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Author SHA1 Message Date
Ricardo Wurmus 5dac9674d4
gnu: r-pupillometryr: Update to 0.0.5. 
* gnu/packages/cran.scm (r-pupillometryr): Update to 0.0.5.
[propagated-inputs]: Remove r-data-table and r-lazyeval; add r-stringr.
 2023-10-05 15:16:27 +02:00
Ricardo Wurmus de4c0a2564
gnu: r-billboarder: Update to 0.4.1. 
* gnu/packages/cran.scm (r-billboarder): Update to 0.4.1.
 2023-10-05 15:16:27 +02:00
Ricardo Wurmus b372a2c8c2
gnu: r-learnr: Update to 0.11.5. 
* gnu/packages/cran.scm (r-learnr): Update to 0.11.5.
[native-inputs]: Add esbuild.
 2023-10-05 15:16:27 +02:00
Ricardo Wurmus 7694563fa1
gnu: r-renv: Update to 1.0.3. 
* gnu/packages/cran.scm (r-renv): Update to 1.0.3.
 2023-10-05 15:16:27 +02:00
Ricardo Wurmus 15688b1c96
gnu: r-rio: Update to 1.0.1. 
* gnu/packages/cran.scm (r-rio): Update to 1.0.1.
[propagated-inputs]: Remove r-openxlsx; add r-lifecycle, r-r-utils, r-stringi, and
r-writexl.
 2023-10-05 15:16:27 +02:00
Ricardo Wurmus 66e46a0260
gnu: r-import: Update to 1.3.1. 
* gnu/packages/cran.scm (r-import): Update to 1.3.1.
 2023-10-05 15:16:27 +02:00
Ricardo Wurmus 42f5162f60
gnu: r-tinytex: Update to 0.47. 
* gnu/packages/cran.scm (r-tinytex): Update to 0.47.
 2023-10-05 15:16:27 +02:00
Ricardo Wurmus df888839a1
gnu: r-psych: Update to 2.3.9. 
* gnu/packages/cran.scm (r-psych): Update to 2.3.9.
 2023-10-05 15:16:27 +02:00
Ricardo Wurmus 7f51c3790f
gnu: r-rmysql: Update to 0.10.26. 
* gnu/packages/cran.scm (r-rmysql): Update to 0.10.26.
 2023-10-05 15:16:27 +02:00
Ricardo Wurmus 994a8523be
gnu: r-limsolve: Update to 1.5.7. 
* gnu/packages/cran.scm (r-limsolve): Update to 1.5.7.
 2023-10-05 15:16:27 +02:00
Ricardo Wurmus e234cecc9e
gnu: r-lamw: Update to 2.2.1. 
* gnu/packages/cran.scm (r-lamw): Update to 2.2.1.
 2023-10-05 15:16:27 +02:00
Ricardo Wurmus 50f7b875a9
gnu: r-sp: Update to 2.1-0. 
* gnu/packages/cran.scm (r-sp): Update to 2.1-0.
 2023-10-05 15:16:27 +02:00
Ricardo Wurmus 9aa7e46c86
gnu: r-prettyunits: Update to 1.2.0. 
* gnu/packages/cran.scm (r-prettyunits): Update to 1.2.0.
 2023-10-05 15:16:27 +02:00
Ricardo Wurmus 47b8f2165a
gnu: r-ctrdata: Update to 1.15.2. 
* gnu/packages/cran.scm (r-ctrdata): Update to 1.15.2.
 2023-10-05 15:16:27 +02:00
Ricardo Wurmus 5b0a691bfa
gnu: r-pkgload: Update to 1.3.3. 
* gnu/packages/cran.scm (r-pkgload): Update to 1.3.3.
[propagated-inputs]: Add r-pkgbuild.
 2023-10-05 15:16:27 +02:00
Ricardo Wurmus 1fc6c1d2ab
gnu: r-gensa: Update to 1.1.10.1. 
* gnu/packages/cran.scm (r-gensa): Update to 1.1.10.1.
 2023-10-05 15:16:26 +02:00
Ricardo Wurmus 5cac6f401c
gnu: r-d3r: Update to 1.1.0. 
* gnu/packages/cran.scm (r-d3r): Update to 1.1.0.
[propagated-inputs]: Remove r-rlang.
 2023-10-05 15:16:26 +02:00
Ricardo Wurmus cb8c68da4b
gnu: r-jqr: Update to 1.3.0. 
