jackhill/guix/guix.git
3 years agodeduplication: pass store directory to replace-with-link.
Caleb Ristvedt [Sat, 8 Aug 2020 15:05:22 +0000 (10:05 -0500)]
deduplication: pass store directory to replace-with-link.

This causes with-writable-file to take into consideration the actual store
being used, as passed to 'deduplicate', rather than
whatever (%store-directory) may return.

* guix/store/deduplication.scm (replace-with-link): new keyword argument
  'store'.  Pass to with-writable-file.
  (with-writable-file, call-with-writable-file): new store argument.
  (deduplicate): pass store to replace-with-link.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
3 years ago.dir-locals.el: fix call-with-{retrying-}transaction indenting.
Caleb Ristvedt [Wed, 24 Jun 2020 06:00:40 +0000 (01:00 -0500)]
.dir-locals.el: fix call-with-{retrying-}transaction indenting.

* .dir-locals.el (call-with-transaction, call-with-retrying-transaction):
  change scheme-indent-function property from 2 to 1.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
3 years agognu: python-wrapper: Mention pip in description.
Pierre Neidhardt [Mon, 14 Sep 2020 08:27:32 +0000 (10:27 +0200)]
gnu: python-wrapper: Mention pip in description.

* gnu/packages/python.scm (python-wrapper)[description]: Mention that `pip'
won't work properly if both python and python-wrapper are installed.

3 years agobuild-system: linux-module: Delete some huge items that we probably don't need.
Danny Milosavljevic [Sun, 13 Sep 2020 22:24:13 +0000 (00:24 +0200)]
build-system: linux-module: Delete some huge items that we probably don't need.

* guix/build-system/linux-module.scm (make-linux-module-builder): Delete
some huge items that we probably don't need.

3 years agognu: sxiv: Use 'cc-for-target'.
Efraim Flashner [Mon, 14 Sep 2020 07:30:42 +0000 (10:30 +0300)]
gnu: sxiv: Use 'cc-for-target'.

* gnu/packages/image-viewers.scm (sxiv)[arguments]: Replace hard-coded
gcc substitution with cc-for-target in make-flags.

3 years agognu: sxiv: Install icons.
Efraim Flashner [Mon, 14 Sep 2020 07:27:46 +0000 (10:27 +0300)]
gnu: sxiv: Install icons.

* gnu/packages/image-viewers.scm (sxiv)[arguments]: Add custom phase to
install icons.

3 years agognu: sxiv: Install desktop file.
Efraim Flashner [Mon, 14 Sep 2020 07:25:34 +0000 (10:25 +0300)]
gnu: sxiv: Install desktop file.

* gnu/packages/image-viewers.scm (sxiv)[arguments]: Add custom
'install-desktop-file phase to install desktop file.

3 years agognu: rofi: Update to 1.6.0.
Gabriel Arazas [Sun, 13 Sep 2020 13:39:12 +0000 (21:39 +0800)]
gnu: rofi: Update to 1.6.0.

* gnu/packages/xdisorg.scm (rofi): Update to 1.6.0.
[inputs]: Add libjpeg-turbo.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
3 years agognu: Update coq and its dependents
Robin Green [Sun, 13 Sep 2020 14:12:18 +0000 (15:12 +0100)]
gnu: Update coq and its dependents

* gnu/packages/coq.scm (coq): Update to 8.11.2
(coq-flocq): Update to 3.3.1
(coq-gappa): Update to 1.4.4
(coq-mathcomp): Update to 1.11.0
(coq-coquelicot): Update to 3.1.0
(coq-bignums): Update to 8.11.0
(coq-interval): Update to 4.0.0
(coq-equations): Update to 1.2.3

Signed-off-by: Julien Lepiller <julien@lepiller.eu>
3 years agognu: youtube-dl: Update to 2020.09.14.
Tobias Geerinckx-Rice [Sun, 13 Sep 2020 22:55:23 +0000 (00:55 +0200)]
gnu: youtube-dl: Update to 2020.09.14.

* gnu/packages/video.scm (youtube-dl): Update to 2020.09.14.

3 years agognu: python-ansi2html: Fix typo in description.
Tobias Geerinckx-Rice [Sun, 13 Sep 2020 21:10:51 +0000 (23:10 +0200)]
gnu: python-ansi2html: Fix typo in description.

