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Author SHA1 Message Date
Ricardo Wurmus
fc9baf4ad2
gnu: r-adamgui: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-adamgui): Update to 1.18.0.

Change-Id: Iabe992f09b65994038340e564de3be62ffdae5e3
 2023-11-03 22:49:11 +01:00
Ricardo Wurmus
2662a6af48
gnu: r-adam: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-adam): Update to 1.18.0.

Change-Id: I33e560dba8bade0b474b8911c82f71bd768e37a5
 2023-11-03 22:49:11 +01:00
Ricardo Wurmus
de5c088e06
gnu: r-adacgh2: Update to 2.42.0. 
* gnu/packages/bioconductor.scm (r-adacgh2): Update to 2.42.0.

Change-Id: I3a08c5e0c0651c3cb35329de5ce97f660e48ae43
 2023-11-03 22:49:11 +01:00
Ricardo Wurmus
7e7d075194
gnu: r-absseq: Update to 1.56.0. 
* gnu/packages/bioconductor.scm (r-absseq): Update to 1.56.0.

Change-Id: I417b2bc58c196fce30a389ae3b999306a0b83893
 2023-11-03 22:49:11 +01:00
Ricardo Wurmus
d08d58d828
gnu: r-abarray: Update to 1.70.0. 
* gnu/packages/bioconductor.scm (r-abarray): Update to 1.70.0.

Change-Id: Ibdbf0deb2efad33dffee619c4f8a80f90c815d37
 2023-11-03 22:49:11 +01:00
Ricardo Wurmus
6ea450f390
gnu: r-debcam: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-debcam): Update to 1.20.0.
[arguments]: Remove old comment and enable tests.
[inputs]: Replace icedtea with openjdk11.

Change-Id: Id8afa7e53d69fa7767901249cab58fe5555d0e48
 2023-11-03 22:49:11 +01:00
Ricardo Wurmus
bcf0ecd1ec
gnu: Add r-hpo-db. 
* gnu/packages/bioconductor.scm (r-hpo-db): New variable.

Change-Id: I4de4bde150f5ff5634e83a6e2e715cddd30db9b2
 2023-11-03 22:49:11 +01:00
Ricardo Wurmus
6304d3cce6
gnu: Add r-mpo-db. 
* gnu/packages/bioconductor.scm (r-mpo-db): New variable.

Change-Id: I88f21ac585d10f2763656b458f015b95a8a8bcfe
 2023-11-03 22:49:11 +01:00
Ricardo Wurmus
48bf30e3b1
gnu: Add r-fancova. 
* gnu/packages/cran.scm (r-fancova): New variable.

Change-Id: I9bfef352be86c08707edfee0bfb171094114d158
 2023-11-03 22:49:10 +01:00
Ricardo Wurmus
75ce5b0466
gnu: Add r-collapse. 
* gnu/packages/cran.scm (r-collapse): New variable.

Change-Id: Ib6690a85987e14930057ed960fdd229706b0c35d
 2023-11-03 22:49:10 +01:00
Ricardo Wurmus
4f85beac2d
gnu: Add r-msexperiment. 
* gnu/packages/bioconductor.scm (r-msexperiment): New variable.

Change-Id: I707addc076f36bab7f6e96953f5fbd614580825e
 2023-11-03 22:49:10 +01:00
Ricardo Wurmus
bbe7ea0d27
gnu: Add r-sparsearray. 
* gnu/packages/bioconductor.scm (r-sparsearray): New variable.

Change-Id: Ibc5b5a518206d492dd5b912294da3967881b5ccd
 2023-11-03 22:49:10 +01:00
Ricardo Wurmus
f80de2f03f
gnu: Add r-metabocoreutils. 
* gnu/packages/bioconductor.scm (r-metabocoreutils): New variable.

Change-Id: I58880565005e05a8a87c97e4611cdba8489515ab
 2023-11-03 22:49:10 +01:00
Ricardo Wurmus
7a14f9365a
guix: Upgrade to Bioconductor 3.18. 
* guix/build-system/r.scm (bioconductor-uri): Bump Bioconductor version to
3.18.
* guix/import/cran.scm (%bioconductor-version): Same.

