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* gnu: r-lmom: Update to 2.9.Ricardo Wurmus2022-05-30
| | | | * gnu/packages/statistics.scm (r-lmom): Update to 2.9.
* gnu: r-chron: Update to 2.3-57.Ricardo Wurmus2022-05-30
| | | | * gnu/packages/statistics.scm (r-chron): Update to 2.3-57.
* gnu: r-tree: Update to 1.0-42.Ricardo Wurmus2022-05-30
| | | | * gnu/packages/cran.scm (r-tree): Update to 1.0-42.
* gnu: r-parameters: Update to 0.18.1.Ricardo Wurmus2022-05-30
| | | | * gnu/packages/cran.scm (r-parameters): Update to 0.18.1.
* gnu: r-clue: Update to 0.3-61.Ricardo Wurmus2022-05-30
| | | | * gnu/packages/cran.scm (r-clue): Update to 0.3-61.
* gnu: r-cobs: Update to 1.3-5.Ricardo Wurmus2022-05-30
| | | | * gnu/packages/cran.scm (r-cobs): Update to 1.3-5.
* gnu: r-gee: Update to 4.13-23.Ricardo Wurmus2022-05-30
| | | | * gnu/packages/cran.scm (r-gee): Update to 4.13-23.
* gnu: r-qpdf: Update to 1.2.0.Ricardo Wurmus2022-05-30
| | | | | | | * gnu/packages/cran.scm (r-qpdf): Update to 1.2.0. [source]: Remove trailing #T from snippet. [arguments]: Remove trailing #T from 'configure phase. [inputs]: Add libjpeg-turbo.
* gnu: r-batchelor: Update to 1.12.1.Ricardo Wurmus2022-05-30
| | | | * gnu/packages/bioconductor.scm (r-batchelor): Update to 1.12.1.
* gnu: gcc-9: Update to 9.5.0.Efraim Flashner2022-05-30
| | | | * gnu/packages/gcc.scm (gcc-9): Update to 9.5.0.
* gnu: hello: Update to 2.12.1.Efraim Flashner2022-05-30
| | | | * gnu/packages/base.scm (hello): Update to 2.12.1.
* gnu: nss: Skip tests on riscv64-linux.Efraim Flashner2022-05-30
| | | | | * gnu/packages/nss.scm (nss)[arguments]: Skip tests when building for riscv64-linux.
* gnu: nss: Adjust make-flags for riscv64-linux.Efraim Flashner2022-05-30
| | | | | * gnu/packages/nss.scm (nss)[arguments]: When building for riscv64-linux don't build the binaries with gtest.
* gnu: Add rust-serde-regex-1.Evgenii Lepikhin2022-05-30
| | | | | | * gnu/packages/crates-io.scm (rust-serde-regex-1): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: rust-nom-7: Update to 7.1.1.Evgenii Lepikhin2022-05-30
| | | | | | | * gnu/packages/crates-io.scm (rust-nom-7): Update to 7.1.1. [arguments]: In cargo-inputs replace rust-minimal-lexical-0.1 with 0.2. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: Add rust-minimal-lexical-0.2.Evgenii Lepikhin2022-05-30
| | | | | | | * gnu/packages/crates-io.scm (rust-minimal-lexical-0.2): New variable. (rust-minimal-lexical-0.1): Inherit from rust-minimal-lexical-0.2. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: Add rust-located-yaml-0.2.Evgenii Lepikhin2022-05-30
| | | | | | * gnu/packages/crates-io.scm (rust-located-yaml-0.2) New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: Add rust-pretty-0.11.Evgenii Lepikhin2022-05-30
| | | | | | | * gnu/packages/crates-io.scm (rust-pretty-0.11) New variable. (rust-pretty-0.5): Inherit from rust-pretty-0.11. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: Add rust-nom-locate-4.Evgenii Lepikhin2022-05-30
| | | | | | * gnu/packages/crates-io.scm (rust-nom-locate-4): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: virtuoso-ose: Register patch.Efraim Flashner2022-05-30
| | | | | | This is a follow-up to 48efbde7a944acfe4fc944bf27bfa9ff82592024. * gnu/local.mk (dist_patch_DATA): Register patch.
* gnu: yt-dlp: Remove trailing #t.Efraim Flashner2022-05-30
| | | | | | * gnu/packages/video.scm (yt-dlp)[source]: Remove trailing #t from snippet. [arguments]: Remove trailing #t from phases.
* gnu: yt-dlp: Update to 2022.05.18.Efraim Flashner2022-05-30
| | | | | * gnu/packages/video.scm (yt-dlp): Update to 2022.05.18. [inputs]: Add python-brotli and python-certifi.
* gnu: links: Update to 2.27.Efraim Flashner2022-05-30
| | | | * gnu/packages/web-browsers.scm (links): Update to 2.27.
* gnu: virtuoso-ose: Update to 7.2.7.Roel Janssen2022-05-30
| | | | | | | * gnu/packages/databases.scm (virtuoso-ose): Update to 7.2.7; Run autogen after applying the patch below. * gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch: New file.
* 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.
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