* gnu/packages/python-xyz.scm (python-ansi2html)[description]: Fix typo.

3 years agognu: wesnoth: Update to 1.14.14.
Tobias Geerinckx-Rice [Sun, 13 Sep 2020 22:22:10 +0000 (00:22 +0200)]
gnu: wesnoth: Update to 1.14.14.

* gnu/packages/games.scm (wesnoth): Update to 1.14.14.

3 years agognu: jasper: Update to 2.0.20 [fixes CVE-2016-9398's revenge].
Tobias Geerinckx-Rice [Sun, 13 Sep 2020 22:21:30 +0000 (00:21 +0200)]
gnu: jasper: Update to 2.0.20 [fixes CVE-2016-9398's revenge].

* gnu/packages/image.scm (jasper): Update to 2.0.20.
[arguments]: Skip tests of the now-disabled MIF image format.

3 years agognu: shellcheck: Update to 0.7.1.
Tobias Geerinckx-Rice [Sun, 13 Sep 2020 22:01:32 +0000 (00:01 +0200)]
gnu: shellcheck: Update to 0.7.1.

* gnu/packages/haskell-apps.scm (shellcheck): Update to 0.7.1.

3 years agognu: bear: Update to 2.4.4.
Tobias Geerinckx-Rice [Sun, 13 Sep 2020 21:43:08 +0000 (23:43 +0200)]
gnu: bear: Update to 2.4.4.

* gnu/packages/build-tools.scm (bear): Update to 2.4.4.

3 years agognu: libhandy: Enable glade_catalog.
Leo Prikler [Tue, 8 Sep 2020 12:08:33 +0000 (14:08 +0200)]
gnu: libhandy: Enable glade_catalog.

* gnu/packages/gnome.scm (libhandy)[configure-flags]: Add glade_catalog.
[inputs]: Add glade and libxml2.
(libhandy-0.0)[configure-flags]: Keep glade_catalog disabled.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
3 years agognu: glade: Add catalog and module search paths.
Leo Prikler [Tue, 8 Sep 2020 12:03:40 +0000 (14:03 +0200)]
gnu: glade: Add catalog and module search paths.

* gnu/packages/gnome.scm (glade3)[native-search-paths]: Add
GLADE_CATALOG_SEARCH_PATH and GLADE_MODULE_SEARCH_PATH.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
3 years agognu: emacs-djvu: Add needed inputs
Morgan Smith [Wed, 9 Sep 2020 02:21:11 +0000 (22:21 -0400)]
gnu: emacs-djvu: Add needed inputs

* gnu/packages/emacs-xyz.scm (emacs-djvu)[inputs, arguments]: New fields.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
3 years agoservices: certbot: Support registration without email.
Timotej Lazar [Fri, 11 Sep 2020 11:55:55 +0000 (13:55 +0200)]
services: certbot: Support registration without email.

* gnu/services/certbot.scm (certbot-configuration): Add default for the
email option.
(certbot-command): Pass email for registration only when specified.
* doc/guix.texi (Certificate Services): "mandatory"→"optional" email.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
3 years agognu: fmt: Update to 7.0.3.
Greg Hogan [Fri, 11 Sep 2020 10:58:03 +0000 (06:58 -0400)]
gnu: fmt: Update to 7.0.3.

From 820d39a55a5673fffac70c919b8cc3b28d94f6e7 Mon Sep 17 00:00:00 2001
From: Greg Hogan <code@greghogan.com>
Date: Fri, 11 Sep 2020 10:53:20 +0000
Subject: [PATCH] gnu: fmt: Update to 7.0.3.

* gnu/packages/pretty-print.scm (fmt): Update to 7.0.3.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
3 years agognu: gcc-toolchain: Reword description.
zimoun [Fri, 11 Sep 2020 16:08:00 +0000 (18:08 +0200)]
gnu: gcc-toolchain: Reword description.

* gnu/packages/commencement.scm (make-gcc-toolchain)[description]: Reword.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
3 years agognu: gccgo: Reword synopsis and description.
zimoun [Fri, 11 Sep 2020 16:07:59 +0000 (18:07 +0200)]
gnu: gccgo: Reword synopsis and description.

Fixes <https://bugs.gnu.org/43303>.
Reported by Jeffrey Walton <noloader@gmail.com>.

