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Author SHA1 Message Date
Ricardo Wurmus 3d352cb9cf
gnu: Add python-sortedcontainers. 
* gnu/packages/python.scm (python-sortedcontainers): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 098cb1e9c4
gnu: Add python-cytoolz. 
* gnu/packages/python.scm (python-cytoolz): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 7cd51cd28e
gnu: Add python-toolz. 
* gnu/packages/python.scm (python-toolz): New variable.
 2018-09-10 16:50:25 +02:00
Ricardo Wurmus 943a4cb601
gnu: Add python-multiprocess. 
* gnu/packages/python.scm (python-multiprocess): New variable.
 2018-09-10 16:50:25 +02:00
Ricardo Wurmus fc62567251
gnu: Add python-dill. 
* gnu/packages/python.scm (python-dill): New variable.
 2018-09-10 16:50:25 +02:00
Tobias Geerinckx-Rice 82d5c7c6de
gnu: python-typing: Update to 3.6.6. 
* gnu/packages/python.scm (python-typing): Update to 3.6.6.
 2018-09-10 15:29:13 +02:00
Tobias Geerinckx-Rice 419aa05e1b
gnu: tinyproxy: Update to 1.10.0. 
* gnu/packages/web.scm (tinyproxy): Update to 1.10.0.
[native-inputs]: Remove asciidoc.
 2018-09-10 15:29:12 +02:00
Tobias Geerinckx-Rice f6c8a97a04
gnu: spectrwm: Update to 3.2.0. 
* gnu/packages/wm.scm (spectrwm): Update to 3.2.0.
[arguments]: Remove 'fix-freetype-include' phase.
 2018-09-10 15:29:12 +02:00
Mădălin Ionel Patrașcu 57d70dbabc
gnu: Add yad. 
* gnu/packages/gtk.scm (yad): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2018-09-10 14:45:15 +02:00
Ludovic Courtès 94b3b6041d
gnu: hpcguix-web: Update to 53e09ea. 
* gnu/packages/web.scm (hpcguix-web): Update to 53e09ea.
 2018-09-10 12:18:14 +02:00
Ludovic Courtès 81317071fb
services: hpcguix-web: Produce a log file and rotate it. 
* gnu/services/web.scm (%hpcguix-web-log-file)
(%hpcguix-web-log-rotations): New variables.
(hpcguix-web-shepherd-service): Pass #:log-file.
(hpcguix-web-service-type): Extend ROTTLOG-SERVICE-TYPE.
 2018-09-10 12:12:52 +02:00
Ludovic Courtès 19de8273ee
services: tailon: Move to (gnu services web). 
This allows (gnu services admin) to remain deeper in the module graph
and to be used by (gnu services web).

* gnu/services/admin.scm (<tailon-configuration-file>)
(tailon-configuration-files-string)
(tailon-configuration-file-compiler, <tailon-configuration>)
(tailon-shepherd-service, %tailon-accounts)
(tailon-service-type): Move to...
* gnu/services/web.scm: ... here.
* gnu/tests/admin.scm: Remove.  Move test to...
* gnu/tests/web.scm (%tailon-os)
(run-tailon-test, %test-tailon): ... here.
 2018-09-10 12:12:50 +02:00
Alex Vong d930374014
gnu: youtube-dl: Update to 2018.08.04. 
* gnu/packages/video.scm (youtube-dl): Update to 2018.08.04.
 2018-09-10 11:31:34 +02:00
Leo Famulari de15ff1a6c
gnu: Add asignify. 
* gnu/packages/crypto.scm (asignify): New variable.
 2018-09-09 20:05:47 -04:00
Leo Famulari d4bd2453ec
gnu: certbot: Update to 0.27.1. 
* gnu/packages/tls.scm (python-acme): Update to 0.27.1.
[arguments]: Use invoke.
(certbot): Update to 0.27.1.
[native-inputs]: Use python-sphinx-1.6.
 2018-09-09 18:52:04 -04:00
Leo Famulari ced98c7e89
gnu: libgd: Fix CVE-2018-{5711,1000222}. 
* gnu/packages/patches/gd-CVE-2018-1000222.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gd.scm (gd/fixed): New variable.
* gnu/packages/php.scm (gd-for-php)[source]: Use 'gd-CVE-2018-1000222.patch'.
