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* gnu: r-org-hs-eg-db: Update to 3.7.0.•••* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.7.0. Ricardo Wurmus2018-11-13
* gnu: r-genomationdata: Update to 1.14.0.•••* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.14.0. Ricardo Wurmus2018-11-13
* gnu: r-go-db: Update to 3.7.0.•••* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.7.0. Ricardo Wurmus2018-11-13
* gnu: r-genomeinfodbdata: Update to 1.2.0.•••* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 1.2.0. Ricardo Wurmus2018-11-13
* gnu: spice-vdagent: Fix typo in desktop file.•••Fixes <https://bugs.gnu.org/33346>. * gnu/packages/spice.scm (spice-vdagent)[arguments]: Fix typo in 'patch-spice-vdagent.desktop' phase. Taegil Bae2018-11-13
* gnu: ImageMagick: Update to 6.9.10-14.•••* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.10-14. Alex Vong2018-11-14
* gnu: libssh: Fetch source over HTTPS.•••* gnu/packages/ssh.scm (libssh)[source]: Use HTTPS URL. Leo Famulari2018-11-13
* gnu: direnv: Build with Go 1.9.•••* gnu/packages/shellutils.scm (direnv)[native-inputs]: Remove go. [inputs]: Add go-1.9. Leo Famulari2018-11-13
* gnu: Poppler: Fix CVE-2018-19149.•••* 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. Leo Famulari2018-11-13
* gnu: certbot, python-acme: Update to 0.28.0.•••* gnu/packages/tls.scm (certbot, python-acme): Update to 0.28.0. Leo Famulari2018-11-13
* gnu: guix: Update to f5a2724.•••* gnu/packages/package-management.scm (guix): Update to f5a2724. Ludovic Courtès2018-11-13
* deduplication: Restore directory mtime and permissions after deduplication.•••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. Ludovic Courtès2018-11-13
* tests: Check file canonicalization for 'restore-file-set'.•••* guix/tests.scm (canonical-file?): New procedure. * tests/nar.scm ("restore-file-set (signed, valid)"): Check that every item of FILES matches 'canonical-file?'. Ludovic Courtès2018-11-13
* tests: Remove check for a feature that appeared in Guile 2.0.10.•••* tests/nar.scm: Remove test for 'open-sha256-input-port'. Ludovic Courtès2018-11-13
* services: nscd: Add 'invalidate' and 'statistics' actions.•••* 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. Ludovic Courtès2018-11-13
* services: mcron: Fix typo in comment.•••* gnu/services/mcron.scm (shepherd-schedule-action): Fix typo in comment. Ludovic Courtès2018-11-13
* nar: Access the database instead of connecting to the daemon.•••* 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?'. Ludovic Courtès2018-11-13
* gnu: restic: Fix build phase.•••* gnu/packages/backup.scm (restic)[arguments]: Set "HOME" environment variable in build phase. Oleg Pykhalov2018-11-13
* gnu: c-toxcore: Fetch sources from git.•••* gnu/packages/messaging.scm (c-toxcore)[source]: Fetch from git. Ricardo Wurmus2018-11-13
* gnu: wine-staging: Update to 3.20.•••* gnu/packages/wine.scm (wine-staging-patchset-data): Update to 3.20. * gnu/packages/wine.scm (wine-staging): Update to 3.20. Rutger Helling2018-11-13
* gnu: php: Update to 7.2.12.•••* gnu/packages/php.scm (php): Update to 7.2.12. Julien Lepiller2018-11-12
* store: Add a functional object cache and use it in 'lower-object'.•••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. Ludovic Courtès2018-11-12
* tests: Add 'test-assertm' to (guix tests).•••* 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. Ludovic Courtès2018-11-12
* gnu: youtube-dl: Update to 2018.11.07.•••* gnu/packages/video.scm (youtube-dl): Update to 2018.11.07. Arun Isaac2018-11-12
* gnu: vifm: Update to 0.10.•••* gnu/packages/vim.scm (vifm): Update to 0.10. Efraim Flashner2018-11-12
* gnu: go-github-com-aarzilli-golua: Fix for go-1.11.•••* gnu/packages/golang.scm (go-github-com-aarzilli-golua)[arguments]: Fix for go-1.11. [native-inputs]: Remove lua. [propagated-inputs]: Add lua. Pierre Neidhardt2018-11-12