* gnu/packages/gcc.scm: (gccgo-4.9): Add synopsis and description

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
3 years agognu: libgccjit: Reword synopsis and description.
zimoun [Fri, 11 Sep 2020 16:07:58 +0000 (18:07 +0200)]
gnu: libgccjit: Reword synopsis and description.

Fixes <https://bugs.gnu.org/43303>.
Reported by Jeffrey Walton <noloader@gmail.com>.

* gnu/packages/gcc.scm: (libgccjit)[synopsis,description]: Reword.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
3 years agognu: zrythm: Update to 0.8.911.
Alexandros Theodotou [Fri, 11 Sep 2020 16:48:40 +0000 (17:48 +0100)]
gnu: zrythm: Update to 0.8.911.

* gnu/packages/music.scm (zrythm): Update to 0.8.911.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
3 years agognu: Add meson 0.55.1.
Alexandros Theodotou [Fri, 11 Sep 2020 16:27:56 +0000 (17:27 +0100)]
gnu: Add meson 0.55.1.

* gnu/packages/build-tools.scm (meson-0.55): New variable.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
3 years agognu: libaudec: Update to 0.2.3.
Alexandros Theodotou [Fri, 11 Sep 2020 16:37:23 +0000 (17:37 +0100)]
gnu: libaudec: Update to 0.2.3.

* gnu/packages/audio.scm (libaudec): Update to 0.2.3.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
3 years agognu: libcyaml: Update to 1.1.0.
Ludovic Courtès [Fri, 11 Sep 2020 15:14:34 +0000 (17:14 +0200)]
gnu: libcyaml: Update to 1.1.0.

* gnu/packages/web.scm (libcyaml): Update to 1.1.0.

3 years agoservices: Fix zram-device-service.
Tobias Geerinckx-Rice [Sun, 13 Sep 2020 21:02:49 +0000 (23:02 +0200)]
services: Fix zram-device-service.

* gnu/services/linux.scm (<zram-device-configuration>): Fix typo.

3 years agognu: Fix a crash in NTP and Chrony.
Leo Famulari [Sat, 12 Sep 2020 00:51:22 +0000 (20:51 -0400)]
gnu: Fix a crash in NTP and Chrony.

Fixes <https://bugs.gnu.org/43321>.

* gnu/packages/ntp.scm (ntp, chrony)[inputs]: Replace libcap with libcap/next.

3 years agognu: josm: Fix formatting and install more files.
Christopher Baines [Sun, 13 Sep 2020 08:31:15 +0000 (09:31 +0100)]
gnu: josm: Fix formatting and install more files.

This means that JOSM appears in the GNOME Shell menu.

* gnu/packages/geo.scm (josm)[source]: Replace tab character.
[arguments]: Reduce line length, and add install-share-directories phase.

3 years agognu: profanity: Change build system.
Raghav Gururajan [Sun, 13 Sep 2020 04:30:10 +0000 (00:30 -0400)]
gnu: profanity: Change build system.

* gnu/package/messaging.scm (profanity) [build-system]: Change from
gnu to glib-or-gtk.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
3 years agognu: profanity: Enable plugins, icons and clipboard.
Raghav Gururajan [Sun, 13 Sep 2020 04:27:19 +0000 (00:27 -0400)]
gnu: profanity: Enable plugins, icons and clipboard.

* gnu/packages/messaging.scm (profanity) [arguments]<#:configure-flags>
[--enable-python-plugins]: New flag.
[--enable-plugins]: New flag.
[--enable-icons-and-clipboard]: New flag.
[--enable-icons]: Remove flag.
[inputs]: Add python-wrapper.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
3 years agognu: profanity: Move some dependencies.
Raghav Gururajan [Sun, 13 Sep 2020 04:22:25 +0000 (00:22 -0400)]
gnu: profanity: Move some dependencies.

* gnu/packages/messaging.scm (profanity) [native-inputs]: Move gtk-2,
libnotify and libsignal-protocol-c to ...
[inputs]: ... here.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
3 years agognu: profanity: Make some cosmetic changes.
Raghav Gururajan [Sun, 13 Sep 2020 04:19:38 +0000 (00:19 -0400)]
gnu: profanity: Make some cosmetic changes.

* gnu/packages/messaging.scm (profanity): Make some cosmetic changes.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
3 years agognu: editorconfig-vim: Update to 1.1.1.
Efraim Flashner [Sat, 12 Sep 2020 19:33:26 +0000 (22:33 +0300)]
gnu: editorconfig-vim: Update to 1.1.1.

