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2018-11-07gnu: r-multtest: Update to 2.38.0....* gnu/packages/bioconductor.scm (r-multtest): Update to 2.38.0. Ricardo Wurmus
2018-11-07gnu: r-qdnaseq: Update to 1.18.0....* gnu/packages/bioconductor.scm (r-qdnaseq): Update to 1.18.0. Ricardo Wurmus
2018-11-07gnu: r-cghcall: Update to 2.44.0....* gnu/packages/bioconductor.scm (r-cghcall): Update to 2.44.0. Ricardo Wurmus
2018-11-07gnu: r-cghbase: Update to 1.42.0....* gnu/packages/bioconductor.scm (r-cghbase): Update to 1.42.0. Ricardo Wurmus
2018-11-07gnu: r-marray: Update to 1.60.0....* gnu/packages/bioconductor.scm (r-marray): Update to 1.60.0. Ricardo Wurmus
2018-11-07gnu: r-diffbind: Update to 2.10.0....* gnu/packages/bioconductor.scm (r-diffbind): Update to 2.10.0. Ricardo Wurmus
2018-11-07gnu: r-hpar: Update to 1.24.0....* gnu/packages/bioconductor.scm (r-hpar): Update to 1.24.0. Ricardo Wurmus
2018-11-07gnu: Add r-biocmanager....* gnu/packages/cran.scm (r-biocmanager): New variable. Ricardo Wurmus
2018-11-07gnu: Add r-ncdf4....* gnu/packages/cran.scm (r-ncdf4): New variable. Ricardo Wurmus
2018-11-07gnu: Add r-rcppannoy....* gnu/packages/cran.scm (r-rcppannoy): New variable. Ricardo Wurmus
2018-11-07gnu: slang: Use a correct location for terminfo dirs....As termcap is disabled and no terminfo directory is given, slang is not able to query terminal capabilities. Specifying a correct path for terminfo will automatically disable termcap support in the configuration. * gnu/packages/slang.scm (slang)[source]: Remove the snippet disabling termcap. [arguments]: Set MISC_TERMINFO_DIRS to a correct location. Mathieu Othacehe
2018-11-07gnu: terminals: Change libtsm and kmscon repositories....Those two packages (from the same author) are no longer maintained and do not even compile. Switch to a fork that is maintained even if it does not have any release yet. * gnu/packages/terminals.scm (libtsm)[origin]: Use "https://github.com/Aetf/libtsm" as new origin and switch to git-fetch method. (kmscon)[origin]: Use "https://github.com/Aetf/kmscon" as new origin and switch to git-fetch method. Mathieu Othacehe
2018-11-07services: kmscon: Add an auto-login option....Add an auto-login option that behaves as the one of mingetty-service. * gnu/services/base.scm (kmscon-configuration)[auto-login]: New field. (kmscon-service-type): Pass it to kmscon command. * doc/guix.texi (Base Services): Document it. Mathieu Othacehe
2018-11-07services: kmscon: Do not switch to vt at start....* gnu/services/base.scm (kmscon-service-type): Add "--no-switchvt" to kmscon command. Mathieu Othacehe
2018-11-07gnu: Add guile-newt....* gnu/packages/guile.scm (guile-newt): New variable. Mathieu Othacehe
2018-11-07gnu: kodi: Fix typo....This is a follow-up to 2c17bd7b2955beef4130d11b33e07e4fb3b234dc. * gnu/packages/kodi.scm (kodi)[arguments]: Remove unwanted symbols. Efraim Flashner
2018-11-06gnu: LibreOffice: Update to 6.1.3.2....* gnu/packages/libreoffice.scm (libreoffice): Update to 6.1.3.2. Leo Famulari
2018-11-06gnu: GnuPG: Update to 2.2.11....* gnu/packages/gnupg.scm (gnupg): Update to 2.2.11. Leo Famulari
2018-11-06pack: Add test for '--relocatable'....* tests/guix-pack-relocatable.sh: New file. * Makefile.am (SH_TESTS): Add it. Ludovic Courtès
2018-11-06store-copy: Canonicalize the mtime and permissions of the store copy....Fixes a bug whereby directories in the output of 'guix pack -f tarball' would not be read-only. * guix/build/store-copy.scm (reset-permissions): New procedure. (populate-store): Pass #:keep-mtime? #t to 'copy-recursively'. Call 'reset-permissions'. * tests/pack.scm ("self-contained-tarball"): In CHECK, define 'canonical?' and use it to check that every file has an mtime of 1 and is read-only. * tests/guix-pack.sh: Invoke "chmod -Rf +w" before "rm -rf" in trap. Ludovic Courtès
