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* gnu: emacs-geiser-gauche: Process autoloads in-tree.Liliana Marie Prikler2023-11-01
| | | | | * gnu/packages/emacs-xyz.scm (emacs-geiser-gauche)[#:phases]<patch-autoloads>: Resolve "geiser-gauche-autoloads.el" in the current working directory.
* gnu: emacs-geiser-guile: Process autoloads in-tree.Liliana Marie Prikler2023-11-01
| | | | | * gnu/packages/emacs-xyz.scm (emacs-geiser-guile)[#:phases]<patch-autoloads>: Resolve "geiser-guile-autoloads.el" in the current working directory.
* gnu: uim: Keep Emacs files in subdirectory.Liliana Marie Prikler2023-11-01
| | | | | | * gnu/packages/xorg.scm (uim)[arguments]<#:configure-flags>: Drop “--with-lispdir”. <#:phases>: Drop ‘fix-install-path’. Adjust ‘make-autoloads’ accordingly.
* gnu: guile-wisp: Build autoloads before installing them.Liliana Marie Prikler2023-11-01
| | | | | * gnu/packages/guile-xyz.scm (guile-wisp)[#:phases]: Move ‘make-autoloads’ after ‘unpack’.
* gnu: crm114: Adjust to changes in emacs-build-system.Liliana Marie Prikler2023-11-01
| | | | | | * gnu/packages/mail.scm (crm114)[#:phases]: Move ‘make-autoloads’ after ‘unpack’. Delete ‘enable-autoloads-compilation’. Adjust ordering of other phases accordingly.
* gnu: emacs-mew: Adjust to changes in emacs-build-system.Liliana Marie Prikler2023-11-01
| | | | | | | | | | * gnu/packages/mail.scm (emacs-mew)[arguments]: Only let-bind icon-dir. <#:modules>: Add (guix build emacs-build-system). <#:imported-modules>: Use %emacs-build-system-modules. <#:configure-flags>: Set elispdir with emacs:elpa-directory. <#:phases>: Move ‘generate-autoloads’ after ‘unpack’. Generate the autoloads locally. Also enable compilation.
* gnu: translate-shell: Compile emacs bytecode.Liliana Marie Prikler2023-11-01
| | | | * gnu/packages/dictionaries.scm (translate-shell)[#:phases]: Add ‘emacs-build’.
* gnu: translate-shell: Build autoloads before installing them.Liliana Marie Prikler2023-11-01
| | | | | * gnu/packages/dictionaries.scm (translate-shell)[#:phases]: Move ‘emacs-make-autoloads’ before ‘unpack’. Drop ‘emacs-autoload-compilation’.
* gnu: skktools: Build autoloads before installing them.Liliana Marie Prikler2023-11-01
| | | | * gnu/packages/language.scm (skktools)[#:phases]: Move ‘make-autoloads’ after ‘unpack’.
* gnu: r-rjava: Use OpenJDK 11.Ricardo Wurmus2023-11-01
| | | | | | | | | 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
* Revert "gnu: lvm2: Remove systemd rule."Simon Tournier2023-10-31
| | | | | | 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>.
* gnu: python-baltica: Add missing R inputs.Afkhami, Navid2023-10-31
| | | | | | | | | * 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
* gnu: r-logspline: Update to 2.1.21.Ricardo Wurmus2023-10-31
| | | | | | * gnu/packages/statistics.scm (r-logspline): Update to 2.1.21. Change-Id: Ib4ec6124282851bcc52eb87f7e30027e801f0531
* gnu: r-withr: Update to 2.5.2.Ricardo Wurmus2023-10-31
| | | | | | * gnu/packages/statistics.scm (r-withr): Update to 2.5.2. Change-Id: Ie4265bc4a6d9c54e3f64ab12ae0d14c716b4e03f
* gnu: r-checkmate: Update to 2.3.0.Ricardo Wurmus2023-10-31
| | | | | | * gnu/packages/statistics.scm (r-checkmate): Update to 2.3.0. Change-Id: I0599e3a4e174cc311c37d7c334087eda15deafc1
* gnu: r-dbplyr: Update to 2.4.0.Ricardo Wurmus2023-10-31
| | | | | | * gnu/packages/statistics.scm (r-dbplyr): Update to 2.4.0. Change-Id: I8cf5c1b47b47a41b606e76d0b5e14425946f0903
* gnu: r-knitr: Update to 1.45.Ricardo Wurmus2023-10-31
| | | | | | * gnu/packages/statistics.scm (r-knitr): Update to 1.45. Change-Id: I1317366a0041f29b284e24d056734498f9d35cd7
