94b3b6041d
gnu: hpcguix-web: Update to 53e09ea.
...
* gnu/packages/web.scm (hpcguix-web): Update to 53e09ea.
2018-09-10 12:18:14 +02:00
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
de15ff1a6c
gnu: Add asignify.
...
* gnu/packages/crypto.scm (asignify): New variable.
2018-09-09 20:05:47 -04:00
02107081da
gnu: double-conversion: Update to 3.1.0.
...
* gnu/packages/maths.scm (double-conversion): Update to 3.1.0.
2018-09-10 01:41:29 +02:00
2bdc73fb26
gnu: double-conversion: Don't use unstable tarball.
...
* gnu/packages/maths.scm (double-conversion)[source]: Use GIT-FETCH.
2018-09-10 01:41:29 +02:00
68a08dfbe5
gnu: libgd: Incorporate grafted changes.
...
* gnu/packages/gd.scm (gd)[replacement]: Remove field.
[source](patches): Add "gd-CVE-2018-5711.patch" and
"gd-CVE-2018-1000222.patch".
(gd/fixed): Remove variable.
* gnu/packages/php.scm (gd-for-php): Remove variable.
(php)[inputs]: Change GD-FOR-PHP to GD.
2018-09-10 01:39:01 +02:00
fe79ce3b1f
Merge branch 'master' into core-updates
2018-09-10 01:37:32 +02:00
fb94354a69
gnu: jbig2dec: Remove graft for 0.15.
...
* gnu/packages/image.scm (jbig2dec): Update to 0.15.
[source]: Reindent.
(jbig2dec-0.15): Remove variable.
2018-09-10 01:00:26 +02:00
18784d8f11
gnu: OpenSSL: Remove obsolete workaround.
...
* gnu/packages/tls.scm (openssl)[arguments]: Remove workaround that is not
needed for GCC version 5.3 and later.
2018-09-10 00:54:03 +02:00
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
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
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
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
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
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
4333d48a82
gnu: mariadb: Move unbundle substitutions to source snippet.
...
* gnu/packages/databases.scm (mariadb)[source](snippet): Add two substitutions
from ...
[arguments]: The 'unbundle' phase here. Rename to 'fix-pcre-detection.
2018-09-09 17:59:37 +02:00
1d957c79b6
gnu: mariadb: Update to 10.1.36.
...
* gnu/packages/databases.scm (mariadb): Update to 10.1.36.
[arguments]: Disable one new test.
2018-09-09 17:59:36 +02:00
5e53722249
gnu: jbig2dec: Don't build libjbig2dec.a.
...
* gnu/packages/image.scm (jbig2dec)[arguments]: New field.
2018-09-09 17:59:36 +02:00
de781c05e7
gnu: util-linux: Remove static library reference from '.la' files.
...
* gnu/packages/linux.scm (util-linux)[arguments]: Substitute all '.la' files.
2018-09-09 17:59:36 +02:00
334bd08c42
gnu: cmake: Update to 3.12.2.
...
* gnu/packages/cmake.scm (cmake): Update to 3.12.2.
2018-09-09 17:59:36 +02:00
a34ce3308e
gnu: gdk-pixbuf: Update to 2.38.0.
...
* gnu/packages/gtk.scm (gdk-pixbuf): Update to 2.38.0.
[build-system]: Switch to MESON-BUILD-SYSTEM.
[arguments]: Don't explicitly enable x11 in #:configure-flags. Prevent tests
from getting installed. Adjust test substitutions. Add phase to fix install.
[native-inputs]: Add GETTEXT-MINIMAL.
(gdk-pixbuf+svg)[arguments]: Adjust accordingly.
2018-09-09 17:59:36 +02:00
7b1ad8b1d9
gnu: gtk+: Update to 3.24.0.
...
* gnu/packages/gtk.scm (gtk+): Update to 3.24.0.
2018-09-09 17:59:36 +02:00
2246c19218
gnu: mesa: Update to 18.1.8.
...
* gnu/packages/gl.scm (mesa): Update to 18.1.8.
2018-09-09 17:59:36 +02:00
589aca1c18
gnu: Python: Delete broken test.
...
* gnu/packages/python.scm (python-3.7)[source](snippet): Delete test which
may crash some systems.
2018-09-09 17:59:36 +02:00
9adaf1f408
gnu: OpenBLAS: Update to 0.3.3.
...
* gnu/packages/maths.scm (openblas): Update to 0.3.3.
2018-09-09 17:59:35 +02:00
9bb8b563a8
gnu: meson: Update to 0.47.2.
...
* gnu/packages/build-tools.scm (meson): Update to 0.47.2.
2018-09-09 17:59:35 +02:00
5d948c0c5d
gnu: python-hypothesis: Update to 3.70.3.
...
* gnu/packages/check.scm (python-hypothesis): Update to 3.70.3.
2018-09-09 17:59:35 +02:00
ad8ae693c8
gnu: python-pytest: Update to 3.8.0.
...
* gnu/packages/check.scm (python-pytest): Update to 3.8.0.
2018-09-09 17:59:35 +02:00
529c36225a
gnu: fontconfig: Update to 2.13.1.
...
* gnu/packages/fontutils.scm (fontconfig): Update to 2.13.1.
2018-09-09 17:59:35 +02:00
6cd715adef
gnu: python-scipy: Update to 1.1.0.
...
* gnu/packages/python.scm (python-scipy): Update to 1.1.0.
2018-09-09 17:59:35 +02:00
f6f8645cc9
gnu: libcmis: Fix FTBFS with Boost >= 1.68.0.
