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2022-05-30gnu: rust-nom-7: Update to 7.1.1.Evgenii Lepikhin
* 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>
2022-05-30gnu: Add rust-minimal-lexical-0.2.Evgenii Lepikhin
* 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>
2022-05-30gnu: Add rust-located-yaml-0.2.Evgenii Lepikhin
* gnu/packages/crates-io.scm (rust-located-yaml-0.2) New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-30gnu: Add rust-pretty-0.11.Evgenii Lepikhin
* 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>
2022-05-30gnu: Add rust-nom-locate-4.Evgenii Lepikhin
* gnu/packages/crates-io.scm (rust-nom-locate-4): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-30gnu: virtuoso-ose: Register patch.Efraim Flashner
This is a follow-up to 48efbde7a944acfe4fc944bf27bfa9ff82592024. * gnu/local.mk (dist_patch_DATA): Register patch.
2022-05-30gnu: yt-dlp: Remove trailing #t.Efraim Flashner
* gnu/packages/video.scm (yt-dlp)[source]: Remove trailing #t from snippet. [arguments]: Remove trailing #t from phases.
2022-05-30gnu: yt-dlp: Update to 2022.05.18.Efraim Flashner
* gnu/packages/video.scm (yt-dlp): Update to 2022.05.18. [inputs]: Add python-brotli and python-certifi.
2022-05-30gnu: links: Update to 2.27.Efraim Flashner
* gnu/packages/web-browsers.scm (links): Update to 2.27.
2022-05-30gnu: virtuoso-ose: Update to 7.2.7.Roel Janssen
* 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.
2022-05-29gnu: icecat: Update to 91.9.1-guix0-preview1 [security fixes].Mark H Weaver
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.
2022-05-29gnu: Add python-gpy.Wiktor Zelazny
* gnu/packages/python-science.scm (python-gpy): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-05-29gnu: Add python-paramz.Wiktor Zelazny
* gnu/packages/python-science.scm (python-paramz): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-05-29gnu: Add python-climin.Wiktor Zelazny
* gnu/packages/python-science.scm (python-climin): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-05-29gnu: wla-dx: Update to 10.1.Felix Gruber
* 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>
2022-05-29store: Record cache lookups in 'references/cached'.Ludovic Courtès
* guix/store.scm (references/cached): Add call to 'record-cache-lookup!'.
2022-05-29gnu: openjdk: Update to 17.0.3.Danny Milosavljevic
* gnu/packages/java.scm (openjdk17): Update to 17.0.3.
2022-05-29gnu: python-translate-toolkit: Update to 3.6.2.Julien Lepiller
* gnu/packages/python-xyz.scm (python-translate-toolkit): Update to 3.6.2.
2022-05-29gnu: python-user-agents: Update to 2.2.0.Julien Lepiller
* gnu/packages/python-xyz.scm (python-user-agents): Update to 2.2.0.
2022-05-29gnu: python-ua-parser: Update to 0.10.0.Julien Lepiller
* gnu/packages/python-xyz.scm (python-ua-parser): Update to 0.10.0.
2022-05-29gnu: lagrange: Update to 1.13.6.Efraim Flashner
* gnu/packages/web-browsers.scm (lagrange): Update to 1.13.6. [source]: Adjust snippet to remove another bundled library.
2022-05-29gnu: wget: Update to 1.21.3.Efraim Flashner
* gnu/packages/wget.scm (wget): Update to 1.21.3.
2022-05-29gnu: mutt: Update to 2.2.5.Efraim Flashner
* gnu/packages/mail.scm (mutt): Update to 2.2.5.
2022-05-29gnu: git-annex: Update to 10.20220525.Efraim Flashner
* gnu/packages/haskell-apps.scm (git-annex): Update to 10.20220525.
2022-05-29gnu: nmap: Honor tests? flag.Efraim Flashner
* gnu/packages/admin.scm (nmap)[arguments]: In custom 'check phase honor the #:tests? flag.
