cityhash.patch: Update.
2018-11-08 09:46:42 +01:00
Ricardo Wurmus 15c9609482
gnu: sra-tools: Update to 2.9.3.
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.9.3.
[arguments]: Remove build phase patch-away-glibc-conflict.
2018-11-08 09:46:05 +01:00
Ricardo Wurmus b17333414f
gnu: plink-ng: Fetch sources from git.
* gnu/packages/bioinformatics.scm (plink-ng)[source]: Fetch from git.
2018-11-08 09:30:59 +01:00
Ricardo Wurmus 87408854ec
gnu: ncbi-vdb: Update to 2.9.3.
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.9.3.
2018-11-08 09:30:16 +01:00
Ricardo Wurmus 8d3eaa9262
gnu: ngs-sdk: Update to 2.9.3.
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.9.3.
2018-11-08 09:29:58 +01:00
Ricardo Wurmus 3da3cedf76
gnu: ngs-sdk: Use INVOKE.
* gnu/packages/bioinformatics.scm (ngs-sdk)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-08 09:15:05 +01:00
Ricardo Wurmus e78e54d029
gnu: emboss: Use INVOKE.
* gnu/packages/bioinformatics.scm (emboss)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-08 09:14:09 +01:00
Ricardo Wurmus 8b685c4720
gnu: taxtastic: Use INVOKE.
* gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-08 09:13:35 +01:00
Ricardo Wurmus 2e2d88539c
gnu: sra-tools: Use INVOKE.
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-08 09:12:43 +01:00
Ricardo Wurmus 179416467f
gnu: muscle: Use INVOKE.
* gnu/packages/bioinformatics.scm (muscle)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-08 09:11:38 +01:00
Ricardo Wurmus 0881d62f25
gnu: newick-utils: Remove custom autoconf phase.
* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Remove.
2018-11-08 09:10:58 +01:00
Ricardo Wurmus e35dce0170
gnu: mash: Remove custom autoconf phase.
* gnu/packages/bioinformatics.scm (mash)[arguments]: Remove autoconf phase.
2018-11-08 09:10:20 +01:00
Ricardo Wurmus 31c41a8cfe
gnu: vsearch: Remove custom autogen phase.
* gnu/packages/bioinformatics.scm (vsearch)[arguments]: Remove.
2018-11-08 09:04:34 +01:00
Ricardo Wurmus c527d36f02
gnu: java-picard-1.113: Use INVOKE.
* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Use INVOKE
and return #T unconditionally.
2018-11-08 09:02:34 +01:00
Ricardo Wurmus e438c96558
gnu: fraggenescan: Use INVOKE.
* gnu/packages/bioinformatics.scm (fraggenescan)[arguments]: Use INVOKE in
build phases and return #T unconditionally.
2018-11-08 08:58:46 +01:00
Ricardo Wurmus c098c49b3e
gnu: sailfish: Fetch sources from git.
* gnu/packages/bioinformatics.scm (sailfish)[source]: Fetch from git.
2018-11-08 08:53:54 +01:00
Ricardo Wurmus 4031e7f1ec
gnu: ngs-sdk: Fetch sources from git.
* gnu/packages/bioinformatics.scm (ngs-sdk)[source]: Fetch from git.
2018-11-08 08:53:53 +01:00
Ricardo Wurmus 6a7d9ee39f
gnu: ncbi-vdb: Use INVOKE and end phases on #T.
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use INVOKE and
unconditionally end phases with #T.
2018-11-08 08:53:53 +01:00
Ricardo Wurmus 3398dfb764
gnu: ncbi-vdb: Fetch sources from git.
* gnu/packages/bioinformatics.scm (ncbi-vdb)[source]: Fetch from git.
[arguments]: Add phase to make checkout writable.
2018-11-08 08:53:53 +01:00
Ricardo Wurmus e0f1aa2d2b
gnu: tadbit: Fetch sources from git.
* gnu/packages/bioinformatics.scm (tadbit)[source]: Fetch from git.
[version]: Use "2.0.0" instead of "2.0".
2018-11-08 08:53:50 +01:00
Kei Kebreau ed33049cdc
gnu: pspp: Update to 1.2.0.
* gnu/packages/statistics.scm (pspp): Update to 1.2.0.
[inputs]: Add spread-sheet-widget.
[native-inputs]: Add autoconf, python-2, and texinfo.
2018-11-07 17:46:25 -05:00
Kei Kebreau e2f36385d3
gnu: Add spread-sheet-widget.
* gnu/packages/gtk.scm (spread-sheet-widget): New public variable.
2018-11-07 17:46:25 -05:00
Ricardo Wurmus f3f34b132c
gnu: filevercmp: Fetch sources from git.
* gnu/packages/bioinformatics.scm (filevercmp)[source]: Fetch from git.
[arguments]: Add #T to the end of the install phase.
2018-11-07 23:17:36 +01:00
Ricardo Wurmus 3b888065da
gnu: ritornello: Update to 2.0.1.
* gnu/packages/bioinformatics.scm (ritornello): Update to 2.0.1.
[arguments]: Adjust file patching.
2018-11-07 23:17:36 +01:00
Ricardo Wurmus 7145f4e519
gnu: ritornello: Fetch sources from git.
* gnu/packages/bioinformatics.scm (ritornello)[source]: Fetch from git.
2018-11-07 23:17:35 +01:00
Ricardo Wurmus e0a8fc85dd
gnu: snap-aligner: Fetch sources from git.
* gnu/packages/bioinformatics.scm (snap-aligner)[source]: Fetch from git.
[arguments]: Use INVOKE.
2018-11-07 23:17:35 +01:00
Ricardo Wurmus 6236524409
gnu: sortmerna: Fetch sources from git.
* gnu/packages/bioinformatics.scm (sortmerna)[source]: Fetch from git.
2018-11-07 23:17:35 +01:00
Ricardo Wurmus 273df99d7d
gnu: vsearch: Fetch source from git.
* gnu/packages/bioinformatics.scm (vsearch)[source]: Fetch from git.
2018-11-07 23:17:35 +01:00
Ricardo Wurmus 67caa4b773
gnu: preseq: Update to 2.0.3.
* gnu/packages/bioinformatics.scm (preseq): Update to 2.0.3.