...
* gnu/packages/libreoffice.scm (libcmis)[arguments]: Add phase to substitute
header file name.
2018-09-09 17:59:35 +02:00
436969904c
gnu: vigra: Fix FTBFS with Numpy >= 1.15.
...
* gnu/packages/image.scm (vigra)[arguments]: Disable one more test.
2018-09-09 17:59:34 +02:00
6bbbdb1a34
gnu: oath-toolkit: Fix FTBFS with Glibc >= 2.28.
...
* gnu/packages/patches/oath-toolkit-glibc-compat.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/authentication.scm (oath-toolkit)[source](patches): New field.
2018-09-09 17:59:34 +02:00
0171019418
gnu: openssl: Update to 1.0.2p.
...
* gnu/packages/patches/openssl-1.0.2-CVE-2018-0495.patch,
gnu/packages/patches/openssl-1.0.2-CVE-2018-0732.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.
* gnu/packages/tls.scm (openssl): Update to 1.0.2p.
[source](patches): Remove obsolete.
2018-09-09 17:57:39 +02:00
16676fc3b1
gnu: curl: Remove graft for 7.61.1.
...
* gnu/packages/curl.scm (curl): Update to 7.61.1.
(curl-7.61.1): Remove variable.
2018-09-09 17:55:33 +02:00
842c44c974
gnu: ghostscript: Remove graft for 9.24.
...
* gnu/packages/patches/ghostscript-CVE-2018-10194.patch,
gnu/packages/patches/ghostscript-runpath.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.
* gnu/packages/ghostscript.scm (ghostscript): Update to 9.24.
(ghostscript/fixed): Remove variable.
2018-09-09 17:54:32 +02:00
0aeb134850
Merge branch 'master' into core-updates
2018-09-09 17:40:35 +02:00
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
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
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
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
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
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
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
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
617cf5de92
gnu: mpfr: Update home page.
...
* gnu/packages/multiprecision.scm (mpfr)[home-page]: Use HTTPS.
2018-09-09 16:43:10 +02:00
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
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
c2311644a5
gnu: signify: Update to 24.
...
* gnu/packages/crypto.scm (signify): Update to 24.
2018-09-09 15:01:54 +02:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
9f1f200c04
gnu: diffoscope: Update to 100.
...
* gnu/packages/package-management.scm (diffoscope): Update to 100.
2018-09-07 17:59:16 +02:00
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
6b4f99102c
gnu: gdb: Update to 8.2.
...
* gnu/packages/gdb.scm (gdb): Update to 8.2.
2018-09-07 17:55:55 +02:00
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
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
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
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
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
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
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
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
b03f270e3d
gnu: guile: Remove "share/guile/site" from GUILE_LOAD_COMPILED_PATH.
...
.go files should always go to lib/guile/2.x/site-ccache, and in
practice, we no longer have packages that don't do that.
* gnu/packages/guile.scm (guile-2.2)[native-search-paths]: Remove
"share/guile/site/2.2" from GUILE_LOAD_COMPILED_PATH spec.
(guile-2.0)[native-search-paths]: Likewise.
2018-09-07 10:47:52 +02:00
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
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
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
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
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
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
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
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
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
d53aeeafcc
Add missing use-modules clause.
...
This is a follow-up to commit 5dfe491290
2018-09-06 04:53:32 +02:00
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
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
a5c70c2e0e
gnu: libmpdclient: Update to 2.15.
...
* gnu/packages/mpd.scm (libmpdclient): Update to 2.15.
2018-09-06 02:33:47 +02:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
b8f6e2f82a
gnu: Add r-ordinal.
...
* gnu/packages/cran.scm (r-ordinal): New variable.
2018-09-05 20:03:07 +02:00
dc66835226
gnu: Add r-ucminf.
...
* gnu/packages/cran.scm (r-ucminf): New variable.
2018-09-05 20:03:07 +02:00
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
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
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
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
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
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
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
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
589bd1c426
gnu: Add r-flextable.
...
* gnu/packages/cran.scm (r-flextable): New variable.
2018-09-05 20:03:06 +02:00
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
f9f4578ba0
Revert "gnu: ghc-tasty: Update to 1.1.0.3."
...
This reverts commit 3ad6b89090
2018-09-05 20:03:06 +02:00
90708323a1
Revert "gnu: ghc-base-compat: Update to 0.10.4."
...
This reverts commit 0fa2c552fc
2018-09-05 20:03:06 +02:00
0fd7d59dc3
gnu: Add r-moonbook.
...
* gnu/packages/cran.scm (r-moonbook): New variable.
2018-09-05 20:03:06 +02:00
aaed237d1b
gnu: Add r-nortest.
...
* gnu/packages/cran.scm (r-nortest): New variable.
2018-09-05 20:03:06 +02:00
1f560b9cdb
gnu: Add r-sjmisc.
...
* gnu/packages/cran.scm (r-sjmisc): New variable.
2018-09-05 20:03:06 +02:00
cfc0631433
gnu: Add r-sjlabelled.
...
* gnu/packages/cran.scm (r-sjlabelled): New variable.
2018-09-05 20:03:06 +02:00
de059e4bd3
gnu: Add r-prediction.
...
* gnu/packages/cran.scm (r-prediction): New variable.
2018-09-05 20:03:06 +02:00
bfee9ce88f
gnu: Add r-snakecase.
...
* gnu/packages/cran.scm (r-snakecase): New variable.
