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45086 Commits

Author SHA1 Message Date
Andreas Enge 4c32f116cd
gnu: Add libhomfly. 
* gnu/packages/sagemath.scm (libhomfly): New variable.
 2019-06-18 00:14:14 +02:00
Andreas Enge 972ef8f591
gnu: Add libbraiding. 
* gnu/packages/sagemath.scm (libbraiding): New variable.
 2019-06-18 00:14:14 +02:00
Gábor Boskovits 1539156231
doc: Fix typo. 
* doc/guix.texi (Base Services)[guix-publish-service-type]:
"guix-publish-configuration" instead of "guix-configuration".
 2019-06-17 23:20:44 +02:00
Danny Milosavljevic c8535731b8
gnu: python-flask-script: Fix tests. 
* gnu/packages/python-web.scm
(python-flask-script)[arguments]<#:phases>[patch-tests]: New phase.
 2019-06-17 22:56:19 +02:00
Ricardo Wurmus 27d6d24e63
gnu: python-scikit-learn: Update to 0.20.3. 
* gnu/packages/machine-learning.scm (python-scikit-learn): Update to 0.20.3.
 2019-06-17 20:22:42 +02:00
Ricardo Wurmus a6f2ced34b
gnu: Add tbsp. 
* gnu/packages/bioinformatics.scm (tbsp): New variable.
 2019-06-17 20:22:38 +02:00
Andreas Enge bf473f0ca0
gnu: Add rw. 
* gnu/packages/graph.scm (rw): New variable.
 2019-06-17 19:47:15 +02:00
Andreas Enge f455d99dfa
gnu: edge-addition-planarity-suite: Move to the (gnu packages graph) module. 
* gnu/packages/maths.scm (edge-addition-planarity-suite): Move from here...
* gnu/packages/maths.scm (edge-addition-planarity-suite): ...to here.
 2019-06-17 19:47:15 +02:00
Nicolas Goaziou 7658904a34
gnu: Fix freeorion build. 
* gnu/packages/games.scm (freeorion)[arguments]: Fix font unbundling.
 2019-06-17 17:37:04 +02:00
Andreas Enge 9f6065237d
gnu: Add edge-addition-planarity-suite. 
* gnu/packages/maths.scm (edge-addition-planarity-suite): New variable.
 2019-06-17 17:02:01 +02:00
Andreas Enge 1e1a65a633
gnu: python-cypari2: Update to 2.1.1. 
* gnu/packages/sagemath.scm (python-cypari2): Update to 2.1.1.
 2019-06-17 16:00:13 +02:00
Andreas Enge 20caeea483
gnu: Add cliquer. 
* gnu/packages/sagemath.scm (cliquer): New variable.
 2019-06-17 16:00:13 +02:00
Efraim Flashner 505459d7cb
gnu: busybox: Don't install to usr. 
* gnu/packages/busybox.scm (busybox)[arguments]: Add a custom phase
to prevent installing to %PREFIX/usr.
 2019-06-17 16:27:16 +03:00
Gábor Boskovits de2d14f2ff
gnu: waybar: Add optional dependencies. 
* gnu/packages/wm.scm(waybar)[inputs]: Add libdbusmenu, libnl,
libmpdclient and pulseaudio.
 2019-06-17 13:33:06 +02:00
Ricardo Wurmus 5cfc16320a
gnu: python-scipy: Update to 1.2.2. 
* gnu/packages/python-xyz.scm (python-scipy): Update to 1.2.2.
 2019-06-17 13:31:23 +02:00
Robert Vollmert f434664cc0
gnu: oil-shell: Update to 0.6pre22. 
It turns out the currently packaged release fails to build for me.
According to upstream, the 0.6 pre-releases are preferable to
currently packaged 0.5.

gnu/packages/shells.scm (oil-shell): Update to 0.6pre22.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-06-17 12:36:13 +02:00
Robert Vollmert 73eacca85e
gnu: kakoune: Remove dependency on boost. 
kakoune builds without boost since a while already.

* gnu/packages/text-editors.scm (kakoune)[inputs]: Remove boost.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-06-17 12:36:13 +02:00
Ludovic Courtès ed504cafa2
vm: 'system-docker-image' builds in a UTF-8 locale. 
Fixes <https://bugs.gnu.org/36215>.
Reported by Björn Höfling <bjoern.hoefling@bjoernhoefling.de>.