2018-11-07 23:17:35 +01:00
Ricardo Wurmus 37e285be43
gnu: preseq: Fetch sources from git.
* gnu/packages/bioinformatics.scm (preseq)[source]: Fetch from git.
2018-11-07 23:17:35 +01:00
Ricardo Wurmus 63f3255e13
gnu: seqtk: Update to 1.3.
* gnu/packages/bioinformatics.scm (seqtk): Update to 1.3.
[source]: Remove outdated snippet.
[arguments]: Use INVOKE and return #T unconditionally.
2018-11-07 23:17:35 +01:00
Ricardo Wurmus 019fcdf20a
gnu: seqtk: Fetch sources from git.
* gnu/packages/bioinformatics.scm (seqtk)[source]: Fetch from git.
2018-11-07 23:17:34 +01:00
Ricardo Wurmus b9d0c3564b
gnu: raxml: Update to 8.2.12.
* gnu/packages/bioinformatics.scm (raxml): Update to 8.2.12.
2018-11-07 23:17:34 +01:00
Ricardo Wurmus d9ba126d17
gnu: python2-biom-format: Fix build.
This is a follow-up to commit 239716fb0b.

* gnu/packages/bioinformatics.scm (python2-biom-format)[arguments]: Modify
phases of base package.
2018-11-07 23:17:34 +01:00
Ricardo Wurmus 4715d4af17
gnu: raxml: Fetch sources from git.
* gnu/packages/bioinformatics.scm (raxml)[source]: Fetch from git.
2018-11-07 23:17:34 +01:00
Ricardo Wurmus 5e242b02c3
gnu: pyicoteo: Fetch sources from git.
* gnu/packages/bioinformatics.scm (pyicoteo)[source]: Fetch from git.
2018-11-07 23:17:34 +01:00
Efraim Flashner b44b1f08f6
gnu: hplip: Remove bundled non-free blobs.
This fixes <https://bugs.gnu.org/32184>.

* gnu/packages/cups.scm (hplip)[source]: Add patch. Update snippet to
remove non-free code and binary blobs.
* gnu/packages/patches/hplip-remove-imageprocessor.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
2018-11-07 23:16:02 +02:00
Ricardo Wurmus 2b773a9273
gnu: sra-tools: Fetch sources from git.
* gnu/packages/bioinformatics.scm (sra-tools)[source]: Fetch from git.
2018-11-07 21:41:56 +01:00
Ricardo Wurmus 55698df260
gnu: libgff: Fetch sources from git.
* gnu/packages/bioinformatics.scm (libgff)[source]: Fetch from git.
2018-11-07 21:41:56 +01:00
Ricardo Wurmus 4257c10ad2
gnu: kentutils: Fetch sources from git.
* gnu/packages/bioinformatics.scm (kentutils)[source]: Fetch from git.
[arguments]: Add phase "fix-permissions".
2018-11-07 21:41:55 +01:00
Ricardo Wurmus 1a20bcadf3
gnu: r-seqgl: Fetch sources from git.
* gnu/packages/bioinformatics.scm (r-seqgl)[source]: Fetch from git.
2018-11-07 21:41:55 +01:00
Ricardo Wurmus a2b9d6a8d0
gnu: pplacer: Fetch sources from git.
* gnu/packages/bioinformatics.scm (pplacer)[source]: Fetch from git.
[arguments]: Make files writable; use INVOKE.
2018-11-07 21:41:55 +01:00
Ricardo Wurmus 6052264b56
gnu: minced: Update to 0.3.2.
* gnu/packages/bioinformatics.scm (minced): Update to 0.3.2.
2018-11-07 21:41:55 +01:00
Ricardo Wurmus 9d94ca0ebf
gnu: minced: Fetch sources from git.
* gnu/packages/bioinformatics.scm (minced)[source]: Fetch from git.
2018-11-07 21:41:55 +01:00
Ricardo Wurmus b58d9e4aa2
gnu: metabat: Fetch sources from git.
* gnu/packages/bioinformatics.scm (metabat)[source]: Fetch from git.
2018-11-07 21:41:55 +01:00
Ricardo Wurmus 5c1f35e71b
gnu: mash: Update to 2.1.
* gnu/packages/bioinformatics.scm (mash): Update to 2.1.
2018-11-07 21:41:55 +01:00
Ricardo Wurmus 497fc04d8f
gnu: mash: Fetch sources from git.
* gnu/packages/bioinformatics.scm (mash)[source]: Fetch from git.
2018-11-07 21:41:55 +01:00
Marius Bakke 55174e668f
Merge branch 'master' into core-updates 2018-11-07 21:09:57 +01:00
Marius Bakke b31e156161
gnu: fio: Update to 3.11.
* gnu/packages/benchmark.scm (fio): Update to 3.11.
[source]: Use bz2 compressed tarball.
2018-11-07 21:09:00 +01:00
Marius Bakke 1badc85068
gnu: ceph: Update to 13.2.2.
* gnu/packages/patches/ceph-skip-unittest_blockdev.patch: Adjust for 13.2.2.
* gnu/packages/patches/ceph-rocksdb-compat.patch: Delete file.
* gnu/packages/patches/ceph-detect-rocksdb.patch,
gnu/packages/patches/ceph-volume-respect-PATH.patch: New files.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/storage.scm (ceph): Update to 13.2.2.
[source]: Don't remove src/dpdk, which has been moved to src/spdk/dpdk and
is purged elsewhere.  Drop bundled rapidjson.  Adjust patch list.
[arguments]: Add "-DWITH_MGR_DASHBOARD_FRONTEND=OFF" and "-DWITH_SPDK=OFF" to
 #:configure-flags.   Drop obsolete "-DWITH_EMBEDDED".  Add workaround for
<https://bugs.gnu.org/30756>.  Remove obsolete test substitution.  Rework
'wrap-python-script' to be less verbose and wrap more scripts.
[native-inputs]: Add GCC-7.
[inputs]: Add OATH-TOOLKIT, RAPIDJSON and PYTHON2-SIX.
2018-11-07 21:01:12 +01:00
Ricardo Wurmus 2dc28391f3
gnu: kaiju: Update to 1.6.3.
* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.3.
