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Author SHA1 Message Date
Alex Vong
3c1edff5ca
gnu: java-fasterxml-jackson-databind: Update to 2.9.4 [fixes CVE-{2017-17485, 2018-5968}]. 
* gnu/packages/java.scm (java-fasterxml-jackson-databind): Update to 2.9.4.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-02-15 17:18:27 -05:00
Alex Vong
38a0fc384a
gnu: java-fasterxml-jackson-core: Update to 2.9.4. 
* gnu/packages/java.scm (java-fasterxml-jackson-core): Update to 2.9.4.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-02-15 17:18:26 -05:00
Alex Vong
93dceea45e
gnu: java-fasterxml-jackson-annotations: Update to 2.9.4. 
* gnu/packages/java.scm (java-fasterxml-jackson-annotations): Update to 2.9.4.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-02-15 17:18:26 -05:00
Ben Woodcroft
5ebc8e7f41
gnu: diamond: Update to 0.9.18. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.18.
 2018-02-16 08:13:24 +10:00
Pjotr Prins
aabcb6e57c
gnu: python-elasticsearch: Update to 6.1.1. 
* gnu/packages/python-web.scm (python-elasticsearch, python2-elasticsearch):
Update to 6.1.1.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-02-15 16:57:12 -05:00
Hartmut Goebel
34581f68c0
gnu: Add bpython. 
* gnu/packages/python.scm (bpython, bpython2): New variables.
 2018-02-15 21:44:07 +01:00
Hartmut Goebel
e79a8424ca
gnu: Add python-curtsies. 
* gnu/packages/terminals.scm (python-curtsies, python2-curtsies): New
  variables.
 2018-02-15 21:44:06 +01:00
Hartmut Goebel
573450e60c
gnu: Add python-blessings. 
* gnu/packages/terminals.scm (python-blessings, python2-blessings): New
  variables.
 2018-02-15 21:44:06 +01:00
Hartmut Goebel
46ddcf4a29
gnu: Add python-pyte. 
* gnu/packages/terminals.scm (python-pyte, python2-pyte): New variables.
 2018-02-15 21:44:06 +01:00
Leo Famulari
3026de3fce
gnu: irssi: Update to 1.1.1 [fixes CVE-2018-{7050,7051,7052,7053,7054}]. 
* gnu/packages/irc.scm (irssi): Update to 1.1.1.
 2018-02-15 14:41:26 -05:00
Oleg Pykhalov
5b23829299
gnu: Add epipe. 
* gnu/packages/emacs.scm (epipe): New public variable.
 2018-02-15 20:45:45 +03:00
Danny Milosavljevic
a124e4258a
gnu: ghc: Make memory allocator decommit memory on Linux < 4.5. 
* gnu/packages/patches/ghc-8.0-fall-back-to-madv_dontneed.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/haskell.scm (ghc-8): Use it.
 2018-02-15 17:27:50 +01:00
Ricardo Wurmus
4aa0a1df2d
gnu: java-jeromq: Update to 0.4.3. 
* gnu/packages/java.scm (java-jeromq): Update to 0.4.3.
[arguments]: Disable DealerSpecTest.
 2018-02-15 17:19:09 +01:00
Ricardo Wurmus
36b39d1618
gnu: java-testng: Update to 6.14.2. 
* gnu/packages/java.scm (java-testng): Update to 6.14.2.
[arguments]: Delete failing tests and those requiring groovy.
[native-inputs]: Add java-mockito-1.
 2018-02-15 17:19:06 +01:00
Ricardo Wurmus
152d30c346
gnu: Add python-loompy. 
* gnu/packages/bioinformatics.scm (python-loompy): New variable.
 2018-02-15 17:19:00 +01:00
Ricardo Wurmus
3082de04c2
gnu: Add r-dropbead. 
* gnu/packages/bioinformatics.scm (r-dropbead): New variable.
 2018-02-15 17:18:54 +01:00
Ricardo Wurmus
05f7296012
gnu: Add r-delayedmatrixstats. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): New variable.