2018-11-06pack: Add test for 'self-contained-tarball' with localstatedir....* tests/pack.scm ("self-contained-tarball + localstatedir"): New test. Ludovic Courtès
2018-11-06pack: Squashfs backend now honors '--localstatedir'....* guix/scripts/pack.scm (squashfs-image)[database]: New variable. [build]: Add (gnu build install) to the closure. Call 'install-database-and-gc-roots' when DATABASE is true, and invoke mksquashfs once more. * tests/pack.scm ("squashfs-image + localstatedir"): New test. Ludovic Courtès
2018-11-06pack: Docker backend now honors '--localstatedir'....* guix/docker.scm (build-docker-image): Add #:database parameter. Create /var/guix/db, /var/guix/profiles, etc. when DATABASE is true. * guix/scripts/pack.scm (docker-image): Export. Remove #:deduplicate? parameter. Define 'database' and pass it to 'docker-image'. * tests/pack.scm (test-assertm): Recompile the derivation of %BOOTSTRAP-GUILE. ("docker-image + localstatedir"): New test. Ludovic Courtès
2018-11-06install: Add 'install-database-and-gc-roots'....* gnu/build/install.scm (%root-profile): New variable. (install-database-and-gc-roots): New procedure. (populate-single-profile-directory): Replace inline code with a call to 'install-database-and-gc-roots'. Ludovic Courtès
2018-11-06pack: Import (guix store database) only when '--localstatedir' is passed....This is another way to address <https://bugs.gnu.org/32184>, which was previously addressed in commit 19c924af4f3726688ca155a905ebf1cb9acdfca2. * gnu/build/install.scm (register-closure): Move to... * gnu/build/vm.scm (register-closure): ... here. New procedure. * guix/scripts/pack.scm (self-contained-tarball)[build]: Remove now unneeded 'with-extensions' form and custom (guix config) module. * tests/guix-pack.sh: Revert the strategy from commit 19c924af4f3726688ca155a905ebf1cb9acdfca2. * tests/pack.scm ("self-contained-tarball"): Likewise. Ludovic Courtès
2018-11-06pack: Move store database creation to a separate derivation....* guix/scripts/pack.scm (store-database): New procedure. (self-contained-tarball): Use it when LOCALSTATEDIR? is true. Remove 'schema' and add 'database'. [build]: Pass DATABASE to 'populate-single-profile-directory'. (squashfs-image): Remove #:deduplicate? parameter. [build]: Remove (gnu build install) and (guix config) from the imported modules. Remove 'with-extensions'. * gnu/build/install.scm (populate-single-profile-directory): Remove #:deduplicate?, #:register?, and #:schema; add #:database. Remove call to 'register-closure' and simply copy DATABASE instead. Ludovic Courtès
2018-11-06gnu: nginx: Update to 1.14.1 [security fixes]....This fixes CVE-2018-16843, CVE-2018-16844, and CVE-2018-16845. * gnu/packages/web.scm (nginx): Update to 1.14.1. Marius Bakke
2018-11-06guix: Update to Bioconductor 3.8....* guix/import/cran.scm (%bioconductor-version): Update to 3.8. * guix/build-system/r.scm (bioconductor-uri): Update archive URL. Ricardo Wurmus
2018-11-06gnu: Syncthing: Update to 0.14.52....* gnu/packages/syncthing.scm (syncthing): Update to 0.14.52. Leo Famulari
2018-11-06gnu: libgit2: Work around test failures on 32-bit platforms....* gnu/packages/patches/libgit2-oom-test.patch: New file. * gnu/packages/version-control.scm (libgit2)[source]: Use it. * gnu/local.mk (dist_patch_DATA): Add it. Ludovic Courtès
2018-11-06gnu: Add xcb-util-errors....* gnu/packages/xorg.scm (xcb-util-errors): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Stefan Stefanović