2022-05-29gnu: wgetpaste: Remove trailing #t from phases.Efraim Flashner
* gnu/packages/wget.scm (wgetpaste)[arguments]: Remove trailing #t from phases.
2022-05-29gnu: wgetpaste: Add missing input.Efraim Flashner
* gnu/packages/wget.scm (wgetpaste)[inputs]: Add bash-minimal.
2022-05-29gnu: telescope: Update to 0.8.1.cage
* 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>
2022-05-29gnu: Add pbuilder.Efraim Flashner
* gnu/packages/debian.scm (pbuilder): New variable.
2022-05-29gnu: apostrophe: Build with correct webkitgtk.Rene Saavedra
* gnu/packages/gnome.scm (apostrophe)[inputs]: Replace webkitgtk with webkitgtk-with-libsoup2. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-29Merge branch 'wip-r'Ricardo Wurmus
2022-05-29gnu: r-bsgenome-hsapiens-ucsc-hg19-masked: Update to 1.3.993.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19-masked): Update to 1.3.993.
2022-05-29gnu: clang-from-llvm: Fix building on riscv64-linux.Efraim Flashner
* gnu/packages/llvm.scm (clang-from-llvm)[arguments]: When building for riscv64-linux add configure-flags and make-flags to ensure linking with '-latomic'.
2022-05-29gnu: Add r-scmap.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-scmap): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-05-29gnu: pigx-sars-cov-2: Fix build.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-sars-cov-2)[arguments]: Add 'autoreconf phase to patch build system.
2022-05-29gnu: pigx-bsseq: Fix build.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-bsseq)[arguments]: Patch build system in 'autoreconf phase.
2022-05-29gnu: pigx-scrnaseq: Fix build.Ricardo Wurmus
* 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.
2022-05-29gnu: pigx-chipseq: Fix build.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-chipseq)[arguments]: Patch build system.
2022-05-29gnu: Add r-googlevis.Mădălin Ionel Patrașcu
* gnu/packages/cran.scm (r-googlevis): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-05-29scripts/import: Use pretty printer from (guix scripts style).Ricardo Wurmus
* guix/scripts/import.scm (guix-import): Use pretty-print-with-comments. (newline-rewriting-port): Remove procedure.
2022-05-28services: elogind: When started by dbus-daemon, wait for the Shepherd service.Ludovic Courtès
Fixes <https://issues.guix.gnu.org/55444>. Previously shepherd and dbus-daemon would race to start elogind. In some cases (for instance if one logs in quickly enough on the tty), dbus-daemon would "win" and start elogind before shepherd has had a chance to do it. Consequently, shepherd would fail to start elogind and mark it as stopped and disabled, in turn preventing services that depend on it such as 'xorg-server' from starting. * gnu/services/desktop.scm (elogind-dbus-service): Rewrite to refer to a wrapper that waits for the 'elogind' Shepherd service.
2022-05-28services: herd: Add 'wait-for-service'.Ludovic Courtès
* gnu/services/herd.scm (wait-for-service): New procedure.
2022-05-28gnu: Add r-msdata.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-msdata): New variable.
2022-05-28gnu: r-tcgabiolinksgui-data: Update to 1.16.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-tcgabiolinksgui-data): Update to 1.16.0.
2022-05-28gnu: r-curatedtcgadata: Update to 1.18.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-curatedtcgadata): Update to 1.18.0. [native-inputs]: Add r-knitr.
2022-05-28gnu: r-gagedata: Update to 2.34.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-gagedata): Update to 2.34.0.
2022-05-28gnu: r-affydata: Update to 1.44.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-affydata): Update to 1.44.0.
2022-05-28gnu: r-all: Update to 1.38.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-all): Update to 1.38.0.
2022-05-28gnu: r-hsmmsinglecell: Update to 1.16.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-hsmmsinglecell): Update to 1.16.0.
2022-05-28gnu: r-pasilla: Update to 1.24.0.Ricardo Wurmus
* 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.
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