2018-11-07 20:47:22 +01:00
Ricardo Wurmus 6fe323bf2e
gnu: kaiju: Fetch sources from git.
* gnu/packages/bioinformatics.scm (kaiju)[source]: Fetch from git.
[arguments]: Remove redundant installation step.
2018-11-07 20:46:36 +01:00
Ricardo Wurmus f0731591a5
gnu: idr: Fetch sources from git.
* gnu/packages/bioinformatics.scm (idr)[source]: Fetch from git.
2018-11-07 20:41:58 +01:00
Ricardo Wurmus b8a6230df3
gnu: java-htsjdk: Fetch sources from git.
* gnu/packages/bioinformatics.scm (java-htsjdk)[source]: Fetch from git.
2018-11-07 20:36:07 +01:00
Ricardo Wurmus 57be690d91
gnu: hisat2: Use versioned source URL.
* gnu/packages/bioinformatics.scm (hisat2)[source]: Use versioned URL.
2018-11-07 20:32:29 +01:00
Ricardo Wurmus c8f02c1dcb
gnu: grit: Update to 2.0.5.
* gnu/packages/bioinformatics.scm (grit): Update to 2.0.5.
[arguments]: Simplify.
2018-11-07 20:30:44 +01:00
Ricardo Wurmus 8d75adbf03
gnu: grit: Fetch sources from git.
* gnu/packages/bioinformatics.scm (grit)[source]: Fetch from git.
2018-11-07 20:27:10 +01:00
Ricardo Wurmus 152bebd9e0
gnu: gemma: Update to 0.98.
* gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu/packages/patches/gemma-intel-compat.patch: Remove file.
* gnu/packages/bioinformatics.scm (gemma): Update to 0.98.
[source]: Remove patch.
[inputs]: Add eigen, gfortran:lib, and openblas.
[arguments]: Add phase "find-eigen".
2018-11-07 20:26:46 +01:00
Ricardo Wurmus b113f39019
gnu: gemma: Fetch sources from git.
* gnu/packages/bioinformatics.scm (gemma)[source]: Fetch from git.
2018-11-07 20:26:45 +01:00
Pierre Langlois f09e8abc5e
gnu: clementine: Build with sqlite-with-column-metadata.
* gnu/packages/music.scm (clementine)[inputs]: Use sqlite-with-column-metadata.

Signed-off-by: Leo Famulari <leo@famulari.name>
2018-11-07 14:25:07 -05:00
Ricardo Wurmus 91b71cfbba
gnu: fxtract: Fetch sources from git.
* gnu/packages/bioinformatics.scm (fxtract)[source]: Fetch from git.
2018-11-07 19:55:50 +01:00
Ricardo Wurmus 7ca49ab57a
gnu: ribodiff: Fetch sources from git.
* gnu/packages/bioinformatics.scm (ribodiff)[source]: Fetch from git.
2018-11-07 19:48:21 +01:00
Ricardo Wurmus 239716fb0b
gnu: python-biom-format: Update to 2.1.7.
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.7.
[arguments]: Add phases "use-cython", "disable-broken-test", and
"make-files-writable".
[propagated-inputs]: Add python-flake8.
[native-inputs]: Add python-cython, python-pytest, and python-pytest-cov.
2018-11-07 19:47:07 +01:00
Ricardo Wurmus 007a81d5cf
gnu: python-biom-format: Fetch source from git.
* gnu/packages/bioinformatics.scm (python-biom-format)[source]: Fetch from
git.
2018-11-07 19:10:36 +01:00
Ricardo Wurmus 383cb7b8e6
gnu: bioawk: Fetch sources from git.
* gnu/packages/bioinformatics.scm (bioawk)[source]: Fetch from git.
2018-11-07 19:06:30 +01:00
Ricardo Wurmus 20ee3e8b76
gnu: bedtools-2.18: Fetch sources from stable URL.
* gnu/packages/bioinformatics.scm (bedtools-2.18)[source]: Use stable release
tarball instead of generated tag tarball.
2018-11-07 18:52:46 +01:00
Ricardo Wurmus 8e58319c45
gnu: bamtools: Fetch sources from git.
* gnu/packages/bioinformatics.scm (bamtools)[source]: Fetch from git.
2018-11-07 18:44:30 +01:00
Ricardo Wurmus 21335fdbec
gnu: ngless: Install links to required tools.
* gnu/packages/bioinformatics.scm (ngless)[arguments]: Install links to tools.
[inputs]: Add prodigal, bwa, samtools, and minimap2.
2018-11-07 17:19:53 +01:00
Ricardo Wurmus fff67cc8a7
gnu: prodigal: Fetch sources from git.
* gnu/packages/bioinformatics.scm (prodigal)[source]: Fetch from git.
2018-11-07 17:19:53 +01:00
Marius Bakke e2568df74e
gnu: rocksdb: Update to 5.15.10.
* gnu/packages/databases.scm (rocksdb): Update to 5.15.10.
2018-11-07 16:06:56 +01:00
Marius Bakke 8dd3665883
gnu: rocksdb: Don't use unstable tarball.
* gnu/packages/databases.scm (rocksdb)[source]: Use GIT-FETCH.
2018-11-07 16:06:56 +01:00
Ludovic Courtès dcb45127e0
services: cuirass: Add 'ttl' configuration field.
* gnu/services/cuirass.scm (<cuirass-configuration>)[ttl]: New field.
(cuirass-shepherd-service): Honor it.
2018-11-07 16:06:42 +01:00
Ludovic Courtès 08759829cf
gnu: cuirass: Update to 0b40dca.
* gnu/packages/ci.scm (cuirass): Update to 0b40dca.
2018-11-07 16:06:42 +01:00
Ludovic Courtès 970c9993f1
linux-initrd: Make sure 'build-initrd' can delete files.
Fixes <https://bugs.gnu.org/33297>.
Reported by Mark H Weaver <mhw@netris.org>.

This fixes a regression introduced in
72dc64f8f7, which made files read-only.

* gnu/build/linux-initrd.scm (build-initrd): Call 'make-file-writable'
on all the files under contents/.
2018-11-07 16:06:42 +01:00
Ricardo Wurmus 9255198423
gnu: r-mzr: Update to 2.16.0.
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.0.
[inputs]: Remove netcdf.