* gnu/packages/vim.scm (editorconfig-vim): Update to 1.1.1.
[source]: Remove snippet.
[arguments]: Remove custom 'patch-editorconfig-path phase.
[inputs]: Remove editorconfig-core-c.

3 years agognu: muse-sequencer: Enable more features.
Ricardo Wurmus [Sat, 12 Sep 2020 12:53:14 +0000 (14:53 +0200)]
gnu: muse-sequencer: Enable more features.

* gnu/packages/music.scm (muse-sequencer)[arguments]: Add phase "fix-include"
to patch header file reference; remove obsolete ENABLE_LV2_SUPPLIED
configuration option; remove ENABLE_RTAUDIO=OFF.
[inputs]: Add lrdf, pulseaudio, rtaudio, and rubberband.

3 years agognu: muse-sequencer: Update to 3.1.1.
Ricardo Wurmus [Sat, 12 Sep 2020 06:42:49 +0000 (08:42 +0200)]
gnu: muse-sequencer: Update to 3.1.1.

* gnu/packages/music.scm (muse-sequencer): Update to 3.1.1.
[arguments]: Set CMAKE_EXE_LINKER_FLAGS and CMAKE_SHARED_LINKER_FLAGS; end
"chdir" phase with #T.

3 years agognu: emacs-pdf-tools: Update to 0.90-1.
Nicolas Goaziou [Sat, 12 Sep 2020 12:09:40 +0000 (14:09 +0200)]
gnu: emacs-pdf-tools: Update to 0.90-1.

* gnu/packages/emacs-xyz.scm (emacs-pdf-tools): Update to 0.90-1.  Fix
indentation.

Update to an unreleased commit to fix an incompatibility with Emacs 27+.

3 years agoRevert "gnu: linux-libre: Update to 5.8.8."
Oleg Pykhalov [Sat, 12 Sep 2020 10:20:19 +0000 (13:20 +0300)]
Revert "gnu: linux-libre: Update to 5.8.8."

This reverts commit ad42c20921235532e80e776fd55090127389208b, which breaks
"guix system build" as described in <https://issues.guix.info/issue/43352>.

3 years agoui: Lexicographically sort transaction entries based on their package name.
Maxim Cournoyer [Wed, 2 Sep 2020 17:08:46 +0000 (13:08 -0400)]
ui: Lexicographically sort transaction entries based on their package name.

* guix/ui.scm (show-manifest-transaction): Sort entries to be displayed in a
tabulated view.

3 years agoui: Refactor the package-strings helper in show-manifest-transaction.
Maxim Cournoyer [Wed, 2 Sep 2020 15:52:16 +0000 (11:52 -0400)]
ui: Refactor the package-strings helper in show-manifest-transaction.

* guix/ui.scm (show-manifest-transaction)[package-strings]: Add an
OLD-VERSIONS keyword parameter.  Absorb the code path previously found in the
upgrade-string.  Remove upgrade-string.
(show-manifest-transaction): Adjust to the above changes.

3 years agodoc: Document the use of snippets vs phases.
Maxim Cournoyer [Fri, 11 Sep 2020 18:08:34 +0000 (14:08 -0400)]
doc: Document the use of snippets vs phases.

* doc/contributing.texi (Snippets versus phases): New section.

3 years agognu: python-aiodns: Propagate python-pycares.
Danny Milosavljevic [Sat, 12 Sep 2020 00:31:26 +0000 (02:31 +0200)]
gnu: python-aiodns: Propagate python-pycares.

* gnu/packages/python-web.scm (python-aiodns)[inputs]: Move python-pycares...
[propagated-inputs]: ...to here.

3 years agognu: Add poezio.
Raghav Gururajan [Fri, 11 Sep 2020 18:04:08 +0000 (14:04 -0400)]
gnu: Add poezio.

* gnu/packages/messaging.scm (poezio): New variable.

3 years agognu: Add python-potr.
Raghav Gururajan [Fri, 11 Sep 2020 16:45:24 +0000 (12:45 -0400)]
gnu: Add python-potr.

* gnu/packages/python-crypto.scm (python-potr): New variable.

