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2018-11-14gnu: Add r-acdm.Ricardo Wurmus
* gnu/packages/cran.scm (r-acdm): New variable.
2018-11-14gnu: Add r-acd.Ricardo Wurmus
* gnu/packages/cran.scm (r-acd): New variable.
2018-11-14gnu: Add r-abn.Ricardo Wurmus
* gnu/packages/cran.scm (r-abn): New variable.
2018-11-14gnu: Add r-rjags.Ricardo Wurmus
* gnu/packages/cran.scm (r-rjags): New variable.
2018-11-14gnu: Add jags.Ricardo Wurmus
* gnu/packages/statistics.scm (jags): New variable.
2018-11-13gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Update to 3.4.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene): Update to 3.4.4.
2018-11-13gnu: r-org-mm-eg-db: Update to 3.7.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.7.0.
2018-11-13gnu: r-org-dm-eg-db: Update to 3.7.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.7.0.
2018-11-13gnu: r-org-ce-eg-db: Update to 3.7.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.7.0.
2018-11-13gnu: r-org-hs-eg-db: Update to 3.7.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.7.0.
2018-11-13gnu: r-genomationdata: Update to 1.14.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.14.0.
2018-11-13gnu: r-go-db: Update to 3.7.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.7.0.
2018-11-13gnu: r-genomeinfodbdata: Update to 1.2.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 1.2.0.
2018-11-13gnu: spice-vdagent: Fix typo in desktop file.Taegil Bae
Fixes <https://bugs.gnu.org/33346>. * gnu/packages/spice.scm (spice-vdagent)[arguments]: Fix typo in 'patch-spice-vdagent.desktop' phase.
2018-11-14gnu: ImageMagick: Update to 6.9.10-14.Alex Vong
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.10-14.
2018-11-13gnu: libssh: Fetch source over HTTPS.Leo Famulari
* gnu/packages/ssh.scm (libssh)[source]: Use HTTPS URL.
2018-11-13gnu: direnv: Build with Go 1.9.Leo Famulari
* gnu/packages/shellutils.scm (direnv)[native-inputs]: Remove go. [inputs]: Add go-1.9.
2018-11-13gnu: Poppler: Fix CVE-2018-19149.Leo Famulari
* gnu/packages/patches/poppler-CVE-2018-19149.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/pdf.scm (poppler)[replacement]: New field. (poppler/fixed): New variable. (poppler-qt4, poppler-qt5): Use package/inherit.
2018-11-13gnu: certbot, python-acme: Update to 0.28.0.Leo Famulari
* gnu/packages/tls.scm (certbot, python-acme): Update to 0.28.0.
2018-11-13gnu: guix: Update to f5a2724.Ludovic Courtès
* gnu/packages/package-management.scm (guix): Update to f5a2724.
2018-11-13deduplication: Restore directory mtime and permissions after deduplication.Ludovic Courtès
Fixes <https://bugs.gnu.org/33361>. * guix/store/deduplication.scm (replace-with-link): Call 'set-file-time' and 'chmod' after 'rename-file'. * tests/nar.scm ("restore-file-set with directories (signed, valid)"): New test.
2018-11-13tests: Check file canonicalization for 'restore-file-set'.Ludovic Courtès
* guix/tests.scm (canonical-file?): New procedure. * tests/nar.scm ("restore-file-set (signed, valid)"): Check that every item of FILES matches 'canonical-file?'.
2018-11-13tests: Remove check for a feature that appeared in Guile 2.0.10.Ludovic Courtès
* tests/nar.scm: Remove test for 'open-sha256-input-port'.
2018-11-13services: nscd: Add 'invalidate' and 'statistics' actions.Ludovic Courtès
* gnu/services/base.scm (nscd-action-procedure, nscd-actions): New procedures. (nscd-shepherd-service): Add 'modules' and 'actions' fields. * gnu/tests/base.scm (run-basic-test)["nscd invalidate action"] ["nscd invalidate action, wrong table"]: New tests. * doc/guix.texi (Services): Mention 'herd doc nscd action'. (Base Services): Document the actions.
2018-11-13services: mcron: Fix typo in comment.Ludovic Courtès
* gnu/services/mcron.scm (shepherd-schedule-action): Fix typo in comment.
2018-11-13nar: Access the database instead of connecting to the daemon.Ludovic Courtès
* guix/store/database.scm (%default-database-file): New variable. (path-id): Export. * guix/nar.scm (finalize-store-file): Use 'with-database' instead of 'with-store', and use 'path-id' instead of 'valid-path?'.
2018-11-13gnu: restic: Fix build phase.Oleg Pykhalov
* gnu/packages/backup.scm (restic)[arguments]: Set "HOME" environment variable in build phase.
2018-11-13gnu: c-toxcore: Fetch sources from git.Ricardo Wurmus
* gnu/packages/messaging.scm (c-toxcore)[source]: Fetch from git.
2018-11-13gnu: wine-staging: Update to 3.20.Rutger Helling
* gnu/packages/wine.scm (wine-staging-patchset-data): Update to 3.20. * gnu/packages/wine.scm (wine-staging): Update to 3.20.
