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2020-06-13gnu: r-genomeinfodb: Update to 1.24.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.24.0.
2020-06-13gnu: r-iranges: Update to 2.22.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.22.2.
2020-06-13gnu: r-s4vectors: Update to 0.26.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.26.1.
2020-06-13gnu: r-bioccheck: Update to 1.24.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.24.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-biocstyle: Update to 2.16.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.16.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-biocviews: Update to 1.56.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.56.0.
2020-06-13gnu: r-grohmm: Update to 1.22.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.22.0.
2020-06-13gnu: r-systempiper: Update to 1.22.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.22.0. [propagated-inputs]: Add r-assertthat, r-magrittr, r-rsvg, r-dot, and r-stringr; remove r-biocgenerics. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-shortread: Update to 1.46.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.46.0.
2020-06-13gnu: r-gostats: Update to 2.54.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.54.0.
2020-06-13gnu: r-category: Update to 2.54.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-category): Update to 2.54.0.
2020-06-13gnu: r-gseabase: Update to 1.50.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.50.1. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-rbgl: Update to 1.64.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.64.0.
2020-06-13gnu: r-annotationforge: Update to 1.30.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.30.1. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-dexseq: Update to 1.34.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.34.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-deseq2: Update to 1.28.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.28.1. [propagated-inputs]: Remove r-hmisc. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-genefilter: Update to 1.70.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.70.0. [native-inputs]: Add r-knitr.
2020-06-13gnu: r-rgraphviz: Update to 2.32.0.Ricardo Wurmus
* gnu/packages/graph.scm (r-rgraphviz): Update to 2.32.0.
2020-06-13gnu: r-preprocesscore: Update to 1.50.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-preprocesscore): Update to 1.50.0.
2020-06-13gnu: Add r-dot.Ricardo Wurmus
* gnu/packages/cran.scm (r-dot): New variable.
2020-06-13gnu: Add r-v8.Ricardo Wurmus
* gnu/packages/cran.scm (r-v8): New variable.
2020-06-13gnu: Add r-scatterpie.Ricardo Wurmus
* gnu/packages/cran.scm (r-scatterpie): New variable.
2020-06-13gnu: Add r-gprofiler2.Ricardo Wurmus
* gnu/packages/cran.scm (r-gprofiler2): New variable.
2020-06-13gnu: node: Build shared library.Ricardo Wurmus
* gnu/packages/node.scm (node)[arguments]: Build shared library.
2020-06-13guix: Update to Bioconductor 3.11.Ricardo Wurmus
* guix/build-system/r.scm (bioconductor-uri): Use new URL. * guix/import/cran.scm (%bioconductor-version): Update to 3.11.
2020-06-13gnu: r-gprofiler: Move to (gnu packages cran).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gprofiler): Move this variable from here... * gnu/packages/cran.scm (r-gprofiler): ...to here.
2020-06-12lint: check-patch-file-names: Use origin-actual-file-name.Christopher Baines
This avoids crashes for the patch-file-names checker where a <origin> is used for a patch, but without a value for the file-name field. This is currently the case with the bash package. * guix/lint.scm (check-patch-file-names): Change origin-file-name to origin-actual-file-name.
2020-06-12gnu: guile-sqlite3: Update to 0.1.1.Ludovic Courtès
* gnu/packages/guile.scm (guile-sqlite3): Update to 0.1.1. [source]: Remove 'patches', 'modules', and 'snippet'. * gnu/packages/patches/guile-sqlite3-fix-cross-compilation.patch: Remove. * gnu/local.mk (dist_patch_DATA): Adjust accordingly.
2020-06-12git-authenticate: Disallow SHA1 (and MD5) signatures.Ludovic Courtès
* guix/git-authenticate.scm (commit-signing-key): Add #:disallowed-hash-algorithms and honor it. (authenticate-commit)[recent-commit?]: New variable. Pass #:disallowed-hash-algorithms to 'commit-signing-key'. * tests/git-authenticate.scm ("signed commits, SHA1 signature"): New test.
2020-06-12gnu: Add liblogging.Katherine Cox-Buday
* gnu/packages/c.scm (liblogging): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-06-12gnu: Add libfastjson.Katherine Cox-Buday
* gnu/packages/c.scm (libfastjson): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-06-12gnu: Add libestr.Katherine Cox-Buday
* gnu/packages/c.scm (libestr): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-06-12gnu: Add emacs-shell-pop.Ryan Desfosses
* gnu/packages/emacs-xyz.scm (emacs-shell-pop): New variable Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-06-12download: Add more apache mirrors.Efraim Flashner
* guix/download.scm (%mirrors): Add more apache mirrors.
