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Author SHA1 Message Date
Ricardo Wurmus
326be9abff
gnu: r-singlecellexperiment: Update to 1.20.1. 
* gnu/packages/bioconductor.scm (r-singlecellexperiment): Update to 1.20.1.
 2023-03-21 09:36:15 +01:00
Ricardo Wurmus
fa048ce50e
gnu: r-variancepartition: Update to 1.28.9. 
* gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.28.9.
 2023-03-21 09:36:15 +01:00
Ricardo Wurmus
481abed581
gnu: r-biocparallel: Update to 1.32.6. 
* gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.32.6.
 2023-03-21 09:36:15 +01:00
Petr Hodina
ac6e5d5b80
gnu: Add mygnuhealth. 
* gnu/packages/medical.scm (mygnuhealth): New variable.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Co-authored-by: Morgan Smith <Morgan.J.Smith@outlook.com>
Modified-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2023-03-20 23:46:16 -04:00
Kaelyn Takata
b4fb941957
gnu: zabbix-agentd: Update to 6.0.14. 
* gnu/packages/monitoring.scm (zabbix-agentd): Update to 6.0.14.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2023-03-20 23:10:15 -04:00
Simon South
e19d215ec9
gnu: tesseract-ocr: Use standard TESSDATA_PREFIX. 
* gnu/packages/ocr.scm (tesseract-ocr-tessdata-fast): Install data to
'share/tessdata' prefix rather than 'share/tesseract-ocr/tessdata'.
(tesseract-ocr) [arguments]: Delete adjust-TESSDATA_PREFIX-macro.
Adjust installation prefix in install-minimal-tessdata phase.
[native-search-paths]: Search for files under share/tessdata directly.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2023-03-20 22:19:35 -04:00
Maxim Cournoyer
34e4761a0f
gnu: emacs-magit-gerrit: Update to 0.4-1.a975215. 
* gnu/packages/emacs-xyz.scm (emacs-magit-gerrit): Update to 0.4-1.a975215.
 2023-03-20 21:07:10 -04:00
Maxim Cournoyer
b019c16b03
gnu: emacs-magit: Update to 3.3.0-4.a760dd1. 
This update resolves a problem where configuring a remote would result in the
error "Symbol’s function definition is void:
transient--with-suspended-override".

* gnu/packages/emacs-xyz.scm (emacs-magit): Update to 3.3.0-4.a760dd1.
 2023-03-20 21:07:10 -04:00
Maxim Cournoyer
35dcd38fc3
gnu: emacs-transient: Update to 0.3.7-1.0ae0de4. 
* gnu/packages/emacs-xyz.scm (emacs-transient): Update to 0.3.7-1.0ae0de4.
[propagated-inputs]: Remove emacs-dash; add emacs-compat.
 2023-03-20 21:07:09 -04:00
Ricardo Wurmus
d2ae00530b
gnu: lepton-eda: Update to 1.9.18-20220529. 
* gnu/packages/engineering.scm (lepton-eda): Update to 1.9.18-20220529.
[inputs]: Add guile-readline.
[arguments]: Adjust build phase 'fix-dynamic-link; add build phase 'fix-tests.
 2023-03-21 00:02:59 +01:00
Ricardo Wurmus
fa0c6defeb
gnu: Add ctrlr. 
* gnu/packages/music.scm (ctrlr): New variable.
 2023-03-21 00:02:59 +01:00
Andreas Enge
30f4b3a7e8
gnu: openjdk10: Apply patch again. 
This partially reverts commit 7636c49b45
where the patch was dropped.

* gnu/packages/java.scm (openjdk10)[source]: Apply patch.
 2023-03-20 19:00:02 +01:00
Mădălin Ionel Patrașcu
2336d5f57a
gnu: Add r-annotationhubdata. 
* gnu/packages/bioconductor.scm (r-annotationhubdata): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2023-03-20 18:25:10 +01:00
Mădălin Ionel Patrașcu
40b79eafee
gnu: Add r-affylmgui. 