3 years agognu: Add python-slixmpp.
Raghav Gururajan [Fri, 11 Sep 2020 18:34:02 +0000 (14:34 -0400)]
gnu: Add python-slixmpp.

* gnu/packages/python-xyz.scm (python-slixmpp): New variable.

3 years agognu: ebusd: Enable MQTT support.
Danny Milosavljevic [Sat, 12 Sep 2020 00:05:57 +0000 (02:05 +0200)]
gnu: ebusd: Enable MQTT support.

* gnu/packages/embedded.scm (ebusd)[inputs]: Add mosquitto.

3 years agognu: Add mosquitto.
Danny Milosavljevic [Sat, 12 Sep 2020 00:04:28 +0000 (02:04 +0200)]
gnu: Add mosquitto.

* gnu/packages/messaging.scm (mosquitto): New variable.

3 years agognu: lldpd: Update to 1.0.6.
Tobias Geerinckx-Rice [Fri, 11 Sep 2020 20:35:32 +0000 (22:35 +0200)]
gnu: lldpd: Update to 1.0.6.

* gnu/packages/networking.scm (lldpd): Update to 1.0.6.

3 years agognu: enet: Update to 1.3.16.
Tobias Geerinckx-Rice [Fri, 11 Sep 2020 20:32:33 +0000 (22:32 +0200)]
gnu: enet: Update to 1.3.16.

* gnu/packages/networking.scm (enet): Update to 1.3.16.

3 years agognu: batctl: Update to 2020.3.
Tobias Geerinckx-Rice [Fri, 11 Sep 2020 20:27:13 +0000 (22:27 +0200)]
gnu: batctl: Update to 2020.3.

* gnu/packages/networking.scm (batctl): Update to 2020.3.

3 years agoRevert "gnu: dovecot: Set moduledir to global directory."
Tobias Geerinckx-Rice [Fri, 11 Sep 2020 21:29:50 +0000 (23:29 +0200)]
Revert "gnu: dovecot: Set moduledir to global directory."

This reverts commit db0109be42547d5dbb0fc1eb8ae30ccc968ed88b.
Same reason as commit d9d88c2ff0d367599d0a851ccf9377c4e21079d6.

3 years agoRevert "services: dovecot: Use modules via symlink to system profile."
Tobias Geerinckx-Rice [Fri, 11 Sep 2020 20:19:02 +0000 (22:19 +0200)]
Revert "services: dovecot: Use modules via symlink to system profile."

This reverts commit bcfe0f0c1e9a2b91049d7c6c591c7f0c6a002c14 for now.

It breaks most current use(r)s of the Dovecot service and needs to be
combined with an extra modules configuration field of some kind.

See <https://issues.guix.gnu.org/43347>.

3 years agognu: padthv1: Update to 0.9.17.
Tobias Geerinckx-Rice [Fri, 11 Sep 2020 17:17:29 +0000 (19:17 +0200)]
gnu: padthv1: Update to 0.9.17.

* gnu/packages/music.scm (padthv1): Update to 0.9.17.
[inputs]: Replace fftw with fftwf.

3 years agognu: libetpan: Update to 1.9.4.
Tobias Geerinckx-Rice [Fri, 11 Sep 2020 15:04:57 +0000 (17:04 +0200)]
gnu: libetpan: Update to 1.9.4.

* gnu/packages/mail.scm (libetpan): Update to 1.9.4.

3 years agognu: bsequencer: Update to 1.6.0.
Ricardo Wurmus [Fri, 11 Sep 2020 20:19:26 +0000 (22:19 +0200)]
gnu: bsequencer: Update to 1.6.0.

* gnu/packages/music.scm (bsequencer): Update to 1.6.0.

3 years agognu: r-adaptivesparsity: End build phase on #T.
Ricardo Wurmus [Fri, 11 Sep 2020 20:04:41 +0000 (22:04 +0200)]
gnu: r-adaptivesparsity: End build phase on #T.

* gnu/packages/cran.scm (r-adaptivesparsity)[arguments]: End phase
"link-against-armadillo" with Boolean.

3 years agognu: r-adaptivesparsity: Fix case of "Gaussian".
Ricardo Wurmus [Fri, 11 Sep 2020 20:04:12 +0000 (22:04 +0200)]
gnu: r-adaptivesparsity: Fix case of "Gaussian".

* gnu/packages/cran.scm (r-adaptivesparsity)[description]: Fix typo.