2018-09-05 20:03:06 +02:00
c183fa2688
gnu: Add r-officer.
...
* gnu/packages/cran.scm (r-officer): New variable.
2018-09-05 20:03:06 +02:00
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
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
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
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
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
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
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
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
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
2848c52c5e
gnu: r-roxygen2: Update to 6.1.0.
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* 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
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
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
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
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
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
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
97c81cc174
gnu: r-stringi: Update to 1.2.4.
...
* gnu/packages/statistics.scm (r-stringi): Update to 1.2.4.
2018-09-05 20:03:05 +02:00
e362be8e89
gnu: Add r-pkgload.
...
* gnu/packages/cran.scm (r-pkgload): New variable.
2018-09-05 20:03:05 +02:00
4f8247b54b
gnu: Add r-pkgbuild.
...
* gnu/packages/cran.scm (r-pkgbuild): New variable.
2018-09-05 20:03:05 +02:00
1ec1989f80
gnu: r-httpuv: Update to 1.4.5.
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* gnu/packages/web.scm (r-httpuv): Update to 1.4.5.
[native-inputs]: Add pkg-config.
2018-09-05 20:03:05 +02:00
f077174178
gnu: r-scran: Update to 1.8.4.
...
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.8.4.
2018-09-05 20:03:05 +02:00
8e44ff0c0d
gnu: r-scater: Update to 1.8.4.
...
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.8.4.
2018-09-05 20:03:05 +02:00
e69c07e61a
gnu: r-hdf5array: Update to 1.8.1.
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* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.8.1.
2018-09-05 20:03:04 +02:00
16527f1cbc
gnu: r-ggbio: Update to 1.28.5.
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* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.28.5.
[propagated-inputs]: Add r-rlang.
2018-09-05 20:03:04 +02:00
70daf9362b
gnu: r-biovizbase: Update to 1.28.2.
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* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.28.2.
[propagated-inputs]: Add r-rlang.
2018-09-05 20:03:04 +02:00
ff7c7d62f4
gnu: r-keggrest: Update to 1.20.1.
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* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.20.1.
2018-09-05 20:03:04 +02:00
3c55304688
gnu: r-edaseq: Update to 2.14.1.
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* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.14.1.
2018-09-05 20:03:04 +02:00
eb251fe524
gnu: r-igraph: Update to 1.2.2.
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* gnu/packages/graph.scm (r-igraph): Update to 1.2.2.
2018-09-05 20:03:04 +02:00
c273bcdfce
gnu: r-diffusionmap: Update to 1.1-0.1.
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* gnu/packages/graph.scm (r-diffusionmap): Update to 1.1-0.1.
2018-09-05 20:03:04 +02:00
6f6aef80e3
gnu: r-seurat: Update to 2.3.4.
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* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.4.
[source]: Remove snippet.
[arguments]: Remove.
[native-inputs]: Remove.
[propagated-inputs]: Remove r-caret, r-diffusionmap, r-fnn, r-gdata, r-ranger,
r-stringr, r-tclust, and rvgam; add r-httr.
2018-09-05 20:03:04 +02:00
07bd90ce90
gnu: r-msnbase: Update to 2.6.3.
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* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.6.3.
2018-09-05 20:03:04 +02:00
4ee8c37cca
gnu: r-maldiquant: Update to 1.18.
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* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.18.
2018-09-05 20:03:04 +02:00
48b21f8b6b
gnu: r-seqminer: Update to 6.1.
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* gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.1.
2018-09-05 20:03:04 +02:00
ad2ed8d01f
gnu: r-genomicfeatures: Update to 1.32.2.
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* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.32.2.
2018-09-05 20:03:04 +02:00
f2e79823c6
gnu: r-rtracklayer: Update to 1.40.6.
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* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.6.
2018-09-05 20:03:04 +02:00
aea1b6fb8a
gnu: r-delayedarray: Update to 0.6.5.
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* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.5.
2018-09-05 20:03:04 +02:00
3e61c2a8b1
gnu: r-rsamtools: Update to 1.32.3.
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* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.32.3.
2018-09-05 20:03:04 +02:00
a02340058c
gnu: r-biocparallel: Update to 1.14.2.
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* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.14.2.
2018-09-05 20:03:04 +02:00
1d56c79f86
gnu: r-genomicranges: Update to 1.32.6.
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* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.32.6.
2018-09-05 20:03:04 +02:00
688cb08527
gnu: r-limma: Update to 3.36.3.
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* gnu/packages/bioinformatics.scm (r-limma): Update to 3.36.3.
2018-09-05 20:03:03 +02:00
33a103a543
gnu: r-variantannotation: Update to 1.26.1.
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* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.26.1.
2018-09-05 20:03:03 +02:00
1adf4596a6
gnu: r-edger: Update to 3.22.3.
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* gnu/packages/bioinformatics.scm (r-edger): Update to 3.22.3.
2018-09-05 20:03:03 +02:00
5728d9c6c0
gnu: r-iranges: Update to 2.14.11.
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* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.14.11.
2018-09-05 20:03:03 +02:00
3c04375614
gnu: r-biocviews: Update to 1.48.3.
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* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.3.
2018-09-05 20:03:03 +02:00
ce0e762bf9
gnu: r-annotationforge: Update to 1.22.2.
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* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.22.2.
2018-09-05 20:03:03 +02:00
65050163e0
gnu: r-chippeakanno: Update to 3.14.1.
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* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.14.1.
2018-09-05 20:03:03 +02:00
88e4ed55d6
gnu: Add r-clipr.