 2018-09-09 18:13:19 -04:00
Ricardo Wurmus 45350539aa
gnu: r-chron: Update to 2.3-53. 
* gnu/packages/statistics.scm (r-chron): Update to 2.3-53.
 2018-09-09 22:26:02 +02:00
Ricardo Wurmus ab50580a9d
gnu: r-annotationhub: Update to 2.12.1. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.12.1.
 2018-09-09 22:26:02 +02:00
Ricardo Wurmus 35c076e619
gnu: r-chippeakanno: Update to 3.14.2. 
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.14.2.
 2018-09-09 22:26:02 +02:00
Roel Janssen c36d972531
gnu: Update texmaker to 5.0.2. 
* gnu/packages/tex.scm (texmaker): Update to 5.0.2.
 2018-09-09 21:59:08 +02:00
Marius Bakke 0084744b3a
gnu: ghostscript: Update replacement to 9.24 [security fixes]. 
The following CVEs are fixed with this release: CVE-2018-15908,
CVE-2018-15909, CVE-2018-15910, CVE-2018-15911, CVE-2018-16509,
CVE-2018-16510, CVE-2018-16511, CVE-2018-16513, CVE-2018-16539,
CVE-2018-16540, CVE-2018-16541, CVE-2018-16542, CVE-2018-16543.

* gnu/packages/patches/ghostscript-CVE-2018-10194.patch: Delete file.
* gnu/packages/patches/ghostscript-CVE-2018-16509.patch,
gnu/packages/patches/ghostscript-bug-699708.patch: New files.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/ghostscript.scm (ghostscript/fixed): Update to 9.24.
[source](patches): Remove 'ghostscript-CVE-2018-10194.patch' and
'ghostscript-runpath.patch'.  Add 'ghostscript-CVE-2018-16509.patch' and
'ghostscript-bug-699708.patch'.
[arguments]: Add LDFLAGS to #:configure-flags, and a phase to create output
directory.
 2018-09-09 16:43:11 +02:00
Marius Bakke 910a20e2b8
gnu: jbig2dec: Replace with 0.15 [security fixes]. 
* gnu/packages/image.scm (jbig2dec-0.15): New public variable.
(jbig2dec)[replacement]: New field.
 2018-09-09 16:43:11 +02:00
Marius Bakke a617fd55df
gnu: OpenBLAS: Update source URI. 
* gnu/packages/maths.scm (openblas)[source](uri): Use the more stable
SourceForge mirror.
 2018-09-09 16:43:11 +02:00
Marius Bakke 1448fa2547
gnu: openal: Update to 1.19.0. 
* gnu/packages/audio.scm (openal): Update to 1.19.0.
 2018-09-09 16:43:11 +02:00
Marius Bakke e9c1492f66
gnu: glm: Update to 0.9.9.1. 
* gnu/packages/maths.scm (glm): Update to 0.9.9.1.
 2018-09-09 16:43:10 +02:00
Marius Bakke 91b3a6d4db
gnu: msmtp: Remove unneeded input. 
* gnu/packages/mail.scm (msmtp)[inputs]: Remove LIBIDN, which is only required
when using OpenSSL (or GnuTLS sans IDN support).
 2018-09-09 16:43:10 +02:00
Marius Bakke 37f9cfae43
gnu: msmtp: Update to 1.8.0. 
* gnu/packages/mail.scm (msmtp): Update to 1.8.0.
 2018-09-09 16:43:10 +02:00
Marius Bakke 249846bfde
gnu: libsoup: Update to 2.64.0. 
* gnu/packages/gnome.scm (libsoup): Update to 2.64.0.
[inputs]: Add LIBPSL.
 2018-09-09 16:43:10 +02:00
Marius Bakke 617cf5de92
gnu: mpfr: Update home page. 
* gnu/packages/multiprecision.scm (mpfr)[home-page]: Use HTTPS.
 2018-09-09 16:43:10 +02:00
Marius Bakke 81bf0fd0d4
gnu: julia: Update objconv input. 
* gnu/packages/julia.scm (julia)[inputs]: Update the hash of "objconv", which
does not have a stable URL.  Add a file name and use HTTPS while at it.
 2018-09-09 16:43:10 +02:00
Tobias Geerinckx-Rice b64e67ad40
gnu: cloc: Update to 1.78. 
* gnu/packages/code.scm (cloc): Update to 1.78.
