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Author SHA1 Message Date
Leo Famulari 8937898af9
gnu: linux-libre 5.4: Update to 5.4.245. 
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.245.
(linux-libre-5.4-pristine-source): Update hash.
 2023-06-05 19:18:56 -04:00
Leo Famulari 00e2d8d8ae
gnu: linux-libre 5.10: Update to 5.10.182. 
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.182.
(linux-libre-5.10-pristine-source): Update hash.
 2023-06-05 19:18:55 -04:00
Leo Famulari f9755ff2ac
gnu: linux-libre 5.15: Update to 5.15.115. 
* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.115.
(linux-libre-5.15-pristine-source): Update hash.
 2023-06-05 19:18:55 -04:00
Leo Famulari 455e88bc84
gnu: linux-libre 6.1: Update to 6.1.32. 
* gnu/packages/linux.scm (linux-libre-6.1-version): Update to 6.1.32.
(linux-libre-6.1-pristine-source): Update hash.
 2023-06-05 19:18:55 -04:00
Leo Famulari b3dfa5b671
gnu: linux-libre: Update to 6.3.6. 
* gnu/packages/linux.scm (linux-libre-6.3-version): Update to 6.3.6.
(linux-libre-6.3-pristine-source): Update hash.
 2023-06-05 19:18:47 -04:00
Efraim Flashner f598f5b870
gnu: blurhash: Update to 0.2.0. 
* gnu/packages/image.scm (blurhash): Update to 0.2.0.
[native-inputs]: Remove cmake. Add pkg-config.
 2023-06-05 22:05:13 +03:00
Efraim Flashner ff6bb37299
gnu: cpp-httplib: Update to 0.12.5. 
* gnu/packages/cpp.scm (cpp-httplib): Update to 0.12.5.
[arguments]: Adjust configure-flags to build the tests.  Add a make-flag
to set CXX.  Adjust custom 'disable-network-tests phase to skip more
network tests. Remove custom 'check phase.
[native-inputs]: Add googletest.
 2023-06-05 22:00:56 +03:00
Efraim Flashner cad86f8dcd
gnu: python-codespell: Update to 2.2.4. 
* gnu/packages/python-xyz.scm (python-codespell): Update to 2.2.4.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Remove python-check-manifest; add python-pygments and
python-tomli.
 2023-06-05 21:36:09 +03:00
Ricardo Wurmus 52e0a77a1b
gnu: proj-7: Add upstream patch. 
* gnu/packages/patches/proj-7-initialize-memory.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/geo.scm (proj-7)[source]: Add it.
 2023-06-05 17:55:38 +02:00
Ricardo Wurmus 4f2ec0f2d1
gnu: python-bulkvis: Reference upstream issue. 
* gnu/packages/bioinformatics.scm (python-bulkvis)[arguments]: Add comment
with link to upstream issue for bokeh compatibility patch.
 2023-06-05 17:20:52 +02:00
Ricardo Wurmus 77d6d5783b
gnu: python-tenacity: Use pyproject-build-system. 
* gnu/packages/python-xyz.scm (python-tenacity)[build-system]: Use
pyproject-build-system.
[arguments]: Remove.
 2023-06-05 17:11:15 +02:00
Ricardo Wurmus 46fc4c01a0
gnu: python-tenacity: Use Tornado 6. 
* gnu/packages/python-xyz.scm (python-tenacity)[native-inputs]: Replace
python-tornado with python-tornado-6.
 2023-06-05 17:11:15 +02:00
Ricardo Wurmus 1671aa25d4
gnu: python-bokeh: Use Tornado 6. 
* gnu/packages/python-xyz.scm (python-bokeh)[propagated-inputs]: Replace
python-tornado with python-tornado-6.
 2023-06-05 17:11:15 +02:00
Navid Afkhami 6559adea29
gnu: Add python-bulkvis. 
* gnu/packages/bioinformatics.scm (python-bulkvis): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2023-06-05 17:11:15 +02:00
Navid Afkhami 91e75bb35f
gnu: Add python-readpaf. 
* gnu/packages/bioinformatics.scm (python-readpaf): New variable.
 2023-06-05 17:11:14 +02:00
Efraim Flashner 940665301d
gnu: gcompris-qt: Update to 3.2. 
* gnu/packages/education.scm (gcompris-qt): Update to 3.2.
[inputs]: Add qtcharts, qtquickcontrols2-5. Remove qtquickcontrols-5,
qtxml-5.
 2023-06-05 11:35:52 +03:00
Timotej Lazar a95edc3d7b
gnu: mupdf: Update to 1.22.1. 
* gnu/packages/pdf.scm (mupdf): Update to 1.22.1.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-06-05 10:29:01 +03:00
Efraim Flashner eed55a6544
gnu: lagrange: Update to 1.16.3. 
* gnu/packages/web-browsers.scm (lagrange): Update to 1.16.3.
 2023-06-04 21:08:30 +03:00
Efraim Flashner c15470671a
gnu: keepassxc: Update to 2.7.5. 
* gnu/packages/password-utils.scm (keepassxc): Update to 2.7.5.
 2023-06-04 21:08:30 +03:00
Efraim Flashner f8b82976d6
gnu: urlscan: Update to 1.0.0. 
* gnu/packages/mail.scm (urlscan): Update to 1.0.0.
[arguments]: Skip the test phase.
[build-system]: Switch to the pyproject-build-system.
[native-inputs]: Add python-hatch-vcs, python-hatchling.
 2023-06-04 21:06:47 +03:00
Efraim Flashner 9d9e793da5
gnu: tree: Update to 2.1.1. 
* gnu/packages/admin.scm (tree): Update to 2.1.1.
[arguments]: Remove unneeded 'fix-manpage-version phase.
 2023-06-04 19:02:15 +03:00
Zheng Junjie ae04b3996b
gnu: jpegoptim: Fix cross-compiling to riscv64. 