Change-Id: Ic3fc2e6ab6b5f6f6e55662f81baee67391158c5b
 2023-11-03 22:49:10 +01:00
Tobias Geerinckx-Rice
2059b9fbe0
system: vm: Include the cirrus driver in the initrd. 
This is Ludo's suggestion at <https://issues.guix.gnu.org/36069#26>,
with an added guard against duplicates and a tweaked comment.

* gnu/system/vm.scm (virtualized-operating-system): Add "cirrus" to the
list of INITRD-MODULES.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
Change-Id: I1a86286586eee0b8c39706544778c7911a86da33
 2023-10-29 02:00:00 +02:00
Afkhami, Navid
c9361460de
gnu: Add r-miamiplot. 
* gnu/packages/bioinformatics.scm (r-miamiplot): New variable.

Change-Id: I41a3a951c6f1835800301e4c168eeeb0dd299f06
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-11-03 14:10:13 +01:00
Skylar Chan
6ae8fd7aa7
gnu: cmark-gfm: Update to 0.29.0.gfm.13. 
* gnu/packages/markup.scm (cmark-gfm): Update to 0.29.0.gfm.13.
[arguments]: Use G-expressions.

Change-Id: Id8f856cfa8020bc8028d9bf3041a7c651b8b0102
Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-11-03 10:14:06 +00:00
Timotej Lazar
021b222cda
gnu: mupdf: Update to 1.23.4. 
* gnu/packages/pdf.scm (mupdf): Update to 1.23.4.
[source]: Switch from gz to lz tarball.

Change-Id: Ie4d20c95e509960390dce3da77315fa2bf2d688f
Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-11-03 10:14:06 +00:00
Timotej Lazar
c9a7cbf0b7
gnu: syncthing: Update to 1.25.0. 
* gnu/packages/syncthing.scm (syncthing): Update to 1.25.0.

Change-Id: I39ebd12e96fb09386cf51bd42cd5241f3820c16c
Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-11-03 10:14:06 +00:00
Artyom V. Poptsov
ada2152893
gnu: go-github-com-hjson-hjson-go: Update to 4.3.1. 
* gnu/packages/golang.scm (go-github-com-hjson-hjson-go): Update to 4.3.1.

Change-Id: Iee2aef614686cbf79f388e2dd9435745d5502e2a
Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-11-03 10:14:06 +00:00
Benjamin
66ff9c82a3
gnu: neovim: Update to 0.9.4. 
* gnu/packages/vim.scm (neovim): Update to 0.9.4.

Change-Id: I7246390c69875cbc1d7442afe38abd31ce85616b
Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-11-03 10:01:29 +00:00
Julien Lepiller
9024524de1
gnu: guile-netlink: Update to 1.2.1. 
* gnu/packages/guile-xyz.scm (guile-netlink): Update to 1.2.1.

Change-Id: I3018cf7e0b6cd460bf27b8bbe1b031cf0dafe547
Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-11-03 10:00:41 +00:00
Jaeme Sifat
809f461ec1
gnu: foot: Update to 1.16.2. 
* gnu/packages/terminals.scm (foot): Update to 1.16.2.
[arguments]: Use gexps.

Change-Id: I0615f6251a918a572369c05b126853f79e9fca4c
Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-11-03 09:59:41 +00:00
Kaelyn Takata
ada7e0d042
gnu: wine-minimal: Update to 8.18. 
* gnu/packages/wine.scm (wine-minimal): Update to 8.18.
[properties]: Set upstream-name.

Change-Id: I018c320a990bf101d193095b68c44312ce9653a4
Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-11-03 09:56:01 +00:00
Simon Tournier
4471cfd099
gnu: emacs-ox-rss: Update upstream URL. 
* gnu/packages/emacs-xyz.scm (emacs-ox-rss)[source]: Update upstream URL.

Change-Id: I66f0aa2cf5ee08705a89d0683e638e3fa1e1fb12
Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-11-03 09:46:02 +00:00
Timotej Lazar
5378149acc
gnu: msmtp: Update to 1.8.25. 
* gnu/packages/mail.scm (msmtp): Update to 1.8.25.

Change-Id: If6a03b52734fa09dc6e8ffa5dd893f7d80b86aac
Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-11-03 09:46:02 +00:00
Timotej Lazar
93b8d2e730
gnu: wlr-randr: Update to 0.3.1. 
* gnu/packages/wm.scm (wlr-randr): Update to 0.3.1.