[propagated-inputs]: Add r-ncdf4.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus 37200dbcc3
gnu: r-rhdf5lib: Update to 1.4.0.
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.0.
[source]: Add snippet to remove bundled binaries.
[arguments]: Replace references to hdf5 with references to hdf5-1.10.
[native-inputs]: Likewise.
[propagated-inputs]: Replace hdf5 with hdf5-1.10.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus 8e48d36f26
gnu: r-hdf5array: Update to 1.10.0.
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.10.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus 611a255d2b
gnu: r-rhdf5: Update to 2.26.0.
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.26.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus a1c2bf8e54
gnu: r-rcas: Update to 1.8.0.
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.8.0.
[native-inputs]: Remove r-testthat and ghc-pandoc-citeproc.
[propagated-inputs]: Add r-annotationdbi, r-genomeinfodb, and r-genomicranges;
remove r-bsgenome-mmusculus-ucsc-mm9, r-bsgenome-celegans-ucsc-ce10,
r-bsgenome-dmelanogaster-ucsc-dm3, r-org-ce-eg-db, r-org-dm-eg-db, and
r-org-mm-eg-db.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus 900ce2bafd
gnu: r-delayedmatrixstats: Update to 1.4.0.
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.4.0.
[propagated-inputs]: Add r-biocparallel and r-hdf5array.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus 70a3a76ba7
gnu: r-scran: Update to 1.10.1.
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.10.1.
[propagated-inputs]: Add r-biocneighbors; remove r-dt, r-fnn, r-ggplot2,
r-shiny, and r-viridis.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus 48f2791496
gnu: r-scater: Update to 1.10.0.
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.10.0.
[propagated-inputs]: Add r-biocparallel; remove r-biobase, r-data-table,
r-edger, r-limma, r-rhdf5, r-rjson, r-shiny, r-shinydashboard, and r-tximport.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus f93ec63ccf
gnu: r-singlecellexperiment: Update to 1.4.0.
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.4.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus 3c833608f3
gnu: r-beachmat: Update to 1.4.0.
* gnu/packages/bioinformatics.scm (r-beachmat): Update to 1.4.0.
[propagated-inputs]: Add r-biocgenerics.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus edb91244c3
gnu: r-qvalue: Update to 2.14.0.
* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.14.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus d055f199a9
gnu: r-hitc: Update to 1.26.0.
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.26.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus 8023912934
gnu: r-fithic: Update to 1.8.0.
* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.8.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus 7468a76480
gnu: r-sushi: Update to 1.20.0.
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.20.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus 85b16c05e8
gnu: r-gwascat: Update to 2.14.0.
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.14.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus d57445c9b2
gnu: r-gviz: Update to 1.26.0.
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus ea55326dc7
gnu: r-gqtlstats: Update to 1.14.0.
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.14.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus da679b5202
gnu: r-ldblock: Update to 1.12.0.
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.12.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus 4b91335566
gnu: r-erma: Update to 0.14.0.
* gnu/packages/bioinformatics.scm (r-erma): Update to 0.14.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus 220ac15e3f
gnu: r-snpstats: Update to 1.32.0.
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.32.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus 181a843143
gnu: r-gqtlbase: Update to 1.14.0.
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.14.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus f20c766413
gnu: r-ggbio: Update to 1.30.0.
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.30.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus e7a0bc1ccf
gnu: r-biovizbase: Update to 1.30.0.
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.30.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus cdab2dcfea
gnu: r-organismdbi: Update to 1.24.0.
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.24.0.
[propagated-inputs]: Remove r-biocinstaller; add r-biocmanager.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus e8e78c4966
gnu: r-ensembldb: Update to 2.6.0.
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus 0c96e4b290
gnu: r-dirichletmultinomial: Update to 1.24.0.
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.24.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus 5ae5a8ebfc
gnu: r-complexheatmap: Update to 1.20.0.
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 1.20.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus d78c6aca55
gnu: r-genomicfiles: Update to 1.18.0.
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.18.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus 122e099e72
gnu: r-gage: Update to 2.32.0.
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.32.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus 4984212786
gnu: r-keggrest: Update to 1.22.0.
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.22.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus 95df764c01
gnu: r-fastseg: Update to 1.28.0.
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.28.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus 147633d4c1
gnu: r-annotationhub: Update to 2.14.1.
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.1.
[propagated-inputs]: Remove r-biocinstaller; add r-biocmanager.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus d7ea34bf99
gnu: r-interactivedisplaybase: Update to 1.20.0.
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.20.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus b03951f26b
gnu: r-edaseq: Update to 2.16.0.
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.16.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus 7812e6b82e
gnu: r-deseq: Update to 1.34.0.
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.34.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus 800954eba4
gnu: r-aroma-light: Update to 3.12.0.
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.12.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus 675d91a035
gnu: r-msnid: Update to 1.16.0.
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.16.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 762aca7270
gnu: r-msnbase: Update to 2.8.0.
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.8.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 73d7475246
gnu: r-pcamethods: Update to 1.74.0.
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.74.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 2c4311dc7c
gnu: r-mzid: Update to 1.20.0.
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.20.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 0e16fc4699
gnu: r-vsn: Update to 3.50.0.
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.50.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 2b085484c0
gnu: r-affy: Update to 1.60.0.
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.60.0.
[propagated-inputs]: Remove r-biocinstaller; add r-biocmanager.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 511abd7add
gnu: r-affyio: Update to 1.52.0.
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.52.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 691ce09fd3
gnu: r-protgenerics: Update to 1.14.0.
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.14.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 8af8688339
gnu: r-sva: Update to 3.30.0.
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.30.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 18604a76e4
gnu: r-methylkit: Update to 1.8.0.
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.8.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 739a856db8
gnu: r-copywriter: Update to 2.14.0.
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.14.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 2e9d8116fb
gnu: r-chipseq: Update to 1.32.0.
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.32.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus cec8f0920b
gnu: r-annotationfilter: Update to 1.6.0.
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.6.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus d2b60be596
gnu: r-tximport: Update to 1.10.0.
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.10.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus ad90921ddc
gnu: r-mutationalpatterns: Update to 1.8.0.
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.8.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 338f860cc6
gnu: r-bamsignals: Update to 1.14.0.