* gnu: r-strex: Update to 1.6.1.Ricardo Wurmus2023-10-31
| | | | | | * gnu/packages/cran.scm (r-strex): Update to 1.6.1. Change-Id: Id37ef19901a3548128816e2677148405b5845297
* gnu: r-seuratobject: Update to 5.0.0.Ricardo Wurmus2023-10-31
| | | | | | | * gnu/packages/cran.scm (r-seuratobject): Update to 5.0.0. [propagated-inputs]: Add r-generics, r-lifecycle, and r-spam. Change-Id: I8486d42c1f9d3e5f4b9fc091a4d4aab7b1c803b6
* gnu: r-rfast: Update to 2.0.9.Ricardo Wurmus2023-10-31
| | | | | | | * gnu/packages/cran.scm (r-rfast): Update to 2.0.9. [propagated-inputs]: Add r-rcppparallel. Change-Id: I551a2b1745b937454b5aad99f4620839f9a89902
* gnu: r-spatstat: Update to 3.0-7.Ricardo Wurmus2023-10-31
| | | | | | * gnu/packages/cran.scm (r-spatstat): Update to 3.0-7. Change-Id: I8c54279b92acb7532b1050613a60ba2e96c115eb
* gnu: r-spatstat-linnet: Update to 3.1-3.Ricardo Wurmus2023-10-31
| | | | | | * gnu/packages/cran.scm (r-spatstat-linnet): Update to 3.1-3. Change-Id: I7f1dadd2e8fecf03cbde3c56de3a3384ba8cf24d
* gnu: r-posterior: Update to 1.5.0.Ricardo Wurmus2023-10-31
| | | | | | * gnu/packages/cran.scm (r-posterior): Update to 1.5.0. Change-Id: I3fa7adca749efcbe0d8b6ab0f707e70a1e895d2d
* gnu: r-adagio: Update to 0.9.2.Ricardo Wurmus2023-10-31
| | | | | | * gnu/packages/cran.scm (r-adagio): Update to 0.9.2. Change-Id: I2131b973194fcf710fed1ac4c425717278269308
* gnu: r-rintrojs: Update to 0.3.3.Ricardo Wurmus2023-10-31
| | | | | | * gnu/packages/cran.scm (r-rintrojs): Update to 0.3.3. Change-Id: I184740e9bd1ed8d087c2985d08b12f4fe31d72b7
* gnu: r-sampling: Update to 2.10.Ricardo Wurmus2023-10-31
| | | | | | * gnu/packages/cran.scm (r-sampling): Update to 2.10. Change-Id: I7a3407c77fb71a8a4355415beeee09edc2a8908c
* gnu: r-polspline: Update to 1.1.24.Ricardo Wurmus2023-10-31
| | | | | | * gnu/packages/cran.scm (r-polspline): Update to 1.1.24. Change-Id: I323fc3b50c1d215d749cd814a684463810e4bfc4
* gnu: r-grimport2: Update to 0.3-1.Ricardo Wurmus2023-10-31
| | | | | | * gnu/packages/cran.scm (r-grimport2): Update to 0.3-1. Change-Id: I6b7de08f4d24a3398e8b788fbe726792ac38a59a
* gnu: r-gridpattern: Update to 1.1.1.Ricardo Wurmus2023-10-31
| | | | | | * gnu/packages/cran.scm (r-gridpattern): Update to 1.1.1. Change-Id: I63bc1df4fc6f8f5e9931a6a82db68df0e933a1cb
* gnu: r-performance: Update to 0.10.8.Ricardo Wurmus2023-10-31
| | | | | | * gnu/packages/cran.scm (r-performance): Update to 0.10.8. Change-Id: Ic0c7a1f1402ae5a63bf433fd2f874e24eab5a216
* gnu: r-wrs2: Update to 1.1-5.Ricardo Wurmus2023-10-31
| | | | | | | * gnu/packages/cran.scm (r-wrs2): Update to 1.1-5. [propagated-inputs]: Remove r-mc2d. Change-Id: I0346e018b401143b4f9cf65845cf4d3b210ed54b
* gnu: r-rbibutils: Update to 2.2.16.Ricardo Wurmus2023-10-31
| | | | | | * gnu/packages/cran.scm (r-rbibutils): Update to 2.2.16. Change-Id: I188dddbb7fa03f43574e50d43f741c5398e7c331
* gnu: r-lambertw: Update to 0.6.9.Ricardo Wurmus2023-10-31
| | | | | | * gnu/packages/cran.scm (r-lambertw): Update to 0.6.9. Change-Id: Ia36a96ddd78585768b88ab662d5c5ba31aa40744
* gnu: r-mbess: Update to 4.9.3.Ricardo Wurmus2023-10-31
| | | | | | * gnu/packages/cran.scm (r-mbess): Update to 4.9.3. Change-Id: I8ada8e1a56b7497145409de82865d5d9d83da6e3
* gnu: r-poorman: Update to 0.2.7.Ricardo Wurmus2023-10-31
| | | | | | * gnu/packages/cran.scm (r-poorman): Update to 0.2.7. Change-Id: I9c23bd2bbba0eb6f6b2b6b6ac1cc11524b5c6980
* gnu: r-consort: Update to 1.2.1.Ricardo Wurmus2023-10-31
| | | | | | * gnu/packages/cran.scm (r-consort): Update to 1.2.1. Change-Id: I28d1749044a38f9a9144eeb5675d6607bf973c53
* gnu: r-abn: Update to 3.0.2.Ricardo Wurmus2023-10-31