* gnu: go-github-com-wtolson-go-taglib: Fix tests and build for go-1.11.•••* 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. Pierre Neidhardt2018-11-12
* gnu: go-gopkg.in-asn1-ber.v1: Fix tests for go-1.11.•••* gnu/packages/syncthing.scm (go-gopkg.in-asn1-ber.v1): Fix tests for go-1.11. Pierre Neidhardt2018-11-12
* gnu: go-github-com-audriusbutkevicius-cli: Fix tests for go-1.11.•••* gnu/packages/syncthing.scm (go-github-com-audriusbutkevicius-cli): Fix tests for go-1.11. Pierre Neidhardt2018-11-12
* gnu: go-github-com-prometheus-common-expfmt: Fix tests for go-1.11.•••* gnu/packages/syncthing.scm (go-github-com-prometheus-common-expfmt): Fix tests for go-1.11. Pierre Neidhardt2018-11-12
* build-system/go: Plan removal of the pkg folder for go-1.11 onward.•••* guix/build/go-build-system.scm (install): New comment. Pierre Neidhardt2018-11-12
* gnu: go: Update default to 1.11.•••* gnu/packages/golang.scm (go): Update default to 1.11. Pierre Neidhardt2018-11-12
* guix system: Invoking 'guix system init' twice keeps timestamps zeroed.•••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. Ludovic Courtès2018-11-11
* guix package: '--show' errors when asked for a non-existent package.•••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. Ludovic Courtès2018-11-11
* doc: Fix typo.•••* doc/guix.texi (Porting to a New Platform): Fix typo. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Laura Lazzati2018-11-11
* gnu: r-s4vectors: Update to 0.20.1.•••* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.20.1. Ricardo Wurmus2018-11-11
* gnu: r-rcmdcheck: Update to 1.3.2.•••* gnu/packages/cran.scm (r-rcmdcheck): Update to 1.3.2. Ricardo Wurmus2018-11-11
* gnu: r-ggpubr: Update to 0.1.9.•••* gnu/packages/cran.scm (r-ggpubr): Update to 0.1.9. Ricardo Wurmus2018-11-11
* gnu: r-dplyr: Update to 0.7.8.•••* gnu/packages/statistics.scm (r-dplyr): Update to 0.7.8. Ricardo Wurmus2018-11-11
* gnu: r-rcpparmadillo: Update to 0.9.200.4.0.•••* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.200.4.0. Ricardo Wurmus2018-11-11
* gnu: r-rtsne: Update to 0.15.•••* gnu/packages/statistics.scm (r-rtsne): Update to 0.15. Ricardo Wurmus2018-11-11
* gnu: r-lme4: Update to 1.1-19.•••* gnu/packages/statistics.scm (r-lme4): Update to 1.1-19. Ricardo Wurmus2018-11-11
* gnu: webkitgtk@2.22: Adjust to documentation output.•••This is a follow-up to commit 0ead0b4d2c025ad1b4a293fb6cbb8a578b7dd87d. * gnu/packages/webkit.scm (webkitgtk)[arguments]: Remove hard coded file list. (webkitgtk-2.22)[arguments]: Inherit phases using SUBSTITUTE-KEYWORD-ARGUMENTS. Marius Bakke2018-11-11
* gnu: libtoxcore: Update to 0.0.0-2.bf69b54.•••* gnu/packages/messaging.scm (libtoxcore): Update to 0.0.0-2.bf69b54. [native-inputs]: Add check. Ricardo Wurmus2018-11-11
* gnu: mumi: Update to 0.0.0-2.bfd96ce7.•••* gnu/packages/mail.scm (mumi): Update to 0.0.0-2.bfd96ce7. Ricardo Wurmus2018-11-11
* gnu: PostgreSQL: Update to 10.6 [fixes CVE-2018-16850].•••* gnu/packages/databases.scm (postgresql): Update to 10.6. Leo Famulari2018-11-11
* gnu: webkitgtk: Include documentation.•••* gnu/packages/webkit.scm (webkitgtk): Include documentation. Pierre Neidhardt2018-11-11
* gnu: gtk-doc: Use local docbook-xsl.•••* gnu/packages/gtk.scm (gtk-doc): Use local docbook-xsl. Pierre Neidhardt2018-11-11
* gnu: faust-2: Update to 2.5.23.•••* gnu/packages/audio.scm (faust-2): Update to 2.5.23. [native-inputs]: Replace llvm-with-rtti with llvm-3.8-with-rtti. * gnu/packages/llvm.scm (llvm-with-rtti): Rename this variable... (llvm-3.8-with-rtti): ...to this variable; inherit from llvm-3.8. Ricardo Wurmus2018-11-11
* gnu: gajim: Move python-docutils from inputs to native-inputs.•••* gnu/packages/messaging.scm (gajim): Move python-docutils from inputs to native-inputs. Clément Lassieur2018-11-11
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