Commit graph

97800 commits

Author SHA1 Message Date
Ricardo Wurmus
41435e0e1c
gnu: r-clusterprofiler: Update to 4.4.2.
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.4.2.
2022-06-12 11:16:29 +02:00
Ricardo Wurmus
640b45d73c
gnu: r-monocle: Update to 2.24.1.
* gnu/packages/bioconductor.scm (r-monocle): Update to 2.24.1.
2022-06-12 11:16:29 +02:00
Ricardo Wurmus
8ed8c8b8da
gnu: r-chippeakanno: Update to 3.30.1.
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.30.1.
2022-06-12 11:16:29 +02:00
Ricardo Wurmus
46aab4d33d
gnu: r-zellkonverter: Update to 1.6.2.
* gnu/packages/bioconductor.scm (r-zellkonverter): Update to 1.6.2.
2022-06-12 11:16:28 +02:00
Ricardo Wurmus
7a344aa9e2
gnu: r-keggrest: Update to 1.36.2.
* gnu/packages/bioconductor.scm (r-keggrest): Update to 1.36.2.
2022-06-12 11:16:28 +02:00
Ricardo Wurmus
1ecac84c73
gnu: r-genomicfeatures: Update to 1.48.3.
* gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.48.3.
2022-06-12 11:16:28 +02:00
Ricardo Wurmus
15e26f97d9
gnu: r-biocparallel: Update to 1.30.3.
* gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.30.3.
[propagated-inputs]: Add r-codetools.
2022-06-12 11:16:28 +02:00
Ricardo Wurmus
f5899fe58b
gnu: r-deepsnv: Update to 1.42.1.
* gnu/packages/bioconductor.scm (r-deepsnv): Update to 1.42.1.
2022-06-12 11:16:23 +02:00
Julien Lepiller
965d54e344
gnu: java-plexus-component-metadata: Fix package.
* gnu/packages/java.scm (java-plexus-component-metadata): Apply fix for
  newer jdom.
2022-06-12 09:07:17 +02:00
Tobias Geerinckx-Rice
75eae3fd78
gnu: emacs-rainbow-mode: Update to 1.0.6.
* gnu/packages/emacs-xyz.scm (emacs-rainbow-mode): Update to 1.0.6.
2022-06-05 02:00:01 +02:00
Tobias Geerinckx-Rice
1dc22f19e8
gnu: emacs-undo-tree: Update to 0.8.2.
* gnu/packages/emacs-xyz.scm (emacs-undo-tree): Update to 0.8.2.
2022-06-05 02:00:01 +02:00
Tobias Geerinckx-Rice
4fc248ada2
gnu: emacs-ghub: Update to 3.5.6.
* gnu/packages/emacs-xyz.scm (emacs-ghub): Update to 3.5.6.
2022-06-05 02:00:01 +02:00
Tobias Geerinckx-Rice
66c5e40762
gnu: emacs-d-mode: Update to 2.0.12.
* gnu/packages/emacs-xyz.scm (emacs-d-mode): Update to 2.0.12.
2022-06-05 02:00:00 +02:00
Tobias Geerinckx-Rice
aef64b9c45
gnu: emacs-kind-icon: Update to 0.1.5.
* gnu/packages/emacs-xyz.scm (emacs-kind-icon): Update to 0.1.5.
2022-06-05 02:00:00 +02:00
Tobias Geerinckx-Rice
67a78c0ad6
gnu: ndctl: Update to 73.
* gnu/packages/disk.scm (ndctl): Update to 73.
[build-system]: Switch to Meson.
[arguments]: Adjust #:configure-flags accordingly.  Remove #:make-flags.
[native-inputs]: Remove automake, autoconf, and libtool.
2022-06-05 02:00:00 +02:00
Tobias Geerinckx-Rice
cd81b3bdfd
gnu: memkind: Update to 1.13.0.
* gnu/packages/disk.scm (memkind): Update to 1.13.0.
2022-06-05 02:00:00 +02:00
Tobias Geerinckx-Rice
7d00cdf44d
gnu: diffoscope: Update to 216.
* gnu/packages/diffoscope.scm (diffoscope): Update to 216.
2022-06-05 02:00:00 +02:00
Tobias Geerinckx-Rice
b8686f1bfc
gnu: python-pyodbc-c: Fix comment.
* gnu/packages/databases.scm (python-pyodbc-c): Fix comment about tests.
2022-06-05 02:00:00 +02:00
Tobias Geerinckx-Rice
898511205c
gnu: irssi: Edit description.
* gnu/packages/irc.scm (irssi)[synopsis, description]: Expound.
2022-06-05 02:00:00 +02:00
Julien Lepiller
1643402950
gnu: offlate: Update to 0.6.1.
* gnu/packages/python-xyz.scm (offlate): Update to 0.6.1.
2022-06-11 22:55:26 +02:00
Tobias Geerinckx-Rice
c23d4871a6
gnu: irssi: Update to 1.4.1.
* gnu/packages/irc.scm (irssi): Update to 1.4.1.
[arguments]: Remove unmaintained "--with-bot".
2022-06-05 02:00:08 +02:00
Tobias Geerinckx-Rice
c794df8490
gnu: python-pyodbc-c: Fix metadata.
It appears to have been copied from python-pyodbc, a different project.

