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* gnu: r-preprocesscore: Update to 1.50.0.Ricardo Wurmus2020-06-13
| | | | * gnu/packages/statistics.scm (r-preprocesscore): Update to 1.50.0.
* gnu: Add r-dot.Ricardo Wurmus2020-06-13
| | | | * gnu/packages/cran.scm (r-dot): New variable.
* gnu: Add r-v8.Ricardo Wurmus2020-06-13
| | | | * gnu/packages/cran.scm (r-v8): New variable.
* gnu: Add r-scatterpie.Ricardo Wurmus2020-06-13
| | | | * gnu/packages/cran.scm (r-scatterpie): New variable.
* gnu: Add r-gprofiler2.Ricardo Wurmus2020-06-13
| | | | * gnu/packages/cran.scm (r-gprofiler2): New variable.
* gnu: node: Build shared library.Ricardo Wurmus2020-06-13
| | | | * gnu/packages/node.scm (node)[arguments]: Build shared library.
* guix: Update to Bioconductor 3.11.Ricardo Wurmus2020-06-13
| | | | | * guix/build-system/r.scm (bioconductor-uri): Use new URL. * guix/import/cran.scm (%bioconductor-version): Update to 3.11.
* gnu: r-gprofiler: Move to (gnu packages cran).Ricardo Wurmus2020-06-13
| | | | | * gnu/packages/bioinformatics.scm (r-gprofiler): Move this variable from here... * gnu/packages/cran.scm (r-gprofiler): ...to here.
* lint: check-patch-file-names: Use origin-actual-file-name.Christopher Baines2020-06-12
| | | | | | | | | 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.
* gnu: guile-sqlite3: Update to 0.1.1.Ludovic Courtès2020-06-12
| | | | | | | * 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.
* git-authenticate: Disallow SHA1 (and MD5) signatures.Ludovic Courtès2020-06-12
| | | | | | | | * 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.
* gnu: Add liblogging.Katherine Cox-Buday2020-06-12
| | | | | | * gnu/packages/c.scm (liblogging): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add libfastjson.Katherine Cox-Buday2020-06-12
| | | | | | * gnu/packages/c.scm (libfastjson): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add libestr.Katherine Cox-Buday2020-06-12
| | | | | | * gnu/packages/c.scm (libestr): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add emacs-shell-pop.Ryan Desfosses2020-06-12
| | | | | | * gnu/packages/emacs-xyz.scm (emacs-shell-pop): New variable Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* download: Add more apache mirrors.Efraim Flashner2020-06-12
| | | | * guix/download.scm (%mirrors): Add more apache mirrors.
* gnu: Fix apache mirror URIs.Efraim Flashner2020-06-12
| | | | | | | | * 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.
* system: image: Do not produce an HFS tree when building an ISO.Mathieu Othacehe2020-06-12
| | | | | | 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".
* gnu: xf86-input-libinput: Reduce closure size.Pierre Neidhardt2020-06-12
| | | | | * gnu/packages/xorg.scm (xf86-input-libinput)[inputs]: Replace libinput by libinput-minimal.
* guix: lint: Support origins in check-patch-file-names.Chris Marusich2020-06-11
| | | | | | * 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.
* gnu: icecat: Fix WebGL support.Ekaitz Zarraga2020-06-12
| | | | | | * gnu/packages/gnuzilla.scm (icecat): Wrap mesa. Signed-off-by: Julien Lepiller <julien@lepiller.eu>
* shepherd: 'read-pid-file/container' terminates the whole process group.Ludovic Courtès2020-06-12
| | | | | | | | 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.
* shepherd: Unblock signals in the child process.Ludovic Courtès2020-06-12
| | | | | | | | | | | | | | | 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'.
* gnu: Add exercism and dependencies.Jakub Kądziołka2020-06-11
| | | | | | | | | | | | | | | | | * 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.
* gnu: linux-libre: Update to 5.4.46.Mark H Weaver2020-06-11
| | | | | * gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.46. (linux-libre-5.4-pristine-source): Update hash.
* gnu: linux-libre@5.7: Update to 5.7.2.Mark H Weaver2020-06-11
| | | | | * gnu/packages/linux.scm (linux-libre-5.7-version): Update to 5.7.128. (linux-libre-5.7-pristine-source): Update hash.
* gnu: linux-libre@5.6: Remove.Mark H Weaver2020-06-11
| | | | | | | | | 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.
* gnu: linux-libre@4.19: Update to 4.19.128.Mark H Weaver2020-06-11
| | | | | * gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.128. (linux-libre-4.19-pristine-source): Update hash.
* gnu: linux-libre@4.14: Update to 4.14.184.Mark H Weaver2020-06-11
| | | | | * gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.184. (linux-libre-4.14-pristine-source): Update hash.