[source]: Update URI.
 2018-09-09 15:01:55 +02:00
Tobias Geerinckx-Rice c2311644a5
gnu: signify: Update to 24. 
* gnu/packages/crypto.scm (signify): Update to 24.
 2018-09-09 15:01:54 +02:00
Tobias Geerinckx-Rice bb105673b8
gnu: musl: Update to 1.1.20. 
* gnu/packages/musl.scm (musl): Update to 1.1.20.
 2018-09-09 15:01:54 +02:00
Tobias Geerinckx-Rice bb5e06a35e
gnu: perl-pegex: Update to 0.67. 
* gnu/packages/perl.scm (perl-pegex): Update to 0.67.
 2018-09-09 15:01:54 +02:00
Tobias Geerinckx-Rice 9ad80992d0
gnu: perl-config-autoconf: Update to 0.317. 
* gnu/packages/perl.scm (perl-config-autoconf): Update to 0.317.
 2018-09-09 15:01:53 +02:00
Tobias Geerinckx-Rice 15dbc911f6
gnu: perl-extutils-installpaths: Update to 0.012. 
* gnu/packages/perl.scm (perl-extutils-installpaths): Update to 0.012.
 2018-09-09 15:01:53 +02:00
Tobias Geerinckx-Rice 4e77b75e11
gnu: perl-extutils-helpers: Update to 0.026. 
* gnu/packages/perl.scm (perl-extutils-helpers): Update to 0.026.
 2018-09-09 15:01:53 +02:00
Tobias Geerinckx-Rice 748e6e1271
gnu: perl-getopt-long-descriptive: Update to 0.103. 
* gnu/packages/perl.scm (perl-getopt-long-descriptive): Update to 0.103.
 2018-09-09 15:01:53 +02:00
Tobias Geerinckx-Rice 04fc0b9489
gnu: perl-namespace-clean: Update to 0.27. 
* gnu/packages/perl.scm (perl-namespace-clean): Update to 0.27.
 2018-09-09 15:01:52 +02:00
Tobias Geerinckx-Rice 49e63e3884
gnu: perl-datetime: Update to 1.50. 
* gnu/packages/perl.scm (perl-datetime): Update to 1.50.
 2018-09-09 15:01:52 +02:00
Tobias Geerinckx-Rice 2d32a6572d
gnu: perl-params-validate: Update to 1.29. 
* gnu/packages/perl.scm (perl-params-validate): Update to 1.29.
 2018-09-09 15:01:52 +02:00
Tobias Geerinckx-Rice a0fad0374e
gnu: links: Update to 2.17. 
* gnu/packages/web-browsers.scm (links): Update to 2.17.
 2018-09-09 15:01:52 +02:00
Tobias Geerinckx-Rice b9114ccbad
gnu: aircrack-ng: Update to 1.3. 
* gnu/packages/networking.scm (aircrack-ng): Update to 1.3.
[native-inputs]: Add autoconf, automake, libtool, and which.
[inputs]: Add libpcap.
[arguments]: Use conventional --options in #:configure-flags.
Restore ‘configure’ phase. Add ‘patch-evalrev’ and customise ‘bootstrap’
phases. Simplify ‘absolutize-tools’ phase.
 2018-09-09 14:50:34 +02:00
Tobias Geerinckx-Rice 6930ea33c9
gnu: aircrack-ng: Use HTTPS. 
* gnu/packages/networking.scm (aircrack-ng)[source, home-page]: Use HTTPS.
 2018-09-09 14:50:34 +02:00
宋文武 d7f99b3b76
gnu: perl: Improve description. 
Fixes <https://bug.gnu.org/32650>.

* gnu/packages/perl.scm (perl)[description]: Use description from 'perlintro'.
 2018-09-09 19:11:52 +08:00
Ludovic Courtès 4ab6a2f23d
tests: base: Add Guile-Gcrypt & co. to the search path. 
Fixes a regression introduced in
ca71942445, whereby (gcrypt hash) would
not be found in the system under test, leading to a failure of the
"/run/current-system is a GC root" test.

* gnu/tests/base.scm (run-basic-test)[guix&co]: New variable.
[test]: Add all of GUIX&CO to %LOAD-PATH.
 2018-09-08 23:02:01 +02:00
Ludovic Courtès e80c725db7
services: nginx: 'stop' returns #f. 
