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2023-11-03guix: Upgrade to Bioconductor 3.18.Ricardo Wurmus
* guix/build-system/r.scm (bioconductor-uri): Bump Bioconductor version to 3.18. * guix/import/cran.scm (%bioconductor-version): Same. Change-Id: Ic3fc2e6ab6b5f6f6e55662f81baee67391158c5b
2023-10-29system: vm: Include the cirrus driver in the initrd.Tobias Geerinckx-Rice
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
2023-11-03gnu: Add r-miamiplot.Afkhami, Navid
* gnu/packages/bioinformatics.scm (r-miamiplot): New variable. Change-Id: I41a3a951c6f1835800301e4c168eeeb0dd299f06 Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-11-03gnu: cmark-gfm: Update to 0.29.0.gfm.13.Skylar Chan
* 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>
2023-11-03gnu: mupdf: Update to 1.23.4.Timotej Lazar
* 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>
2023-11-03gnu: syncthing: Update to 1.25.0.Timotej Lazar
* gnu/packages/syncthing.scm (syncthing): Update to 1.25.0. Change-Id: I39ebd12e96fb09386cf51bd42cd5241f3820c16c Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-11-03gnu: go-github-com-hjson-hjson-go: Update to 4.3.1.Artyom V. Poptsov
* 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>
2023-11-03gnu: neovim: Update to 0.9.4.Benjamin
* gnu/packages/vim.scm (neovim): Update to 0.9.4. Change-Id: I7246390c69875cbc1d7442afe38abd31ce85616b Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-11-03gnu: guile-netlink: Update to 1.2.1.Julien Lepiller
* gnu/packages/guile-xyz.scm (guile-netlink): Update to 1.2.1. Change-Id: I3018cf7e0b6cd460bf27b8bbe1b031cf0dafe547 Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-11-03gnu: foot: Update to 1.16.2.Jaeme Sifat
* gnu/packages/terminals.scm (foot): Update to 1.16.2. [arguments]: Use gexps. Change-Id: I0615f6251a918a572369c05b126853f79e9fca4c Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-11-03gnu: wine-minimal: Update to 8.18.Kaelyn Takata
* 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>
2023-11-03gnu: emacs-ox-rss: Update upstream URL.Simon Tournier
* gnu/packages/emacs-xyz.scm (emacs-ox-rss)[source]: Update upstream URL. Change-Id: I66f0aa2cf5ee08705a89d0683e638e3fa1e1fb12 Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-11-03gnu: msmtp: Update to 1.8.25.Timotej Lazar
* gnu/packages/mail.scm (msmtp): Update to 1.8.25. Change-Id: If6a03b52734fa09dc6e8ffa5dd893f7d80b86aac Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-11-03gnu: wlr-randr: Update to 0.3.1.Timotej Lazar
* gnu/packages/wm.scm (wlr-randr): Update to 0.3.1. Change-Id: I1b0d9ae20c9c4a249b3679431101edfa61e39d44 Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-11-03gnu: emacs-mastodon: Update to 1.0.13.Cayetano Santos
* gnu/packages/emacs-xyz.scm (emacs-mastodon): Update to 1.0.13. Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-11-03gnu: asciinema: Update to 2.4.0.Timotej Lazar
* gnu/packages/terminals.scm (asciinema): Update to 2.4.0. Change-Id: I3e0fc7cc16aaebdf8346bb715f07021a5d568163 Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-11-03gnu: strawberry: Update to 1.0.21.Felix Gruber
* gnu/packages/music.scm (strawberry): Update to 1.0.21. [inputs]: Add libebur128. Change-Id: I2f0094ab1f87301cbf05c13ca5742bb03703b0b4 Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-11-03gnu: dragonfly-reverb: Update to 3.2.10.kiasoc5
* gnu/packages/music.scm (dragonfly-reverb): Update to 3.2.10. Change-Id: I4b0dc4e7aeae381467690305b9551e53341ef8b7 Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-11-02gnu: Add r-matrixtests.Afkhami, Navid
* gnu/packages/cran.scm (r-matrixtests): New variable. Change-Id: I62f7bd760fc8603425906c304ef4293da1c0cf61 Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-11-02gnu: Add r-nestedcv.Afkhami, Navid
* gnu/packages/cran.scm (r-nestedcv): New variable. Change-Id: Id998b4192565c220f8d238963ef61217aed12bd3
2023-11-02gnu: emacs-cider: Include enrich-classpath wrapper scripts.Jelle Licht
* 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>
2023-11-02gnu: emacs-cider: Update to 1.9.0.Jelle Licht
* gnu/packages/emacs-xyz.scm (emacs-cider): Update to 1.9.0. Change-Id: I25c511e93bdd7ec19a74ef10d0b5527a9e0b922d Signed-off-by: Andrew Tropin <andrew@trop.in>
2023-11-02gnu: emacs-clj-refactor: Update to 3.10.0.Jelle Licht
* gnu/packages/emacs-xyz.scm (emacs-clj-refactor): Update to 3.10.0. Change-Id: Idef5f44e2e3a8ed149d46ba2307184ffee21de4b Signed-off-by: Andrew Tropin <andrew@trop.in>
2023-11-02gnu: emacs-clojure-mode: Update to 5.18.0.Jelle Licht
* gnu/packages/emacs-xyz.scm (emacs-clojure-mode): Update to 5.18.0. Change-Id: I84cadfe0af5e1635abd02593e4f5f02b53645b39 Signed-off-by: Andrew Tropin <andrew@trop.in>
2023-11-02gnu: emacs-org-contrib: Remove dependency on emacs-cider.Jelle Licht
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>
2023-11-01gnu: r-rjava: Use OpenJDK 11.Ricardo Wurmus
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
2023-11-01teams.scm: Add file-local variable prop line for the mode.Maxim Cournoyer
This tells Emacs to use the scheme-mode to edit the file. * etc/teams.scm (mode): New file-local variable. Change-Id: I9a48f552e831317402673d95cf6c1de506d388b5
2023-11-01doc: contributiong: Fix ref usage.Julien Lepiller
Previous usage renders as "see See Teams". * doc/contributing.texi: Fix ref usage. Change-Id: I97a91697ecb87d07cc3c962a79d87dd290a70a7c
2023-10-31nls: Update translations.Florian Pelz
Change-Id: I432aec0ea31ead192d6444c96dc42038f5c7ab9a
2023-10-31Revert "gnu: lvm2: Remove systemd rule."Simon Tournier
This reverts commit c0895371c5759c7d9edb330774e90f192cc4cf2c, which does not correctly fix the issue, as reported by Josselin Poiret <dev@jpoiret.xyz> in <https://issues.guix.gnu.org/issue/66586#6>.