* gnu/packages/image.scm (jpegoptim)[arguments]: When cross-compiling t
riscv64, add phase to update-config-scripts.
[native-inputs]: When cross-compiling to riscv64, add config.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-06-04 15:28:53 +03:00
Zheng Junjie 4f3e5548fc
gnu: libicns: Fix cross-compiling to riscv64. 
* gnu/packages/image.scm (libicns)[arguments]: When cross-compiling to
riscv64, add phase to update-config-scripts.
[native-inputs]: When cross-compiling to riscv64, add config.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-06-04 15:28:20 +03:00
Zheng Junjie 713da38002
gnu: gsettings-desktop-schemas: Fix cross-compiling. 
* gnu/packages/gnome.scm(gsettings-desktop-schemas)[inputs]: Add
gobject-introspection.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-06-04 15:02:07 +03:00
Zheng Junjie 3f45c3b12b
gnu: gobject-introspection: Fix cross-compiling. 
* gnu/packages/glib.scm(gobject-introspection)[native-inputs]: When
cross-compiling add python.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-06-04 14:58:28 +03:00
Zheng Junjie 188da31fe5
gnu: mtdev: Fix cross-compiling to riscv64. 
* gnu/packages/xdisorg.scm (mtdev)[arguments]: When cross-compiling to
riscv64 add a phase to update config.{guess,sub}.
[native-inputs]: When cross-compiling to riscv64 add config.
 2023-06-04 14:56:09 +03:00
Zheng Junjie 0ee6c9ea01
gnu: xcb-util-wm: Fix cross-compiling to riscv64. 
* gnu/packages/xorg.scm (xcb-util-wm)[arguments]: Add
update-config-scripts phase when cross-compiling to riscv64.
[native-inputs]: Add config when cross-compiling to riscv64.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-06-04 14:46:56 +03:00
Zheng Junjie 81515a4029
gnu: libxtst: Fix cross-compiling to riscv64. 
* gnu/packages/xorg.scm (libxtst)[arguments]: When cross-compiling to
riscv64, add phase to update config.{guess,sub}.
[native-inputs]: When cross-compiling to riscv64, add config.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-06-04 14:44:55 +03:00
Efraim Flashner d845178050
gnu: libdeflate: Use default tests. 
* gnu/packages/compression.scm (libdeflate)[arguments]: Adjust
configure-flags to build the test suite. Remove custom 'check phase.
 2023-06-04 14:18:23 +03:00
Josselin Poiret e198fe4e94
gnu: agda-ial: Update to ded30c410d5d40142249686572aa1acd1b2f8cc7. 
* gnu/packages/agda.scm (agda-ial): Update to
ded30c410d5d40142249686572aa1acd1b2f8cc7, use agda-build-system, switch to
G-Exps, reorder fields.
 2023-06-04 11:04:54 +02:00
Josselin Poiret 067e75e17a
gnu: Add agda-1lab. 
* gnu/packages/agda.scm: New variable agda-1lab.
 2023-06-04 10:59:36 +02:00
Josselin Poiret cf2c3f7970
gnu: Add agda-cubical. 
* gnu/packages/agda.scm: New variable agda-cubical.
 2023-06-04 10:59:36 +02:00
Josselin Poiret 8203e8f3c9
gnu: Add agda-categories. 
* gnu/packages/patches/agda-categories-use-find.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/agda.scm: New variable agda-categories.
 2023-06-04 10:59:35 +02:00
Josselin Poiret c1f8bcbbda
gnu: Add agda-stdlib. 
* gnu/packages/patches/agda-stdlib-use-runhaskell.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/agda.scm: New variable agda-stdlib.
 2023-06-04 10:59:34 +02:00
Josselin Poiret 7a00ab0532
gnu: agda: Add AGDA_LIBDIRS search-path. 
* gnu/packages/patches/agda-libdirs-env-variable.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/agda.scm (agda): Patch agda, and add search path.
 2023-06-04 10:59:33 +02:00
Josselin Poiret ae29c9d26e
gnu: emacs-agda2-mode: Switch to G-Exps. 
* gnu/packages/agda.scm (emacs-agda2-mode): Switch it up.
 2023-06-04 10:59:32 +02:00
Josselin Poiret fe6c31e333
gnu: emacs-agda2-mode: No longer inherit from agda. 
* gnu/packages/agda.scm (emacs-agda2-mode): Remove it. Made no sense, as we only
need the source, which we can refer to without inheriting the whole thing.
 2023-06-04 10:59:31 +02:00
Josselin Poiret 789db27c51
gnu: agda: Build info manual. 
* gnu/packages/agda.scm (agda): Build the user manual as an info manual.
 2023-06-04 10:59:31 +02:00
Josselin Poiret af5d228b13
gnu: agda: Update to 2.6.3 and switch to git-fetch. 
* gnu/packages/agda.scm (agda): Update to 2.6.3, switch to fetching using git so
that doc files are included, and add new dependency ghc-vector-hashtables.
 2023-06-04 10:59:30 +02:00
Josselin Poiret cc67085077
gnu: Add ghc-vector-hashtables. 
* gnu/packages/haskell-xyz.scm (ghc-vector-hashtables): New variable.
 2023-06-04 10:59:30 +02:00
Josselin Poiret 89f8fc9c95
gnu: Add ghc-peano. 
* gnu/packages/haskell-xyz.scm (ghc-peano): New variable.
 2023-06-04 10:59:29 +02:00
kiasoc5 f72f3a909a
gnu: sbsigntools: Update to 0.9.5. 
This fixes a build failure with openssl-3.