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.14.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 48196899cd
gnu: r-rhtslib: Update to 1.14.0.
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.14.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 7d7c702c03
gnu: r-zlibbioc: Update to 1.28.0.
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.28.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 2919fefe12
gnu: r-motifrg: Update to 1.26.0.
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.26.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus 34f1c60c78
gnu: r-seqlogo: Update to 1.48.0.
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.48.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus c5b0815c44
gnu: r-genomation: Update to 1.14.0.
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.14.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus 45ba2caedb
gnu: r-seqpattern: Update to 1.14.0.
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.14.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus d11bc259a8
gnu: r-impute: Update to 1.56.0.
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.56.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus 78ecdbc00a
gnu: r-bsgenome: Update to 1.50.0.
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.50.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus 44fa14dfa3
gnu: r-topgo: Update to 2.34.0.
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.34.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus 8a0d57d26e
gnu: r-genomicfeatures: Update to 1.34.1.
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.1.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus c5f1d1ce80
gnu: r-rtracklayer: Update to 1.42.0.
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.42.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus 52b95337e8
gnu: r-genomicalignments: Update to 1.18.0.
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.18.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus 9fd4350e5a
gnu: r-summarizedexperiment: Update to 1.12.0.
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.12.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus de4c38f80b
gnu: r-delayedarray: Update to 0.8.0.
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.8.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus 7f3778eb06
gnu: r-rsamtools: Update to 1.34.0.
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.34.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus 4804c59227
gnu: r-biostrings: Update to 2.50.0.
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus cd8828918f
gnu: r-biocparallel: Update to 1.16.0.
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.16.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus 3359d44210
gnu: r-biomart: Update to 2.38.0.
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.38.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus 3986e0dee5
gnu: r-annotationdbi: Update to 1.44.0.
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.44.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus 5b82e12a99
gnu: r-biobase: Update to 2.42.0.
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.42.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus 8d3906a95f
gnu: r-genomicranges: Update to 1.34.0.
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.34.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus fb10fb72ba
gnu: r-xvector: Update to 0.22.0.
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.22.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus 78d2ffdc73
gnu: r-limma: Update to 3.38.2.
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.38.2.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus ca2945c316
gnu: r-variantannotation: Update to 1.28.1.
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.1.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus 08cd2d5b59
gnu: r-edger: Update to 3.24.0.
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.24.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus 12871693fe
gnu: r-genomeinfodb: Update to 1.18.0.
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.18.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus 9a8dd51979
gnu: r-iranges: Update to 2.16.0.
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.16.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus a037453554
gnu: r-s4vectors: Update to 0.20.0.
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.20.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus 70f2758f71
gnu: r-dnacopy: Update to 1.56.0.
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.56.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus a127d3522a
gnu: r-bioccheck: Update to 1.18.0.
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.18.0.
[propagated-inputs]: Add r-knitr and r-biocmanager; remove r-biocinstaller.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus 6087f5ce37
gnu: r-biocstyle: Update to 2.10.0.
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.10.0.
[propagated-inputs]: Add biocmanager.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus c8dbb5fa7f
gnu: r-biocviews: Update to 1.50.1.
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.1.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus 36d7d823a4
gnu: r-biocinstaller: Update to 1.32.1.
* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.32.1.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus 2f28ffd81d
gnu: r-biocgenerics: Update to 0.28.0.
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.28.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus 5c996cab4c
gnu: r-grohmm: Update to 1.16.0.
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.16.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus bf25930cf6
gnu: r-systempiper: Update to 1.16.0.
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.16.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus 9adf78c21e
gnu: r-shortread: Update to 1.40.0.
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.40.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus 4a4b5b8537
gnu: r-gostats: Update to 2.48.0.
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.48.0.
2018-11-07 12:27:12 +01:00
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 3bd83e6db2
gnu: qtbase: Remove obsolete patch.
This patch is no longer needed since 7930cfc989
was merged to core-updates.

* gnu/packages/patches/qtbase-glibc-compat.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/qt.scm (qtbase)[source](patches): Drop it.
2018-11-06 00:04:31 +01:00
Marius Bakke f4a5faa9dc
Merge branch 'master' into core-updates 2018-11-05 23:56:22 +01:00
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
Leo Famulari 288d24800d
gnu: ruby-rack: Update to 2.0.6 [fixes CVE-2018-{16470,16471}].
* gnu/packages/ruby.scm (ruby-rack): Update to 2.0.6.
2018-11-05 16:22:11 -05:00
Pierre Neidhardt 426ffb830a
gnu: emacs-mu4e-conversation: Update to 20181105.
* gnu/packages/emacs.scm (emacs-mu4e-conversation): Update to 20181105.
2018-11-05 20:22:06 +01:00
Pierre Neidhardt 695db2f98a
gnu: Add emacs-helm-slime.
* gnu/packages/emacs.scm (emacs-helm-slime): New variable.
2018-11-05 13:58:33 +01:00
Mark H Weaver c9f3d38be4
gnu: linux-libre: Update to 4.19.1.
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.19.1.
(%linux-libre-hash): Update hash.
2018-11-05 04:00:45 -05:00
Mark H Weaver 28c717213d
gnu: linux-libre@4.14: Update to 4.14.79.
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.79.
(%linux-libre-4.14-hash): Update hash.
2018-11-05 04:00:43 -05:00
Eric Bavier cddc044ce7
libreoffice: honor '--cores=...' during build.
* gnu/packages/libreoffice.scm (libreoffice)[configure-flags]: Add
'--with-parallelism' flag.
2018-11-04 21:56:39 -06:00
Danny Milosavljevic 64eb038eef
gnu: Add fswatch.
* gnu/packages/monitoring.scm (fswatch): New variable.
2018-11-05 03:01:21 +01:00
Luther Thompson 1417f50317
gnu: python-ilinkedlist: Update to 0.2.0.
* gnu/packages/python.scm (python-ilinkedlist): Update to 0.2.0.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-05 00:08:47 +01:00
Vagrant Cascadian b6e9514864
gnu: pelican: Update to 3.7.1.
* gnu/packages/python.scm (pelican): Update to 3.7.1.
  [home-page]: Use HTTPS URL.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-05 00:08:47 +01:00
Pkill -9 c834bd3bb2
gnu: xonotic: Add icon and category to desktop files.
