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* gnu: icecat: Update to 91.9.1-guix0-preview1 [security fixes].base-for-series-12531base-for-series-12529Mark H Weaver2022-05-29
| | | | | | | Includes fixes for CVE-2022-1529 and CVE-2022-1802. * gnu/packages/gnuzilla.scm (%icecat-version, %icecat-build-id): Update. (icecat-source): Update gnuzilla commit, base version, and hashes.
* gnu: Add python-gpy.Wiktor Zelazny2022-05-29
| | | | | | * gnu/packages/python-science.scm (python-gpy): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add python-paramz.Wiktor Zelazny2022-05-29
| | | | | | * gnu/packages/python-science.scm (python-paramz): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add python-climin.Wiktor Zelazny2022-05-29
| | | | | | * gnu/packages/python-science.scm (python-climin): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: wla-dx: Update to 10.1.Felix Gruber2022-05-29
| | | | | | | | * gnu/packages/assembly.scm (wla-dx): Update to 10.1. [native-inputs]: Use new style. [arguments]: Add custom 'check phase to run run_tests.sh. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* store: Record cache lookups in 'references/cached'.Ludovic Courtès2022-05-29
| | | | | * guix/store.scm (references/cached): Add call to 'record-cache-lookup!'.
* gnu: openjdk: Update to 17.0.3.Danny Milosavljevic2022-05-29
| | | | * gnu/packages/java.scm (openjdk17): Update to 17.0.3.
* gnu: python-translate-toolkit: Update to 3.6.2.Julien Lepiller2022-05-29
| | | | | * gnu/packages/python-xyz.scm (python-translate-toolkit): Update to 3.6.2.
* gnu: python-user-agents: Update to 2.2.0.Julien Lepiller2022-05-29
| | | | * gnu/packages/python-xyz.scm (python-user-agents): Update to 2.2.0.
* gnu: python-ua-parser: Update to 0.10.0.Julien Lepiller2022-05-29
| | | | * gnu/packages/python-xyz.scm (python-ua-parser): Update to 0.10.0.
* gnu: lagrange: Update to 1.13.6.Efraim Flashner2022-05-29
| | | | | * gnu/packages/web-browsers.scm (lagrange): Update to 1.13.6. [source]: Adjust snippet to remove another bundled library.
* gnu: wget: Update to 1.21.3.Efraim Flashner2022-05-29
| | | | * gnu/packages/wget.scm (wget): Update to 1.21.3.
* gnu: mutt: Update to 2.2.5.Efraim Flashner2022-05-29
| | | | * gnu/packages/mail.scm (mutt): Update to 2.2.5.
* gnu: git-annex: Update to 10.20220525.Efraim Flashner2022-05-29
| | | | * gnu/packages/haskell-apps.scm (git-annex): Update to 10.20220525.
* gnu: nmap: Honor tests? flag.Efraim Flashner2022-05-29
| | | | | * gnu/packages/admin.scm (nmap)[arguments]: In custom 'check phase honor the #:tests? flag.
* gnu: wgetpaste: Remove trailing #t from phases.Efraim Flashner2022-05-29
| | | | | * gnu/packages/wget.scm (wgetpaste)[arguments]: Remove trailing #t from phases.
* gnu: wgetpaste: Add missing input.Efraim Flashner2022-05-29
| | | | * gnu/packages/wget.scm (wgetpaste)[inputs]: Add bash-minimal.
* gnu: telescope: Update to 0.8.1.cage2022-05-29
| | | | | | | * gnu/packages/web-browsers.scm (telescope): Update to 0.8.1. [home-page]: Update to new upstream home-page. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: Add pbuilder.Efraim Flashner2022-05-29
| | | | * gnu/packages/debian.scm (pbuilder): New variable.
* gnu: apostrophe: Build with correct webkitgtk.Rene Saavedra2022-05-29
| | | | | | | * gnu/packages/gnome.scm (apostrophe)[inputs]: Replace webkitgtk with webkitgtk-with-libsoup2. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* Merge branch 'wip-r'Ricardo Wurmus2022-05-29
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| * gnu: r-bsgenome-hsapiens-ucsc-hg19-masked: Update to 1.3.993.Ricardo Wurmus2022-05-29
| | | | | | | | * gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19-masked): Update to 1.3.993.
| * gnu: pigx-sars-cov-2: Fix build.Ricardo Wurmus2022-05-29
| | | | | | | | | | * gnu/packages/bioinformatics.scm (pigx-sars-cov-2)[arguments]: Add 'autoreconf phase to patch build system.
| * gnu: pigx-bsseq: Fix build.Ricardo Wurmus2022-05-29
| | | | | | | | | | * gnu/packages/bioinformatics.scm (pigx-bsseq)[arguments]: Patch build system in 'autoreconf phase.
| * gnu: pigx-scrnaseq: Fix build.Ricardo Wurmus2022-05-29
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Add autoreconf step to work around m4 macro bug and missing VERSION file. [native-inputs]: Add autoconf and automake.
| * gnu: pigx-chipseq: Fix build.Ricardo Wurmus2022-05-29
| | | | | | | | | | * gnu/packages/bioinformatics.scm (pigx-chipseq)[arguments]: Patch build system.
| * gnu: Add r-msdata.Ricardo Wurmus2022-05-28
| | | | | | | | * gnu/packages/bioconductor.scm (r-msdata): New variable.