Previously we'd return #t, which the Shepherd would consider a failure
to stop the service.

* gnu/services/web.scm (nginx-shepherd-service): In 'nginx-action',
return #f when stopping the service.
 2018-09-08 23:02:00 +02:00
Ludovic Courtès 985975ae80
services: nginx: Don't read PID file when passed a custom config file. 
Fixes <https://bugs.gnu.org/32665>.

* gnu/services/web.scm (nginx-shepherd-service): Check whether FILE is
true and don't read the PID file if it is; use 'read-pid-file' instead
of a potentially endless loop.
 2018-09-08 23:02:00 +02:00
Jan Nieuwenhuizen c665774a1c
gnu: mes: Update to 0.17.1. 
* gnu/packages/patches/mes-nyacc-0.86.0.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/mes.scm (mes): Update to 0.17.1, depend on latest Nyacc 0.86.0.
(nyacc-for-mes): Remove.
 2018-09-08 20:36:30 +02:00
Jan Nieuwenhuizen 445ecce923
gnu: nyacc: Update to 0.86.0. 
* gnu/packages/patches/nyacc-binary-literals.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/mes.scm (nyacc): Update to 0.86.0, add patch.
 2018-09-08 20:36:30 +02:00
Benjamin Slade 39b5d8fd9d
gnu: Add frotz, frotz-dumb-terminal, and frotz-sdl. 
* gnu/packages/games.scm (frotz, frotz-dumb-terminal, frotz-sdl): New
variables.

Signed-off-by: Kei Kebreau <kkebreau@posteo.net>
 2018-09-08 13:41:10 -04:00
Mark H Weaver 090e3768e8
gnu: linux-libre: Update to 4.18.6. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.6.
(%linux-libre-hash): Update hash.
 2018-09-07 21:05:14 -04:00
Mark H Weaver 4be8fdd3cc
gnu: linux-libre@4.14: Update to 4.14.68. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.68.
(%linux-libre-4.14-hash): Update hash.
 2018-09-07 21:03:03 -04:00
Mark H Weaver ddb419ce04
gnu: linux-libre@4.9: Update to 4.9.125. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.125.
 2018-09-07 21:02:30 -04:00
Mark H Weaver 48d17ba1d3
gnu: linux-libre@4.4: Update to 4.4.154. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.154.
 2018-09-07 21:01:48 -04:00
Ludovic Courtès 9b6c435564
services: 'instantiate-missing-services' reaches fixed point. 
Fixes a bug whereby services indirectly depended on would not be
automatically instantiated.

* gnu/services.scm (instantiate-missing-services): Loop back when the
length of ADJUSTED is greater than that of INSTANCES.
* tests/services.scm ("instantiate-missing-services, indirect"): New test.
 2018-09-07 23:00:39 +02:00
Ludovic Courtès 9f1f200c04
gnu: diffoscope: Update to 100. 
* gnu/packages/package-management.scm (diffoscope): Update to 100.
 2018-09-07 17:59:16 +02:00
Ludovic Courtès afdd1555c4
gnu: indent: Add version 2.2.12. 
* gnu/packages/code.scm (indent-2.2.12): New variable.
 2018-09-07 17:57:04 +02:00
Ludovic Courtès 6b4f99102c
gnu: gdb: Update to 8.2. 
* gnu/packages/gdb.scm (gdb): Update to 8.2.
 2018-09-07 17:55:55 +02:00
Ludovic Courtès 15214828a5
gnu: guile-json: Update to 1.2.0. 
* gnu/packages/guile.scm (guile-json): Update to 1.2.0.
[license]: Change to GPL3+.
 2018-09-07 17:55:51 +02:00
pimi 214452ffd3
gnu: Add r-ggformula. 
* gnu/packages/cran.scm (r-ggformula): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-07 11:40:06 +02:00
pimi c61f7bc543
gnu: Add r-mosaiccore. 
* gnu/packages/cran.scm (r-mosaiccore): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-07 11:40:06 +02:00
pimi 77b33e0ede
gnu: Add r-ggstance. 
gnu/packages/cran.scm (r-ggstance): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-07 11:40:06 +02:00
pimi 12da2a5e58
gnu: Add r-abctools. 
* gnu/packages/cran.scm (r-abctools): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-07 11:40:06 +02:00
pimi cadc10a513
gnu: Add r-abcrf. 