 2018-02-15 17:18:52 +01:00
Ricardo Wurmus
fc162dbaec
gnu: Add python-typing. 
* gnu/packages/python.scm (python-typing, python2-typing): New variables.
 2018-02-15 17:18:50 +01:00
Ricardo Wurmus
130d290e29
gnu: Add python-future-fstrings. 
* gnu/packages/python.scm (python-future-fstrings): New variable.
 2018-02-15 17:18:46 +01:00
Ricardo Wurmus
8b2ad13b19
gnu: Add python-tokenize-rt. 
* gnu/packages/python.scm (python-tokenize-rt): New variable.
 2018-02-15 17:18:43 +01:00
Ricardo Wurmus
e035589482
gnu: augeas: Update to 1.10.1. 
* gnu/packages/augeas.scm (augeas): Update to 1.10.1.
 2018-02-15 17:17:19 +01:00
Ludovic Courtès
ec0f3d0a5b
gnu: ifdtool: Fix Texinfo markup. 
* gnu/packages/flashing-tools.scm (ifdtool)[description]: Fix Texinfo
markup.
 2018-02-15 16:35:39 +01:00
Danny Milosavljevic
8e60743d8b
gnu: me-cleaner: Update synopsis. 
* gnu/packages/flashing-tools.scm (me-cleaner)[synopsis]: Modify.
 2018-02-15 15:01:39 +01:00
Danny Milosavljevic
7e0a6fac0b
services: mingetty: Move tty optionality to agetty. 
Follow-up to 5a9902c8ac.

* gnu/services/base.scm (mingetty-shepherd-service): Move tty optionality check to...
(agetty-shepherd-service): ...here.
 2018-02-15 12:32:18 +01:00
Danny Milosavljevic
0297a160a0
gnu: Add me-cleaner. 
* gnu/packages/flashing-tools.scm (me-cleaner): New variable.
 2018-02-15 12:05:25 +01:00
Danny Milosavljevic
9721c0b6ef
gnu: Add intelmetool. 
* gnu/packages/flashing-tools.scm (intelmetool): New variable.
 2018-02-15 12:05:24 +01:00
Danny Milosavljevic
501e184716
gnu: Add ifdtool. 
* gnu/packages/flashing-tools.scm (ifdtool): New variable.
 2018-02-15 12:05:24 +01:00
Danny Milosavljevic
5a9902c8ac
services: agetty: Add agetty instance to base services. Make its tty optional. 
* gnu/services/base.scm (%base-services): Instantiate agetty-service.
(default-serial-port): New variable.
(agetty-shepherd-service): Make tty optional, default to the above.
* doc/guix.texi (agetty-configuration): Update "tty" documentation.
* gnu/system/install.scm (agetty-default-service): Delete variable.
(embedded-installation-os): Remove agetty-default-service instance.
Add "console" kernel-argument.
 2018-02-15 12:05:21 +01:00
Ludovic Courtès
2b870303e7
gnu: cuirass: Update to 4ab2f2c. 
Previous revision had (web server fiberized) installed in the wrong
place, and would thus fail to start.

* gnu/packages/ci.scm (cuirass): Update to 4ab2f2c.
 2018-02-15 10:32:20 +01:00
Pierre Langlois
6ca15c9ef6
gnu: crypto++: Update to 6.0.0. 
* gnu/packages/crypto.scm (crypto++): Update to 6.0.0.
* gnu/packages/patches/crypto++-fix-dos-in-asn.1-decoders.patch: Delete
file.
* gnu/local.mk (dist_patch_DATA): Remove it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-02-15 10:23:42 +01:00
Ludovic Courtès
9859b5c190
gnu: nss-mdns: Update to 0.12.0. 
* gnu/packages/avahi.scm (nss-mdns): Update to 0.12 + patch.
(nss-mdns-0.10.0): Remove.
* gnu/services/avahi.scm (avahi-service-type): Use NSS-MDNS again.
 2018-02-15 10:16:00 +01:00
Ludovic Courtès
d1688e6ad4
gnu: cuirass: Update to 8080c17. 