| * gnu: r-tcgabiolinksgui-data: Update to 1.16.0.Ricardo Wurmus2022-05-28
| | | | | | | | * gnu/packages/bioconductor.scm (r-tcgabiolinksgui-data): Update to 1.16.0.
| * gnu: r-curatedtcgadata: Update to 1.18.0.Ricardo Wurmus2022-05-28
| | | | | | | | | | * gnu/packages/bioconductor.scm (r-curatedtcgadata): Update to 1.18.0. [native-inputs]: Add r-knitr.
| * gnu: r-gagedata: Update to 2.34.0.Ricardo Wurmus2022-05-28
| | | | | | | | * gnu/packages/bioconductor.scm (r-gagedata): Update to 2.34.0.
| * gnu: r-affydata: Update to 1.44.0.Ricardo Wurmus2022-05-28
| | | | | | | | * gnu/packages/bioconductor.scm (r-affydata): Update to 1.44.0.
| * gnu: r-all: Update to 1.38.0.Ricardo Wurmus2022-05-28
| | | | | | | | * gnu/packages/bioconductor.scm (r-all): Update to 1.38.0.
| * gnu: r-hsmmsinglecell: Update to 1.16.0.Ricardo Wurmus2022-05-28
| | | | | | | | * gnu/packages/bioconductor.scm (r-hsmmsinglecell): Update to 1.16.0.
| * gnu: r-pasilla: Update to 1.24.0.Ricardo Wurmus2022-05-28
| | | | | | | | | | | | * gnu/packages/bioconductor.scm (r-pasilla): Update to 1.24.0. [propagated-inputs]: Remove r-biocstyle, r-knitr, and r-rmarkdown. [native-inputs]: Add r-knitr.
| * gnu: r-genomationdata: Update to 1.28.0.Ricardo Wurmus2022-05-28
| | | | | | | | * gnu/packages/bioconductor.scm (r-genomationdata): Update to 1.28.0.
| * gnu: r-genelendatabase: Update to 1.32.0.Ricardo Wurmus2022-05-28
| | | | | | | | * gnu/packages/bioconductor.scm (r-genelendatabase): Update to 1.32.0.
| * gnu: r-copyhelper: Update to 1.28.0.Ricardo Wurmus2022-05-28
| | | | | | | | * gnu/packages/bioconductor.scm (r-copyhelper): Update to 1.28.0.
| * gnu: r-chromstardata: Update to 1.22.0.Ricardo Wurmus2022-05-28
| | | | | | | | * gnu/packages/bioconductor.scm (r-chromstardata): Update to 1.22.0.
| * gnu: r-celldex: Update to 1.6.0.Ricardo Wurmus2022-05-28
| | | | | | | | * gnu/packages/bioconductor.scm (r-celldex): Update to 1.6.0.
| * gnu: r-biscuiteerdata: Update to 1.10.0.Ricardo Wurmus2022-05-28
| | | | | | | | * gnu/packages/bioconductor.scm (r-biscuiteerdata): Update to 1.10.0.
| * gnu: r-arrmdata: Update to 1.32.0.Ricardo Wurmus2022-05-28
| | | | | | | | * gnu/packages/bioconductor.scm (r-arrmdata): Update to 1.32.0.
| * gnu: r-aneufinderdata: Update to 1.24.0.Ricardo Wurmus2022-05-28
| | | | | | | | * gnu/packages/bioconductor.scm (r-aneufinderdata): Update to 1.24.0.
| * gnu: r-adductdata: Update to 1.12.0.Ricardo Wurmus2022-05-28
| | | | | | | | * gnu/packages/bioconductor.scm (r-adductdata): Update to 1.12.0.
| * gnu: r-pfam-db: Update to 3.15.0.Ricardo Wurmus2022-05-28
| | | | | | | | * gnu/packages/bioconductor.scm (r-pfam-db): Update to 3.15.0.
| * gnu: r-txdb-hsapiens-ucsc-hg38-knowngene: Update to 3.15.0.Ricardo Wurmus2022-05-28
| | | | | | | | | | * gnu/packages/bioconductor.scm (r-txdb-hsapiens-ucsc-hg38-knowngene): Update to 3.15.0. [propagated-inputs]: Add r-annotationdbi.
| * gnu: r-bsgenome-hsapiens-ucsc-hg38: Update to 1.4.4.Ricardo Wurmus2022-05-28
| | | | | | | | * gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg38): Update to 1.4.4.
| * gnu: r-bsgenome-hsapiens-ucsc-hg19: Update to 1.4.3.Ricardo Wurmus2022-05-28
| | | | | | | | * gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19): Update to 1.4.3.
| * gnu: r-leidenbase: Update to 0.1.9.Ricardo Wurmus2022-05-28
| | | | | | | | * gnu/packages/bioconductor.scm (r-leidenbase): Update to 0.1.9.
| * gnu: r-phyloseq: Update to 1.40.0.Ricardo Wurmus2022-05-28
| | | | | | | | * gnu/packages/bioconductor.scm (r-phyloseq): Update to 1.40.0.
| * gnu: r-tximeta: Update to 1.14.0.Ricardo Wurmus2022-05-28
| | | | | | | | * gnu/packages/bioconductor.scm (r-tximeta): Update to 1.14.0.
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