* gnu: linux-libre@4.9: Update to 4.9.227.Mark H Weaver2020-06-11
| | | | | * gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.227. (linux-libre-4.9-pristine-source): Update hash.
* gnu: linux-libre@4.4: Update to 4.4.227.Mark H Weaver2020-06-11
| | | | | * gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.227. (linux-libre-4.4-pristine-source): Update hash.
* gnu: adns: Update to 1.6.0.Efraim Flashner2020-06-11
| | | | | | * gnu/packages/adns.scm (adns): Update to 1.6.0. [source]: Use https. [native-inputs]: Add m4.
* gnu: subversion: Update to 1.14.0.Efraim Flashner2020-06-11
| | | | | * gnu/packages/version-control.scm (subversion): Update to 1.14.0. [source]: Update source URI.
* gnu: nghttp2: Replace with version 1.41 [fixes CVE-2020-11080].Ludovic Courtès2020-06-11
| | | | | * gnu/packages/web.scm (nghttp2-1.41): New variable. (nghttp2)[replacement]: New field.
* packages: 'package-grafts' returns grafts for all the relevant outputs.Ludovic Courtès2020-06-11
| | | | | | | | | | | | | | | Fixes <https://bugs.gnu.org/41796>. Reported by Jakub Kądziołka <kuba@kadziolka.net>. * guix/packages.scm (input-graft): Add 'output' parameter and honor it. Add OUTPUT to the cache key. (input-cross-graft): Likewise. (fold-bag-dependencies): Operate on inputs instead of nodes. Turn VISITED into a vhash instead of a set. Pass PROC HEAD and OUTPUT instead of just HEAD. (bag-grafts): Adjust accordingly. * tests/packages.scm ("package-grafts, dependency on several outputs"): New test.
* gnu: r-with-tests, r-minimal: Update to 4.0.1.Ricardo Wurmus2020-06-11
| | | | * gnu/packages/statistics.scm (r-with-tests, r-minimal): Update to 4.0.1.
* gnu: r-brms: Update to 2.13.0.Ricardo Wurmus2020-06-11
| | | | * gnu/packages/cran.scm (r-brms): Update to 2.13.0.
* gnu: r-crochet: Update to 2.3.0.Ricardo Wurmus2020-06-11
| | | | | * gnu/packages/cran.scm (r-crochet): Update to 2.3.0. [native-inputs]: Add r-knitr.
* gnu: r-openmx: Update to 2.17.4.Ricardo Wurmus2020-06-11
| | | | * gnu/packages/cran.scm (r-openmx): Update to 2.17.4.
* gnu: r-stanheaders: Update to 2.21.0-5.Ricardo Wurmus2020-06-11
| | | | | * gnu/packages/cran.scm (r-stanheaders): Update to 2.21.0-5. [propagated-inputs]: Add r-rcppeigen and r-rcppparallel.
* gnu: r-semtools: Update to 0.5-3.Ricardo Wurmus2020-06-11
| | | | * gnu/packages/cran.scm (r-semtools): Update to 0.5-3.
* gnu: r-sem: Update to 3.1-11.Ricardo Wurmus2020-06-11
| | | | * gnu/packages/cran.scm (r-sem): Update to 3.1-11.
* gnu: r-emplik: Update to 1.1-1.Ricardo Wurmus2020-06-11
| | | | * gnu/packages/cran.scm (r-emplik): Update to 1.1-1.
* gnu: r-rsvg: Update to 2.1.Ricardo Wurmus2020-06-11
| | | | | * gnu/packages/cran.scm (r-rsvg): Update to 2.1. [native-inputs]: Add r-knitr.
* gnu: r-actuar: Update to 3.0-0.Ricardo Wurmus2020-06-11
| | | | * gnu/packages/cran.scm (r-actuar): Update to 3.0-0.
* gnu: r-gdina: Update to 2.8.0.Ricardo Wurmus2020-06-11
| | | | * gnu/packages/cran.scm (r-gdina): Update to 2.8.0.
* gnu: r-seewave: Update to 2.1.6.Ricardo Wurmus2020-06-11
| | | | | * gnu/packages/cran.scm (r-seewave): Update to 2.1.6. [inputs]: Add libsndfile.
* gnu: r-elasticnet: Update to 1.3.Ricardo Wurmus2020-06-11
| | | | * gnu/packages/cran.scm (r-elasticnet): Update to 1.3.
* gnu: r-showtext: Update to 0.8-1.Ricardo Wurmus2020-06-11
| | | | * gnu/packages/cran.scm (r-showtext): Update to 0.8-1.
* gnu: r-showtextdb: Update to 3.0.Ricardo Wurmus2020-06-11
| | | | * gnu/packages/cran.scm (r-showtextdb): Update to 3.0.
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