* gnu/packages/ci.scm (cuirass): Update to 8080c17.
[inputs]: Add GUILE-FIBERS.
[arguments] <wrap-program>: Add Fibers to the search path in the
wrapper.
 2018-02-14 23:44:28 +01:00
Ludovic Courtès
499e499b8e
gnu: guile-sqlite3: Update to 10c13a7. 
* gnu/packages/guile.scm (guile-sqlite3): Update to 10c13a7.
 2018-02-14 23:38:22 +01:00
Julien Lepiller
08da664d10
gnu: Add cat-avatar-generator-service. 
* gnu/services/web.scm (cat-avatar-generator-service): New variable.
* doc/guix.text (Web Services): Document it.
 2018-02-14 23:18:41 +01:00
Julien Lepiller
3bedac5057
gnu: Add cat-avatar-generator. 
* gnu/packages/web.scm (cat-avatar-generator): New variable.
 2018-02-14 23:15:16 +01:00
Tobias Geerinckx-Rice
f2ba6fc8bb
gnu: yadifa: Update to 2.3.8. 
* gnu/packages/dns.scm (yadifa): Update to 2.3.8.
 2018-02-14 20:39:53 +01:00
Marius Bakke
1bd08a268a
gnu: strace: Update to 4.21. 
* gnu/packages/linux.scm (strace): Update to 4.21.
[source](uri): Releases are now served from GitHub.
 2018-02-14 20:23:19 +01:00
Marius Bakke
1a46a6d02d
gnu: fio: Update to 3.4. 
* gnu/packages/benchmark.scm (fio): Update to 3.4.
 2018-02-14 20:23:19 +01:00
Oleg Pykhalov
ac07b94ab5
gnu: Add emacs-scratch-el. 
* gnu/packages/emacs.scm (emacs-scratch-el): New public variable.
 2018-02-14 15:54:26 +03:00
Mark H Weaver
5fe9ba59ba
gnu: magit: Do not set 'magit-git-executable' to absolute file name. 
Fixes <https://bugs.gnu.org/30434>.
Reported by Ricardo Wurmus <rekado@elephly.net>.

* gnu/packages/emacs.scm (magit)[arguments]: Do not modify the default value
of 'magit-git-executable'.  Remove "#:modules" and "#:imported-modules".
 2018-02-14 03:48:20 -05:00
Mark H Weaver
84fe44201b
gnu: magit: Do not set 'magit-git-executable' to absolute file name. 
Fixes <https://bugs.gnu.org/30434>.
Reported by Ricardo Wurmus <rekado@elephly.net>.

* gnu/packages/emacs.scm (magit)[arguments]: Do not modify the default value
of 'magit-git-executable'.  Remove "#:modules" and "#:imported-modules".
 2018-02-14 03:42:07 -05:00
Mark H Weaver
02843215d8
gnu: shepherd: 'herd status' now sorts the result. 
Add a patch by Ludovic Courtès <ludo@gnu.org> from the upstream
shepherd repository to partially fix <https://bugs.gnu.org/30299>.

* gnu/packages/patches/shepherd-herd-status-sorted.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/admin.scm (shepherd)[source]: Add patch.
 2018-02-14 03:42:02 -05:00
Mark H Weaver
932c98326d
Merge branch 'master' into core-updates 2018-02-14 03:40:08 -05:00
Rutger Helling
870541d6a7
gnu: mpv: Enable Vulkan support. 
* gnu/packages/video.scm (mpv)[inputs]: Add shaderc and vulkan-icd-loader.
 2018-02-14 08:18:58 +01:00
Rutger Helling
5b69baf0ad
gnu: Add shaderc. 
* gnu/packages/vulkan.scm (shaderc): New variable.
 2018-02-14 08:18:58 +01:00
Mark H Weaver
c5971d473d
gnu: icecat: Add more fixes from upstream mozilla-esr52. 
* gnu/packages/gnuzilla.scm (icecat)[source]: Add selected fixes from the
upstream mozilla-esr52 repository.