| | | | | | * gnu/packages/bioconductor.scm (r-abn): Update to 3.0.2. Change-Id: Icf3de104b61e79b9a7c9fbfecb0e071d6e46ef9d
* gnu: r-htmltable: Update to 2.4.2.Ricardo Wurmus2023-10-31
| | | | | | | | * gnu/packages/cran.scm (r-htmltable): Update to 2.4.2. [arguments]: Replace minified JavaScript. [native-inputs]: Add esbuild and js-jquery. Change-Id: Iacc17957c2a773ca651d3a9e980a3e4281874829
* gnu: r-rsqlite: Update to 2.3.2.Ricardo Wurmus2023-10-31
| | | | | | * gnu/packages/statistics.scm (r-rsqlite): Update to 2.3.2. Change-Id: I97532cd5834e0aad84d7072f7f93bae612ad93bf
* gnu: b43-tools: Use make-flags.Efraim Flashner2023-10-31
| | | | | | | | * gnu/packages/firmware.scm (b43-tools)[arguments]: Add make-flags. Use make-flags in custom 'build and 'install phases. Remove trailing #t from phases. Change-Id: I8576351ecd571d191598943a2d143ab3e3e9da09
* gnu: python-radio-beam: Update to 0.3.6.Maxim Cournoyer2023-10-31
| | | | | | | * gnu/packages/astronomy.scm (python-radio-beam): Update to 0.3.6. [native-inputs]: Add python-setuptools-scm. Change-Id: I3be87a22b701119699d37104f8df4f3fab44d0c8
* gnu: python-spectral-cube: Update to 0.6.3.Maxim Cournoyer2023-10-31
| | | | | | | * gnu/packages/astronomy.scm (python-spectral-cube): Update to 0.6.3. [native-inputs]: Add python-setuptools-scm. Change-Id: I8b701081d2c8ea2fd8f25ca845e8e26760fdc094
* gnu: Add python-spectral-cube.Sharlatan Hellseher2023-10-31
| | | | | | * gnu/packages/astronomy.scm (python-spectral-cube): New variable. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
* gnu: Add python-aplpy.Sharlatan Hellseher2023-10-31
| | | | | | * gnu/packages/astronomy.scm (python-aplpy): New variable. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
* gnu: Add python-pyregion.Sharlatan Hellseher2023-10-31
| | | | | | * gnu/packages/astronomy.scm (python-pyregion): New variable. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
* gnu: Add python-pyavm.Sharlatan Hellseher2023-10-31
| | | | | | * gnu/packages/astronomy.scm (python-pyavm): New variable. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
* gnu: Add python-radio-beam.Sharlatan Hellseher2023-10-31
| | | | | | * gnu/packages/astronomy.scm (python-radio-beam): New variable. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
* gnu: opensmtpd: Update to 7.4.0p0 (bis).Tobias Geerinckx-Rice2023-10-29
| | | | | | | | | | | | | | | | | | | This time fixing a segfault reported & debugged entirely by graywolf. See: <https://github.com/OpenSMTPD/OpenSMTPD/issues/1233> So, what went wrong here? Mostly me being entirely convinced, to the point of not even looking, that we have no opensmtpd system test. We do. Instead, I tested the update on my own mail server, which for entirely unhysterical raisins happens to link OpenSMTPd against OpenSSL and so just happens to sidestep this bug. Aiya. * gnu/packages/mail.scm (opensmtpd): Update to 7.4.0p0. [native-inputs]: Add pkg-config. [inputs]: Add libbsd. [arguments]: Add "--with-libbsd" to #:configure-flags. Co-authored-by: graywolf in #guix Change-Id: I5536b828eecd16f041ed9381b16bd7aa54158155
* gnu: Add r-radiogx.Mădălin Ionel Patrașcu2023-10-31
| | | | | | | * gnu/packages/bioconductor.scm (r-radiogx): New variable. Change-Id: I8fd06a18bd68f9a3baa2cc129d62aef06528bc97 Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: Add r-coregx.Mădălin Ionel Patrașcu2023-10-31
| | | | | | | * gnu/packages/bioconductor.scm (r-coregx): New variable. Change-Id: Ib54ba3c7bebdcc90748d4e4b0b2ce63b7f0fc1b8 Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
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