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2022-04-14gnu: scregseg: Remove cythonized file.Efraim Flashner
* gnu/packages/bioinformatics.scm (scregseg)[source]: Add snippet to remove cythonized file.
2022-04-14gnu: cl-py4cl: Update to 0.0.0-1.2f2a008.Paul A. Patience
* gnu/packages/lisp-xyz.scm (sbcl-py4cl): Update to 0.0.0-1.2f2a008. [arguments]<#:phases>: Adjust substitutions to renamed files. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2022-04-14gnu: Add emacs-org-modern.jgart
* gnu/packages/emacs-xyz.scm (emacs-org-modern): New variable. Signed-off-by: Raghav Gururajan <rg@raghavgururajan.name>
2022-04-14gnu: Add cl-numpy-file-format.Paul A. Patience
* gnu/packages/lisp-xyz.scm (cl-numpy-file-format, ecl-numpy-file-format, sbcl-numpy-file-format): New variables. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2022-04-14gnu: cl-who: Update to 1.1.4-3.07dafe9.Foo Chuan Wei
* gnu/packages/lisp-xyz.scm (sbcl-cl-who): Update to 1.1.4-3.07dafe9. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2022-04-14gnu: linux-libre 5.10: Update to 5.10.111.Leo Famulari
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.111. (linux-libre-5.10-pristine-source): Update hash.
2022-04-14gnu: linux-libre 5.15: Update to 5.15.34.Leo Famulari
* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.34. (linux-libre-5.15-pristine-source): Update hash.
2022-04-14gnu: linux-libre: Update to 5.16.20.Leo Famulari
* gnu/packages/linux.scm (linux-libre-5.16-version): Update to 5.16.20. (linux-libre-5.16-pristine-source): Update hash.
2022-04-14gnu: linux-libre 5.17: Update to 5.17.3.Leo Famulari
* gnu/packages/linux.scm (linux-libre-5.17-version): Update to 5.17.3. (linux-libre-5.17-pristine-source): Update hash.
2022-04-14gnu: Update linux-libre 5.17 configuration files.Leo Famulari
This option that adds new hardware support appeared after the 5.17 release. * gnu/packages/aux-files/linux-libre/5.17-arm.conf, gnu/packages/aux-files/linux-libre/5.17-arm64.conf, gnu/packages/aux-files/linux-libre/5.17-i686.conf, gnu/packages/aux-files/linux-libre/5.17-x86_64.conf: Enable support for Realtek Ethernet switch chips.
2022-04-14gnu: Add r-xcir.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-xcir): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2022-04-14gnu: sundials: Remove input labels.Ludovic Courtès
* gnu/packages/maths.scm (sundials)[native-inputs, inputs]: Remove labels. (sundials-openmpi)[inputs]: Remove labels.
2022-04-14gnu: sundials: Update to 6.1.1.Ludovic Courtès
* gnu/packages/maths.scm (sundials): Update to 6.1.1. [inputs]: Add PETSC. (sundials-openmpi)[inputs]: Remove PETSC. [arguments]: Remove now unnecessary flags. Change "MPI_ENABLE" to "ENABLE_MPI".
2022-04-14daemon: Support systemd-style socket activation.Ludovic Courtès
* nix/nix-daemon/guix-daemon.cc (SD_LISTEN_FDS_START): New macro. (systemd_activation_sockets): New function. (main): Use it. Remove obsolete 'printMsg' call. * doc/guix.texi (Invoking guix-daemon): Document socket activation.
2022-04-14publish: Support systemd-style socket activation.Ludovic Courtès
* guix/scripts/publish.scm (systemd-socket): New procedure. (guix-publish): Add 'style' variable. Adjust startup message depending on whether STYLE is 'systemd. * doc/guix.texi (Invoking guix publish): Mention socket activation.
2022-04-14publish: Use SRFI-71 instead of SRFI-11.Ludovic Courtès
* guix/scripts/publish.scm (make-request-handler): Use 'let' instead of 'let-values'.
2022-04-14gnu: guile-fibers@1.1: Support cross-compilation.Ludovic Courtès
Fixes <https://issues.guix.gnu.org/54793>. Reported by Mathieu Othacehe <othacehe@gnu.org>. * gnu/packages/guile-xyz.scm (guile-fibers-1.1)[arguments]: Add 'support-cross-compilation' phase.