 2018-02-13 19:53:35 -05:00
Marius Bakke
4af55f7657
gnu: freeipmi: Update to 1.6.1. 
* gnu/packages/freeipmi.scm (freeipmi): Update to 1.6.1.
 2018-02-13 23:52:39 +01:00
Danny Milosavljevic
a32f9b59ab
system: make-u-boot-package: Install configuration file. 
* gnu/packages/bootloaders.scm (make-u-boot-package): Install configuration
file.
 2018-02-13 23:23:25 +01:00
Marius Bakke
b2b2ba40c3
gnu: efivar: Update to 34. 
* gnu/packages/linux.scm (efivar): Update to 34.
[arguments]: Add CC_FOR_BUILD=gcc to #:make-flags.
 2018-02-13 23:02:03 +01:00
Marius Bakke
8b114e5bd9
gnu: feh: Update to 2.23.2. 
* gnu/packages/image-viewers.scm (feh): Update to 2.23.2.
 2018-02-13 23:02:03 +01:00
Ben Woodcroft
119c09c219
gnu: vsearch: Update to 2.7.0. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.7.0.
 2018-02-14 07:43:19 +10:00
Efraim Flashner
34a7b7d713
gnu: libdvdnav@4: Remove variable. 
* gnu/packages/video.scm (libdvdnav@4): Remove variable.
 2018-02-13 22:56:51 +02:00
Efraim Flashner
0976ea38b1
gnu: libdvdnav: Update to 6.0.0. 
* gnu/packages/video.scm (libdvdnav): Update to 6.0.0.
 2018-02-13 22:56:50 +02:00
Efraim Flashner
3c9deb0b11
gnu: libdvdread: Update to 6.0.0. 
* gnu/packages/video.scm (libdvdread): Update to 6.0.0.
 2018-02-13 22:56:50 +02:00
Efraim Flashner
975c715a41
gnu: x265: Update to 2.6. 
* gnu/packages/video.scm (x265): Update to 2.6.
 2018-02-13 22:56:48 +02:00
Efraim Flashner
1373ce7ce0
gnu: ffmpeg: Update to 3.4.2. 
* gnu/packages/video.scm (ffmpeg): Update to 3.4.2.
 2018-02-13 22:56:44 +02:00
Leo Famulari
5c4fd60416
gnu: python-icalendar: Update to 4.0.1. 
* gnu/packages/python.scm (python-icalendar): Update to 4.0.1.
 2018-02-13 14:33:22 -05:00
Mark H Weaver
288b8fd5e9
Merge branch 'master' into core-updates 2018-02-13 13:17:15 -05:00
Mark H Weaver
acff6aa004
gnu: linux-libre: Update to 4.15.3. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.15.3.
(%linux-libre-hash): Update hash.
 2018-02-13 13:08:30 -05:00
Mark H Weaver
146be91dda
gnu: linux-libre@4.14: Update to 4.14.19. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.19.
(%linux-libre-4.14-hash): Update hash.
 2018-02-13 13:07:48 -05:00
Mark H Weaver
47b731b372
gnu: linux-libre@4.9: Update to 4.9.81. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.81.
 2018-02-13 13:06:28 -05:00
Ricardo Wurmus
117c83bdc7
gnu: r-htmltable: Update to 1.11.2. 
* gnu/packages/web.scm (r-htmltable): Update to 1.11.2.
[propagated-inputs]: Remove r-dplyr and r-tidyr.
 2018-02-13 16:18:45 +01:00
Ricardo Wurmus
7d358f33d8
gnu: r-htmlwidgets: Update to 1.0. 
* gnu/packages/web.scm (r-htmlwidgets): Update to 1.0.
 2018-02-13 16:18:45 +01:00
Ricardo Wurmus
1ee14481d2
gnu: r-lubridate: Update to 1.7.2. 
* gnu/packages/statistics.scm (r-lubridate): Update to 1.7.2.
 2018-02-13 16:18:45 +01:00
Ricardo Wurmus
4ff5fc6fa0
gnu: r-ranger: Update to 0.9.0. 
