Age | Commit message (Collapse) | Author |
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* 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>
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* 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>
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* gnu/packages/crates-io.scm (rust-located-yaml-0.2) New variable.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
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* 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>
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* gnu/packages/crates-io.scm (rust-nom-locate-4): New variable.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
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This is a follow-up to 48efbde7a944acfe4fc944bf27bfa9ff82592024.
* gnu/local.mk (dist_patch_DATA): Register patch.
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* gnu/packages/video.scm (yt-dlp)[source]: Remove trailing #t from
snippet.
[arguments]: Remove trailing #t from phases.
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* gnu/packages/video.scm (yt-dlp): Update to 2022.05.18.
[inputs]: Add python-brotli and python-certifi.
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* gnu/packages/web-browsers.scm (links): Update to 2.27.
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* 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.
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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.
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* gnu/packages/python-science.scm (python-gpy): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/python-science.scm (python-paramz): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/python-science.scm (python-climin): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* 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>
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* guix/store.scm (references/cached): Add call to
'record-cache-lookup!'.
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* gnu/packages/java.scm (openjdk17): Update to 17.0.3.
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* gnu/packages/python-xyz.scm (python-translate-toolkit): Update to
3.6.2.
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* gnu/packages/python-xyz.scm (python-user-agents): Update to 2.2.0.
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* gnu/packages/python-xyz.scm (python-ua-parser): Update to 0.10.0.
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* gnu/packages/web-browsers.scm (lagrange): Update to 1.13.6.
[source]: Adjust snippet to remove another bundled library.
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* gnu/packages/wget.scm (wget): Update to 1.21.3.
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* gnu/packages/mail.scm (mutt): Update to 2.2.5.
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* gnu/packages/haskell-apps.scm (git-annex): Update to 10.20220525.
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* gnu/packages/admin.scm (nmap)[arguments]: In custom 'check phase honor
the #:tests? flag.
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* gnu/packages/wget.scm (wgetpaste)[arguments]: Remove trailing #t from
phases.
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* gnu/packages/wget.scm (wgetpaste)[inputs]: Add bash-minimal.
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* 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>
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* gnu/packages/debian.scm (pbuilder): New variable.
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* gnu/packages/gnome.scm (apostrophe)[inputs]: Replace webkitgtk with
webkitgtk-with-libsoup2.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
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* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19-masked): Update to 1.3.993.
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* gnu/packages/llvm.scm (clang-from-llvm)[arguments]: When building for
riscv64-linux add configure-flags and make-flags to ensure linking with
'-latomic'.
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* gnu/packages/bioconductor.scm (r-scmap): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
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* gnu/packages/bioinformatics.scm (pigx-sars-cov-2)[arguments]: Add
'autoreconf phase to patch build system.
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* gnu/packages/bioinformatics.scm (pigx-bsseq)[arguments]: Patch build system
in 'autoreconf phase.
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* 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.
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* gnu/packages/bioinformatics.scm (pigx-chipseq)[arguments]: Patch build
system.
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* gnu/packages/cran.scm (r-googlevis): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
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* guix/scripts/import.scm (guix-import): Use pretty-print-with-comments.
(newline-rewriting-port): Remove procedure.
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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.
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* gnu/services/herd.scm (wait-for-service): New procedure.
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* gnu/packages/bioconductor.scm (r-msdata): New variable.
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* gnu/packages/bioconductor.scm (r-tcgabiolinksgui-data): Update to 1.16.0.
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* gnu/packages/bioconductor.scm (r-curatedtcgadata): Update to 1.18.0.
[native-inputs]: Add r-knitr.
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* gnu/packages/bioconductor.scm (r-gagedata): Update to 2.34.0.
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* gnu/packages/bioconductor.scm (r-affydata): Update to 1.44.0.
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* gnu/packages/bioconductor.scm (r-all): Update to 1.38.0.
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* gnu/packages/bioconductor.scm (r-hsmmsinglecell): Update to 1.16.0.
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* 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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