2022-04-14style: Correctly read dots in pairs and improper lists.Ludovic Courtès
Until now dots were read as symbols. * guix/scripts/style.scm (read-with-comments)[dot]: New variable. [dot?, reverse/dot]: New procedures. Use 'reverse/dot' instead of 'reverse' when reading lists. * tests/style.scm ("read-with-comments: dot notation") ("((a . 1) (b . 2))", "(a b c . boom)"): New tests.
2022-04-14gnu: r-illuminahumanmethylation450kanno-ilmn12-hg19: Move to annotation section.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-illuminahumanmethylation450kanno-ilmn12-hg19): Move this variable up to the annotation section.
2022-04-14gnu: r-snplocs-hsapiens-dbsnp144-grch37: Move to annotation section.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-snplocs-hsapiens-dbsnp144-grch37): Move this variable up to the annotation section.
2022-04-14gnu: r-chromvarmotifs: Move to (gnu packages bioinformatics).Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-chromvarmotifs): Move this variable from here... * gnu/packages/bioinformatics.scm (r-chromvarmotifs): ...to here.
2022-04-14gnu: r-absseq: Move out of experiments section.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-absseq): Move definition out of experiments section.
2022-04-14gnu: r-abarray: Move out of experiments section.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-abarray): Move definition out of experiments section.
2022-04-14gnu: r-aneufinder: Move to packages section.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-aneufinder): Move this definition out of the section for Bioconductor experiments packages.
2022-04-14gnu: Add r-absseq.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-absseq): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-04-14gnu: Add r-abarray.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-abarray): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-04-14gnu: Add r-acde.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-acde): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-04-14gnu: Add r-wppi.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-wppi): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-04-14gnu: Add r-acme.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-acme): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-04-14gnu: Add r-acgh.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-acgh): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-04-14gnu: libfprint: Fix build, add python for the tests.Attila Lendvai
* gnu/packages/freedesktop.scm (libfprint)[native-inputs]: Add python-minimal as it's needed by the tests. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-04-14gnu: Add r-ace.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-ace): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-04-14gnu: r-catalyst: Update description.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-catalyst)[description]: Add Texinfo markup and clarify a sentence. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-04-14gnu: r-tcgabiolinks: Update to 2.22.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.22.4.
2022-04-14gnu: r-omnipathr: Update to 3.2.8.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-omnipathr): Update to 3.2.8.
2022-04-14gnu: r-bgeedb: Update to 2.20.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bgeedb): Update to 2.20.1.
2022-04-14gnu: r-gviz: Update to 1.38.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-gviz): Update to 1.38.4.
2022-04-14gnu: r-catalyst: Update to 1.18.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-catalyst): Update to 1.18.1.
2022-04-14gnu: r-mscoreutils: Update to 1.6.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-mscoreutils): Update to 1.6.2.
2022-04-14gnu: r-singler: Update to 1.8.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-singler): Update to 1.8.1.
2022-04-14gnu: r-s4vectors: Update to 0.32.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.32.4.
2022-04-14gnu: r-experimenthub: Update to 2.2.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-experimenthub): Update to 2.2.1.
2022-04-14gnu: r-universalmotif: Update to 1.12.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.12.4.
2022-04-14gnu: r-variancepartition: Update to 1.24.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.24.1. [propagated-inputs]: Add r-aod, r-rdpack, and r-rhpcblasctl.
2022-04-14gnu: r-cytolib: Update to 2.6.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-cytolib): Update to 2.6.2.
2022-04-14gnu: r-rsubread: Update to 2.8.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.8.2.
2022-04-14gnu: r-ropls: Update to 1.26.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ropls): Update to 1.26.4.
2022-04-14gnu: r-birewire: Update to 3.26.5.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-birewire): Update to 3.26.5. [propagated-inputs]: Remove r-tsne; add r-rtsne.
2022-04-14gnu: r-biocfilecache: Update to 2.2.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocfilecache): Update to 2.2.1.
2022-04-14gnu: r-massspecwavelet: Update to 1.60.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-massspecwavelet): Update to 1.60.1.
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