* gnu/packages/cran.scm (r-abcrf): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-07 11:40:06 +02:00
pimi 40c10917bc
gnu: Add r-abcp2. 
* gnu/packages/cran.scm (r-abcp2): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-07 11:40:06 +02:00
Alex Branham 12498b59e7
gnu: emacs-ess: Update to 17.11. 
* gnu/packages/emacs.scm (emacs-ess): Update to 17.11
[url]: Use github for https
[snippet]: update julia-mode substitution, only build info doc, bypass failing test
[propagated-inputs]: Add emacs-julia-mode
[description]: Mention that ESS supports Julia and JAGS (which replaces OpenBUGS)
[arguments]: Remove 'set-home' phase.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-07 11:40:06 +02:00
Ludovic Courtès 1540075c79
vm: Make UUID computation really deterministic. 
Fixes <https://bugs.gnu.org/32652>.

* gnu/system/vm.scm (operating-system-uuid)[service-name,
file-system-digest]: New procedures.
Map these over services and file systems and hash the result.
* tests/guix-system.sh: Add test.
 2018-09-07 11:40:05 +02:00
Tobias Geerinckx-Rice 0012e0dd56
gnu: knot: Update to 2.7.2. 
* gnu/packages/dns.scm (knot): Update to 2.7.2.
 2018-09-07 03:01:40 +02:00
Leo Famulari 91cc2a38de
gnu: Wireshark: Update to 2.6.3 [fixes CVE-2018-{14994,16056,16057,16058}]. 
* gnu/packages/networking.scm (wireshark): Update to 2.6.3.
 2018-09-06 17:05:42 -04:00
Leo Famulari 1e066f0706
gnu: curl: Update replacement to 7.61.1 [fixes CVE-2018-14618]. 
* gnu/packages/curl.scm (curl)[replacement]: Update to 7.61.1.
(curl-7.61.0): Replace variable with ...
(curl-7.61.1): ... new variable.
 2018-09-06 17:02:52 -04:00
Kei Kebreau 21f5f351fb
gnu: libgme: Update to 0.6.2. 
* gnu/packages/music.scm (libgme): Update to 0.6.2.
[native-inputs]: Add gcc-4.9.
 2018-09-06 11:01:52 -04:00
Ludovic Courtès 7df945656c
services: hpcguix-web: Set SSL_CERT_DIR. 
Previously Git pulls over HTTPS would fail with:

  guix/git.scm:132:7: In procedure update-cached-checkout:
  Throw to key `git-error' with args `(#<<git-error> code: -17 message: "the SSL certificate is invalid" class: 16>)'.

* gnu/services/web.scm (hpcguix-web-shepherd-service): Pass
"SSL_CERT_DIR=/etc/ssl/certs".
* doc/guix.texi (Web Services): Mention certificates.
 2018-09-06 13:49:06 +02:00
Eric Brown f66be84d08
gnu: gfortran, gcc-objc, gcc-objc++: Add version 8. 
* gnu/packages/gcc.scm (gfortran-8, gcc-objc-8, gcc-objc++-8): New
variables.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-06 11:12:40 +02:00
Ludovic Courtès b290a631a0
gnu: guile-present: Install .go files to libdir. 
* gnu/packages/plotutils.scm (guile-present)[source](modules, snippet):
Remove.
 2018-09-06 10:49:42 +02:00
Ludovic Courtès 89874fd156
gnu: guile-charting: Install .go files to libdir. 
* gnu/packages/plotutils.scm (guile-charting)[source](modules, snippet):
Remove.
 2018-09-06 10:48:44 +02:00
Ludovic Courtès b3ca2d8883
gnu: hpcguix-web: Update to 9ff40fc. 
* gnu/packages/web.scm (hpcguix-web): Update to 9ff40fc.
[arguments]: In 'wrap-program' phase, add guile-gcrypt, guile-git, and
guile-bytestructures to DEPS.
 2018-09-06 10:46:07 +02:00
Ludovic Courtès 96d6c41dfa
gnu: guile-commonmark: Install .go files to libdir. 
* gnu/packages/guile.scm (guile-commonmark)[source](snippet): Change the
"modir = " and "godir = " line separately, allowing .go files to be
installed to $(libdir).
 2018-09-06 10:43:01 +02:00
Ricardo Wurmus d53aeeafcc
Add missing use-modules clause. 