3 years agognu: r-qtl: Use CRAN-URI.
Ricardo Wurmus [Fri, 11 Sep 2020 20:02:22 +0000 (22:02 +0200)]
gnu: r-qtl: Use CRAN-URI.

* gnu/packages/cran.scm (r-qtl)[source]: Use CRAN-URI instead of explicit
mirror URL.

3 years agognu: r-qtl: Correct indentation.
Ricardo Wurmus [Fri, 11 Sep 2020 20:00:30 +0000 (22:00 +0200)]
gnu: r-qtl: Correct indentation.

* gnu/packages/cran.scm (r-qtl): Reindent.
[description]: Reflow paragraphs.

3 years agognu: r-absfiltergsea: Move to (gnu packages cran).
zimoun [Fri, 11 Sep 2020 18:08:48 +0000 (20:08 +0200)]
gnu: r-absfiltergsea: Move to (gnu packages cran).

* gnu/packages/bioinformatics.scm (r-absfiltergsea): Move from here...
* gnu/packages/cran.scm (r-absfiltergsea): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
3 years agognu: r-diversitree: Move to (gnu packages cran).
zimoun [Fri, 11 Sep 2020 18:08:47 +0000 (20:08 +0200)]
gnu: r-diversitree: Move to (gnu packages cran).

* gnu/packages/bioinformatics.scm (r-diversitree): Move from here...
* gnu/packages/cran.scm (r-diversitree): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
3 years agognu: r-phangorn: Move to (gnu packages cran).
zimoun [Fri, 11 Sep 2020 18:08:49 +0000 (20:08 +0200)]
gnu: r-phangorn: Move to (gnu packages cran).

* gnu/packages/bioinformatics.scm (r-phangorn): Move from here...
* gnu/packages/cran.scm (r-phangorn): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
3 years agognu: r-seurat: Move to (gnu packages cran).
zimoun [Fri, 11 Sep 2020 18:08:46 +0000 (20:08 +0200)]
gnu: r-seurat: Move to (gnu packages cran).

* gnu/packages/bioinformatics.scm (r-seurat): Move from here...
* gnu/packages/cran.scm (r-seurat): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
3 years agognu: r-maldiquant: Move to (gnu packages cran).
zimoun [Fri, 11 Sep 2020 18:08:45 +0000 (20:08 +0200)]
gnu: r-maldiquant: Move to (gnu packages cran).

* gnu/packages/bioinformatics.scm (r-maldiquant): Move from here...
* gnu/packages/cran.scm (r-maldiquant): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
3 years agognu: r-seqminer: Move to (gnu packages cran).
zimoun [Fri, 11 Sep 2020 18:08:44 +0000 (20:08 +0200)]
gnu: r-seqminer: Move to (gnu packages cran).

* gnu/packages/bioinformatics.scm (r-seqminer): Move from here...
* gnu/packages/cran.scm (r-seqminer): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
3 years agognu: r-qtl2: Move to (gnu packages cran).
zimoun [Fri, 11 Sep 2020 18:08:43 +0000 (20:08 +0200)]
gnu: r-qtl2: Move to (gnu packages cran).

* gnu/packages/bioinformatics.scm (r-qtl2): Move from here...
* gnu/packages/cran.scm (r-qtl2): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
3 years agognu: r-qtl: Move to (gnu packages cran).
zimoun [Fri, 11 Sep 2020 18:08:42 +0000 (20:08 +0200)]
gnu: r-qtl: Move to (gnu packages cran).

* gnu/packages/bioinformatics.scm (r-qtl): Move from here...
* gnu/packages/cran.scm (r-qtl): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
3 years agognu: r-igraph: Move to (gnu packages cran).
zimoun [Fri, 11 Sep 2020 18:08:41 +0000 (20:08 +0200)]
gnu: r-igraph: Move to (gnu packages cran).

* gnu/packages/graph.scm (r-igraph): Move from here...
* gnu/packages/cran.scm (r-igraph): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
3 years agognu: r-diffusionmap: Move to (gnu packages cran).
zimoun [Fri, 11 Sep 2020 18:08:40 +0000 (20:08 +0200)]
gnu: r-diffusionmap: Move to (gnu packages cran).