* gnu/packages/cran.scm (r-jqr): Update to 1.3.0.
 2023-10-05 15:16:26 +02:00
Ricardo Wurmus 92fce36949
gnu: r-curl: Update to 5.1.0. 
* gnu/packages/cran.scm (r-curl): Update to 5.1.0.
 2023-10-05 15:16:26 +02:00
Ricardo Wurmus 4d9908cd61
gnu: r-jade: Update to 2.0-4. 
* gnu/packages/cran.scm (r-jade): Update to 2.0-4.
 2023-10-05 15:16:26 +02:00
Ricardo Wurmus 6d2df3bd9e
gnu: r-gunifrac: Update to 1.8. 
* gnu/packages/cran.scm (r-gunifrac): Update to 1.8.
[propagated-inputs]: Add r-inline.
 2023-10-05 15:16:26 +02:00
Ricardo Wurmus fa97d8c2d0
gnu: r-ggstatsplot: Update to 0.12.1. 
* gnu/packages/cran.scm (r-ggstatsplot): Update to 0.12.1.
 2023-10-05 15:16:26 +02:00
Ricardo Wurmus b253dbe7a0
gnu: r-datawizard: Update to 0.9.0. 
* gnu/packages/cran.scm (r-datawizard): Update to 0.9.0.
 2023-10-05 15:16:26 +02:00
Ricardo Wurmus c64777cfe0
gnu: r-activepathways: Update to 2.0.2. 
* gnu/packages/bioconductor.scm (r-activepathways): Update to 2.0.2.
 2023-10-05 15:16:26 +02:00
Ricardo Wurmus f1259b80be
gnu: r-valr: Update to 0.7.0. 
* gnu/packages/bioconductor.scm (r-valr): Update to 0.7.0.
[propagated-inputs]: Add r-lifecycle.
 2023-10-05 15:16:26 +02:00
Ricardo Wurmus 8c22cc96f0
gnu: r-biomartr: Update to 1.0.5. 
* gnu/packages/bioconductor.scm (r-biomartr): Update to 1.0.5.
 2023-10-05 15:16:26 +02:00
Ricardo Wurmus 3fba8cd274
refresh: Fix sorting of updates by file and line number. 
* guix/scripts/refresh.scm (guix-refresh): Add cascade-sort procedure and use
it to sort specs by package location.
 2023-10-05 15:16:26 +02:00
Ekaitz Zarraga 044a76c280
doc: contributing: Add alternative setups section. 
Start with Guile Studio and Vim/NeoVim.

* doc/contributing.texi (Alternative Setups): Add section explaining
other setups that are similar to the one in The Perfect Setup.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2023-10-05 15:05:41 +03:00
Andrew Tropin eeb7132ec3
gnu: emacs-telega: Update to 0.8.03-1.17bfa50. 
* gnu/packages/emacs-xyz.scm (emacs-telega-server): Update to
0.8.03-1.17bfa50.
 2023-10-05 14:16:39 +04:00
Andrew Tropin 9e963c9d75
gnu: tdlib: Update to 1.8.16-0.4d1d22d. 
* gnu/packages/messaging.scm (tdlib): Update to 1.8.16-0.4d1d22d.
 2023-10-05 14:16:38 +04:00
Ricardo Wurmus 276b9287c1
gnu: r-aplot: Update to 0.2.1. 
* gnu/packages/cran.scm (r-aplot): Update to 0.2.1.
 2023-10-05 10:31:09 +02:00
Ricardo Wurmus d841c23dc5
gnu: r-tximeta: Update to 1.18.3. 
* gnu/packages/bioconductor.scm (r-tximeta): Update to 1.18.3.
 2023-10-05 10:23:27 +02:00
Ricardo Wurmus b53f7a87b2
gnu: r-biodb: Update to 1.8.1. 
* gnu/packages/bioconductor.scm (r-biodb): Update to 1.8.1.
[propagated-inputs]: Add r-git2r.
 2023-10-05 10:23:27 +02:00
Ricardo Wurmus bf7c049147
gnu: r-gviz: Update to 1.44.2. 
* gnu/packages/bioconductor.scm (r-gviz): Update to 1.44.2.
 2023-10-05 10:23:27 +02:00
Ricardo Wurmus 9220702479
gnu: r-s4vectors: Update to 0.38.2. 
* gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.38.2.
 2023-10-05 10:23:27 +02:00
Ricardo Wurmus 6492c6496b
gnu: r-biocstyle: Update to 2.28.1. 