This is a follow-up to commit 5dfe491290.
Sorry!

* gnu/packages/bioinformatics.scm, gnu/packages/graph.scm: Use (gnu packages
bioconductor).
 2018-09-06 04:53:32 +02:00
Tobias Geerinckx-Rice 79b283e433
gnu: ccache: Update to 3.4.3. 
* gnu/packages/ccache.scm (ccache): Update to 3.4.3.
[arguments]: Remove obsolete 'munge-failing-test' phase.
 2018-09-06 02:33:47 +02:00
Tobias Geerinckx-Rice d83477adf9
gnu: font-fira-code: Update to 1.205. 
* gnu/packages/fonts.scm (font-fira-code): Update to 1.205.
 2018-09-06 02:33:47 +02:00
Tobias Geerinckx-Rice a5c70c2e0e
gnu: libmpdclient: Update to 2.15. 
* gnu/packages/mpd.scm (libmpdclient): Update to 2.15.
 2018-09-06 02:33:47 +02:00
Ricardo Wurmus 00a43cb81c
gnu: pigx-scrnaseq: Use latest version of Pandoc. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus c2b4f81e51
gnu: pigx-bsseq: Use latest version of Pandoc. 
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus 7cd40c8c5d
gnu: pigx-chipseq: Use latest version of Pandoc. 
* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus ca248f1db9
gnu: pigx-rnaseq: Use latest version of Pandoc. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus dff5640a59
gnu: r-rcas: Use standard version of ghc-pandoc-citeproc. 
* gnu/packages/bioinformatics.scm (r-rcas)[native-inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc".
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus f33a4748b7
gnu: r-modelmetrics: Update to 1.2.0. 
* gnu/packages/statistics.scm (r-modelmetrics): Update to 1.2.0.
[propagated-inputs]: Add r-data-table.
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus 0d279d607a
gnu: r-robustbase: Update to 0.93-2. 
* gnu/packages/statistics.scm (r-robustbase): Update to 0.93-2.
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus 8e499d756a
gnu: r-rann: Update to 2.6. 
* gnu/packages/statistics.scm (r-rann): Update to 2.6.
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus 314e8e763f
gnu: r-ggthemes: Update to 4.0.1. 
* gnu/packages/statistics.scm (r-ggthemes): Update to 4.0.1.
[propagated-inputs]: Remove r-assertthat and r-colorspace; add r-purrr,
r-stringr, and r-tibble.
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus e5db6890ad
gnu: r-ztable: Update to 0.2.0. 
* gnu/packages/statistics.scm (r-ztable): Update to 0.2.0.
[propagated-inputs]: Add r-flextable, r-magrittr, r-moonbook, r-officer,
r-rcolorbrewer, r-scales, and r-stringr.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus f0519c8fae
gnu: r-zoo: Update to 1.8-3. 
* gnu/packages/statistics.scm (r-zoo): Update to 1.8-3.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 8da236a377
gnu: r-gtools: Update to 3.8.1. 
* gnu/packages/statistics.scm (r-gtools): Update to 3.8.1.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus c28d8d8db0
gnu: r-kernlab: Update to 0.9-27. 
* gnu/packages/machine-learning.scm (r-kernlab): Update to 0.9-27.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus c0608f815c
gnu: r-adaptivesparsity: Update to 1.6. 
* gnu/packages/machine-learning.scm (r-adaptivesparsity): Update to 1.6.
[propagated-inputs]: Add r-mass and r-matrix.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus a207bca2ad
gnu: r-codedepends: Move from cran to bioconductor. 
* gnu/packages/cran.scm (r-codedepends): Move from here...
* gnu/packages/bioconductor.scm (r-codedepends): ...to here.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 5dfe491290
gnu: r-graph: Move from bioinformatics to bioconductor. 
* gnu/packages/bioinformatics.scm (r-graph): Move from here...
* gnu/packages/bioconductor.scm (r-graph): ...to here.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus caaec88651
gnu: r-ggpubr: Update to 0.1.8. 
* gnu/packages/cran.scm (r-ggpubr): Update to 0.1.8.
[propagated-inputs]: Add r-glue and r-polynom.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus a9b02ddd73
gnu: r-codedepends: Update to 0.6.5. 
* gnu/packages/cran.scm (r-codedepends): Update to 0.6.5.