Change-Id: I1b0d9ae20c9c4a249b3679431101edfa61e39d44
Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-11-03 09:46:02 +00:00
Cayetano Santos
a4ec0c6ca0
gnu: emacs-mastodon: Update to 1.0.13. 
* gnu/packages/emacs-xyz.scm (emacs-mastodon): Update to 1.0.13.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-11-03 09:46:02 +00:00
Timotej Lazar
399cd64bc9
gnu: asciinema: Update to 2.4.0. 
* gnu/packages/terminals.scm (asciinema): Update to 2.4.0.

Change-Id: I3e0fc7cc16aaebdf8346bb715f07021a5d568163
Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-11-03 09:46:02 +00:00
Felix Gruber
1853fd9c2f
gnu: strawberry: Update to 1.0.21. 
* gnu/packages/music.scm (strawberry): Update to 1.0.21.
[inputs]: Add libebur128.

Change-Id: I2f0094ab1f87301cbf05c13ca5742bb03703b0b4
Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-11-03 09:46:02 +00:00
kiasoc5
e20ef7d2d1
gnu: dragonfly-reverb: Update to 3.2.10. 
* gnu/packages/music.scm (dragonfly-reverb): Update to 3.2.10.

Change-Id: I4b0dc4e7aeae381467690305b9551e53341ef8b7
Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-11-03 09:46:02 +00:00
Afkhami, Navid
28ebbe2be8
gnu: Add r-matrixtests. 
* gnu/packages/cran.scm (r-matrixtests): New variable.

Change-Id: I62f7bd760fc8603425906c304ef4293da1c0cf61
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-11-02 18:34:09 +01:00
Afkhami, Navid
64dbce8381
gnu: Add r-nestedcv. 
* gnu/packages/cran.scm (r-nestedcv): New variable.

Change-Id: Id998b4192565c220f8d238963ef61217aed12bd3
 2023-11-02 18:34:09 +01:00
Jelle Licht
f5346094f0
gnu: emacs-cider: Include enrich-classpath wrapper scripts. 
* gnu/packages/emacs-xyz.scm (emacs-cider)[arguments]<#:include>: Add
"^lein\\.sh$" and "^clojure\\.sh$" to the list of regexes for installed files.

Change-Id: I02507d3cd012dbe827751a21870e4bc1f13d93b5
Signed-off-by: Andrew Tropin <andrew@trop.in>
 2023-11-02 10:01:22 +04:00
Jelle Licht
0f2ec2117b
gnu: emacs-cider: Update to 1.9.0. 
* gnu/packages/emacs-xyz.scm (emacs-cider): Update to 1.9.0.

Change-Id: I25c511e93bdd7ec19a74ef10d0b5527a9e0b922d
Signed-off-by: Andrew Tropin <andrew@trop.in>
 2023-11-02 10:01:21 +04:00
Jelle Licht
7c2d36d014
gnu: emacs-clj-refactor: Update to 3.10.0. 
* gnu/packages/emacs-xyz.scm (emacs-clj-refactor): Update to 3.10.0.

Change-Id: Idef5f44e2e3a8ed149d46ba2307184ffee21de4b
Signed-off-by: Andrew Tropin <andrew@trop.in>
 2023-11-02 10:01:20 +04:00
Jelle Licht
1ebc1651a6
gnu: emacs-clojure-mode: Update to 5.18.0. 
* gnu/packages/emacs-xyz.scm (emacs-clojure-mode): Update to 5.18.0.

Change-Id: I84cadfe0af5e1635abd02593e4f5f02b53645b39
Signed-off-by: Andrew Tropin <andrew@trop.in>
 2023-11-02 10:01:19 +04:00
Jelle Licht
a5c7ceda0a
gnu: emacs-org-contrib: Remove dependency on emacs-cider. 
Since version 0.4 the ob-clojure-literate.el file with a dependency on cider
was removed from org-contrib.

* gnu/packages/emacs-xyz.scm (emacs-org-contrib)[native-inputs]: Remove
emacs-cider.