* gnu/packages/efi.scm (sbsigntools): Update to 0.9.5.
[arguments]: Remove trailing #t's. Use Gexps. Use "this-package-input". Simplify lambdas.
[inputs]: Remove labels.

Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
 2023-06-04 10:33:59 +02:00
Josselin Poiret b741218e91
gnu: proot: Update to 5.4.0 and fix clone3 behavior. 
* gnu/packages/patches/proot-add-clone3.patch: New patch.
* gnu/packages/linux.scm (proot): Update to 5.4.0, and add pending upstream
patch to fix buggy pthread support.
* gnu/local.mk (dist_patch_DATA): Register it.
 2023-06-04 10:33:59 +02:00
Felix Lechner d89247150f
gnu: heimdal: Drop obsolete and insecure user tools. 
According to messages from the Heimdal maintainers Brian May and Nico
Williams, no one should be using their version of 'su' anymore. It was deleted
from the development branch five years ago [1] and is only being shipped
because the 7.8.0 is based on an older, stable branch.

[1] 8a77f45aff

Following the directions from the maintainers, this commit drops all
executables built from the ./appl folder via deletion of that SUBDIR from
the top-level Makefile.am.

Unfortunately, the heimdal-discuss mailing list does not appear to have a
public archive. The relevant SMTP Message-Id was:

    <MDAEMON-F202305111940.AA401569md5001000003030@sequoia-grove.ad.secure-endpoints.com>

* gnu/packages/kerberos.scm (heimdal): Drop obsolete and insecure user tools.

Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
 2023-06-04 10:33:58 +02:00
Felix Lechner 94879ff743
gnu: heimdal: Run autoreconf. 
* gnu/packages/kerberos.scm (heimdal): Run autoreconf.

Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
 2023-06-04 10:33:57 +02:00
muradm f4f5ee6ad6
services: screen-locker-service-type: Configurable PAM and setuid. 
screen-locker-service-type by default does both define PAM entry
and make program setuid binary. Normally both methods are
mutually exclusive, if binary has setuid set it does not really
needs PAM, otherway around also similar, if PAM is enabled
binary should not relay on setuid.

Recent swaylock package now compiled with PAM support. When PAM
support is compiled in, swaylock rejects executing if binary is
also setuid program.

This change turns screen-locker-configuration from strict
PAM AND setuid to more flexible PAM AND/OR setuid. Allowing
swaylock to be configured properly while supporting other
screen locker preferences.

* gnu/services/xorg.scm (screen-locker-configuration): Switch from
define-record-type to define-configuration.
[using-pam?]: New field to control PAM entry existence.
[using-setuid?]: New field to control setuid binary existence.
(screen-locker-pam-services): Should not make unix-pam-service if
using-pam? is set to #f.
(screen-locker-setuid-programs): Should not make program setuid
program if using-setuid? is set to #f.
(screen-locker-generate-doc): Internal function to generate
configuration documentation.
(screen-locker-service): Adapt to new screen-locker-configuration.
* gnu/services/desktop.scm (desktop-services-for-system): Adapt to
new screen-locker-configuration.
* doc/guix.texi: Reflect new changes to screen-locker-configuration.

Signed-off-by: Josselin Poiret <dev@jpoiret.xyz>
 2023-06-04 10:33:55 +02:00
Bruno Victal 65bce4d9f9
gnu: mpd: Split outputs. 
The HTML manual accounts for more than 40% of the package size.