2020-06-12gnu: Fix apache mirror URIs.Efraim Flashner
* gnu/packages/web.scm (serf)[source]: Remove redundant part of URI. * gnu/packages/java.scm (ant-bootstrap, java-commons-httpclient, java-jakarta-oro)[source]: Same. * gnu/packages/maven.scm (maven-shared-utils, maven-plugin-annotations, maven-wagon-provider-api, maven-artifact)[source]: Same.
2020-06-12system: image: Do not produce an HFS tree when building an ISO.Mathieu Othacehe
Use "mbr_only" mode to make sure that no HFS+ tree are generated. * gnu/system/image.scm (system-image): Set MKRESCUE_SED_MODE to "mbr_only".
2020-06-12gnu: xf86-input-libinput: Reduce closure size.Pierre Neidhardt
* gnu/packages/xorg.scm (xf86-input-libinput)[inputs]: Replace libinput by libinput-minimal.
2020-06-11guix: lint: Support origins in check-patch-file-names.Chris Marusich
* guix/lint.scm (check-patch-file-names)[starts-with-package-name?]: New procedure, extracted from the existing logic. Using it, add a clause to the match-lambda to handle origin records.
2020-06-12gnu: icecat: Fix WebGL support.Ekaitz Zarraga
* gnu/packages/gnuzilla.scm (icecat): Wrap mesa. Signed-off-by: Julien Lepiller <julien@lepiller.eu>
2020-06-12shepherd: 'read-pid-file/container' terminates the whole process group.Ludovic Courtès
This mirrors a change made in the Shepherd 0.8.0. Previously, upon startup failure, we could have left processes behind. * gnu/build/shepherd.scm (read-pid-file/container): Kill (- PID) instead of PID.
2020-06-12shepherd: Unblock signals in the child process.Ludovic Courtès
Fixes <https://bugs.gnu.org/41791>. Reported by Tobias Geerinckx-Rice <me@tobias.gr>. This change mirrors changes made in the Shepherd 0.8.1, where signals are blocked in the shepherd process in support of 'signalfd'. The regression was introduced with the switch to 0.8.1 in 3f9c62d1a8b345909adaeb22f454ad22554c55a1: child processes would not receive SIGTERM upon 'herd stop SERVICE'. * gnu/build/shepherd.scm <top level>: Autoload (shepherd system). (make-forkexec-constructor/container): Call call to 'sigaction' and 'unblock-signals'.
2020-06-11gnu: Add exercism and dependencies.Jakub Kądziołka
* gnu/packages/education.scm (exercism): New variable. * gnu/packages/patches/exercism-disable-self-update.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/golang.scm (go-github-com-spf13-afero) (go-github-com-spf13-cast) (go-github-com-spf13-cobra) (go-github-com-spf13-jwalterweatherman) (go-github-com-spf13-viper) (go-github-com-fsnotify-fsnotify) (go-github-com-magiconair-properties) (go-github-com-pelletier-go-toml) (go-github-com-subosito-gotenv) (go-gopkg-in-ini-v1) (go-github-com-mitchellh-mapstructure): New variables.
2020-06-11gnu: linux-libre: Update to 5.4.46.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.46. (linux-libre-5.4-pristine-source): Update hash.
2020-06-11gnu: linux-libre@5.7: Update to 5.7.2.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-5.7-version): Update to 5.7.128. (linux-libre-5.7-pristine-source): Update hash.
2020-06-11gnu: linux-libre@5.6: Remove.Mark H Weaver
Users of linux-libre-5.6 should migrate to version 5.7. * gnu/packages/linux.scm (deblob-scripts-5.6, linux-libre-5.6-version) (linux-libre-5.6-pristine-source, linux-libre-5.6-source) (linux-libre-headers-5.6, linux-libre-arm-generic-5.6) (linux-libre-arm64-generic-5.6): Remove variables.
2020-06-11gnu: linux-libre@4.19: Update to 4.19.128.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.128. (linux-libre-4.19-pristine-source): Update hash.
2020-06-11gnu: linux-libre@4.14: Update to 4.14.184.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.184. (linux-libre-4.14-pristine-source): Update hash.
2020-06-11gnu: linux-libre@4.9: Update to 4.9.227.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.227. (linux-libre-4.9-pristine-source): Update hash.
2020-06-11gnu: linux-libre@4.4: Update to 4.4.227.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.227. (linux-libre-4.4-pristine-source): Update hash.
2020-06-11gnu: adns: Update to 1.6.0.Efraim Flashner
* gnu/packages/adns.scm (adns): Update to 1.6.0. [source]: Use https. [native-inputs]: Add m4.
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