This is a followup to 9c941364bf.

* gnu/system/vm.scm (system-docker-image)[build]: Set GUIX_LOCPATH and
call 'setlocale'.
 2019-06-17 12:36:13 +02:00
Ludovic Courtès 123b9c02dd
gnu: open-zwave: Unbundle hidapi. 
* gnu/packages/patches/open-zwave-hidapi.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/zwave.scm (open-zwave)[source](patches): New field.
(snippet): Delete 'cpp/hidapi'.
[native-inputs]: Add PKG-CONFIG.
[inputs]: Add HIDAPI.
 2019-06-17 12:36:13 +02:00
Andreas Enge bf95a142bb
gnu: gap: Update to 4.10.1. 
* gnu/packages/algebra.scm (gap): Update to 4.10.1.
Install headers and library files by hand, since the make targets have
disappeared. Delete the special check phase, since the "make check" target
has appeared. Remove a package that is no longer recommended, and enable
two recommended packages with clarified licenses.
 2019-06-17 12:15:21 +02:00
Efraim Flashner 55350f8316
gnu: cmst: Don't install files to usr. 
* gnu/packages/connman.scm (cmst)[arguments]: Move custom 'fix-Makefiles
phase before 'build. Add more substitutions.
 2019-06-17 10:02:47 +03:00
Efraim Flashner 9e3e80baa3
gnu: cava: Don't install files to usr. 
* gnu/packages/audio.scm (cava)[arguments]: In configure-flags change
FONT_DIR to not use 'usr'.
 2019-06-17 10:02:46 +03:00
Efraim Flashner ee0b4733e1
gnu: toybox: Don't install files to usr. 
* gnu/packages/busybox.scm (toybox)[arguments]: Add custom phase to
remove any files installed in $PREFIX/usr.
 2019-06-17 10:02:45 +03:00
Rutger Helling c9f0331152
gnu: xpra: Update to 2.5.2. 
* gnu/packages/xorg.scm (xpra): Update to 2.5.2.
 2019-06-17 08:28:38 +02:00
Chris Marusich 0bc010dacd
gnu: Add emacs-extend-smime. 
* gnu/packages/emacs-xyz.scm (emacs-extend-smime): New variable.
 2019-06-16 21:25:59 -07:00
Chris Marusich 3c33931c80
gnu: Upgrade emacs-default-encrypt to 4.4. 
* gnu/packages/emacs-xyz.scm (emacs-default-encrypt) <version>: Upgrade
to 4.4.
<sha256>: Update accordingly.
<uri, home-page>: Honor changes to upstream's website.
 2019-06-16 21:25:59 -07:00
Ricardo Wurmus 932a6c422a
gnu: r-rhisat2: Update to 1.0.3. 
* gnu/packages/bioconductor.scm (r-rhisat2): Update to 1.0.3.
 2019-06-17 04:55:12 +02:00
Ricardo Wurmus 42df44f645
gnu: r-seurat: Update to 3.0.2. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.0.2.
 2019-06-17 04:55:03 +02:00
Ricardo Wurmus 6dc3c58728
gnu: r-tximport: Update to 1.12.1. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.12.1.
 2019-06-17 04:54:56 +02:00
Ricardo Wurmus 7bbd06ed59
gnu: r-systempiper: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.18.1.
 2019-06-17 04:54:51 +02:00
Ricardo Wurmus fd61e9c5d6
gnu: r-r-utils: Update to 2.9.0. 
* gnu/packages/statistics.scm (r-r-utils): Update to 2.9.0.
 2019-06-17 04:54:46 +02:00
Ricardo Wurmus 0f4182a137
gnu: r-dt: Update to 0.7. 
* gnu/packages/statistics.scm (r-dt): Update to 0.7.
 2019-06-17 04:54:40 +02:00
Ricardo Wurmus 074dd1806c
gnu: r-rcpparmadillo: Update to 0.9.500.2.0. 
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.500.2.0.
