Commit graph

100890 commits

Author SHA1 Message Date
Konrad Hinsen
9529384c92
gnu: snakemake-7: Convert dependencies to propagated-inputs
* gnu/packages/python-xyz.scm (snakemake-7)[inputs]: Change to ...
[propagated-inputs]: ... this, to ensure that "python -m snakemake"
works (because snakemake uses it internally).

Signed-off-by: Marius Bakke <marius@gnu.org>
2022-08-29 18:22:59 +02:00
Konrad Hinsen
6a31fb6e7b
gnu: snakemake-6: Convert dependencies to propagated-inputs
* gnu/packages/python-xyz.scm (snakemake-6)[inputs]: Change to ...
[propagated-inputs]: ... this, to ensure that "python -m snakemake"
works (because snakemake uses it internally).

Signed-off-by: Marius Bakke <marius@gnu.org>
2022-08-29 18:22:59 +02:00
Konrad Hinsen
5831155175
gnu: snakemake-7: Fix cluster execution bug
* gnu/packages/python-xyz.scm (snakemake-7)[arguments]: Revise the patch for
the cluster execution script

Signed-off-by: Marius Bakke <marius@gnu.org>
2022-08-29 18:22:58 +02:00
Maxime Devos
52aa21cc9a
gnu: gnupg: Use mirror URL.
In commit 38747a27f3, the package switched from
a mirror:// URL to a ftp:// URL, but there doesn't appear to have been any
particular reason for that.

* gnu/packages/gnupg.scm (gnupg)[source]{uri}: Use a mirror:// again.

Signed-off-by: Marius Bakke <marius@gnu.org>
2022-08-29 18:22:58 +02:00
Michael Rohleder
309935a016
gnu: uncrustify: Update to 0.75.1.
* gnu/packages/code.scm (uncrustify): Update to 0.75.1.

Signed-off-by: Marius Bakke <marius@gnu.org>
2022-08-29 18:22:58 +02:00
Michael Rohleder
ed9558b17a
gnu: rr: Update to 5.6.0.
* gnu/packages/debug.scm (rr): Update to 5.6.0.
[arguments]<#:configure-flags>: Add -rpath to zlib to satisfy
validate-runpath.
[inputs]: Add zlib.

Signed-off-by: Marius Bakke <marius@gnu.org>
2022-08-29 18:22:58 +02:00
Luis Felipe
72cfcf1735
gnu: Add python-django-cleanup.
* gnu/packages/django.scm (python-django-cleanup): New variable.

Signed-off-by: Marius Bakke <marius@gnu.org>
2022-08-29 18:22:58 +02:00
Clément Lassieur
6e83d294ce
gnu: emacs-clang-format: Remove inherited propagated inputs.
* gnu/packages/llvm.scm (emacs-clang-format)[propagated-inputs]: Remove them.
2022-08-29 18:05:39 +02:00
Marius Bakke
be01b13fb7
gnu: zathura-pdf-mupdf: Remove input labels.
* gnu/packages/pdf.scm (zathura-pdf-mupdf)[inputs]: Remove labels.
2022-08-29 17:49:58 +02:00
Marius Bakke
7c9cf349f3
gnu: zathura-pdf-mupdf: Update to 0.3.9.
* gnu/packages/pdf.scm (zathura-pdf-mupdf): Update to 0.3.9.
[inputs]: Add GUMBO-PARSER and TESSERACT-OCR.
[arguments]: Remove obsolete configure flag.  Adjust mupdf substitutions.
2022-08-29 17:49:58 +02:00
Pierre-Henry Fröhring
f26b9d5ced
gnu: mupdf: Update to 1.20.3.
* Copy/paste is fixed.

The build now uses the patched version of freeglut that is included in the
thirdparty directory so that copy/paste works.

* gnu/packages/pdf.scm (mupdf)[source](snippet): Preserve freeglut.
[inputs]: Add LIBXRANDR and LIBXI.
[arguments]: Explicitly add configure flags for system libraries.

Signed-off-by: Marius Bakke <marius@gnu.org>
2022-08-29 17:49:58 +02:00
Marius Bakke
608f9efc34
gnu: tesseract-ocr: Propagate leptonica.
* gnu/packages/ocr.scm (tesseract-ocr)[inputs]: Move LEPTONICA ...
[propagated-inputs]: ... here.
2022-08-29 17:49:58 +02:00
Remco van 't Veer
83c86fa446
gnu: ruby: Replace with 2.7.6 [security fixes].
Includes fixes for: CVE-2022-28739, CVE-2021-41816, and CVE-2021-41817.