[propagated-inputs]: Add r-graph.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 2e6909baf0
gnu: r-later: Update to 0.7.4. 
* gnu/packages/cran.scm (r-later): Update to 0.7.4.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 12132229b0
gnu: r-maptools: Update to 0.9-3. 
* gnu/packages/cran.scm (r-maptools): Update to 0.9-3.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 7a96c4e0a0
gnu: r-fnn: Update to 1.1.2.1. 
* gnu/packages/cran.scm (r-fnn): Update to 1.1.2.1.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 19950821d7
gnu: r-heatmaply: Update to 0.15.2. 
* gnu/packages/cran.scm (r-heatmaply): Update to 0.15.2.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus 1fe9919a57
gnu: r-tsa: Update to 1.2. 
* gnu/packages/cran.scm (r-tsa): Update to 1.2.
[propagated-inputs]: Remove r-tseries.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus be5642eb69
gnu: r-statnet-common: Update to 4.1.4. 
* gnu/packages/cran.scm (r-statnet-common): Update to 4.1.4.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus e32368c130
gnu: r-metap: Update to 1.0. 
* gnu/packages/cran.scm (r-metap): Update to 1.0.
[propagated-inputs]: Add r-rdpack.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus d97d98e142
gnu: r-tinytex: Update to 0.8. 
* gnu/packages/cran.scm (r-tinytex): Update to 0.8.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 6f5b157e3d
gnu: r-pillar: Update to 1.3.0. 
* gnu/packages/cran.scm (r-pillar): Update to 1.3.0.
[propagated-inputs]: Add r-fansi.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 69bf449bf1
gnu: r-xts: Update to 0.11-0. 
* gnu/packages/cran.scm (r-xts): Update to 0.11-0.
[native-inputs]: Remove.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 1b3b2a72ee
gnu: r-mice: Update to 3.3.0. 
* gnu/packages/cran.scm (r-mice): Update to 3.3.0.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus a7265593d3
gnu: r-pan: Update to 1.6. 
* gnu/packages/cran.scm (r-pan): Update to 1.6.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus e7630cc931
gnu: r-jomo: Update to 2.6-4. 
* gnu/packages/cran.scm (r-jomo): Update to 2.6-4.
[propagated-inputs]: Add r-ordinal.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus b8f6e2f82a
gnu: Add r-ordinal. 
* gnu/packages/cran.scm (r-ordinal): New variable.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus dc66835226
gnu: Add r-ucminf. 
* gnu/packages/cran.scm (r-ucminf): New variable.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 45c156bf81
gnu: r-broom: Update to 0.5.0. 
* gnu/packages/cran.scm (r-broom): Update to 0.5.0.
[propagated-inputs]: Add r-backports, r-dplyr, r-purrr, and r-tibble; remove
r-plyr and r-psych.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 2d2b95d151
gnu: r-ipred: Update to 0.9-7. 
* gnu/packages/cran.scm (r-ipred): Update to 0.9-7.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus c73752cac5
gnu: r-pls: Update to 2.7-0. 
* gnu/packages/cran.scm (r-pls): Update to 2.7-0.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus b00e8ae771
gnu: r-glue: Update to 1.3.0. 
* gnu/packages/cran.scm (r-glue): Update to 1.3.0.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus b72de5b3f6
gnu: r-callr: Update to 3.0.0. 
* gnu/packages/cran.scm (r-callr): Update to 3.0.0.
[propagated-inputs]: Add r-base64enc.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus e3c1e93e35
gnu: r-reprex: Update to 0.2.0. 
* gnu/packages/cran.scm (r-reprex): Update to 0.2.0.
[propagated-inputs]: Add r-clipr, r-rlang, and r-withr.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 2cdd9d4f83
gnu: r-reticulate: Update to 1.10. 
* gnu/packages/cran.scm (r-reticulate): Update to 1.10.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus cb96d81be4
gnu: r-doby: Update to 4.6-2. 
* gnu/packages/cran.scm (r-doby): Update to 4.6-2.
 2018-09-05 20:03:07 +02:00
Ricardo Wurmus 589bd1c426
gnu: Add r-flextable. 
* gnu/packages/cran.scm (r-flextable): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus 78f2c08c0b
gnu: r-rmarkdown: Use latest version of Pandoc. 