* gnu/packages/games.scm (xonotic): Add icon ("xonotic") and category
("Game") to the .desktop files for Xonotic.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-11-05 00:08:47 +01:00
Ludovic Courtès 688d1a01e4
artwork: Clone over HTTPS.
Suggested by Leo Famulari <leo@famulari.name>
at <https://lists.gnu.org/archive/html/help-guix/2018-11/msg00039.html>.

* gnu/artwork.scm (%artwork-repository): Switch to HTTPS URL.
2018-11-05 00:08:47 +01:00
Ludovic Courtès ab3c60ace3
install: Parameterize the profile name for 'populate-single-profile-directory'.
* gnu/build/install.scm (populate-single-profile-directory): Add
 #:profile-name.  Replace hard-coded occurrences of "guix-profile" with
PROFILE-NAME.  Make the symlink part under /root a function of
PROFILE-NAME.
2018-11-05 00:08:46 +01:00
Pierre Neidhardt 97b7b96efc
gnu: go-github-com-urfave-cli: Remove duplicate declaration.
* gnu/packages/golang.scm (go-github-com-urfave-cli): Remove duplicate declaration.
2018-11-04 23:33:24 +01:00
Efraim Flashner 30012b7408
gnu: myrepos: Wrap the webcheckout binary.
* gnu/packages/version-control.scm (myrepos)[arguments]: Add a custom
'wrap-webcheckout phase to wrap webcheckout with its perl libraries.
[inputs]: Add perl-encode-locale, perl-html-parser, perl-http-date,
perl-http-message, perl-libwww, perl-try-tiny, perl-uri.
2018-11-04 12:45:27 +02:00
Efraim Flashner f909e21797
gnu: debian-archive-keyring: Update to 2018.1.
* gnu/packages/debian.scm (debian-archive-keyring): Update to 2018.1.
[source]: Download from git repository.
2018-11-04 12:00:13 +02:00
Efraim Flashner 2e77bbed71
gnu: ruby@2.3: Update to 2.3.8.
* gnu/packages/ruby.scm (ruby@2.3): Update to 2.3.8.
2018-11-04 12:00:13 +02:00
Efraim Flashner d4b5e4bb73
gnu: debootstrap: Update to 1.0.109.
* gnu/packages/debian.scm (debootstrap): Update to 1.0.109.
2018-11-04 12:00:10 +02:00
Arun Isaac 3e84ce51fb
gnu: mpop: Update to 1.4.0.
* gnu/packages/mail.scm (mpop): Update to 1.4.0.
2018-11-04 10:36:17 +05:30
Efraim Flashner e9f305a1c8
gnu: sbcl-lift: Don't keep the bundled website.
* gnu/packages/lisp.scm (sbcl-lift)[source]: Remove bundled website.
[arguments]: Remove custom 'make-gzips-writable phase.
2018-11-03 20:43:35 +02:00
Ludovic Courtès 0e091b3e93
gnu: totem: Update to 3.26.2.
* gnu/packages/gnome.scm (totem): Update to 3.26.2.
2018-11-03 15:44:40 +01:00
Ludovic Courtès 504f0cf198
gnu: emacs-debbugs: Update to 0.16.
* gnu/packages/emacs.scm (emacs-debbugs): Update to 0.16.
2018-11-03 15:44:24 +01:00
Ludovic Courtès a7c8574f39
gnu: perl-image-exiftool: Update to 11.11.
* gnu/packages/photo.scm (perl-image-exiftool): Update to 11.11.
2018-11-03 15:16:42 +01:00
Ludovic Courtès 46c8f53ba8
gnu: emacs-dired-du: Update to 0.5.1.
* gnu/packages/emacs.scm (emacs-dired-du): Update to 0.5.1.
2018-11-03 15:16:20 +01:00
Ludovic Courtès 8e5c59868c
gnu: diffoscope: Update to 104.
* gnu/packages/package-management.scm (diffoscope): Update to 104.
2018-11-03 15:16:02 +01:00
Arun Isaac b1c7f5fff9
gnu: emacs-emms: Update to 5.1.
* gnu/packages/emacs.scm (emacs-emms): Update to 5.1.
2018-11-03 19:14:05 +05:30
Tobias Geerinckx-Rice 3995e85462
gnu: tor: Update to 0.3.4.9.
* gnu/packages/tor.scm (tor): Update to 0.3.4.9.
2018-11-02 19:51:12 +01:00
Julien Lepiller ff349415b2
gnu: python-apache-libcloud: Update to 2.3.0.
* gnu/packages/python.scm (python-apache-libcloud)
(python2-apache-libcloud): Update to 2.3.0.
2018-11-02 14:32:24 +01:00
Danny Milosavljevic 722aac1ea1
Merge remote-tracking branch 'origin/wip-rust' into master. 2018-11-02 11:01:45 +01:00
Leo Famulari b3325eb306
gnu: Go 1.11: Avoid unnecessary store references.
This shrinks the closure of Go 1.11 from 1379 MiB to 581 MiB.

Fixes <https://bugs.gnu.org/32949>.

* gnu/packages/golang.scm (go-1.11)[arguments]: Add a 'delete-extraneous-files'
phase.
2018-11-01 23:23:09 -04:00
Julien Lepiller 16b89ecc1f
gnu: Add openjdk10.
* gnu/packages/java.scm (openjdk10): New variable.
2018-11-01 21:16:59 +01:00
Julien Lepiller dd74105925
gnu: Add openjdk9.
* gnu/packages/java.scm (openjdk9): New variable.
2018-11-01 20:34:08 +01:00
Leo Famulari 7571ec3576
gnu: MPD: Update to 0.20.23.
* gnu/packages/mpd.scm (mpd): Update to 0.20.23.
2018-11-01 15:30:05 -04:00
Leo Famulari 33279c2a19
gnu: mpd-mpc: Update to 0.31.
* gnu/packages/mpd.scm (mpd-mpc): Update to 0.31.
[native-inputs]: Add python-sphinx.
2018-11-01 15:30:05 -04:00
Leo Famulari 361dd8a556
gnu: icecast: Update to 2.4.4 [fixes CVE-2018-18820].
* gnu/packages/xiph.scm (icecast): Update to 2.4.4.