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* gnu/packages/cran.scm (r-clipr): New variable.
2018-09-05 20:03:03 +02:00
6a8469755c
gnu: Add r-rdpack.
...
* gnu/packages/cran.scm (r-rdpack): New variable.
2018-09-05 20:03:03 +02:00
dd954dd743
gnu: Add r-gbrd.
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* gnu/packages/cran.scm (r-gbrd): New variable.
2018-09-05 20:03:03 +02:00
53718658d2
gnu: Add r-polynom.
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* gnu/packages/cran.scm (r-polynom): New variable.
2018-09-05 20:03:03 +02:00
356230da4a
gnu: Add r-fansi.
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* gnu/packages/cran.scm (r-fansi): New variable.
2018-09-05 20:03:03 +02:00
3b0153bd82
gnu: guix-daemon: Add dependency on Guile-Gcrypt.
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This is a followup to 53166aec98
2018-09-05 15:48:04 +02:00
7903f00a74
gnu: cuirass: Add dependency on Guile-Gcrypt.
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This is a followup to 53166aec98
2018-09-05 15:35:54 +02:00
5e3082df1c
gnu: guile-fibers: Install .go files to "…/site-ccache".
...
* gnu/packages/guile.scm (guile-fibers)[arguments]: New field.
2018-09-05 15:35:54 +02:00
3f5e6ccf9b
slepc: Upgrade to 3.9.2.
...
* gnu/packages/maths.scm (slepc): Upgrade to 3.9.2.
2018-09-05 08:10:38 -05:00
c15be1280e
petsc: Upgrade to 3.9.3.
...
* gnu/packages/maths.scm (petsc): Upgrade to 3.9.3.
[arguments]: Remove unnecessary configure flags.
2018-09-05 08:10:37 -05:00
a3a99e27bb
petsc: Move example code to "examples" output.
...
* gnu/packages/maths.scm (petsc)[arguments]: New 'move-examples' phase.
2018-09-05 08:10:37 -05:00
b26e4f26ff
gnu: Add SUNDIALS.
...
* gnu/packages/maths.scm (sundials, sundials-openmpi): New variables.
2018-09-05 08:10:31 -05:00
296f091b48
gnu: packages: mp3: Use HTTPS where possible.
...
* gnu/packages/mp3.scm (libmad)[home-page]: Use HTTPS.
(libid3tag)[home-page]: Likewise.
(mp3info)[source, home-page]: Likewise.
(mpg123)[source]: Likewise.
(libmpcdec)[source, home-page]: Likewise.
Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
2018-09-05 20:56:55 +08:00
998100e6e8
gnu: eyed3: Update home page.
...
* gnu/packages/mp3.scm (eyed3)[home-page]: Update to redirected HTTPS URL.
Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
2018-09-05 20:56:55 +08:00
53166aec98
gnu: guix: Update to 3d43017.
...
* gnu/packages/package-management.scm (guix): Update to 3d43017
2018-09-05 14:31:48 +02:00
185948b8a8
gnu: xorg: Fix typo.
...
* gnu/packages/xorg.scm: Fix typo in Benjamin's email address.
2018-09-05 13:57:43 +02:00
4fd2622df8
gnu: python-tables: Update to 3.4.4.
...
* gnu/packages/python.scm (python-tables): Update to 3.4.4.
2018-09-05 12:01:23 +02:00
8afdeb8751
gnu: python-pybigwig: Update to 0.3.12.
...
* gnu/packages/bioinformatics.scm (python-pybigwig): Update to 0.3.12.
[propagated-inputs]: Add python-numpy.
2018-09-05 12:01:23 +02:00
0d7974c376
gnu: libbigwig: Update to 0.4.2.
...
* gnu/packages/bioinformatics.scm (libbigwig): Update to 0.4.2.
[source]: Fetch from git.
[arguments]: Disable tests; remove build phases "disable-curl-test" and
"create-target-dirs".
[native-inputs]: Add python-2.
2018-09-05 12:01:23 +02:00
ca1dc4c76a
gnu: nss-pam-ldapd: Update to 0.9.10.
...
* gnu/packages/openldap.scm (nss-pam-ldapd): Update to 0.9.10.
2018-09-05 11:44:52 +02:00
fefe17b088
gnu: dolphin-emu: Update to commit 5f0d825.
...
* gnu/packages/emulators.scm (dolphin-emu): Update to commit 5f0d825.
2018-09-05 10:23:20 +02:00
fcf4841c0e
gnu: Zsh: Patch some tests that began failing in 5.6.
...
* gnu/packages/shells.scm (zsh)[arguments]: Patch the tests rather than deleting
them.
2018-09-04 18:34:01 -04:00
95681e5586
gnu: Zsh: Update to 5.6 [fixes CVE-2018-{0502,13259}].
...
* gnu/packages/shells.scm (zsh): Update to 5.6.
[arguments]: Skip some tests.
2018-09-04 18:10:53 -04:00
ca71942445
Switch to Guile-Gcrypt.
...
This removes (guix hash) and (guix pk-crypto), which now live as part of
Guile-Gcrypt (version 0.1.0.)
* guix/gcrypt.scm, guix/hash.scm, guix/pk-crypto.scm,
tests/hash.scm, tests/pk-crypto.scm: Remove.
* configure.ac: Test for Guile-Gcrypt. Remove LIBGCRYPT and
LIBGCRYPT_LIBDIR assignments.
* m4/guix.m4 (GUIX_ASSERT_LIBGCRYPT_USABLE): Remove.