* gnu/packages/statistics.scm (r-ranger): Update to 0.9.0.
 2018-02-13 16:18:45 +01:00
Ricardo Wurmus
f9ee1741f9
gnu: r-lme4: Update to 1.1-15. 
* gnu/packages/statistics.scm (r-lme4): Update to 1.1-15.
 2018-02-13 16:18:45 +01:00
Ricardo Wurmus
45ec40818b
gnu: r-quantreg: Update to 5.35. 
* gnu/packages/statistics.scm (r-quantreg): Update to 5.35.
 2018-02-13 16:18:45 +01:00
Ricardo Wurmus
725673ad6f
gnu: r-rcppeigen: Update to 0.3.3.4.0. 
* gnu/packages/statistics.scm (r-rcppeigen): Update to 0.3.3.4.0.
 2018-02-13 16:18:45 +01:00
Ricardo Wurmus
c71cd58240
gnu: r-pbapply: Update to 1.3-4. 
* gnu/packages/statistics.scm (r-pbapply): Update to 1.3-4.
 2018-02-13 16:18:45 +01:00
Ricardo Wurmus
f66a34fcc4
gnu: r-vgam: Update to 1.0-5. 
* gnu/packages/statistics.scm (r-vgam): Update to 1.0-5.
 2018-02-13 16:18:45 +01:00
Ricardo Wurmus
09da3d4403
gnu: r-fpc: Update to 2.1-11. 
* gnu/packages/statistics.scm (r-fpc): Update to 2.1-11.
 2018-02-13 16:18:45 +01:00
Ricardo Wurmus
23fb604725
gnu: r-pcapp: Update to 1.9-73. 
* gnu/packages/statistics.scm (r-pcapp): Update to 1.9-73.
 2018-02-13 16:18:45 +01:00
Ricardo Wurmus
fe394eac82
gnu: r-zoo: Update to 1.8-1. 
* gnu/packages/statistics.scm (r-zoo): Update to 1.8-1.
 2018-02-13 16:18:45 +01:00
Ricardo Wurmus
b216fdf21f
gnu: r-hmisc: Update to 4.1-1. 
* gnu/packages/statistics.scm (r-hmisc): Update to 4.1-1.
 2018-02-13 16:18:45 +01:00
Ricardo Wurmus
c4f148ab0a
gnu: r-tidyr: Update to 0.8.0. 
* gnu/packages/statistics.scm (r-tidyr): Update to 0.8.0.
 2018-02-13 16:18:44 +01:00
Ricardo Wurmus
be8db0a0ab
gnu: r-viridislite: Update to 0.3.0. 
* gnu/packages/statistics.scm (r-viridislite): Update to 0.3.0.
 2018-02-13 16:18:44 +01:00
Ricardo Wurmus
9604af890d
gnu: r-viridis: Update to 0.5.0. 
* gnu/packages/statistics.scm (r-viridis): Update to 0.5.0.
 2018-02-13 16:18:44 +01:00
Ricardo Wurmus
a46c71924c
gnu: r-matrixstats: Update to 0.53.1. 
* gnu/packages/statistics.scm (r-matrixstats): Update to 0.53.1.
 2018-02-13 16:18:44 +01:00
Ricardo Wurmus
e04b71a83b
gnu: r-mvtnorm: Update to 1.0-7. 
* gnu/packages/statistics.scm (r-mvtnorm): Update to 1.0-7.
 2018-02-13 16:18:44 +01:00
Ricardo Wurmus
f7d7dd41f1
gnu: r-r-rsp: Update to 0.42.0. 
* gnu/packages/statistics.scm (r-r-rsp): Update to 0.42.0.
[propagated-inputs]: Add r-digest.
 2018-02-13 16:18:44 +01:00
Ricardo Wurmus
2cd6bb5da4
gnu: r-r-cache: Update to 0.13.0. 
* gnu/packages/statistics.scm (r-r-cache): Update to 0.13.0.