2018-11-01 12:33:14 -04:00
Rutger Helling d7ca1899aa
gnu: mame: Update to 0.203.
* gnu/packages/emulators.scm (mame): Update to 0.203.
2018-11-01 09:24:52 +01:00
Rutger Helling a769a4d432
gnu: xpra: Update to 2.4.1.
* gnu/packages/xorg.scm (xpra): Update to 2.4.1.
2018-11-01 08:32:45 +01:00
Rutger Helling e7039f10ec
gnu: dolphin-emu: Use ffmpeg instead of ffmpeg@3.4.
* gnu/packages/emulators.scm (dolphin-emu): Use ffmpeg instead of ffmpeg@3.4.
2018-11-01 08:20:13 +01:00
Rutger Helling ee3dd7a83a
gnu: sdl2: Update to 2.0.9.
* gnu/packages/sdl.scm (sdl2): Update to 2.0.9.
2018-11-01 08:20:13 +01:00
Tobias Geerinckx-Rice 66a2a47117
gnu: whois: Update to 5.4.0.
* gnu/packages/networking.scm (whois): Update to 5.4.0.
2018-11-01 04:34:25 +01:00
Tobias Geerinckx-Rice 38fda1cc36
gnu: highlight: Update to 3.47.
* gnu/packages/pretty-print.scm (highlight): Update to 3.47.
2018-11-01 04:34:25 +01:00
Tobias Geerinckx-Rice a72d337fbc
gnu: python-jsonrpclib-pelix: Update to 0.3.2.
* gnu/packages/python.scm (python-jsonrpclib-pelix): Update to 0.3.2.
[arguments]: Disable #:tests?.
2018-11-01 04:34:25 +01:00
Tobias Geerinckx-Rice 60ed87871d
gnu: python-pynacl: Update to 1.3.0.
* gnu/packages/python-crypto.scm (python-pynacl): Update to 1.3.0.
2018-11-01 04:34:24 +01:00
Tobias Geerinckx-Rice 351a12b0a7
gnu: oniguruma: Update to 6.9.0.
* gnu/packages/textutils.scm (oniguruma): Update to 6.9.0.
2018-11-01 04:34:24 +01:00
Tobias Geerinckx-Rice 33bddd309c
gnu: motion: Install translations.
* gnu/packages/video.scm (motion)[native-inputs]: Add gettext-minimal.
2018-11-01 04:34:24 +01:00
Tobias Geerinckx-Rice 2ea678fabf
gnu: motion: Don't use unstable tarball.
* gnu/packages/video.scm (motion)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
2018-11-01 04:34:24 +01:00
Tobias Geerinckx-Rice 4fbcfc1482
Keep (gnu packages video) module imports in order.
* gnu/packages/video.scm (define-module): Re-order module imports
alphabetically.
2018-11-01 04:33:54 +01:00
Tobias Geerinckx-Rice c3069cd183
gnu: motion: Update to 4.2.
* gnu/packages/video.scm (motion): Update to 4.2.
2018-11-01 04:32:35 +01:00
Tobias Geerinckx-Rice 2930a39b16
gnu: julia: Update objconv input to 2018-10-07.
* gnu/packages/julia.scm (julia)[input]: Update objconf to 2018-10-07.
2018-11-01 04:32:35 +01:00
Efraim Flashner c16913d34d
gnu: myrepos: Update to 1.20180726.
* gnu/packages/version-control.scm (myrepos): Update to 1.20180726.
[source]: Remove patch.
* gnu/packages/patches/myrepos-CVE-2018-7032.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2018-10-31 21:57:02 +02:00
Leo Famulari c438e0cc74
gnu: curl: Update grafted replacement to 7.62.0 [security fixes].
Fixes CVE-2018-{16839,16840,16842}.

* gnu/packages/curl.scm (curl)[replacement]: Update to 7.62.0.
(curl-7.61.1): Replace with ...
(curl-7.62.0): ... new variable.
2018-10-31 13:54:20 -04:00
Rutger Helling 124e9d6e0a
gnu: dolphin-emu: Update to commit 22ddd11.
* gnu/packages/emulators.scm (dolphin-emu): Update to commit 22ddd11.
[arguments]: Return #t with phase 'fixgcc7.
2018-10-31 10:40:04 +01:00
Rutger Helling 3126bee69a
gnu: wine-staging: Update to 3.19.
* gnu/packages/wine.scm (wine-staging-patchset-data): Update to 3.19.
* gnu/packages/wine.scm (wine-staging): Update to 3.19.
2018-10-31 09:39:55 +01:00
Mark H Weaver a45a92ccd8
gnu: webkitgtk@2.22: Update to 2.22.3.
* gnu/packages/webkit.scm (webkitgtk-2.22): Update to 2.22.3.
2018-10-31 01:47:52 -04:00
Arun Isaac c7ac8e36e2
gnu: quaternion: Update to 0.0.9.3.
* gnu/packages/messaging.scm (quaternion): Update to 0.0.9.3.
[inputs]: Add qtquickcontrols, qtsvg and qttools.
[arguments]: Remove fix-libqmatrixclient-dynamic-linking phase. Add
wrap-program phase.
2018-10-31 09:31:59 +05:30
Arun Isaac c6588749a6
gnu: libqmatrixclient: Update to 0.4.0.
* gnu/packages/messaging.scm (libqmatrixclient): Update to 0.4.0.
2018-10-31 09:31:59 +05:30
Tobias Geerinckx-Rice b590951ff2
gnu: meandmyshadow: Update home page.
* gnu/packages/games.scm (meandmyshadow)[home-page]: Follow permanent
redirect.
2018-10-31 02:31:18 +01:00
Tobias Geerinckx-Rice 1d9a9d27ae
gnu: meandmyshadow: Update to 0.5.
* gnu/packages/games.scm (meandmyshadow): Update to 0.5.
[source]: Add unreleased bugfix patch.
[arguments]: Remove obsolete ‘set-sdl'paths’ phase.
[inputs]: Switch to SDL 2. Add lua. Remove libx11, mesa, and glu.
* gnu/packages/patches/meandmyshadow-define-paths-earlier.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
2018-10-31 02:31:18 +01:00
Tobias Geerinckx-Rice 4cae7e67f3
gnu: hyperrogue: Update to 10.4x.