* README: Add Guile-Gcrypt to the dependencies; move libgcrypt as
"required unless --disable-daemon".
* doc/guix.texi (Requirements): Likewise.
* gnu/packages/bash.scm, guix/derivations.scm, guix/docker.scm,
guix/git.scm, guix/http-client.scm, guix/import/cpan.scm,
guix/import/cran.scm, guix/import/crate.scm, guix/import/elpa.scm,
guix/import/gnu.scm, guix/import/hackage.scm,
guix/import/texlive.scm, guix/import/utils.scm, guix/nar.scm,
guix/pki.scm, guix/scripts/archive.scm,
guix/scripts/authenticate.scm, guix/scripts/download.scm,
guix/scripts/hash.scm, guix/scripts/pack.scm,
guix/scripts/publish.scm, guix/scripts/refresh.scm,
guix/scripts/substitute.scm, guix/store.scm,
guix/store/deduplication.scm, guix/tests.scm, tests/base32.scm,
tests/builders.scm, tests/challenge.scm, tests/cpan.scm,
tests/crate.scm, tests/derivations.scm, tests/gem.scm,
tests/nar.scm, tests/opam.scm, tests/pki.scm,
tests/publish.scm, tests/pypi.scm, tests/store-deduplication.scm,
tests/store.scm, tests/substitute.scm: Adjust imports.
* gnu/system/vm.scm: Likewise.
(guile-sqlite3&co): Rename to...
(gcrypt-sqlite3&co): ... this. Add GUILE-GCRYPT.
(expression->derivation-in-linux-vm)[config]: Remove.
(iso9660-image)[config]: Remove.
(qemu-image)[config]: Remove.
(system-docker-image)[config]: Remove.
* guix/scripts/pack.scm: Adjust imports.
(guile-sqlite3&co): Rename to...
(gcrypt-sqlite3&co): ... this. Add GUILE-GCRYPT.
(self-contained-tarball)[build]: Call 'make-config.scm' without
#:libgcrypt argument.
(squashfs-image)[libgcrypt]: Remove.
[build]: Call 'make-config.scm' without #:libgcrypt.
(docker-image)[config, json]: Remove.
[build]: Add GUILE-GCRYPT to the extensions Remove (guix config) from
the imported modules.
* guix/self.scm (specification->package): Remove "libgcrypt", add
"guile-gcrypt".
(compiled-guix): Remove #:libgcrypt.
[guile-gcrypt]: New variable.
[dependencies]: Add it.
[*core-modules*]: Remove #:libgcrypt from 'make-config.scm' call.
Add #:extensions.
[*config*]: Remove #:libgcrypt from 'make-config.scm' call.
(%dependency-variables): Remove %libgcrypt.
(make-config.scm): Remove #:libgcrypt.
* build-aux/build-self.scm (guile-gcrypt): New variable.
(make-config.scm): Remove #:libgcrypt.
(build-program)[fake-gcrypt-hash]: New variable.
Add (gcrypt hash) to the imported modules. Adjust load path
assignments.
* gnu/packages/package-management.scm (guix)[propagated-inputs]: Add
GUILE-GCRYPT.
[arguments]: In 'wrap-program' phase, add GUILE-GCRYPT to the search
path.
2018-09-04 17:25:11 +02:00
1bf758767d
gnu: Add emacs-picpocket.
...
* gnu/packages/emacs.scm (emacs-picpocket): New public variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-09-04 15:39:43 +02:00
71ca16b58d
gnu: petsc-openmpi: Configure with support for hdf5 data format.
...
* gnu/packages/maths.scm (petsc-openmpi)[inputs]: Add
hdf5-parallel-openmpi.
[arguments]: Add '--with-hdf5-include' and '--with-hdf5-lib'
flags. Add 'set-test-environment' phase.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-09-04 15:22:48 +02:00
b50658fe8a
gnu: kicad: Update to 5.0.0.
...
* gnu/packages/engineering.scm (kicad): Update to 5.0.0.
[source]: Change from git to url-fetch.
[arguments]: Remove now unneeded build version parameter.
[inputs]: Add opencascade-oce.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-09-04 15:02:59 +02:00
906a396bff
gnu: ghc-zlib: Enable tests.
...
* gnu/packages/haskell.scm (ghc-zlib)[arguments]: Enable tests. Allow building
with newer tasty.
[native-inputs]: Add ghc-quickcheck, ghc-tasty, ghc-tasty-hunit and
ghc-tasty-quickcheck.
2018-09-04 17:31:09 +05:30
6300ba5b66
gnu: ghc-integer-logarithms: Allow building with newer tasty.
...
* gnu/packages/haskell.scm (ghc-integer-logarithms)[arguments]: Allow building
with newer tasty.
2018-09-04 15:24:32 +05:30
8374cc4b05
gnu: ghc-tasty-ant-xml: Update to 1.1.4.
...
* gnu/packages/haskell-check.scm (ghc-tasty-ant-xml): Update to 1.1.4.
2018-09-04 15:21:56 +05:30
3ad6b89090
gnu: ghc-tasty: Update to 1.1.0.3.
...
* gnu/packages/haskell-check.scm (ghc-tasty): Update to 1.1.0.3.
[inputs]: Add ghc-wcwidth.
(ghc-attoparsec-bootstrap, ghc-integer-logarithms-bootstrap,
ghc-scientific-bootstrap): New variables.
(ghc-wcwidth)[inputs]: Replace ghc-attoparsec with ghc-attoparsec-bootstrap.