* gnu/packages/bioconductor.scm (r-affylmgui): New variable.
 2023-03-20 18:25:10 +01:00
Mădălin Ionel Patrașcu
628c22ec9e
gnu: Add r-tkrplot. 
* gnu/packages/cran.scm (r-tkrplot): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
 2023-03-20 18:25:10 +01:00
Mădălin Ionel Patrașcu
9f09ac6b21
gnu: Add r-affyplm. 
* gnu/packages/bioconductor.scm (r-affyplm): New variable.
 2023-03-20 18:25:10 +01:00
Mădălin Ionel Patrașcu
284b5eca60
gnu: Add r-affyilm. 
* gnu/packages/bioconductor.scm (r-affyilm): New variable.
 2023-03-20 18:25:10 +01:00
Efraim Flashner
f80215c7c4
gnu: python-google-api-client: Update to 1.12.8. 
* gnu/packages/python-web.scm (python-google-api-client): Update to
1.12.8.
[arguments]: Remove custom phase to adjust setup.py.
[native-inputs]: Remove python-oauth2client, python-uritemplate. Move
python-httplib2, python-six ...
[propagated-inputs]: ... here. Add python-google-api-core-1,
python-google-auth-1, python-google-auth-httplib2, python-uritemplate-3.
 2023-03-20 18:27:45 +02:00
Efraim Flashner
f541989f95
gnu: python-googleapis-common-protos: Update to 1.56.4. 
* gnu/packages/python-web.scm (python-googleapis-common-protos): Update
to 1.56.4.
[arguments]: Enable test suite.
 2023-03-20 18:27:44 +02:00
Efraim Flashner
86f1a3643e
gnu: Add python-google-api-core-1. 
* gnu/packages/python-web.scm (python-google-api-core-1): New variable.
 2023-03-20 18:27:44 +02:00
Efraim Flashner
e0deaf0a85
gnu: Add python-google-auth-1. 
* gnu/packages/python-web.scm (python-google-auth-1): New variable.
 2023-03-20 18:27:44 +02:00
Efraim Flashner
a39aac3352
gnu: Add python-google-auth-httplib2. 
* gnu/packages/python-web.scm (python-google-auth-httplib2): New
variable.
 2023-03-20 18:27:44 +02:00
Efraim Flashner
6ec585fb3e
gnu: Add python-uritemplate-3. 
* gnu/packages/python-web.scm (python-uritemplate-3): New variable.
 2023-03-20 18:27:43 +02:00
Efraim Flashner
0f4800e93a
gnu: python-httplib2: Update to 0.15.0. 
* gnu/packages/python-web.scm (python-httplib2): Update to 0.15.0.
[source]: Download using git.
[arguments]: Add a phase to adjust the test package version
requirements.
[native-inputs]: Add python-flake8, python-future, python-mock,
python-pytest, python-pytest-cov, python-pytest-forked,
python-pytest-randomly, python-pytest-timeout, python-pytest-xdist,
python-six.
[home-page]: Switch to new upstream homepage.
 2023-03-20 18:27:43 +02:00
Efraim Flashner
9d93c0c789
gnu: zig: Increase max-silent-time. 
* gnu/packages/zig.scm (zig-0.10)[properties]: Set max-silent-time to 3
hours.
 2023-03-20 18:27:40 +02:00
Ricardo Wurmus
5dcbe80da8
gnu: Add transanno. 
* gnu/packages/bioinformatics.scm (transanno): New variable.
 2023-03-20 17:22:33 +01:00
Ricardo Wurmus
6a1638fe97
gnu: Add rust-autocompress-0.2. 
* gnu/packages/crates-io.scm (rust-autocompress-0.2): New variable.
 2023-03-20 17:22:33 +01:00
Ricardo Wurmus
cc2f5cd998
gnu: Add rust-temp-testdir-0.2. 
* gnu/packages/crates-io.scm (rust-temp-testdir-0.2): New variable.