2018-11-12gnu: php: Update to 7.2.12.Julien Lepiller
* gnu/packages/php.scm (php): Update to 7.2.12.
2018-11-12store: Add a functional object cache and use it in 'lower-object'.Ludovic Courtès
This leads to ~25% improvements on things like: guix system build desktop.tmpl --no-grafts -d * guix/store.scm (<nix-server>)[object-cache]: New field. * guix/store.scm (open-connection): Initialize it. (cache-object-mapping, lookup-cached-object, %mcached): New procedures. (mcached): New macro. * guix/gexp.scm (lower-object): Use it. * guix/grafts.scm (grafting?): New procedure.
2018-11-12tests: Add 'test-assertm' to (guix tests).Ludovic Courtès
* guix/tests.scm (test-assertm): New macro. * tests/gexp.scm (test-assertm): Remove. * tests/profiles.scm (test-assertm): Remove. * tests/challenge.scm (%store, test-assertm): Remove. * tests/debug-link.scm (%store, test-assertm): Remove. * tests/size.scm (%store, test-assertm): Remove.
2018-11-12gnu: youtube-dl: Update to 2018.11.07.Arun Isaac
* gnu/packages/video.scm (youtube-dl): Update to 2018.11.07.
2018-11-12gnu: vifm: Update to 0.10.Efraim Flashner
* gnu/packages/vim.scm (vifm): Update to 0.10.
2018-11-12gnu: go-github-com-aarzilli-golua: Fix for go-1.11.Pierre Neidhardt
* gnu/packages/golang.scm (go-github-com-aarzilli-golua)[arguments]: Fix for go-1.11. [native-inputs]: Remove lua. [propagated-inputs]: Add lua.
2018-11-12gnu: go-github-com-wtolson-go-taglib: Fix tests and build for go-1.11.Pierre Neidhardt
* gnu/packages/golang.scm (go-github-com-wtolson-go-taglib)[arguments]: Fix tests for go-1.11. [native-inputs]: Remove pkg-config and taglib. [propagated-inputs]: Add pkg-config and taglib.
2018-11-12gnu: go-gopkg.in-asn1-ber.v1: Fix tests for go-1.11.Pierre Neidhardt
* gnu/packages/syncthing.scm (go-gopkg.in-asn1-ber.v1): Fix tests for go-1.11.
2018-11-12gnu: go-github-com-audriusbutkevicius-cli: Fix tests for go-1.11.Pierre Neidhardt
* gnu/packages/syncthing.scm (go-github-com-audriusbutkevicius-cli): Fix tests for go-1.11.
2018-11-12gnu: go-github-com-prometheus-common-expfmt: Fix tests for go-1.11.Pierre Neidhardt
* gnu/packages/syncthing.scm (go-github-com-prometheus-common-expfmt): Fix tests for go-1.11.
2018-11-12build-system/go: Plan removal of the pkg folder for go-1.11 onward.Pierre Neidhardt
* guix/build/go-build-system.scm (install): New comment.
2018-11-12gnu: go: Update default to 1.11.Pierre Neidhardt
* gnu/packages/golang.scm (go): Update default to 1.11.
2018-11-11guix system: Invoking 'guix system init' twice keeps timestamps zeroed.Ludovic Courtès
Fixes a bug whereby running 'guix system init config.scm /mnt' twice would, on the second run, change timestamps in /mnt/gnu/store from the Epoch to now. This is because the 'register-path' call would bypass the 'reset-timestamps' phase altogether in that case, as a consequence of commit bb3b6ccb05550fbfbeb459c68819a752327d6e1e. Reported by Christopher Baines. * guix/scripts/system.scm (install): When TARGET/var/guix exists, delete it. As a side-effect, this ensures that later on, the 'register-path' call invokes 'reset-timestamps' on all the copied store items.
2018-11-11guix package: '--show' errors when asked for a non-existent package.Ludovic Courtès
Fixes <https://bugs.gnu.org/33323>. Reported by swedebugia <swedebugia@riseup.net>. * guix/scripts/package.scm (process-query): Call 'leave' when 'find-packages-by-name' returns the empty list. * tests/guix-package.sh: Test it.
2018-11-11doc: Fix typo.Laura Lazzati
* doc/guix.texi (Porting to a New Platform): Fix typo. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2018-11-11gnu: r-s4vectors: Update to 0.20.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.20.1.
2018-11-11gnu: r-rcmdcheck: Update to 1.3.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-rcmdcheck): Update to 1.3.2.
2018-11-11gnu: r-ggpubr: Update to 0.1.9.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggpubr): Update to 0.1.9.
2018-11-11gnu: r-dplyr: Update to 0.7.8.Ricardo Wurmus
* gnu/packages/statistics.scm (r-dplyr): Update to 0.7.8.
2018-11-11gnu: r-rcpparmadillo: Update to 0.9.200.4.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.200.4.0.
2018-11-11gnu: r-rtsne: Update to 0.15.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rtsne): Update to 0.15.
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