* gnu/packages/mpd.scm (mpd)[outputs]: Add 'doc' output.
[arguments]<#:phases>: Add ‘split-package’.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2023-06-04 08:20:14 +02:00
Bruno Victal 709fd0e5e0
gnu: mpd: Enable tests. 
With this, ninja will no longer report “no work to do” when inside the
`check' phase.

* gnu/packages/mpd.scm [arguments]<#:configure-flags>: Add “-Dtest=true”.
[native-inputs]: Add googletest and zip.  Remove cmake.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2023-06-04 08:20:14 +02:00
Leo Famulari 0d6749be37
gnu: mpd: Update to 0.23.13. 
* gnu/packages/mpd.scm (mpd): Update to 0.23.13.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2023-06-04 08:20:14 +02:00
Zhu Zihao 07ac0cb722
gnu: d-feet: Fix build errors when using Meson 1.1.0. 
Fix the build error:

data/meson.build:15:0: ERROR: Function does not take positional arguments.
data/meson.build:27:0: ERROR: Function does not take positional arguments.

* gnu/packages/patches/d-feet-drop-unused-meson-argument.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it here.
* gnu/packages/gnome.scm (d-feet)[source]: Use it here.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2023-06-04 08:20:13 +02:00
Arun Isaac b3492964c2
gnu: font-charter: Remove woff2 output. 
The font-build-system now installs web fonts too. So, a separate woff2 output
is not necessary.

* gnu/packages/fonts.scm (font-charter)[outputs, arguments]: Delete.
 2023-06-03 22:13:08 +01:00
Efraim Flashner bb3454a83f
gnu: notcurses: Enable building without pandoc. 
* gnu/packages/notcurses.scm (notcurses)[arguments]: Adjust
configure-flags to not use pandoc on systems where pandoc isn't
supported.
[native-inputs]: Don't include pandoc on systems where it isn't
supported.
 2023-06-03 22:10:51 +03:00
Hilton Chain 66c9b82fed
gnu: emacs-straight-el: Update to 0-2.039e5c9. 
* gnu/packages/emacs-xyz.scm (emacs-straight-el): Update to 0-2.039e5c9.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-06-03 12:35:05 +01:00
Artyom V. Poptsov e8eb389594
gnu: guile-png: Update to 0.5.0. 
* gnu/packages/guile-xyz.scm (guile-png): Update to 0.5.0.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-06-03 12:34:43 +01:00
gemmaro f30f8ecc69
gnu: python-zulip: Fix test failure. 
* gnu/packages/messaging.scm (python-zulip): Fix test failure.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-06-03 12:33:52 +01:00
Christopher Baines c5aeb15267
gnu: guix-build-coordinator: Update to 0-85.c44d485. 
* gnu/packages/package-management.scm (guix-build-coordinator): Update to
0-85.c44d485.
 2023-06-03 12:21:31 +01:00
Andy Tai 9cf6833033
gnu: Remove obs-spectralizer. 
As project no longer developed and not building with current obs.