* gnu/packages/games.scm (hyperrogue): Update to 10.4x.
2018-10-30 23:40:43 +01:00
Tobias Geerinckx-Rice 21fc352bad
gnu: yosys: Don't use unstable tarball.
* gnu/packages/fpga.scm (yosys)[source]: Use GIT-FETCH and GIT-FILE-NAME.
2018-10-30 23:40:43 +01:00
Tobias Geerinckx-Rice becee7029f
gnu: disorderfs: Update to 0.5.5.
* gnu/packages/file-systems.scm (disorderfs): Update to 0.5.5.
2018-10-30 23:40:42 +01:00
Tobias Geerinckx-Rice 58cd3123ac
gnu: pulseview: Update to 0.4.1.
* gnu/packages/electronics.scm (pulseview): Update to 0.4.1.
[arguments]: Remove CMAKE_CXX_FLAGS from #:configure-flags. (Keep)
build(ing) the unit tests. Add a ‘remove-empty-doc-directory’ phase.
2018-10-30 23:40:42 +01:00
Tobias Geerinckx-Rice 61c58b7827
gnu: sigrok-cli: Update to 0.7.1.
* gnu/packages/electronics.scm (sigrok-cli): Update to 0.7.1.
2018-10-30 23:40:42 +01:00
Tobias Geerinckx-Rice 295fc4152a
gnu: cloc: Update to 1.80.
* gnu/packages/code.scm (cloc): Update to 1.80.
2018-10-30 23:40:42 +01:00
Tobias Geerinckx-Rice 1204402a90
gnu: python-partd: Update to 0.3.9.
* gnu/packages/python.scm (python-partd): Update to 0.3.9.
2018-10-30 23:40:42 +01:00
Ricardo Wurmus fd649d1e68
gnu: Add r-r2glmm.
* gnu/packages/cran.scm (r-r2glmm): New variable.
2018-10-30 22:47:35 +01:00
Ricardo Wurmus 7c02dd6268
gnu: Add r-lmertest.
* gnu/packages/cran.scm (r-lmertest): New variable.
2018-10-30 22:47:26 +01:00
Ricardo Wurmus 49863fd695
gnu: Add r-afex.
* gnu/packages/cran.scm (r-afex): New variable.
2018-10-30 22:47:18 +01:00
Ricardo Wurmus 20ff6e3a34
gnu: Add r-mvabund.
* gnu/packages/cran.scm (r-mvabund): New variable.
2018-10-30 22:47:10 +01:00
Ricardo Wurmus 4fb35ebd8d
gnu: Add r-rcppgsl.
* gnu/packages/cran.scm (r-rcppgsl): New variable.
2018-10-30 22:47:00 +01:00
Ricardo Wurmus 373cef0a0c
gnu: Add r-tweedie.
* gnu/packages/cran.scm (r-tweedie): New variable.
2018-10-30 22:46:47 +01:00
Ricardo Wurmus 32499b26e6
gnu: Add r-clusteval.
* gnu/packages/cran.scm (r-clusteval): New variable.
2018-10-30 22:13:01 +01:00
Ricardo Wurmus 7a06cdfa8c
gnu: r-analytics: Update to 3.0.
* gnu/packages/cran.scm (r-analytics): Update to 3.0.
[propagated-inputs]: Add r-vim.
2018-10-30 21:48:10 +01:00
Ricardo Wurmus e5f9e9fa79
gnu: r-radiant-data: Update to 0.9.7.
* gnu/packages/cran.scm (r-radiant-data): Update to 0.9.7.
[propagated-inputs]: Add r-shinyfiles and r-summarytools.
2018-10-30 21:48:10 +01:00
Ricardo Wurmus 39528a5ee9
gnu: r-pracma: Update to 2.1.8.
* gnu/packages/maths.scm (r-pracma): Update to 2.1.8.
[propagated-inputs]: Remove r-quadprog.
2018-10-30 21:48:10 +01:00
Ricardo Wurmus 4633c8e6fc
gnu: r-shinydashboard: Update to 0.7.1.
* gnu/packages/web.scm (r-shinydashboard): Update to 0.7.1.
[propagated-inputs]: Add r-promises.
2018-10-30 21:48:10 +01:00
Ricardo Wurmus 65279cc8f3
gnu: Add r-shinyfiles.
* gnu/packages/web.scm (r-shinyfiles): New variable.
2018-10-30 21:48:10 +01:00
Ricardo Wurmus a056e2251e
gnu: r-htmlwidgets: Update to 1.3.
* gnu/packages/web.scm (r-htmlwidgets): Update to 1.3.
2018-10-30 21:48:10 +01:00
Ricardo Wurmus f697ef4a0d
gnu: r-servr: Update to 0.11.
* gnu/packages/web.scm (r-servr): Update to 0.11.
2018-10-30 21:48:10 +01:00
Ricardo Wurmus 8871a51350
gnu: r-webshot: Update to 0.5.1.
* gnu/packages/cran.scm (r-webshot): Update to 0.5.1.
[propagated-inputs]: Add r-callr; remove r-processx and r-withr.
2018-10-30 21:48:09 +01:00
Ricardo Wurmus d42f741035
gnu: r-dendextend: Update to 1.9.0.
* gnu/packages/cran.scm (r-dendextend): Update to 1.9.0.
2018-10-30 21:48:09 +01:00
Ricardo Wurmus 31c8d9fe00
gnu: r-emmeans: Update to 1.3.0.
* gnu/packages/cran.scm (r-emmeans): Update to 1.3.0.
2018-10-30 21:48:09 +01:00
Ricardo Wurmus bec74196ea
gnu: r-abps: Update to 0.3.
* gnu/packages/cran.scm (r-abps): Update to 0.3.
2018-10-30 21:48:09 +01:00
Ricardo Wurmus 464676a970
gnu: r-proc: Update to 1.13.0.
* gnu/packages/cran.scm (r-proc): Update to 1.13.0.
2018-10-30 21:48:03 +01:00
Ricardo Wurmus 71d995392b
gnu: r-rdpack: Update to 0.10-1.
* gnu/packages/cran.scm (r-rdpack): Update to 0.10-1.
2018-10-30 21:47:54 +01:00