* gnu/packages/databases.scm (python-pyodbc-c)[synopsis, description]:
Describe this project instead, and how it differs.
[home-page]: Point elsewhere.
2022-06-05 02:00:08 +02:00
Tobias Geerinckx-Rice
89c7a2c891
gnu: python-pyodbc-c: Update to 3.1.5.
* gnu/packages/databases.scm (python-pyodbc-c): Update to 3.1.5.
2022-06-05 02:00:08 +02:00
Tobias Geerinckx-Rice
289b521584
gnu: python-pyodbc-c: Don't use unstable tarball.
* gnu/packages/databases.scm (python-pyodbc-c)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
2022-06-05 02:00:08 +02:00
Tobias Geerinckx-Rice
64b12a1abf
gnu: python-pyodbc: Update to 4.0.32.
* gnu/packages/databases.scm (python-pyodbc): Update to 4.0.32.
2022-06-05 02:00:08 +02:00
Tobias Geerinckx-Rice
07edc13f04
gnu: python-pyodbc: Document the test situation.
* gnu/packages/databases.scm (python-pyodbc)[arguments]: Replace
counterfactual comment with one that isn't.  Add a custom 'check phase,
which doesn't run.
2022-06-05 02:00:08 +02:00
Tobias Geerinckx-Rice
f0fa2b25ba
gnu: python-pyodbc: Remove precompiled .pyc files from source.
* gnu/packages/databases.scm (python-pyodbc)[source]: Add a snippet.
Remove no-op file-name.
2022-06-05 02:00:07 +02:00
Haider Mirza
2d7548f0cf
gnu: Add emacs-org-auto-tangle.
* gnu/packages/emacs-xyz.scm (emacs-org-auto-tangle): New variable.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2022-06-11 09:19:34 +02:00
Josselin Poiret
a99015c878
system: Align zram priority with swap-space spec to clarify.
Fixes <https://issues.guix.gnu.org/54783>.

* gnu/services/linux.scm (zram-device-configuration)
[priority]: Adapt to use #f or an integer from 0 to 32767.  Add sanitizer to
warn for the change and delay the field.
(zram-device-configuration->udev-string): Adapt as above.
* doc/guix.texi (Zram Device Service): Remove double copyright line.
Change priority description to refer to the Swap Space one, and suggest not
leaving the default #f on to properly use zram.

Reported-by: Stefan Baums <baums@stefanbaums.com>
Modified-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-06-11 00:57:13 -04:00
Maxim Cournoyer
8649ac5eaa
services: jami-configuration: Rename 'jamid' field to 'libjami'.
* gnu/services/telephony.scm (gnu):
(jami-configuration)[jamid]: Rename field to...
[libjami]: ... this.
(jami-configuration->command-line-arguments): Adjust accordingly.
(jami-shepherd-services): Likewise.
2022-06-10 23:52:34 -04:00
Maxim Cournoyer
8994e13b9f
least-authority: Fix typo.
* guix/least-authority.scm (least-authority-wrapper): Fix typo in doc.
2022-06-10 23:52:34 -04:00
Maxim Cournoyer
85b4dabd94
services: jami: Modernize to adjust to Shepherd 0.9+ changes.
This partially fixes <https://issues.guix.gnu.org/54786>, allowing the 'jami'
and 'jami-provisioning' system tests to pass again.