* gnu/packages/video.scm (obs-spectralizer): Remove variable.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-06-03 12:16:17 +01:00
Antero Mejr 76b7c50645
gnu: Add s7. 
* gnu/packages/lisp.scm (s7): New variable.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2023-06-03 16:35:52 +08:00
Antero Mejr 1569f7d77e
gnu: Add s7-bootstrap. 
* gnu/packages/lisp.scm (s7-bootstrap): New variable.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2023-06-03 16:35:52 +08:00
Antero Mejr f2f8e2fa2f
gnu: notcurses: Update to 3.0.9. 
* gnu/packages/notcurses.scm (notcurses): Update to 3.0.9.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2023-06-03 16:35:52 +08:00
Ricardo Wurmus da71721db1
gnu: r-biased-urn: Update to 2.0.10. 
* gnu/packages/statistics.scm (r-biased-urn): Update to 2.0.10.
 2023-06-03 08:32:03 +02:00
Ricardo Wurmus 79b52c60e9
gnu: r-matrixstats: Update to 1.0.0. 
* gnu/packages/statistics.scm (r-matrixstats): Update to 1.0.0.
 2023-06-03 08:32:03 +02:00
Ricardo Wurmus 3f8a983cae
gnu: r-mvtnorm: Update to 1.2-0. 
* gnu/packages/statistics.scm (r-mvtnorm): Update to 1.2-0.
 2023-06-03 08:32:03 +02:00
Ricardo Wurmus fccc10b655
gnu: r-stringfish: Update to 0.15.8. 
* gnu/packages/cran.scm (r-stringfish): Update to 0.15.8.
 2023-06-03 08:32:03 +02:00
Ricardo Wurmus 6c321bbded
gnu: r-scico: Update to 1.4.0. 
* gnu/packages/cran.scm (r-scico): Update to 1.4.0.
 2023-06-03 08:32:03 +02:00
Ricardo Wurmus a066040856
gnu: r-shapforxgboost: Update to 0.1.3. 
* gnu/packages/cran.scm (r-shapforxgboost): Update to 0.1.3.
 2023-06-03 08:32:03 +02:00
Ricardo Wurmus e786bef048
gnu: r-projpred: Update to 2.6.0. 
* gnu/packages/cran.scm (r-projpred): Update to 2.6.0.
[propagated-inputs]: Remove r-ucminf; add r-scales.
 2023-06-03 08:32:03 +02:00
Ricardo Wurmus 944bcae0d4
gnu: r-stanheaders: Update to 2.26.26. 
* gnu/packages/cran.scm (r-stanheaders): Update to 2.26.26.
 2023-06-03 08:32:02 +02:00
Ricardo Wurmus 885811d599
gnu: r-regsem: Update to 1.9.5. 
* gnu/packages/cran.scm (r-regsem): Update to 1.9.5.
 2023-06-03 08:32:02 +02:00
Ricardo Wurmus d3bf7c1852
gnu: r-adabag: Update to 5.0. 
* gnu/packages/cran.scm (r-adabag): Update to 5.0.
[propagated-inputs]: Add r-consrank, r-dplyr, and r-tidyr.
 2023-06-03 08:32:02 +02:00
Ricardo Wurmus 0ca364577a
gnu: r-assertive-code: Update to 0.0-4. 
* gnu/packages/cran.scm (r-assertive-code): Update to 0.0-4.
 2023-06-03 08:32:02 +02:00
Ricardo Wurmus 385b7f6ce6
gnu: r-ontologyindex: Update to 2.11. 
* gnu/packages/cran.scm (r-ontologyindex): Update to 2.11.
 2023-06-03 08:32:02 +02:00
Ricardo Wurmus 399657122b
gnu: r-performance: Update to 0.10.4. 
* gnu/packages/cran.scm (r-performance): Update to 0.10.4.
 2023-06-03 08:32:02 +02:00
Ricardo Wurmus 1a9d42ad1e
gnu: r-biasedurn: Update to 2.0.10. 
* gnu/packages/cran.scm (r-biasedurn): Update to 2.0.10.
 2023-06-03 08:32:02 +02:00
Ricardo Wurmus e0e8974176
gnu: r-maptools: Update to 1.1-7. 
* gnu/packages/cran.scm (r-maptools): Update to 1.1-7.
 2023-06-03 08:32:02 +02:00
Ricardo Wurmus 2ebd2d1050
gnu: r-catdap: Update to 1.3.7. 
* gnu/packages/cran.scm (r-catdap): Update to 1.3.7.
[propagated-inputs]: Add r-rcolorbrewer.
 2023-06-03 08:32:01 +02:00
Ricardo Wurmus c34e0df73e
gnu: r-ucminf: Update to 1.2.0. 
* gnu/packages/cran.scm (r-ucminf): Update to 1.2.0.
 2023-06-03 08:32:01 +02:00
Ricardo Wurmus 4c14c0a574
gnu: r-sp: Update to 1.6-1. 
* gnu/packages/cran.scm (r-sp): Update to 1.6-1.
 2023-06-03 08:32:01 +02:00
Ricardo Wurmus 6b07e52752
gnu: r-ggrastr: Update to 1.0.2. 
* gnu/packages/cran.scm (r-ggrastr): Update to 1.0.2.
 2023-06-03 08:32:01 +02:00
Ricardo Wurmus a8ac423090
gnu: r-ggpicrust2: Update to 1.7.0. 
* gnu/packages/bioconductor.scm (r-ggpicrust2): Update to 1.7.0.
[propagated-inputs]: Add r-circlize.
[native-inputs]: Add r-knitr.
 2023-06-03 08:32:01 +02:00
Ricardo Wurmus 01d9a691be
gnu: r-rmarkdown: Update to 2.22. 
* gnu/packages/statistics.scm (r-rmarkdown): Update to 2.22.
[properties]: Add hints to the updater.
 2023-06-03 08:31:20 +02:00
Ricardo Wurmus f69e0f7927
gnu: r-rgdal: Update to 1.6-7. 
* gnu/packages/cran.scm (r-rgdal): Update to 1.6-7.
[properties]: Add hints to the updater.
 2023-06-03 08:30:37 +02:00
Ricardo Wurmus 51f2fe6542
gnu: Add r-consrank. 
* gnu/packages/cran.scm (r-consrank): New variable.
 2023-06-03 08:27:39 +02:00
Ricardo Wurmus c11b92a8aa
gnu: Add r-singlet. 
* gnu/packages/bioinformatics.scm (r-singlet): New variable.
 2023-06-02 21:18:26 +02:00
Ricardo Wurmus 76eda50717
gnu: Add r-rcppml/devel. 
* gnu/packages/machine-learning.scm (r-rcppml/devel): New variable.
 2023-06-02 19:54:27 +02:00
Navid Afkhami f09944461f
gnu: Add python-cell2cell. 
* gnu/packages/bioinformatics.scm (python-cell2cell): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-06-02 19:54:27 +02:00
Jean-Pierre De Jesus DIAZ 7469d9c106
gnu: Add coccinelle. 
* gnu/packages/patchutils.scm (coccinelle): New variable.