 2023-03-20 17:22:33 +01:00
Ricardo Wurmus
50e63a675b
gnu: Add rust-bio-0.41. 
* gnu/packages/crates-io.scm (rust-bio-0.41): New variable.
 2023-03-20 17:22:33 +01:00
Maxim Cournoyer
45fd01ac5d
gnu: ruby-rugged: Update to 1.6.2-0.6379f23 and enable tests. 
* gnu/packages/ruby.scm (ruby-rugged): Update to 1.6.2-0.6379f23.
[source]: Fetch via git.
[arguments]: Enable tests.  Add #:phases.
[native-inputs]: Add git-minimal/pinned.  Remove ruby-minitest and ruby-pry.
 2023-03-20 11:12:18 -04:00
Maxim Cournoyer
008a2f1803
gnu: python-django-rq: Update to 2.7.0. 
* gnu/packages/django.scm (python-django-rq): Update to 2.7.0.
[arguments]: Replace django-admin.py with django-admin in check phase.
 2023-03-20 08:38:20 -04:00
Maxim Cournoyer
10d5535c78
gnu: python-aioredis: Deprecate by python-redis. 
* gnu/packages/databases.scm (python-aioredis): Mark as deprecated by
python-redis.
 2023-03-20 08:38:19 -04:00
Maxim Cournoyer
c3b110b27a
gnu: python-fakeredis: Update to 2.10.1 and enable tests. 
* gnu/packages/databases.scm (python-fakeredis): Update to 2.10.1.
[source]: Fetch via git.
[build-system]: Use pyproject-build-system.
[arguments]: Enable tests.  Add #:phases.
[native-inputs]: New field.
[propagated-inputs]: Remove python-aioredis and python-packaging.
[home-page]: Update URL.
 2023-03-20 08:38:19 -04:00
Maxim Cournoyer
1a902eb21a
gnu: python-redis: Update to 4.5.2 and enable tests. 
* gnu/packages/databases.scm (python-redis): Update to 4.5.2.
[source]: Fetch from git.
[build-system]: Use pyproject-build-system.
[arguments]: Enable tests.  Add #:test-flags and #:phases.
[native-inputs]: Add field.
[propagated-inputs]: Add field.
[home-page]: Update URL.
 2023-03-20 08:38:07 -04:00
Maxim Cournoyer
20fa738123
gnu: python-hiredis: Update to 2.2.2 and enable tests. 
* gnu/packages/databases.scm (python-hiredis): Update to 2.2.2.
[source]: Fetch via git and apply patches.
[build-system]: Use pyproject-build-system.
[arguments]: Enable tests.  Add #:phases.
[native-inputs]: New field.
[inputs]: Likewise.
* gnu/packages/patches/python-hiredis-fix-header.patch: New file.
* gnu/packages/patches/python-hiredis-use-system-hiredis.patch: Likewise.
* gnu/local.mk (dist_patch_DATA): Register them.
 2023-03-20 08:32:32 -04:00
Maxim Cournoyer
9956638943
gnu: hiredis: Update to 1.1.0. 
* gnu/packages/databases.scm (hiredis): Update to 1.1.0.
 2023-03-20 08:32:32 -04:00
Maxim Cournoyer
4413b09fa3
gnu: redis: Use gexps and streamline. 
* gnu/packages/databases.scm (redis) [arguments]: Merge the use-correct-tclsh
into the patch-paths phase.  Use 'which' instead of assoc-ref.  Move
the #:make-flags argument before the #:phases one.  Use cc-for-target as the
value of the CC make flag.
[native-inputs]: Move field below arguments.
 2023-03-20 08:32:31 -04:00
Maxim Cournoyer
458b791f35
gnu: redis: Update to 7.0.9 [security fixes]. 
Fixes CVE-2023-25155, CVE-2022-36021 and more; see
https://raw.githubusercontent.com/redis/redis/7.0/00-RELEASENOTES.