In version 0.9.0, Shepherd constructors are now run concurrently, via
cooperative scheduling (Guile Fibers).  The Jami service previously relied on
blocking sleeps while polling for D-Bus services to become ready after forking
a process; this wouldn't work anymore since while blocking the service process
wouldn't be given the chance to finish starting.  The new reliance on Fibers
in Shepherd's fork+exec-command in the helper 'send-dbus' procedure also meant
that it wouldn't work outside of Shepherd anymore.  Finally, the
'start-service' Shepherd procedure used in the test suite would cause the Jami
daemon to be spawned multiple times (a bug introduced in Shepherd 0.9.0).

To fix/simplify these problems, this change does the following:

1. Use the Guile AC/D-Bus library for D-Bus communication, which simplify
things, such as avoiding the need to fork 'dbus-send' processes.

2. The non-blocking 'sleep' version of Fiber is used for the 'with-retries'
waiting syntax.

3. A 'dbus' package variant is used to adjust the session bus configuration,
tailoring it for the use case at hand.

4. Avoid start-service in the tests, preferring 'jami-service-available?' for
now.

* gnu/build/jami-service.scm (parse-dbus-reply, strip-quotes)
(deserialize-item, serialize-boolean, dbus-dict->alist)
(dbus-array->list, parse-account-ids, parse-account-details)
(parse-contacts): Delete procedures.
(%send-dbus-binary, %send-dbus-bus, %send-dbus-user, %send-dbus-group)
(%send-dbus-debug): Delete parameters.
(jami-service-running?): New procedure.
(send-dbus/configuration-manager): Rename to...
(call-configuration-manager-method): ... this.  Turn METHOD into a positional
argument.  Turn ARGUMENTS into an optional argument.  Invoke
`call-dbus-method' instead of `send-dbus', adjusting callers accordingly.
(get-account-ids, id->account-details, id->account-details)
(id->volatile-account-details, username->id, add-account remove-account)
(username->contacts, remove-contact, add-contact, set-account-details)
(set-all-moderators, username->all-moderators?, username->moderators)
(set-moderator): Adjust accordingly.
(with-retries, send-dbus, dbus-available-services)
(dbus-service-available?): Move to ...
* gnu/build/dbus-service.scm: ... this new module.
(send-dbus): Rewrite to use the Guile AC/D-Bus library.
(%dbus-query-timeout, sleep*): New variables.
(%current-dbus-connection): New parameter.
(initialize-dbus-connection!, argument->signature-type)
(call-dbus-method): New procedures.
(dbus-available-services): Adjust accordingly.
* gnu/local.mk (GNU_SYSTEM_MODULES): Register new module.
* gnu/packages/glib.scm (dbus-for-jami): New variable.
* gnu/services/telephony.scm: (jami-configuration)[dbus]: Default to
dbus-for-jami.
(jami-dbus-session-activation): Write a D-Bus daemon configuration file at
'/var/run/jami/session-local.conf'.
(jami-shepherd-services): Add the closure of guile-ac-d-bus and guile-fibers
as extensions.  Adjust imported modules.  Remove no longer used parameters.
<jami-dbus-session>: Use a PID file, avoiding the need for the manual
synchronization.
<jami>:  Set DBUS_SESSION_BUS_ADDRESS environment variable.  Poll using
'jami-service-available?' instead of 'dbus-service-available?'.
* gnu/tests/telephony.scm (run-jami-test): Add needed Guile extensions.  Set
DBUS_SESSION_BUS_ADDRESS environment variable.  Adjust all tests to use
'jami-service-available?' to determine if the service is started rather than
the now problematic Shepherd's 'start-service'.
2022-06-10 23:52:33 -04:00
Tobias Geerinckx-Rice
b8edfdb008
gnu: qtox: Update to 1.17.6.
* gnu/packages/messaging.scm (qtox): Update to 1.17.6.
2022-06-05 02:00:01 +02:00
Tobias Geerinckx-Rice
ddd265b033
gnu: galera: Update to 26.4.12.
* gnu/packages/databases.scm (galera): Update to 26.4.12.
2022-06-05 02:00:01 +02:00
Tobias Geerinckx-Rice
1023bd85cc
gnu: Add nmon.
* gnu/packages/admin.scm (nmon): New public variable.
2022-06-05 02:00:00 +02:00
Tobias Geerinckx-Rice
8c2c5c2c9c
gnu: oneko: Edit description.
* gnu/packages/toys.scm (oneko)[description]: Use full sentences.
Name the only two species of animated character actually available.
Add an unfortunate note about Wayland.
2022-06-05 02:00:00 +02:00
Tobias Geerinckx-Rice
a7255dd13f
gnu: oneko: Remove trailing #t from phases.
* gnu/packages/toys.scm (oneko)[source]: Don't explicitly return #t from snippet…
[arguments]: …nor from phases.
2022-06-05 02:00:00 +02:00
Tobias Geerinckx-Rice
7c52cad046
pull: Fail if cache directory ownership is suspect.
New users frequently run ‘sudo guix pull’ which breaks subsequent
unprivileged ‘guix pull’s until manually fixed with chmod -R.