Signed-off-by: Jean-Pierre De Jesus DIAZ <jean@foundationdevices.com>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-06-02 16:27:41 +02:00
Jean-Pierre De Jesus DIAZ 5461ff1e54
gnu: Add ocaml-pyml. 
* gnu/packages/ocaml.ml (ocaml-pyml): New variable.

Signed-off-by: Jean-Pierre De Jesus DIAZ <jean@foundationdevices.com>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-06-02 16:27:39 +02:00
Jean-Pierre De Jesus DIAZ 4017fae4e0
gnu: Add ocaml-stdcompat. 
* gnu/packages/ocaml.scm (ocaml-stdcompat): New variable.

Signed-off-by: Jean-Pierre De Jesus DIAZ <jean@foundationdevices.com>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-06-02 16:27:34 +02:00
Jean-Pierre De Jesus DIAZ bb7f978e60
gnu: Add ocaml-parmap. 
* gnu/packages/ocaml.scm (ocaml-parmap): New variable.

Signed-off-by: Jean-Pierre De Jesus DIAZ <jean@foundationdevices.com>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-06-02 16:27:29 +02:00
Greg Hogan d756564db5
gnu: Add tmux-plugin-mem-cpu-load. 
* gnu/packages/tmux.scm (tmux-plugin-mem-cpu-load): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-06-02 16:25:44 +02:00
Brian Cully dbbc7e9461
services: Error in MODIFY-SERVICES when services don't exist 
This patch causes MODIFY-SERVICES to raise an error if a reference is made to
a service which isn't in its service list. This it to help users notice if
they have an invalid rule, which is currently silently ignored.

* gnu/services.scm (%delete-service):  new procedure
(%apply-clauses): new syntax rule
(%modify-service): remove syntax rule

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-06-02 16:23:03 +02:00
Ludovic Courtès decf5fed65
gnu: cuirass: Update to b825967. 
Fixes a regression introduced with the guile-squee update in
63e5975cac (which brings
non-blocking/asynchronous 'exec-query') whereby Cuirass would call
'exec-query' whereby another command was being processed.

* gnu/packages/ci.scm (cuirass): Update to b825967.
 2023-06-02 16:13:35 +02:00
Greg Hogan 7d7dcc3600
gnu: python-ipython-documentation: Update dependencies. 
* gnu/packages/python-xyz.scm (python-ipython-documentation)
[native-inputs]: Add python-ipykernel.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-06-02 16:08:43 +02:00
Greg Hogan f1af4fbeec
gnu: python-ipython-documentation: Remove patches. 
* gnu/packages/python-xyz.scm (python-ipython-documentation)[source]:
Remove upstreamed patches.
* gnu/packages/patches/python-ipython-documentation-chars.patch,
gnu/packages/patches/python-ipython-documentation-repro.patch:
Delete files.
* gnu/local.mk: Remove files.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-06-02 16:08:39 +02:00
Greg Hogan 53c47c4f28
gnu: python-docrepr: Fix tests. 
* gnu/packages/patches/python-docrepr-fix-tests.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it here.
* gnu/packages/documentation.scm (python-docrepr)[source]<patches>: Use
  it here.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-06-02 16:08:28 +02:00
Denis 'GNUtoo' Carikli c3f9445144
gnu: cpp-mustache: Update to 5.0 to fix build. 
* gnu/packages/cpp.scm (cpp-mustache): Update to 5.0.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-06-02 16:05:25 +02:00
Ludovic Courtès 48c7e71cd7
gnu: gcc-boot0: Do not use 'coreutils-boot0' on GNU/Hurd. 
Fixes <https://issues.guix.gnu.org/63789>.
Reported by Janneke Nieuwenhuizen <janneke@gnu.org>.