 2018-02-13 16:18:44 +01:00
Ricardo Wurmus
48237fde89
gnu: r-bigmemory: Update to 4.5.33. 
* gnu/packages/statistics.scm (r-bigmemory): Update to 4.5.33.
 2018-02-13 16:18:44 +01:00
Ricardo Wurmus
a566b3f9e6
gnu: r-synchronicity: Update to 1.3.2. 
* gnu/packages/statistics.scm (r-synchronicity): Update to 1.3.2.
[propagated-inputs]: Add r-uuid.
 2018-02-13 16:18:44 +01:00
Ricardo Wurmus
8ff6853c13
gnu: r-irlba: Update to 2.3.2. 
* gnu/packages/statistics.scm (r-irlba): Update to 2.3.2.
 2018-02-13 16:18:44 +01:00
Ricardo Wurmus
a63117c8ae
gnu: r-dt: Update to 0.4. 
* gnu/packages/statistics.scm (r-dt): Update to 0.4.
[propagated-inputs]: Add r-crosstalk.
 2018-02-13 16:18:44 +01:00
Ricardo Wurmus
1324f85b43
gnu: r-rprojroot: Update to 1.3-2. 
* gnu/packages/statistics.scm (r-rprojroot): Update to 1.3-2.
 2018-02-13 16:18:44 +01:00
Ricardo Wurmus
edab1c049b
gnu: r-hms: Update to 0.4.1. 
* gnu/packages/statistics.scm (r-hms): Update to 0.4.1.
 2018-02-13 16:18:44 +01:00
Ricardo Wurmus
80f72101b4
gnu: r-withr: Update to 2.1.1. 
* gnu/packages/statistics.scm (r-withr): Update to 2.1.1.
[propagated-inputs]: Remove r-lattice.
 2018-02-13 16:18:44 +01:00
Ricardo Wurmus
ecba783c29
gnu: r-git2r: Update to 0.21.0. 
* gnu/packages/statistics.scm (r-git2r): Update to 0.21.0.
 2018-02-13 16:18:44 +01:00
Ricardo Wurmus
9fb6e62ef5
gnu: r-openssl: Update to 1.0. 
* gnu/packages/statistics.scm (r-openssl): Update to 1.0.
 2018-02-13 16:18:44 +01:00
Ricardo Wurmus
78e03a761c
gnu: r-xml2: Update to 1.2.0. 
* gnu/packages/statistics.scm (r-xml2): Update to 1.2.0.
[native-inputs]: Add pkg-config.
[propagated-inputs]: Remove r-bh.
[inputs]: Add zlib.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus
2afbaab56c
gnu: r-chron: Update to 2.3-52. 
* gnu/packages/statistics.scm (r-chron): Update to 2.3-52.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus
172b63e436
gnu: r-dbplyr: Update to 1.2.0. 
* gnu/packages/statistics.scm (r-dbplyr): Update to 1.2.0.
[propagated-inputs]: Add r-tidyselect.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus
59b62f197d
gnu: r-tibble: Update to 1.4.2. 
* gnu/packages/statistics.scm (r-tibble): Update to 1.4.2.
[propagated-inputs]: Add r-cli, r-crayon, and r-pillar; remove r-rcpp.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus
7387d35228
gnu: r-rlang: Update to 0.1.6. 
* gnu/packages/statistics.scm (r-rlang): Update to 0.1.6.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus
c36ac74005
gnu: r-microbenchmark: Update to 1.4-4. 
* gnu/packages/statistics.scm (r-microbenchmark): Update to 1.4-4.
[propagated-inputs]: Remove r-ggplot2.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus
ab3330e174
gnu: r-knitr: Update to 1.19. 
* gnu/packages/statistics.scm (r-knitr): Update to 1.19.
[propagated-inputs]: Remove r-digest.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus
d222070ad4
gnu: r-estimability: Update to 1.3. 
* gnu/packages/statistics.scm (r-estimability): Update to 1.3.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus
71d2f03be3
gnu: r-digest: Update to 0.6.15. 