(ghc-scientific)[inputs]: Replace ghc-integer-logarithms with
ghc-integer-logarithms-bootstrap.
(ghc-attoparsec)[inputs]: Replace ghc-scientific with
ghc-scientific-bootstrap.
2018-09-04 12:15:17 +05:30
9c4b522f15
gnu: Add ghc-wcwidth.
...
* gnu/packages/haskell.scm (ghc-wcwidth): New variable.
2018-09-04 12:15:10 +05:30
fd95f37f36
Revert "gnu: perl: Add support for cross-compilation"
...
This reverts commit 5108c18e7e
2018-09-03 23:49:12 +02:00
5108c18e7e
gnu: perl: Add support for cross-compilation
...
* gnu/packages/perl.scm (perl): use cross-libc when cross-compiling
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-09-03 23:41:08 +02:00
38fe6449c0
gnu: Add transset-df.
...
* gnu/packages/xorg.scm (transset-df): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-09-03 23:40:23 +02:00
65a58f3907
gnu: ppp: Use OpenSSL for cryptography.
...
* gnu/packages/samba.scm (ppp)[source](patches): Add upstream patch.
[inputs]: Add OPENSSL.
[arguments]: Add substitution for OpenSSL headers.
2018-09-03 19:25:28 +02:00
70dc8db8e7
Merge branch 'master' into core-updates
2018-09-03 19:20:06 +02:00
c702749dfd
gnu: arpack-ng: Update to 3.6.2.
...
* gnu/packages/maths.scm (arpack-ng): Update to 3.6.2.
2018-09-03 19:09:01 +02:00
91bb495b85
gnu: arpack-ng: Drop redundant phase.
...
* gnu/packages/maths.scm (arpack-ng)[arguments]: Remove.
2018-09-03 19:09:01 +02:00
1f7d142000
gnu: python-matplotlib: Update to 2.2.3.
...
* gnu/packages/python.scm (python-matplotlib): Update to 2.2.3.
2018-09-03 19:09:00 +02:00
cbd7c65709
gnu: ppp: Return #t from all phases.
...
* gnu/packages/samba.scm (ppp)[arguments]: Return #t from phase.
2018-09-03 18:58:47 +02:00
84aa18ff7f
gnu: re2: Update to 2018-09-01.
...
* gnu/packages/regex.scm (re2): Update to 2018-09-01.
2018-09-03 18:58:47 +02:00
fcde1d27bb
gnu: openexr: Update to 2.3.0.
...
* gnu/packages/graphics.scm (openexr): Update to 2.3.0.
[source](uri): Change to new download location.
[source](snippet): Remove workaround.
[source](patches): Remove.
* gnu/packages/patches/openexr-missing-samples.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2018-09-03 18:58:47 +02:00
1ae2c577a6
gnu: ilmbase: Update to 2.3.0.
...
* gnu/packages/graphics.scm (ilmbase): Update to 2.3.0.
[source](uri): Change to new download location.
2018-09-03 18:58:46 +02:00
9156206199
gnu: simplescreenrecorder: Build against modular Qt.
...
* gnu/packages/video.scm (simplescreenrecorder)[inputs]: Remove QT. Add
QTBASE and QTX11EXTRAS.
2018-09-03 18:58:46 +02:00
65e686d6cb
Merge branch 'security-updates'
2018-09-03 18:58:20 +02:00
a5896da34e
gnu: gnu-pw-mgr: Update to 2.4.2.
...
* gnu/packages/gnu-pw-mgr.scm (gnu-pw-mgr): Update to 2.4.2.
2018-09-03 19:34:24 +03:00
38a8cd329d
gnu: python-nbxmpp: Update to 0.6.7.
...
* gnu/packages/messaging.scm (python-nbxmpp): Update to 0.6.7.
2018-09-03 18:21:43 +02:00
b619b7f67b
gnu: libircclient: Update to 1.10.
...
* gnu/packages/messaging.scm (libircclient): Update to 1.10.
2018-09-03 18:21:43 +02:00
cfcfc6ab62
Fix some typos.
...
* doc/guix.texi (Sound Services, DNS Services): Fix typos.
* gnu/packages/cpp.scm (json-modern-cxx)[description]: Likewise.
* gnu/packages/emacs.scm (emacs-fancy-narrow)[synopsis, description]:
Likewise. Edit & mark up while we're here.
* gnu/packages/mail.scm (alot)[synopsis, description]: Ditto.
2018-09-03 18:21:43 +02:00
fb458bf3bc
gnu: sudo: Update to 1.8.25.
...
* gnu/packages/admin.scm (sudo): Update to 1.8.25.
2018-09-03 18:21:42 +02:00
0cc6447669
gnu: python-efl: Update to 1.21.0.
...
* gnu/packages/enlightenment.scm (python-efl): Update to 1.21.0.
[source]: Don't use pypi source.
[arguments]: Delete network tests.
2018-09-03 17:32:44 +03:00
290bef39f6
gnu: efl: Update to 1.21.0.
...
* gnu/packages/enlightenment.scm (efl): Update to 1.21.0.
2018-09-03 17:32:44 +03:00
02ddafef55
gnu: python-scipy: Disable broken tests.
...
* gnu/packages/python.scm (python-scipy)[arguments]: Skip two broken tests.
2018-09-03 13:49:32 +02:00
26baaaf49b
gnu: c-toxcore: Update to 0.2.7.
...
* gnu/packages/messaging.scm (c-toxcore): Update to 0.2.7.
2018-09-03 08:22:51 +02:00
aa613d71ec
gnu: openrct2: Update to 0.2.1.