* gnu/packages/statistics.scm (r-rmarkdown)[propagated-inputs]: Replace
"ghc-pandoc-1" with "ghc-pandoc".
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus f9f4578ba0
Revert "gnu: ghc-tasty: Update to 1.1.0.3." 
This reverts commit 3ad6b89090.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus 90708323a1
Revert "gnu: ghc-base-compat: Update to 0.10.4." 
This reverts commit 0fa2c552fc.

We may not upgrade base-compat at this point because we haven't upgraded the
default GHC yet.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus 0fd7d59dc3
gnu: Add r-moonbook. 
* gnu/packages/cran.scm (r-moonbook): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus aaed237d1b
gnu: Add r-nortest. 
* gnu/packages/cran.scm (r-nortest): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus 1f560b9cdb
gnu: Add r-sjmisc. 
* gnu/packages/cran.scm (r-sjmisc): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus cfc0631433
gnu: Add r-sjlabelled. 
* gnu/packages/cran.scm (r-sjlabelled): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus de059e4bd3
gnu: Add r-prediction. 
* gnu/packages/cran.scm (r-prediction): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus bfee9ce88f
gnu: Add r-snakecase. 
* gnu/packages/cran.scm (r-snakecase): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus c183fa2688
gnu: Add r-officer. 
* gnu/packages/cran.scm (r-officer): New variable.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus 5dbe7aa920
gnu: r-googlesheets: Update to 0.3.0. 
* gnu/packages/statistics.scm (r-googlesheets): Update to 0.3.0.
[propagated-inputs]: Add r-tibble.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus 88cb7aa9e7
gnu: r-plotly: Update to 4.8.0. 
* gnu/packages/statistics.scm (r-plotly): Update to 4.8.0.
[propagated-inputs]: Add r-promises and r-rlang.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus 195eec737c
gnu: r-matrixstats: Update to 0.54.0. 
* gnu/packages/statistics.scm (r-matrixstats): Update to 0.54.0.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus e2a2c3378e
gnu: r-r-rsp: Update to 0.43.0. 
* gnu/packages/statistics.scm (r-r-rsp): Update to 0.43.0.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus eefa7c7f3d
gnu: r-r-utils: Update to 2.7.0. 
* gnu/packages/statistics.scm (r-r-utils): Update to 2.7.0.
 2018-09-05 20:03:06 +02:00
Ricardo Wurmus e926159eb3
gnu: r-e1071: Update to 1.7-0. 
* gnu/packages/statistics.scm (r-e1071): Update to 1.7-0.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 2aafa73a94
gnu: r-xml: Update to 3.98-1.16. 
* gnu/packages/statistics.scm (r-xml): Update to 3.98-1.16.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 41f6685388
gnu: r-rcpparmadillo: Update to 0.9.100.5.0. 
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.100.5.0.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 19cb93be55
gnu: r-git2r: Update to 0.23.0. 
* gnu/packages/statistics.scm (r-git2r): Update to 0.23.0.
[native-inputs]: Add pkg-config.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 2848c52c5e
gnu: r-roxygen2: Update to 6.1.0. 
* gnu/packages/statistics.scm (r-roxygen2): Update to 6.1.0.
[propagated-inputs]: Add r-pkgload and r-purrr.
[native-inputs]: Add r-knitr.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 9b7e8df85b
gnu: r-ade4: Update to 1.7-13. 
* gnu/packages/statistics.scm (r-ade4): Update to 1.7-13.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 7f38b31ecb
gnu: r-xtable: Update to 1.8-3. 
* gnu/packages/statistics.scm (r-xtable): Update to 1.8-3.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 6b02569f1d
gnu: r-dbplyr: Update to 1.2.2. 
* gnu/packages/statistics.scm (r-dbplyr): Update to 1.2.2.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 3299bc1c5e
gnu: r-yaml: Update to 2.2.0. 
* gnu/packages/statistics.scm (r-yaml): Update to 2.2.0.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 2a96a093ec
gnu: r-evaluate: Update to 0.11. 
* gnu/packages/statistics.scm (r-evaluate): Update to 0.11.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 3bf390279d
gnu: r-scales: Update to 1.0.0. 
* gnu/packages/statistics.scm (r-scales): Update to 1.0.0.
[propagated-inputs]: Remove r-dichromat and r-plyr.
 2018-09-05 20:03:05 +02:00