* gnu/packages/statistics.scm (r-digest): Update to 0.6.15.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus
ff1197c86e
gnu: r-rpart: Update to 4.1-12. 
* gnu/packages/statistics.scm (r-rpart): Update to 4.1-12.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus
6aa4be9c3c
gnu: r-mgcv: Update to 1.8-23. 
* gnu/packages/statistics.scm (r-mgcv): Update to 1.8-23.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus
4c9264c1b9
gnu: r-mass: Update to 7.3-48. 
* gnu/packages/statistics.scm (r-mass): Update to 7.3-48.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus
97bf74076c
gnu: r-gprofiler: Update to 0.6.3. 
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.3.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus
169942368f
gnu: r-ensembldb: Update to 2.2.1. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.2.1.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus
34d077b8bc
gnu: r-gage: Update to 2.28.2. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.28.2.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus
f5f9442703
gnu: r-keggrest: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.18.1.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus
26e3e28cc9
gnu: r-seurat: Update to 2.2.0. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.2.0.
[propagated-inputs]: Remove r-ggjoy; add r-rcppeigen and r-ggridges.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
53f0dea9d7
gnu: r-msnbase: Update to 2.4.2. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.4.2.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
b1f2753627
gnu: r-methylkit: Update to 1.4.1. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.4.1.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
5ef76bc28c
gnu: r-gkmsvm: Update to 0.79.0. 
* gnu/packages/bioinformatics.scm (r-gkmsvm): Update to 0.79.0.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
0b24dc95b5
gnu: r-wgcna: Update to 1.62. 
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.62.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
e1129446ec
gnu: r-genomation: Update to 1.11.3. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.11.3.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
0b18856532
gnu: r-genomicfeatures: Update to 1.30.3. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.30.3.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
99b3236e65
gnu: r-rtracklayer: Update to 1.38.3. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.3.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
c37b361e44
gnu: r-summarizedexperiment: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.8.1.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
373430672d
gnu: r-biomart: Update to 2.34.2. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.34.2.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
024f19c68b
gnu: r-genomicranges: Update to 1.30.1. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.1.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
0674657908
gnu: r-limma: Update to 3.34.8. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.8.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
5fb1fee67b
gnu: r-variantannotation: Update to 1.24.5. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.24.5.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
d22abe1e5d
gnu: r-edger: Update to 3.20.8. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.8.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
66ae706c24
gnu: r-bookdown: Update to 0.6. 
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.6.
[propagated-inputs]: Add r-xfun and ghc-pandoc.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus
2e9da3390c
gnu: r-vegan: Update to 2.4-6. 
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-6.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus
0f001b3c5a
gnu: r-drr: Update to 0.0.3. 
* gnu/packages/cran.scm (r-drr): Update to 0.0.3.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus
92e4534ca8
gnu: r-lava: Update to 1.6. 
* gnu/packages/cran.scm (r-lava): Update to 1.6.
[propagated-inputs]: Add r-squarem.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus
093acd0de1
gnu: r-sp: Update to 1.2-7. 
* gnu/packages/cran.scm (r-sp): Update to 1.2-7.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus
de1c0332d9
gnu: r-proxy: Update to 0.4-21. 
* gnu/packages/cran.scm (r-proxy): Update to 0.4-21.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus
e30b878ec8
gnu: r-hexbin: Update to 1.27.2. 
* gnu/packages/statistics.scm (r-hexbin): Update to 1.27.2.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus
64fe220cbe
gnu: r-dendextend: Update to 1.7.0. 
* gnu/packages/cran.scm (r-dendextend): Update to 1.7.0.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus
cb471b7eaa
gnu: r-ddalpha: Update to 1.3.1.1. 
* gnu/packages/cran.scm (r-ddalpha): Update to 1.3.1.1.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus
1d13426bed
gnu: r-recipes: Update to 0.1.2. 
* gnu/packages/cran.scm (r-recipes): Update to 0.1.2.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus
637584253f
gnu: r-pracma: Update to 2.1.4. 