2018-11-06self: Install shell completion files....* guix/self.scm (miscellaneous-files): New procedure. (whole-package): Remove #:substitute-keys, add #:miscellany. [build]: Remove code for SUBSTITUTE-KEYS and add code to copy MISCELLANY to OUTPUT. (compiled-guix): Adjust call to 'whole-package'. Ludovic Courtès
2018-11-06nls: Update 'de' translation.Ludovic Courtès
2018-11-06self: Rename 'sub-directory' to 'file-append*'....* guix/self.scm (sub-directory): Rename to... (file-append*): ... this. Add #:recursive? parameter and pass it to 'local-file'. (locale-data, info-manual, compiled-guix): Adjust accordingly. Ludovic Courtès
2018-11-06gnu: guile-sqlite3: Update home page....* gnu/packages/guile.scm (guile-sqlite3)[home-page]: Update. Ludovic Courtès
2018-11-06gnu: Add r-weights....* gnu/packages/cran.scm (r-weights): New variable. Signed-off-by: Gábor Boskovits <boskovits@gmail.com> lakshmi
2018-11-06gnu: youtube-dl: Update to 2018.11.03....* gnu/packages/video.scm (youtube-dl): Update to 2018.11.03. Tobias Geerinckx-Rice
2018-11-06gnu: terraform-docs: Update to 0.5.0....* gnu/packages/terraform.scm (terraform-docs): Update to 0.5.0. [native-inputs]: Remove them all. Tobias Geerinckx-Rice
2018-11-06gnu: jq: Don't use NAME in source URI....* gnu/packages/web.scm (jq)[source]: Code more hard. Tobias Geerinckx-Rice
2018-11-06gnu: jq: Update to 1.6....* gnu/packages/web.scm (jq): Update to 1.6. [source]: Remove upstreamed patch. * gnu/packages/patches/jq-CVE-2015-8863.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. Tobias Geerinckx-Rice
2018-11-06gnu: ffmpeg: Update to 4.1....* gnu/packages/video.scm (ffmpeg): Update to 4.1. Rutger Helling
2018-11-06Revert "gnu: c-ares: Update to 1.15.0."...c-ares has more than 3000 dependant packages. This reverts commit b588adc96feec4498857ecb6d3537f746b0c0463. Efraim Flashner
2018-11-06gnu: c-ares: Update to 1.15.0....* gnu/packages/adns.scm (c-ares): Update to 1.15.0. Efraim Flashner
2018-11-06gnu: services: dns: Fix 'ddclient-activation'....* gnu/services/dns.scm (ddclient-activation): Fix procedure. Oleg Pykhalov
2018-11-05ssh: Honor the SOCKET-NAME argument of connect-to-remote-daemon....* guix/ssh.scm (connect-to-remote-daemon): Pass the `socket-name' variable to the `open-connection' call so that it is honored. Maxim Cournoyer
2018-11-06self: Install substitute keys....* guix/self.scm (whole-package): Add #:substitute-keys and honor it. (compiled-guix): Pass #:substitute-keys to 'whole-package' when PULL-VERSION is one. Ludovic Courtès
2018-11-06maint: Move substitute public keys to etc/substitutes....* berlin.guixsd.org.pub, hydra.gnu.org.pub: Move to... * etc/substitutes: ... here. New directory. * Makefile.am (dist_pkgdata_DATA): Adjust accordingly. Ludovic Courtès
2018-11-06self: Remove extra paren in manual version string....* guix/self.scm (info-manual)[build]: Remove extra closing paren in VERSION. Ludovic Courtès
2018-11-06pull: Make '--dry-run' behave as expected....* guix/scripts/pull.scm (show-help): Document '--dry-run'. (build-and-install): Add #:dry-run? parameter and honor it. (guix-pull): Remove (assoc-ref opts 'dry-run?) condition. Instead, pass it as #:dry-run? to 'build-and-install'. * doc/guix.texi (Invoking guix pull): Document '--dry-run'. Move '--verbose' to the bottom. Ludovic Courtès
2018-11-06bash completion: Restore completion of available packages for 'guix build'....Fixes a regression introduced in 9b0a755f642542dd96065ad05ec9d844d8077fd7 whereby 'guix build TAB' would not suggest any completion. * etc/completion/bash/guix (_guix_complete): Arrange so 'guix build TAB' completes available packages. Ludovic Courtès