2023-10-31gnu: python-baltica: Add missing R inputs.Afkhami, Navid
* 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
2023-10-31gnu: r-logspline: Update to 2.1.21.Ricardo Wurmus
* gnu/packages/statistics.scm (r-logspline): Update to 2.1.21. Change-Id: Ib4ec6124282851bcc52eb87f7e30027e801f0531
2023-10-31gnu: r-withr: Update to 2.5.2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-withr): Update to 2.5.2. Change-Id: Ie4265bc4a6d9c54e3f64ab12ae0d14c716b4e03f
2023-10-31gnu: r-checkmate: Update to 2.3.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-checkmate): Update to 2.3.0. Change-Id: I0599e3a4e174cc311c37d7c334087eda15deafc1
2023-10-31gnu: r-dbplyr: Update to 2.4.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-dbplyr): Update to 2.4.0. Change-Id: I8cf5c1b47b47a41b606e76d0b5e14425946f0903
2023-10-31gnu: r-knitr: Update to 1.45.Ricardo Wurmus
* gnu/packages/statistics.scm (r-knitr): Update to 1.45. Change-Id: I1317366a0041f29b284e24d056734498f9d35cd7
2023-10-31gnu: r-strex: Update to 1.6.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-strex): Update to 1.6.1. Change-Id: Id37ef19901a3548128816e2677148405b5845297
2023-10-31gnu: r-seuratobject: Update to 5.0.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-seuratobject): Update to 5.0.0. [propagated-inputs]: Add r-generics, r-lifecycle, and r-spam. Change-Id: I8486d42c1f9d3e5f4b9fc091a4d4aab7b1c803b6
2023-10-31gnu: r-rfast: Update to 2.0.9.Ricardo Wurmus
* gnu/packages/cran.scm (r-rfast): Update to 2.0.9. [propagated-inputs]: Add r-rcppparallel. Change-Id: I551a2b1745b937454b5aad99f4620839f9a89902
2023-10-31gnu: r-spatstat: Update to 3.0-7.Ricardo Wurmus
* gnu/packages/cran.scm (r-spatstat): Update to 3.0-7. Change-Id: I8c54279b92acb7532b1050613a60ba2e96c115eb
2023-10-31gnu: r-spatstat-linnet: Update to 3.1-3.Ricardo Wurmus
* gnu/packages/cran.scm (r-spatstat-linnet): Update to 3.1-3. Change-Id: I7f1dadd2e8fecf03cbde3c56de3a3384ba8cf24d
2023-10-31gnu: r-posterior: Update to 1.5.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-posterior): Update to 1.5.0. Change-Id: I3fa7adca749efcbe0d8b6ab0f707e70a1e895d2d
2023-10-31gnu: r-adagio: Update to 0.9.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-adagio): Update to 0.9.2. Change-Id: I2131b973194fcf710fed1ac4c425717278269308
2023-10-31gnu: r-rintrojs: Update to 0.3.3.Ricardo Wurmus
* gnu/packages/cran.scm (r-rintrojs): Update to 0.3.3. Change-Id: I184740e9bd1ed8d087c2985d08b12f4fe31d72b7
2023-10-31gnu: r-sampling: Update to 2.10.Ricardo Wurmus
* gnu/packages/cran.scm (r-sampling): Update to 2.10. Change-Id: I7a3407c77fb71a8a4355415beeee09edc2a8908c
2023-10-31gnu: r-polspline: Update to 1.1.24.Ricardo Wurmus
* gnu/packages/cran.scm (r-polspline): Update to 1.1.24. Change-Id: I323fc3b50c1d215d749cd814a684463810e4bfc4
2023-10-31gnu: r-grimport2: Update to 0.3-1.Ricardo Wurmus
* gnu/packages/cran.scm (r-grimport2): Update to 0.3-1. Change-Id: I6b7de08f4d24a3398e8b788fbe726792ac38a59a
2023-10-31gnu: r-gridpattern: Update to 1.1.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-gridpattern): Update to 1.1.1. Change-Id: I63bc1df4fc6f8f5e9931a6a82db68df0e933a1cb
2023-10-31gnu: r-performance: Update to 0.10.8.Ricardo Wurmus
* gnu/packages/cran.scm (r-performance): Update to 0.10.8. Change-Id: Ic0c7a1f1402ae5a63bf433fd2f874e24eab5a216
2023-10-31gnu: r-wrs2: Update to 1.1-5.Ricardo Wurmus
* gnu/packages/cran.scm (r-wrs2): Update to 1.1-5. [propagated-inputs]: Remove r-mc2d. Change-Id: I0346e018b401143b4f9cf65845cf4d3b210ed54b
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