...
* gnu/packages/games.scm (openrct2-objects): Update to 1.0.6.
* gnu/packages/games.scm (openrct2): Update to 0.2.1.
2018-09-03 08:22:50 +02:00
647465ace9
gnu: jellyfish: Update to 2.2.10.
...
* gnu/packages/bioinformatics.scm (jellyfish): Update to 2.2.10.
[supported-systems]: Add aarch64-linux, mips64el-linux.
2018-09-03 08:32:33 +03:00
3910977823
gnu: monitoring.scm: Fix copyright line.
...
This is a follow-up to ead46692ec
2018-09-02 19:18:16 +03:00
2bd6ed9e4c
gnu: haskell-mode: Fix test failure.
...
Fixes <https://bugs.gnu.org/31726 >.
Thanks to Jack Hill <jackhill@jackhill.us> for exploring different solutions
at <https://debbugs.gnu.org/cgi/bugreport.cgi?bug=31726 >.
* gnu/packages/patches/haskell-mode-unused-variables.patch,
gnu/packages/patches/haskell-mode-make-check.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/emacs.scm (haskell-mode)[source]: Use them.
[arguments]: Adjust 'pre-build' phase to embed file name.
Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2018-09-02 17:06:43 +02:00
b21a55a9f2
gnu: emacs-helpful: Update to 0.13.
...
* gnu/packages/emacs.scm (emacs-helpful): Update to 0.13.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-09-02 16:58:06 +02:00
351b6463af
gnu: emacs-elisp-refs: Update to 1.3.
...
* gnu/packages/emacs.scm (emacs-elisp-refs): Update to 1.3.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-09-02 16:56:22 +02:00
87284c6b48
gnu: wine-staging: Update to 3.15.
...
* gnu/packages/wine.scm (wine-staging): Update to 3.15.
2018-09-02 08:53:03 +02:00
ab2e38e206
gnu: wine-staging-patchset-data: Update to 3.15.
...
* gnu/packages/wine.scm (wine-staging-patchset-data): Update to 3.15.
2018-09-02 08:53:03 +02:00
9bf98520f2
gnu: rosegarden: Update to 18.06.
...
* gnu/packages/music.scm (rosegarden): Update to 18.06.
[home-page]: Use HTTPS.
2018-09-02 13:18:28 +08:00
24d298b459
gnu: rust: Move rust-1.19 down.
2018-09-02 00:22:53 +02:00
3159ef7c99
gnu: rust: Bootstrap (only) Rust 1.19.0 by mrustc.
...
* gnu/packages/patches/rust-1.19-mrustc.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/rust.scm (rust-1.19)[source]: Add patch
"rust-1.19-mrustc.patch".
[arguments]<#:modules>: New field.
<#:phases>[patch-cargo-tomls]: New phase.
<#:phases>[build]: Modify.
<#:phases>[install]: Modify.
[native-inputs]: Replace rust-bootstrap by mrustc.
(rust-1.23)[native-inputs]: New field.
[arguments]<#:phases>: Delete phase "patch-cargo-tomls".
2018-09-02 00:09:34 +02:00
a0a273c1ee
gnu: Add perftest.
...
* gnu/packages/linux.scm (perftest): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2018-09-01 17:51:29 -04:00
37a0f47073
gnu: Add ruby-jekyll-paginate-v2.
...
* gnu/packages/ruby.scm (ruby-jekyll-paginate-v2): New variable.
2018-09-01 23:09:14 +02:00
49e1dde53f
gnu: Add jekyll.
...
* gnu/packages/ruby.scm (jekyll): New variable.
2018-09-01 23:09:09 +02:00
3729611379
gnu: Add ruby-pathutil.
...
* gnu/packages/ruby.scm (ruby-pathutil): New variable.
2018-09-01 23:09:06 +02:00
49395112c4
gnu: Add ruby-forwardable-extended.
...
* gnu/packages/ruby.scm (ruby-forwardable-extended): New variable.
2018-09-01 23:09:04 +02:00
a13d451e18
gnu: Add ruby-liquid.
...
* gnu/packages/ruby.scm (ruby-liquid): New variable.
2018-09-01 23:09:02 +02:00
f1ec4d7611
gnu: Add ruby-mercenary.
...
* gnu/packages/ruby.scm (ruby-mercenary): New variable.
2018-09-01 23:09:00 +02:00
f8ae2ee528
gnu: Add ruby-safe-yaml.
...
* gnu/packages/ruby.scm (ruby-safe-yaml): New variable.
2018-09-01 23:08:58 +02:00
73bfc125ef
gnu: Add ruby-heredoc-unindent.
...
* gnu/packages/ruby.scm (ruby-heredoc-unindent): New variable.
2018-09-01 23:08:56 +02:00
2e072e37aa
gnu: Add ruby-hashie.
...
* gnu/packages/ruby.scm (ruby-hashie): New variable.
2018-09-01 23:08:55 +02:00
2c5028bd97
gnu: Add ruby-rouge-2.
...
* gnu/packages/ruby.scm (ruby-rouge-2): New variable.
2018-09-01 23:08:53 +02:00
4ce0414bca
gnu: Add ruby-rouge.
...
* gnu/packages/ruby.scm (ruby-rouge): New variable.
2018-09-01 23:08:46 +02:00
5e2f74bdb8
gnu: Add ruby-em-websocket.
...
* gnu/packages/ruby.scm (ruby-em-websocket): New variable.