Change-Id: I838e965a819d9793424b6310ae324460b260afcc
Signed-off-by: Andrew Tropin <andrew@trop.in>
 2023-11-02 10:01:18 +04:00
Ricardo Wurmus
0647f308b4
gnu: r-rjava: Use OpenJDK 11. 
See https://github.com/s-u/rJava/issues/307.

* gnu/packages/cran.scm (r-rjava)[arguments]: Use search-input-file.
[inputs]: Replace icedtea-8 with openjdk11.

Change-Id: I9e67210f1bfd585fb53845dad55a56a639a5d806
 2023-11-01 19:33:38 +01:00
Maxim Cournoyer
a96f1c1bc0
teams.scm: Add file-local variable prop line for the mode. 
This tells Emacs to use the scheme-mode to edit the file.

* etc/teams.scm (mode): New file-local variable.

Change-Id: I9a48f552e831317402673d95cf6c1de506d388b5
 2023-11-01 12:24:29 -04:00
Julien Lepiller
c95104c2e9
doc: contributiong: Fix ref usage. 
Previous usage renders as "see See Teams".

* doc/contributing.texi: Fix ref usage.

Change-Id: I97a91697ecb87d07cc3c962a79d87dd290a70a7c
 2023-11-01 17:20:17 +01:00
Florian Pelz
938a47c86d
nls: Update translations. 
Change-Id: I432aec0ea31ead192d6444c96dc42038f5c7ab9a
 2023-10-31 23:01:37 +01:00
Simon Tournier
3991d9e4d9
Revert "gnu: lvm2: Remove systemd rule." 
This reverts commit c0895371c5, which does not
correctly fix the issue, as reported by Josselin Poiret <dev@jpoiret.xyz> in
<https://issues.guix.gnu.org/issue/66586#6>.
 2023-10-31 22:15:33 +01:00
Afkhami, Navid
b963bf6b1d
gnu: python-baltica: Add missing R inputs. 
* gnu/packages/bioinformatics.scm (python-baltica)[propagated-inputs]: Add
r-biocmanager, r-dplyr, r-genomicranges, r-here, r-openxlsx, r-optparse,
r-readr, r-rsamtools, r-stringr, r-tidyr, r-upsetr, and r-yaml.
[description]: Add an extra space after a period.

Change-Id: I8c1bb556048b406b95e081155a46da17a6be5676
 2023-10-31 22:03:24 +01:00
Ricardo Wurmus
4254269ad5
gnu: r-logspline: Update to 2.1.21. 
* gnu/packages/statistics.scm (r-logspline): Update to 2.1.21.

Change-Id: Ib4ec6124282851bcc52eb87f7e30027e801f0531
 2023-10-31 21:57:59 +01:00
Ricardo Wurmus
0858b9c472
gnu: r-withr: Update to 2.5.2. 
* gnu/packages/statistics.scm (r-withr): Update to 2.5.2.

Change-Id: Ie4265bc4a6d9c54e3f64ab12ae0d14c716b4e03f
 2023-10-31 21:57:59 +01:00
Ricardo Wurmus
90a8594c7b
gnu: r-checkmate: Update to 2.3.0. 
* gnu/packages/statistics.scm (r-checkmate): Update to 2.3.0.

Change-Id: I0599e3a4e174cc311c37d7c334087eda15deafc1
 2023-10-31 21:57:59 +01:00
Ricardo Wurmus
76a12b07d1
gnu: r-dbplyr: Update to 2.4.0. 
* gnu/packages/statistics.scm (r-dbplyr): Update to 2.4.0.

Change-Id: I8cf5c1b47b47a41b606e76d0b5e14425946f0903
 2023-10-31 21:57:59 +01:00
Ricardo Wurmus
e2d4dd5e1c
gnu: r-knitr: Update to 1.45. 
* gnu/packages/statistics.scm (r-knitr): Update to 1.45.

Change-Id: I1317366a0041f29b284e24d056734498f9d35cd7
 2023-10-31 21:57:59 +01:00
Ricardo Wurmus
4f4ab05dc4
gnu: r-strex: Update to 1.6.1. 
* gnu/packages/cran.scm (r-strex): Update to 1.6.1.

Change-Id: Id37ef19901a3548128816e2677148405b5845297
 2023-10-31 21:57:59 +01:00