* gnu/packages/commencement.scm (gcc-boot0)[source]: Use
'%bootstrap-coreutils&co' when on GNU/Hurd.
 2023-06-02 15:47:28 +02:00
Arvid Krein a7d9cd742c
gnu: Add pcsc-cyberjack. 
* gnu/packages/security-token.scm (pcsc-cyberjack): New variable.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
 2023-06-02 19:24:21 +08:00
Peter Polidoro 7307b05abd
gnu: kicad: Update to 7.0.5. 
* gnu/packages/engineering.scm (kicad): Update to 7.0.5.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2023-06-02 13:13:23 +02:00
Ricardo Wurmus 41b6f213c1
gnu: r-tcgabiolinks: Update to 2.28.2. 
* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.28.2.
 2023-06-02 12:53:15 +02:00
Ricardo Wurmus 6d194c1ba8
gnu: r-biocthis: Update to 1.10.1. 
* gnu/packages/bioconductor.scm (r-biocthis): Update to 1.10.1.
 2023-06-02 12:53:15 +02:00
Ricardo Wurmus 302b916b2b
gnu: r-basilisk-utils: Update to 1.12.1. 
* gnu/packages/bioconductor.scm (r-basilisk-utils): Update to 1.12.1.
 2023-06-02 12:53:15 +02:00
Ricardo Wurmus 6d54b5cc23
gnu: r-megadepth: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-megadepth): Update to 1.10.0.
 2023-06-02 12:53:15 +02:00
Ricardo Wurmus 0beada7cb0
gnu: r-s4arrays: Update to 1.0.4. 
* gnu/packages/bioconductor.scm (r-s4arrays): Update to 1.0.4.
 2023-06-02 12:53:15 +02:00
Ricardo Wurmus f06bd3e740
gnu: r-biocviews: Update to 1.68.1. 
* gnu/packages/bioconductor.scm (r-biocviews): Update to 1.68.1.
 2023-06-02 12:53:15 +02:00
Ricardo Wurmus 438d2b80f7
gnu: r-rsubread: Update to 2.14.2. 
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.14.2.
 2023-06-02 12:53:15 +02:00
Ricardo Wurmus 08e1e36942
gnu: r-treeio: Update to 1.24.1. 
* gnu/packages/bioconductor.scm (r-treeio): Update to 1.24.1.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus 93350d89a2
gnu: r-apeglm: Update to 1.22.1. 
* gnu/packages/bioconductor.scm (r-apeglm): Update to 1.22.1.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus e6faedd0c9
gnu: r-zellkonverter: Update to 1.10.1. 
* gnu/packages/bioconductor.scm (r-zellkonverter): Update to 1.10.1.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus 071c31583b
gnu: r-scmap: Update to 1.22.3. 
* gnu/packages/bioconductor.scm (r-scmap): Update to 1.22.3.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus 2a35673351
gnu: r-limma: Update to 3.56.1. 
* gnu/packages/bioconductor.scm (r-limma): Update to 3.56.1.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus 21342c3bcf
gnu: r-edger: Update to 3.42.4. 
* gnu/packages/bioconductor.scm (r-edger): Update to 3.42.4.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus 15ffd4014e
gnu: r-biostrings: Update to 2.68.1. 
* gnu/packages/bioconductor.scm (r-biostrings): Update to 2.68.1.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus 9e9e21dc46
gnu: r-biocparallel: Update to 1.34.2. 
* gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.34.2.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus 6693480b46
gnu: r-densvis: Update to 1.10.2. 
* gnu/packages/bioconductor.scm (r-densvis): Update to 1.10.2.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus 3b20a9e600
gnu: r-delayedarray: Update to 0.26.3. 
* gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.26.3.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus f947aa3ac9
gnu: r-dearseq: Update to 1.12.1. 
* gnu/packages/bioconductor.scm (r-dearseq): Update to 1.12.1.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus ca0c012d4a
gnu: r-bambu: Update to 3.2.3. 
* gnu/packages/bioconductor.scm (r-bambu): Update to 3.2.3.
 2023-06-02 12:53:14 +02:00
Ricardo Wurmus 83bd8d51c3
gnu: r-alpine: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-alpine): Update to 1.26.0.
 2023-06-02 12:53:13 +02:00
Ricardo Wurmus f4639380ae
gnu: r-anvil: Update to 1.12.3. 
* gnu/packages/bioconductor.scm (r-anvil): Update to 1.12.3.
 2023-06-02 12:53:13 +02:00
Ricardo Wurmus 4f7efc8db9
gnu: r-biocviews: Sort inputs. 
* gnu/packages/bioconductor.scm (r-biocviews)[propagated-inputs]: Sort them.
 2023-06-02 12:51:15 +02:00
Ricardo Wurmus 52546a4512
gnu: r-biocparallel: Sort inputs. 
* gnu/packages/bioconductor.scm (r-biocparallel)[propagated-inputs]: Sort
them.
 2023-06-02 12:50:47 +02:00
Ricardo Wurmus bb27e3b8b1
gnu: r-dismo: Replace bundled jars. 
Fixes <https://issues.guix.gnu.org/63783>.