* gnu/packages/databases.scm (redis): Update to 7.0.9.
[native-inputs]: Add pkg-config and which.
[arguments]: Add a patch-paths phase.  Skip the AOF-related tests.
[properties]: Add a lint-hidden-cve property.
 2023-03-20 08:32:31 -04:00
Andrew Tropin
3a2200e1ad
services: network-manager: Add missing shadowing of 'iwd?' field. 
* gnu/services/networking.scm (network-manager-shepherd-service): Add missing
shadowing of 'iwd?' field by using let* instead of let.
 2023-03-20 12:08:36 +04:00
Sergey Trofimov
1f36534c7e
home: 'home-environment-with-provenance' uses the HE location info. 
* gnu/home.scm (home-environment-with-provenance): Make `config-file`
optional, with the default taken from the HE location info.

Signed-off-by: Andrew Tropin <andrew@trop.in>
 2023-03-20 09:14:23 +04:00
conses
d429ff12e5
gnu: emacs-eshell-syntax-highlighting: Update to 0.3-0.1ba39a9. 
* gnu/packages/emacs-xyz.scm (emacs-eshell-syntax-highlighting): Update to
0.3-0.1ba39a9.

Signed-off-by: Andrew Tropin <andrew@trop.in>
 2023-03-20 09:11:04 +04:00
Andrew Tropin
8f5f505d90
gnu: Add emacs-geiser-eros. 
* gnu/packages/emacs-xyz.scm (emacs-geiser-eros): New variable.
 2023-03-20 09:10:37 +04:00
Leo Famulari
80d31a7478
gnu: linux-libre: Update kernel configs for 6.2.7. 
* gnu/packages/aux-files/linux-libre/6.2-arm.conf,
gnu/packages/aux-files/linux-libre/6.2-arm64.conf,
gnu/packages/aux-files/linux-libre/6.2-i686.conf,
gnu/packages/aux-files/linux-libre/6.2-x86_64.conf: Set some new configuration
options.
 2023-03-19 18:01:00 -04:00
Leo Famulari
90c8f62328
gnu: linux-libre 4.14: Update to 4.14.310. 
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.310.
(linux-libre-4.14-pristine-source, deblob-scripts-4.14): Update hashes.
 2023-03-19 18:00:59 -04:00
Leo Famulari
5617381fc1
gnu: linux-libre 4.19: Update to 4.19.278. 
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.278.
(linux-libre-4.19-pristine-source, deblob-scripts-4.19): Update hashes.
 2023-03-19 18:00:59 -04:00
Leo Famulari
fed3cf520e
gnu: linux-libre 5.4: Update to 5.4.237. 
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.237.
(linux-libre-5.4-pristine-source, deblob-scripts-5.4): Update hashes.
 2023-03-19 18:00:59 -04:00
Leo Famulari
400cb5cf58
gnu: linux-libre 5.10: Update to 5.10.175. 
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.175.
(linux-libre-5.10-pristine-source, deblob-scripts-5.10): Update hashes.
 2023-03-19 18:00:59 -04:00
Leo Famulari
fccf2b2fb5
gnu: linux-libre 5.15: Update to 5.15.103. 
* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.103.
(linux-libre-5.15-pristine-source, deblob-scripts-5.15): Update hashes.
 2023-03-19 18:00:58 -04:00
Leo Famulari
d683261b23
gnu: linux-libre 6.1: Update to 6.1.20. 
* gnu/packages/linux.scm (linux-libre-6.1-version): Update to 6.1.20.
(linux-libre-6.1-pristine-source, deblob-scripts-6.1): Update hashes.
 2023-03-19 18:00:58 -04:00
Leo Famulari
0824203a22
gnu: linux-libre: Update to 6.2.7. 
* gnu/packages/linux.scm (linux-libre-6.2-version): Update to 6.2.7.
(linux-libre-6.2-pristine-source, deblob-scripts-6.2): Update hashes.
 2023-03-19 18:00:58 -04:00