* guix/scripts/pull.scm (guix-pull): Fail if the cache directory (or
its innermost extant parent) is not owned by the user pulling the Guix,
with a hint about ‘sudo -i’.
2022-06-05 02:00:00 +02:00
Tobias Geerinckx-Rice
34c7c922f5
gnu: c-blosc: Remove input labels.
* gnu/packages/compression.scm (c-blosc)[inputs]:
Remove input labels.
2022-06-05 02:00:00 +02:00
Tobias Geerinckx-Rice
2d80b869f0
gnu: c-blosc: Remove bundled libraries from source.
* gnu/packages/compression.scm (c-blosc)[source]: Add snippet.
2022-06-05 02:00:00 +02:00
Tobias Geerinckx-Rice
495c248920
gnu: c-blosc: Omit static library.
* gnu/packages/compression.scm (c-blosc)[arguments]: Add "-DBUILD_STATIC=OFF" to #:configure-flags.
2022-06-05 02:00:00 +02:00
Tobias Geerinckx-Rice
9f01229c95
gnu: c-blosc: Update to 1.21.1.
* gnu/packages/compression.scm (c-blosc): Update to 1.21.1.
[arguments]: Remove obsolete PREFER_EXTERNAL_SNAPPY from #:configure-flags.
2022-06-05 02:00:00 +02:00
Vagrant Cascadian
2f3dec3de7
gnu: tch-ipv6: Build reproducibly.
* gnu/packages/networking.scm (thc-ipv6)[arguments]: Add
  'use-source-date-epoch-in-manpages phase.
2022-06-10 16:56:57 -07:00
Michael Rohleder
010426e2c3
gnu: emacs-dimmer: Update to 0.4.2-1-2f915b1.
To build with Emacs28.

* gnu/packages/emacs-xyz.scm (emacs-dimmer): Update to 0.4.2-1-2f915b1.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-06-10 23:28:55 +02:00
Paul A. Patience
f2d9d283b6
gnu: meshlab: Update to 2022.02.
Note that the previous version no longer compiled (this one does).

* gnu/packages/engineering.scm (meshlab): Update to 2022.02.
[inputs]: Remove the no longer required qtscript and
qtxmlpatterns. Add (uncomment) qhull.
[arguments]: Use G-expressions.
<#:configure-flags>: Set the rpath to fix missing libraries (presumably
new since the previous version) detected during the 'validate-runpath'
phase.
<#:phases>: Remove trailing boolean from 'go-to-source-dir' phase.
Remove the 'move-files' phase, which was made redundant by the manually
provided rpath.
[description]: Move a word and add some commas to improve the
readability. Typeset a program name in @samp{}.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-06-10 23:14:29 +02:00
jgart
c09cc71724
gnu: direnv: Update to 2.31.0.
* gnu/packages/shellutils.scm (direnv): Update to 2.31.0.
[arguments]: Remove trailing boolean in lambda block.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-06-10 23:04:14 +02:00
JOULAUD François
8d4a69eb90
gnu: Add go-github-com-google-go-jsonnet.
* gnu/packages/golang.scm (go-github-com-google-go-jsonnet): New
variable.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2022-06-10 23:00:20 +02:00
JOULAUD François
fa0ead00d9
gnu: Add go-sigs-k8s-io-yaml.
* gnu/packages/golang.scm (go-sigs-k8s-io-yaml): New variable.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2022-06-10 23:00:11 +02:00
Andrew Tropin
d859d8873c
doc: Update example of a minimalistic home environment.
* doc/he-config-bare-bones.scm: Adujst example according to changes in
bash-service-type and home-files-service-type.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-06-10 22:42:49 +02:00
Leo Famulari
30967b0dc4
gnu: linux-libre 5.10: Update to 5.10.121.
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.121.
(linux-libre-5.10-pristine-source, deblob-scripts-5.10): Update hashes.
2022-06-10 15:34:42 -04:00