* gnu/packages/ruby.scm (ruby-2.7-fixed): New variable.
(ruby-2.7)[replacement]: Graft.

Signed-off-by: Marius Bakke <marius@gnu.org>
2022-08-29 16:55:30 +02:00
Remco van 't Veer
939c998160
gnu: ruby: Update to 3.1.2 [security fixes].
Includes fixes for: CVE-2022-28738, and CVE-2022-28739.

* gnu/packages/ruby.scm (ruby-3.1): Update to 3.1.2.

Signed-off-by: Marius Bakke <marius@gnu.org>
2022-08-29 16:55:30 +02:00
Remco van 't Veer
2654acea27
gnu: ruby: Update to 3.0.4 [security fixes].
Includes fixes for: CVE-2022-28738, CVE-2022-28739, CVE-2021-41819,
CVE-2021-41816, and CVE-2021-41817.

* gnu/packages/ruby.scm (ruby-3.0): Update to 3.0.4.

Signed-off-by: Marius Bakke <marius@gnu.org>
2022-08-29 16:55:30 +02:00
Remco van 't Veer
a500e1a061
gnu: ruby: Update to 2.6.10 [security fixes].
Includes fixes for: CVE-2022-28739, CVE-2021-41819, CVE-2021-41817,
CVE-2021-31810, CVE-2021-32066, CVE-2021-28965, CVE-2020-25613, and
CVE-2020-10933.

* gnu/packages/ruby.scm (ruby-2.6): Update to 2.6.10.

Signed-off-by: Marius Bakke <marius@gnu.org>
2022-08-29 16:55:30 +02:00
Marius Bakke
8ab7125265
gnu: Remove ruby@2.5.
* gnu/packages/ruby.scm (ruby-2.5): Remove variable.
2022-08-29 16:55:30 +02:00
Marius Bakke
ae9b3d7cf1
gnu: Remove ruby@2.4.
* gnu/packages/ruby.scm (ruby-2.4): Remove variable.
2022-08-29 16:55:30 +02:00
Efraim Flashner
f4f225e482
gnu: accountsservice: Adjust inputs.
This fixes the builds of gdm and some other packages.

* gnu/packages/freedesktop.scm (accountsservice)[inputs]: Move polkit ...
[propagated-inputs]: ... to here.
2022-08-29 17:18:14 +03:00
jgart
3aac843826
gnu: Add cl-safe-read.
* gnu/packages/lisp-xyz.scm (cl-safe-read, ecl-safe-read, sbcl-safe-read): New
  variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2022-08-29 16:02:09 +02:00
Nikolay Korotkiy
cc6c079230
gnu: cmus: Update to 2.10.0.
* gnu/packages/music.scm (cmus): Update to 2.10.0.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-08-29 16:25:08 +03:00
Nicolas Goaziou
a52473e219
gnu: wireshark: Update to 3.6.7.
* gnu/packages/networking.scm (wireshark): Update to 3.6.7.
2022-08-29 10:32:42 +02:00
Efraim Flashner
de66e21580
gnu: r-keggrest: Update to 1.36.3.
* gnu/packages/bioconductor.scm (r-keggrest): Update to 1.36.3.
2022-08-29 11:26:56 +03:00
Andrew Tropin
75d7317290
gnu: fennel: Update to 1.2.0.
* gnu/packages/lua.scm (fennel): Update to 1.2.0.
[arguments]: Migrate to gexps.
2022-08-29 09:55:44 +03:00
Maxim Cournoyer
0ea62e84a7
services: Add lightdm-service-type.
* gnu/services/lightdm.scm: New service.
* tests/services/lightdm.scm: Test it.
* doc/guix.texi (X Window): Document it.
* gnu/local.mk (GNU_SYSTEM_MODULES): Register it.