* gnu/packages/cran.scm (r-dismo)[source]: Delete bundled jars.
[inputs]: Add java-maxent.
[native-inputs]: Add JDK and zip.
[arguments]: Add phases 'build-jars and 'strip-jar-timestamps.
 2023-06-02 11:34:17 +02:00
Ricardo Wurmus 341b4b2a97
gnu: Add java-maxent. 
* gnu/packages/bioinformatics.scm (java-maxent): New variable.
 2023-06-02 11:34:17 +02:00
Andrew Tropin 75bdd4b052
gnu: swaylock-effects: Update to 1.6.11. 
* gnu/packages/wm.scm (swaylock-effects): Update to 1.6.11.
 2023-06-02 10:47:06 +04:00
Andrew Tropin f9af75b2c3
gnu: xdg-desktop-portal-wlr: Update to 0.7.0. 
* gnu/packages/freedesktop.scm (xdg-desktop-portal-wlr): Update to 0.7.0.
[inputs]: Add mesa.
 2023-06-02 08:59:08 +04:00
Andrew Tropin 69c3aa561d
gnu: xdg-desktop-portal-gtk: Update to 1.14.1. 
* gnu/packages/freedesktop.scm (xdg-desktop-portal-gtk): Update to 1.14.1.
 2023-06-02 08:59:08 +04:00
Andrew Tropin 51c8e86350
gnu: xdg-desktop-portal: Update to 1.16.0. 
* gnu/packages/freedesktop.scm (xdg-desktop-portal): Update to 1.16.0.
 2023-06-02 08:59:08 +04:00
Andrew Tropin a9c8e8fd38
gnu: libportal: Update to 0.6. 
* gnu/packages/freedesktop.scm (libportal): Update to 0.6.
[arguments]: Remove deprecated backends option from #:configure-flags.  Add
set-qt-environment-variables phase.
 2023-06-02 08:59:07 +04:00
Katherine Cox-Buday 195c91b793
gnu: gopls: Update to 0.12.0. 
* gnu/packages/golang.scm (gopls): Update to 0.12.0.
 2023-06-01 23:00:44 -05:00
jgart 9dacecb111
gnu: Update waybar to 0.9.18. 
* gnu/packages/wm.scm (waybar): Update to 0.9.18.
 2023-06-01 22:59:38 -05:00
jgart ab4347a1ad
gnu: python-fire: Update to 0.5.0. 
* gnu/packages/python-xyz.scm (python-fire): Update to 0.5.0.
[inputs]: Remove python-six and python-termcolor.
[propagated-inputs]: Add python-six and python-termcolor.
 2023-06-01 22:59:38 -05:00
Ricardo Wurmus b4382b294e
gnu: Add python-colored. 
* gnu/packages/python-xyz.scm (python-colored): New variable.
 2023-06-01 20:48:17 +02:00
Ricardo Wurmus eb2918aa96
gnu: Add python-plotext. 
* gnu/packages/python-xyz.scm (python-plotext): New variable.
 2023-06-01 20:48:17 +02:00
Ricardo Wurmus d411b7d5e7
gnu: Add python-pyani. 
* gnu/packages/bioinformatics.scm (python-pyani): New variable.
 2023-06-01 20:48:17 +02:00
Ricardo Wurmus 525ef60ff4
gnu: Add python-illumina-utils. 
* gnu/packages/bioinformatics.scm (python-illumina-utils): New variable.
 2023-06-01 20:48:17 +02:00
Efraim Flashner cf388642ce
gnu: libtommath: Honor the #:tests? flag. 
* gnu/packages/multiprecision.scm (libtommath)[arguments]: Adjust custom
'check phase to honor the #:tests? flag.
 2023-06-01 15:52:37 +03:00
Efraim Flashner b428b49d8f
gnu: libtommath: Prevent possible integer overflow. 
* gnu/packages/multiprecision.scm (libtommath)[source]: Add patch.
* gnu/packages/patches/libtommath-integer-overflow.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2023-06-01 15:52:37 +03:00
Efraim Flashner 7c52ae295b
gnu: bear: Update to 3.1.2. 
* gnu/packages/build-tools.scm (bear): Update to 3.1.2.
 2023-06-01 15:24:23 +03:00
Ricardo Wurmus ced6e0fe94
gnu: Add python-ete3. 
* gnu/packages/bioinformatics.scm (python-ete3): New variable.
 2023-06-01 14:10:04 +02:00
Andy Tai e6705f994f
gnu: parallel: Update to 20230522. 
* gnu/packages/parallel.scm (parallel): Update to 20230522.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-06-01 12:55:09 +03:00
Greg Hogan 9511488941
gnu: zenity: Update to 3.44.1. 
* gnu/packages/gnome.scm (zenity): Update to 3.44.1.
[native-inputs]: Add gtk+:bin.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-06-01 12:44:58 +03:00
Greg Hogan 21388dce63
gnu: iperf: Update to 3.13. 
* gnu/packages/networking.scm (iperf): Update to 3.13.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-06-01 12:42:43 +03:00
Greg Hogan 3ab95b2753
gnu: iotop: Update to 1.23. 
* gnu/packages/linux.scm (iotop): Update to 1.23.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-06-01 12:41:37 +03:00
Greg Hogan fd76ffb974
gnu: html-xml-utils: Update to 8.6. 
* gnu/packages/xml.scm (html-xml-utils): Update to 8.6.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-06-01 12:39:58 +03:00
Greg Hogan e6fb7f6467
gnu: hstr: Update to 3.1. 
* gnu/packages/shellutils.scm (hstr): Update to 3.1.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-06-01 12:38:13 +03:00
Greg Hogan dc61b7fcf7
gnu: glances: Update to 3.4.0.3. 
* gnu/packages/python-xyz.scm (glances): Update to 3.4.0.3.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-06-01 12:36:35 +03:00
Greg Hogan f7d5722d36
gnu: fish: Update to 3.6.1. 
* gnu/packages/shells.scm (fish): Update to 3.6.1.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-06-01 12:18:31 +03:00
Greg Hogan 247ac4b73f
gnu: fio: Update to 3.35. 
* gnu/packages/benchmark.scm (fio): Update to 3.35.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-06-01 12:15:01 +03:00