* gnu/packages/maths.scm (r-pracma): Update to 2.1.4.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus
1c7919251a
gnu: Add r-uuid. 
* gnu/packages/cran.scm (r-uuid): New variable.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus
c555ccabcf
gnu: Add r-pillar. 
* gnu/packages/cran.scm (r-pillar): New variable.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus
f244296822
gnu: Add r-utf8. 
* gnu/packages/cran.scm (r-utf8): New variable.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus
c5f033e0f6
gnu: Add r-squarem. 
* gnu/packages/cran.scm (r-squarem): New variable.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus
fe5b889365
gnu: r-shape: Update to 1.4.4. 
* gnu/packages/cran.scm (r-shape): Update to 1.4.4.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus
33d8699da5
gnu: r-rcpp: Update to 0.12.15. 
* gnu/packages/cran.scm (r-rcpp): Update to 0.12.15.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus
f6d2b45ca8
gnu: Add r-xfun. 
* gnu/packages/cran.scm (r-xfun): New variable.
 2018-02-13 16:18:41 +01:00
Leo Famulari
77737e0354
gnu: unzip: Mitigate CVE-2018-1000035. 
* gnu/packages/compression.scm (unzip)[replacement]: New field.
(unzip/fixed): New variable.
 2018-02-13 09:51:07 -05:00
Ricardo Wurmus
ad5de226e7
gnu: Add ghc-megaparsec. 
* gnu/packages/haskell.scm (ghc-megaparsec): New variable.
 2018-02-13 13:37:41 +01:00
Ricardo Wurmus
aeecabd43c
gnu: Add ghc-parser-combinators. 
* gnu/packages/haskell.scm (ghc-parser-combinators): New variable.
 2018-02-13 13:37:41 +01:00
Ricardo Wurmus
f941a52a14
gnu: Add ghc-text-binary. 
* gnu/packages/haskell.scm (ghc-text-binary): New variable.
 2018-02-13 13:37:41 +01:00
Ricardo Wurmus
183d1b1aaf
gnu: ghc-trifecta: Update to 1.7.1.1. 
* gnu/packages/haskell.scm (ghc-trifecta): Update to 1.7.1.1.
[inputs]: Add ghc-doctest.
[native-inputs]: Add cabal-doctest.
 2018-02-13 13:37:41 +01:00
Ricardo Wurmus
2815963b8d
gnu: ghc-reducers: Update to 3.12.2. 
* gnu/packages/haskell.scm (ghc-reducers): Update to 3.12.2.
 2018-02-13 13:37:41 +01:00
Ricardo Wurmus
67e86e58e0
gnu: ghc-directory: Add note. 
* gnu/packages/haskell.scm (ghc-directory): Add comment not to use this
package as an input.
 2018-02-13 13:37:41 +01:00
Ricardo Wurmus
0498d1689d
gnu: darcs: Update to 2.12.5. 
* gnu/packages/version-control.scm (darcs): Update to 2.12.5.
[arguments]: Relax version constraint on shelly.
 2018-02-13 13:37:41 +01:00
Ricardo Wurmus
97bfe0d759
gnu: darcs: Remove ghc-directory from inputs. 
* gnu/packages/version-control.scm (darcs)[inputs]: Remove ghc-directory.
 2018-02-13 13:37:41 +01:00
Ricardo Wurmus
4b1f2166fe
gnu: ghc-graphviz: Fix build with newer QuickCheck. 
* gnu/packages/haskell.scm (ghc-graphviz)[arguments]: Allow building with
newer QuickCheck.
 2018-02-13 13:37:41 +01:00
Ricardo Wurmus
f25c95d384
gnu: ghc-tar: Disable tests. 
* gnu/packages/haskell.scm (ghc-tar)[arguments]: Disable tests.
 2018-02-13 13:37:41 +01:00
Ricardo Wurmus
1b58d289fd
gnu: ghc-system-filepath: Update to 0.4.14. 
* gnu/packages/haskell.scm (ghc-system-filepath): Update to 0.4.14.
[arguments]: Disable tests.
 2018-02-13 13:37:41 +01:00