* gnu/packages/graph.scm (r-diffusionmap): Move from here...
* gnu/packages/cran.scm (r-diffusionmap): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
3 years agognu: r-adaptivesparsity: Move to (gnu packages cran).
zimoun [Fri, 11 Sep 2020 18:08:39 +0000 (20:08 +0200)]
gnu: r-adaptivesparsity: Move to (gnu packages cran).

* gnu/packages/machine-learning.scm (r-adaptivesparsity): Move from here...
* gnu/packages/cran.scm (r-adaptivesparsity): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
3 years agognu: r-codedepends: Comment why it is in bioconductor.scm.
zimoun [Fri, 11 Sep 2020 18:08:38 +0000 (20:08 +0200)]
gnu: r-codedepends: Comment why it is in bioconductor.scm.

* gnu/packages/bioconductor.scm (r-codedepends): Add comment.

3 years agognu: Add r-fhtest.
Peter Lo [Fri, 11 Sep 2020 19:01:53 +0000 (21:01 +0200)]
gnu: Add r-fhtest.

* gnu/packages/bioconductor.scm (r-fhtest): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
3 years agognu: Add r-interval.
Peter Lo [Fri, 11 Sep 2020 19:01:30 +0000 (21:01 +0200)]
gnu: Add r-interval.

* gnu/packages/bioconductor.scm (r-interval): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
3 years agognu: Add r-perm.
Peter Lo [Mon, 29 Jun 2020 08:03:38 +0000 (16:03 +0800)]
gnu: Add r-perm.

* gnu/packages/cran.scm (r-perm): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
3 years agognu: Add r-mlecens.
Peter Lo [Mon, 29 Jun 2020 08:03:37 +0000 (16:03 +0800)]
gnu: Add r-mlecens.

* gnu/packages/cran.scm (r-mlecens): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
3 years agognu: Add r-icens.
Peter Lo [Mon, 29 Jun 2020 08:03:36 +0000 (16:03 +0800)]
gnu: Add r-icens.

* gnu/packages/bioconductor.scm (r-icens): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
3 years agognu: r-tidymodels: Update to 0.1.1.
Ricardo Wurmus [Fri, 11 Sep 2020 17:04:21 +0000 (19:04 +0200)]
gnu: r-tidymodels: Update to 0.1.1.

* gnu/packages/cran.scm (r-tidymodels): Update to 0.1.1.
[propagated-inputs]: Remove r-pillar, r-tidyposterior, r-tidypredict, and
r-tidytext; add r-modeldata and r-tidyr.
[native-inputs]: Add r-rmarkdown, pandoc, and pandoc-citeproc.

3 years agognu: r-infer: Update to 0.5.3.
Ricardo Wurmus [Fri, 11 Sep 2020 17:06:33 +0000 (19:06 +0200)]
gnu: r-infer: Update to 0.5.3.

* gnu/packages/cran.scm (r-infer): Update to 0.5.3.

3 years agognu: Add r-modeldata.
Ricardo Wurmus [Fri, 11 Sep 2020 17:06:26 +0000 (19:06 +0200)]
gnu: Add r-modeldata.

* gnu/packages/cran.scm (r-modeldata): New variable.

3 years agognu: r-parsnip: Update to 0.1.3.
Ricardo Wurmus [Fri, 11 Sep 2020 17:04:10 +0000 (19:04 +0200)]
gnu: r-parsnip: Update to 0.1.3.

* gnu/packages/cran.scm (r-parsnip): Update to 0.1.3.

3 years agognu: r-tidytext: Update to 0.2.5.
Ricardo Wurmus [Fri, 11 Sep 2020 17:04:06 +0000 (19:04 +0200)]
gnu: r-tidytext: Update to 0.2.5.

* gnu/packages/cran.scm (r-tidytext): Update to 0.2.5.
[propagated-inputs]: Remove r-stopwords; add r-tibble.

3 years agognu: r-tidypredict: Update to 0.4.6.
Ricardo Wurmus [Fri, 11 Sep 2020 17:04:01 +0000 (19:04 +0200)]
gnu: r-tidypredict: Update to 0.4.6.

* gnu/packages/cran.scm (r-tidypredict): Update to 0.4.6.

3 years agognu: r-tune: Update to 0.1.1.
Ricardo Wurmus [Fri, 11 Sep 2020 17:03:58 +0000 (19:03 +0200)]
gnu: r-tune: Update to 0.1.1.