2018-09-01 23:08:44 +02:00
fa0063bcf4
gnu: Add ruby-http-parser.rb.
...
* gnu/packages/ruby.scm (ruby-http-parser.rb): New variable.
2018-09-01 23:08:42 +02:00
0312706955
gnu: Add ruby-kramdown.
...
* gnu/packages/ruby.scm (ruby-kramdown): New variable.
2018-09-01 23:08:40 +02:00
197ca8ecd2
gnu: Add ruby-prawn-table.
...
* gnu/packages/ruby.scm (ruby-prawn-table): New variable.
2018-09-01 23:08:38 +02:00
7ad8dd086c
gnu: Add ruby-prawn.
...
* gnu/packages/ruby.scm (ruby-prawn): New variable.
2018-09-01 23:08:36 +02:00
37fbced73c
gnu: Add ruby-yard.
...
* gnu/packages/ruby.scm (ruby-yard): New variable.
2018-09-01 23:08:34 +02:00
770e3b535e
gnu: Add ruby-pdf-core.
...
* gnu/packages/ruby.scm (ruby-pdf-core): New variable.
2018-09-01 23:08:31 +02:00
461fb8598e
gnu: Add ruby-pdf-inspector.
...
* gnu/packages/ruby.scm (ruby-pdf-inspector): New variable.
2018-09-01 23:08:29 +02:00
abbe629c6a
gnu: Add ruby-pdf-reader.
...
* gnu/packages/ruby.scm (ruby-pdf-reader): New variable.
2018-09-01 23:08:27 +02:00
00d71efca6
gnu: Add ruby-morecane.
...
* gnu/packages/ruby.scm (ruby-morecane): New variable.
2018-09-01 23:08:10 +02:00
83d9f67221
gnu: Add ruby-cane.
...
* gnu/packages/ruby.scm (ruby-cane): New variable.
2018-09-01 23:08:06 +02:00
3224a5a84a
gnu: Add ruby-parallel.
...
* gnu/packages/ruby.scm (ruby-parallel): New variable.
2018-09-01 23:08:04 +02:00
ceac6f6f5b
gnu: Add ruby-jekyll-watch.
...
* gnu/packages/ruby.scm (ruby-jekyll-watch): New variable.
2018-09-01 23:08:02 +02:00
88ed727fc5
gnu: Add ruby-listen-3.0.
...
* gnu/packages/ruby.scm (ruby-listen-3.0): New variable.
2018-09-01 23:08:00 +02:00
5e242cb44c
gnu: Add ruby-jekyll-sass-converter.
...
* gnu/packages/ruby.scm (ruby-jekyll-sass-converter): New variable.
2018-09-01 23:07:58 +02:00
f00f449223
gnu: Add ruby-sass.
...
* gnu/packages/ruby.scm (ruby-sass): New variable.
2018-09-01 23:07:56 +02:00
6456beef01
gnu: Add ruby-sass-spec.
...
* gnu/packages/ruby.scm (ruby-sass-spec): New variable.
2018-09-01 23:07:54 +02:00
ddc3a66798
gnu: Add ruby-diffy.
...
* gnu/packages/ruby.scm (ruby-diffy): New variable.
2018-09-01 23:07:52 +02:00
0c8eedc153
gnu: Add ruby-terminfo.
...
* gnu/packages/ruby.scm (ruby-terminfo): New variable.
2018-09-01 23:07:50 +02:00
18077ffc46
gnu: Add ruby-sass-listen.
...
* gnu/packages/ruby.scm (ruby-sass-listen): New variable.
2018-09-01 23:07:48 +02:00
6bba8ecf7b
gnu: Add ruby-rdoc.
...
* gnu/packages/ruby.scm (ruby-rdoc): New variable.
2018-09-01 23:07:46 +02:00
f22c038799
gnu: Add ruby-command-line-reporter-3.
...
* gnu/packages/ruby.scm (ruby-command-line-reporter-3): New variable.
2018-09-01 23:07:44 +02:00
78b9c291f6
gnu: Add ruby-command-line-reporter.
...
* gnu/packages/ruby.scm (ruby-command-line-reporter): New variable.
2018-09-01 23:07:42 +02:00
9c7f15c048
gnu: Add ruby-colorator.
...
* gnu/packages/ruby.scm (ruby-colorator): New variable.
2018-09-01 23:07:39 +02:00
6f2c4efb56
gnu: Add ruby-addressable.
...
* gnu/package/ruby.scm (ruby-addressable): New variable.
2018-09-01 23:07:37 +02:00
0d16905b60
gnu: Add ruby-public-suffix.
...
* gnu/packages/ruby.scm (ruby-public-suffix): New variable.
2018-09-01 23:07:35 +02:00
afb7a3e8d5
gnu: ruby-ttfunk: Update to 1.5.1.
...
* gnu/packages/ruby.scm (ruby-ttfunk): Update to 1.5.1.
2018-09-01 23:07:32 +02:00
ef381322d5
gnu: ruby-activesupport: Update to 5.2.1.
...
* gnu/packages/ruby.scm (ruby-activesupport): Update to 5.2.1.
2018-09-01 23:07:30 +02:00
cbb50182ad
gnu: ruby-i18n: Update to 1.1.0.
...
* gnu/packages/ruby.scm (ruby-i18n): Update to 1.1.0.
2018-09-01 23:07:28 +02:00
352b5d7e74
gnu: Add ruby-concurrent.
...
* gnu/packages/ruby.scm (ruby-concurrent): New variable.
2018-09-01 23:07:06 +02:00
Ludovic Courtès