 2019-06-17 04:54:36 +02:00
Ricardo Wurmus e89e4bb634
gnu: r-mime: Update to 0.7. 
* gnu/packages/statistics.scm (r-mime): Update to 0.7.
 2019-06-17 04:54:32 +02:00
Ricardo Wurmus 24868ae72e
gnu: r-formatr: Update to 1.7. 
* gnu/packages/statistics.scm (r-formatr): Update to 1.7.
 2019-06-17 04:54:27 +02:00
Ricardo Wurmus 4661effbd5
gnu: r-ggplot2: Update to 3.2.0. 
* gnu/packages/statistics.scm (r-ggplot2): Update to 3.2.0.
[propagated-inputs]: Remove r-plyr.
 2019-06-17 04:54:11 +02:00
Ricardo Wurmus 18242e4b52
gnu: r-servr: Update to 0.14. 
* gnu/packages/cran.scm (r-servr): Update to 0.14.
 2019-06-17 04:54:05 +02:00
Ricardo Wurmus 9fea25cf32
gnu: r-polspline: Update to 1.1.15. 
* gnu/packages/cran.scm (r-polspline): Update to 1.1.15.
 2019-06-17 04:54:00 +02:00
Ricardo Wurmus 663a50e8f9
gnu: r-deldir: Update to 0.1-21. 
* gnu/packages/cran.scm (r-deldir): Update to 0.1-21.
 2019-06-17 04:53:55 +02:00
Ricardo Wurmus 776c62d1b2
gnu: r-nor1mix: Update to 1.3-0. 
* gnu/packages/cran.scm (r-nor1mix): Update to 1.3-0.
 2019-06-17 04:53:51 +02:00
Ricardo Wurmus 5cc896546b
gnu: r-tractor-base: Update to 3.3.2. 
* gnu/packages/cran.scm (r-tractor-base): Update to 3.3.2.
 2019-06-17 04:53:47 +02:00
Ricardo Wurmus 935c6532ac
gnu: r-rspectra: Update to 0.15-0. 
* gnu/packages/cran.scm (r-rspectra): Update to 0.15-0.
 2019-06-17 04:53:42 +02:00
Ricardo Wurmus a7794b7243
gnu: r-emmeans: Update to 1.3.5. 
* gnu/packages/cran.scm (r-emmeans): Update to 1.3.5.
 2019-06-17 04:53:37 +02:00
Ricardo Wurmus 89afd03172
gnu: r-abcrf: Update to 1.8. 
* gnu/packages/cran.scm (r-abcrf): Update to 1.8.
[propagated-inputs]: Add r-doparallel and r-foreach.
 2019-06-17 04:53:20 +02:00
Ricardo Wurmus 45dcc89de7
gnu: r-sjmisc: Update to 2.8.0. 
* gnu/packages/cran.scm (r-sjmisc): Update to 2.8.0.
[propagated-inputs]: Remove r-haven; add r-insight.
 2019-06-17 04:53:04 +02:00
Ricardo Wurmus e0cd8f7340
gnu: r-extradistr: Update to 1.8.11. 
* gnu/packages/cran.scm (r-extradistr): Update to 1.8.11.
 2019-06-17 04:52:57 +02:00
Ricardo Wurmus bb6c8f207b
gnu: guile-gi: Update to 0.0.2. 
* gnu/packages/guile-xyz.scm (guile-gi): Update to 0.0.2.
[source]: Fetch using url-fetch.
[arguments]: Add make flags to remove unexpectedly passing test from
XFAIL_TESTS.
[native-inputs]: Remove autoconf, automake, and texinfo.
 2019-06-17 04:52:22 +02:00
Ricardo Wurmus d1a3a8e15e
gnu: guile-picture-language: Update to 0.0.1-1-91d10c9. 
* gnu/packages/guile-xyz.scm (guile-picture-language): Update to
0.0.1-1-91d10c9.
[build-system]: Use gnu-build-system.
[native-inputs]: Add autoconf, automake, imagemagick, pkg-config, and texinfo.
 2019-06-17 03:06:53 +02:00
Tobias Geerinckx-Rice 58637415be
gnu: youtube-viewer: Refer to youtube-dl. 
* gnu/packages/video.scm (youtube-viewer)[inputs]: Add youtube-dl.
[arguments]: Add ‘refer-to-inputs’ phase.
 2019-06-17 03:04:31 +02:00
Tobias Geerinckx-Rice a157fb2723
gnu: radare2: Download over HTTPS. 
* gnu/packages/engineering.scm (radare2)[source]: Use HTTPS.
 2019-06-17 03:04:31 +02:00