* gnu/packages/cran.scm (r-tune): Update to 0.1.1.
[propagated-inputs]: Add r-vctrs.

3 years agognu: r-dials: Update to 0.0.8.
Ricardo Wurmus [Fri, 11 Sep 2020 17:03:54 +0000 (19:03 +0200)]
gnu: r-dials: Update to 0.0.8.

* gnu/packages/cran.scm (r-dials): Update to 0.0.8.

3 years agognu: r-yardstick: Update to 0.0.7.
Ricardo Wurmus [Fri, 11 Sep 2020 17:03:51 +0000 (19:03 +0200)]
gnu: r-yardstick: Update to 0.0.7.

* gnu/packages/cran.scm (r-yardstick): Update to 0.0.7.
[propagated-inputs]: Remove r-rcpp.

3 years agognu: r-workflows: Update to 0.1.3.
Ricardo Wurmus [Fri, 11 Sep 2020 17:03:46 +0000 (19:03 +0200)]
gnu: r-workflows: Update to 0.1.3.

* gnu/packages/cran.scm (r-workflows): Update to 0.1.3.

3 years agognu: r-hardhat: Update to 0.1.4.
Ricardo Wurmus [Fri, 11 Sep 2020 17:03:43 +0000 (19:03 +0200)]
gnu: r-hardhat: Update to 0.1.4.

* gnu/packages/cran.scm (r-hardhat): Update to 0.1.4.

3 years agognu: Add r-tidymodels.
Peter Lo [Mon, 29 Jun 2020 05:50:42 +0000 (13:50 +0800)]
gnu: Add r-tidymodels.

* gnu/packages/cran.scm (r-tidymodels): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
3 years agognu: Add r-infer.
Peter Lo [Mon, 29 Jun 2020 05:50:41 +0000 (13:50 +0800)]
gnu: Add r-infer.

* gnu/packages/cran.scm (r-infer): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
3 years agognu: Add r-parsnip.
Peter Lo [Mon, 29 Jun 2020 05:50:40 +0000 (13:50 +0800)]
gnu: Add r-parsnip.

* gnu/packages/cran.scm (r-parsnip): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
3 years agognu: Add r-tidytext.
Peter Lo [Mon, 29 Jun 2020 05:50:39 +0000 (13:50 +0800)]
gnu: Add r-tidytext.

* gnu/packages/cran.scm (r-tidytext): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
3 years agognu: Add r-hunspell.
Peter Lo [Mon, 29 Jun 2020 05:50:38 +0000 (13:50 +0800)]
gnu: Add r-hunspell.

* gnu/packages/cran.scm (r-hunspell): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
3 years agognu: Add r-tokenizers.
Peter Lo [Mon, 29 Jun 2020 05:50:37 +0000 (13:50 +0800)]
gnu: Add r-tokenizers.

* gnu/packages/cran.scm (r-tokenizers): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
3 years agognu: Add r-janeaustenr.
Peter Lo [Mon, 29 Jun 2020 05:50:36 +0000 (13:50 +0800)]
gnu: Add r-janeaustenr.

* gnu/packages/cran.scm (r-janeaustenr): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
3 years agognu: Add r-tidypredict.
Peter Lo [Mon, 29 Jun 2020 05:50:35 +0000 (13:50 +0800)]
gnu: Add r-tidypredict.

* gnu/packages/cran.scm (r-tidypredict): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
3 years agognu: Add r-tidyposterior.
Peter Lo [Mon, 29 Jun 2020 05:50:34 +0000 (13:50 +0800)]
gnu: Add r-tidyposterior.

* gnu/packages/cran.scm (r-tidyposterior): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
3 years agognu: Add r-tune.
Peter Lo [Mon, 29 Jun 2020 05:50:33 +0000 (13:50 +0800)]
gnu: Add r-tune.

* gnu/packages/cran.scm (r-tune): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
3 years agognu: Add r-dials.
Peter Lo [Mon, 29 Jun 2020 05:50:32 +0000 (13:50 +0800)]
gnu: Add r-dials.

* gnu/packages/cran.scm (r-dials): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
3 years agognu: Add r-dicedesign.
Peter Lo [Mon, 29 Jun 2020 05:50:31 +0000 (13:50 +0800)]
gnu: Add r-dicedesign.

* gnu/packages/cran.scm (r-dicedesign): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>