Co-authored-by: L p R n d n <guix@lprndn.info>
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2022-08-28 22:28:47 -04:00
Maxim Cournoyer
42fee6d0f1
build: marionette: Add support for Tesseract OCR.
* gnu/build/marionette.scm (invoke-ocrad-ocr): New procedure.
(invoke-tesseract-ocr): Likewise.
(marionette-screen-text): Rename the #:ocrad argument to #:ocr.  Dispatch the
matching OCR invocation procedure.
(wait-for-screen-text): Rename the #:ocrad argument to #:ocr.
* gnu/tests/base.scm (run-basic-test): Adjust accordingly.
* gnu/tests/install.scm (enter-luks-passphrase): Likewise.
(enter-luks-passphrase-for-home): Likewise.
2022-08-28 22:10:20 -04:00
Maxim Cournoyer
697b797160
marionette: Improve the error message of 'wait-for-screen-text'.
* gnu/build/marionette.scm (wait-for-screen-text): Return the last OCR'd text
when the predicate fails to match instead of the not useful predicate object.
2022-08-28 22:10:20 -04:00
Maxim Cournoyer
b096b939f7
gnu: lightdm: Apply patch to fix color depth issue with VNC.
* gnu/packages/patches/lightdm-vnc-color-depth.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/display-managers.scm (lightdm): Apply it.
2022-08-28 22:10:20 -04:00
Maxim Cournoyer
a4fd1840ab
gnu: lightdm: Apply patch to allow using VNC options.
* gnu/packages/patches/lightdm-arguments-ordering.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/display-managers.scm (lightdm): Apply it.
2022-08-28 22:10:20 -04:00
Maxim Cournoyer
da3c784c68
gnu: lightdm: Apply patch to fix a problem with VNC integration.
* gnu/packages/patches/lightdm-vncserver-check.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/display-managers.scm (lightdm): Apply it.
2022-08-28 22:10:20 -04:00
Maxim Cournoyer
0e76781df4
gnu: lightdm-gtk-greeter: Adjust --enable-at-spi-command value.
* gnu/packages/display-managers.scm (lightdm-gtk-greeter)
[configure-flags]: Add the '--launch-immediately' option to the
at-spi-bus-launcher to match what is used in the source.
2022-08-28 22:10:19 -04:00
Maxim Cournoyer
20c8fb042c
gnu: lightdm-gtk-greeter: Adjust default config file path.
* gnu/packages/display-managers.scm (lightdm-gtk-greeter)
[phases]{customize-default-config-path}: New phase.
2022-08-28 22:10:19 -04:00
Maxim Cournoyer
d0046bc13b
gnu: lightdm-gtk-greeter: Enable libklavier support.
* gnu/packages/display-managers.scm (lightdm-gtk-greeter)
[configure-flags]: Add '--with-libxklavier'.
[inputs]: Add libxklavier.
2022-08-28 22:10:19 -04:00
Maxim Cournoyer
0d23e9cda2
gnu: lightdm-gtk-greeter: Use the glib-or-gtk-wrap phase as-is.
* gnu/packages/display-managers.scm (lightdm-gtk-greeter)
[configure-flags]: Install binaries to bin/, so the wrap phase of glib-or-gtk
handles them.
[phases]{wrap-program}: Delete.
{custom-wrap}: New phase, wrapping the wrapper with a few extra environment
variables.
2022-08-28 22:10:19 -04:00
Maxim Cournoyer
9376411fbe
gnu: lightdm-gtk-greeter: Add GDK_PIXBUF_MODULE_FILE to wrapper.
* gnu/packages/display-managers.scm (lightdm-gtk-greeter)
[build-system]: Use glib-or-gtk-build-system.
[phases]{wrap-program}: Add GDK_PIXBUF_MODULE_FILE to wrapper.
[inputs]: Add librsvg.
2022-08-28 22:10:19 -04:00
Maxim Cournoyer
6da5eed4e7
gnu: accountsservice: Provide a means to locate extensions.
* gnu/packages/patches/accountsservice-extensions.patch: New patch.
* gnu/packages/freedesktop.scm (accountsservice)[source]: Apply it.
[phases]{wrap-with-xdg-data-dirs}: New phase.
2022-08-28 22:10:18 -04:00
Maxim Cournoyer
12bb1c6db1
gnu: accountsservice: Update to 22.08.8, enable doc and test suite.
* gnu/packages/freedesktop.scm (accountsservice): Update to 22.08.8.
[tests?]: Delete argument.
[configure-flags]: Remove obsolete "-Dsystemd" flag.  Add "-Ddocbook=true" and
"-Dgtk_doc=true".
[phases]{patch-docbook-references}: New phase.
{patch-/bin/cat}: Delete and merge into...
[patch-paths]: ... this phase, renamed from pre-configure.  Use
search-input-file.
[native-inputs]: Add docbook-xml-4.1.2, docbook-xsl, gtk-doc, libxml2,
libxslt, python-dbusmock, python-pygobject, vala and xmlto.
2022-08-28 22:10:18 -04:00
muradm
3c2d2b4538
gnu: security: Add fail2ban-service-type.
* gnu/services/security.scm: New module.
* gnu/tests/security.scm: New module.
* gnu/local.mk: Add new security module and tests.
* doc/guix.text: Add fail2ban-service-type documentation.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-08-28 21:46:30 -04:00
Maxim Cournoyer
ba0dbe3bf2
gexp: directory-union: Fix documentation.
* guix/gexp.scm (directory-union): Fix documentation.
2022-08-28 21:14:18 -04:00
Josselin Poiret
3294fa2ba4
tests: Add test for menu-entry roundtrips as sexps.
* tests/boot-parameters.scm (%uuid-menu-entry,
%file-system-label-menu-entry): New variables.
("menu-entry roundtrip, uuid", "menu-entry roundtrip,
file-system-label"): New tests.