* gnu/packages/bioconductor.scm (r-biocstyle): Update to 2.28.1.
 2023-10-05 10:23:27 +02:00
Ricardo Wurmus 27fd2d2c2a
gnu: r-yapsa: Update to 1.26.8. 
* gnu/packages/bioconductor.scm (r-yapsa): Update to 1.26.8.
 2023-10-05 10:23:27 +02:00
Ricardo Wurmus 6a1b46e7ab
gnu: r-enrichplot: Update to 1.20.3. 
* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.20.3.
[propagated-inputs]: Add r-ggfun.
 2023-10-05 10:23:27 +02:00
Ricardo Wurmus 3f3c986001
gnu: r-spectra: Update to 1.10.3. 
* gnu/packages/bioconductor.scm (r-spectra): Update to 1.10.3.
 2023-10-05 10:23:27 +02:00
Ricardo Wurmus b82dc9b724
gnu: r-keggrest: Update to 1.40.1. 
* gnu/packages/bioconductor.scm (r-keggrest): Update to 1.40.1.
 2023-10-05 10:23:27 +02:00
Ricardo Wurmus b56dabc7a3
gnu: r-genomeinfodb: Update to 1.36.4. 
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.36.4.
 2023-10-05 10:23:27 +02:00
Ricardo Wurmus 28b2b7c367
gnu: r-ensembldb: Update to 2.24.1. 
* gnu/packages/bioconductor.scm (r-ensembldb): Update to 2.24.1.
 2023-10-05 10:23:27 +02:00
Ricardo Wurmus fefad76048
gnu: r-ancombc: Update to 2.2.2. 
* gnu/packages/bioconductor.scm (r-ancombc): Update to 2.2.2.
 2023-10-05 10:23:27 +02:00
Ricardo Wurmus caf9f847ef
gnu: r-omnipathr: Update to 3.8.2. 
* gnu/packages/bioconductor.scm (r-omnipathr): Update to 3.8.2.
 2023-10-05 10:23:27 +02:00
Liliana Marie Prikler 759b55712e
gnu: curl: Update to 8.3.0. 
According to upstream, the current version has 19 security issues.
See also <https://curl.se/docs/vuln-7.85.0.html>.

* gnu/packages/curl.scm (curl/fixed): New variable.
(curl): Use it as replacement.
 2023-10-05 09:41:31 +02:00
Efraim Flashner a31725ff90
gnu: openjdk-10: Fix building on aarch64-linux. 
* gnu/packages/java.scm (openjdk-10)[arguments]: Replace inherited
'patch-for-aarch64 phase for changes in source code layout.

Co-authored-by: Christopher Baines <mail@cbaines.net>
Co-authored-by: Tim Johann <t1m@phrogstar.de>
 2023-10-05 09:54:04 +03:00
Efraim Flashner 6f8f98f334
gnu: universal-ctags: Update to 6.0.20231001.0. 
* gnu/packages/code.scm (universal-ctags): Update to 6.0.20231001.0.
 2023-10-05 09:54:04 +03:00
Kjartan Oli Agustsson c3f47bb2ee
gnu: tree-sitter-java: Update to 0.20.1. 
* gnu/packages/tree-sitter.scm (tree-sitter-java): Update to 0.20.1.

Signed-off-by: Andrew Tropin <andrew@trop.in>
 2023-10-05 09:54:23 +04:00
Maxim Cournoyer ecb1b335d4
gnu: emacs-elpy: Update to 1.35.0-2.7ff8ffa. 
* gnu/packages/emacs-xyz.scm (emacs-elpy): Update to 1.35.0-2.7ff8ffa.
[origin]: Apply patch.
[arguments]: Disable a new test in the disable-broken-tests phase.
* gnu/packages/patches/emacs-elpy-dup-test-name.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2023-10-05 01:34:21 -04:00
Maxim Cournoyer 22d2f94eb2
gnu: phoronix-test-suite: Do not propagate gcc-toolchain. 
* gnu/packages/benchmark.scm (gcc-toolchain*): Replace gcc-toolchain-12
reference with gcc-toolchain.
* gnu/packages/benchmark.scm (phoronix-test-suite): Augment wrap-binary phase
with GCC variables.
[propagated-inputs]: Delete field, moving gcc-toolchain to...
[inputs]: ... here.
[search-paths]: New field.
 2023-10-04 23:30:42 -04:00