Signed-off-by: Marius Bakke <marius@gnu.org>
2022-08-28 23:37:28 +02:00
Josselin Poiret
0811d2cb8d
bootloader: Convert device in menu-entry to proper sexp.
Previously, menu-entry->sexp didn't try to convert `device` to a
proper sexp, which was inserted directly into the boot parameters
G-exp, leading to a G-exp input error.  Now convert both uuid and
file-system-label possibilities to sexps, and add parsing code to
sexp->menu-entry.  This fixes #57307.

* gnu/bootloader.scm (menu-entry->sexp, sexp->menu-entry): Take
non-string devices into account.

Signed-off-by: Marius Bakke <marius@gnu.org>
2022-08-28 23:37:28 +02:00
Nicolas Goaziou
b9322d7819
gnu: emacs-crdt: Update to 0.3.3.
* gnu/packages/emacs-xyz.scm (emacs-crdt): Update to 0.3.3.
2022-08-28 22:46:12 +02:00
Liliana Marie Prikler
f592decd4d
gnu: Remove shlomif-cmake-modules.
This origin was added for the now removed fortune-mod, so let's remove it
as well.

* gnu/packages/games.scm (shlomif-cmake-modules): Delete variable.
2022-08-28 19:17:28 +02:00
Liliana Marie Prikler
5e17480574
gnu: Remove rinutils.
This package was introduced as native input to the now removed fortune-mod,
so let's remove it as well.

* gnu/packages/games.scm (rinutils): Delete variable.
2022-08-28 19:17:28 +02:00
Liliana Marie Prikler
6b6b947b61
gnu: Remove fortune-mod.
Since the addition of fortune-jkirchartz, it is no longer necessary to
keep around a package that propagates various non-nice things.
For a complete list, see <https://bugs.gnu.org/54691>.

* gnu/packages/games.scm (fortune-mod): Delete variable.
2022-08-28 19:17:28 +02:00
Liliana Marie Prikler
560b365c2c
gnu: Add fortunes-jkirchartz.
* gnu/packages/toys.scm (fortunes-jkirchartz): New variable.
2022-08-28 19:17:28 +02:00
Liliana Marie Prikler
2a010ba81d
gnu: Add daikichi.
* gnu/packages/toys.scm (daikichi): New variable.
2022-08-28 19:17:27 +02:00
Marius Bakke
57f8f69562
gnu: gnome-shell: Adjust for polkit 121.
* gnu/packages/patches/gnome-shell-polkit-autocleanup.patch: New file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/gnome.scm (gnome-shell)[source](patches): New field.
2022-08-28 15:41:49 +02:00
Marius Bakke
a44e08337d
gnu: gnome-maps: Update to 42.2.
* gnu/packages/geo.scm (gnome-maps): Update to 42.2.
[inputs]: Change from LIBGWEATHER to LIBGWEATHER4.
2022-08-28 15:41:49 +02:00
Marius Bakke
17f646aeba
gnu: Add libgweather4.
* gnu/packages/gnome.scm (libgweather4): New variable.
2022-08-28 15:41:49 +02:00