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2018-11-07gnu: r-regioner: Update to 1.14.0....* gnu/packages/bioconductor.scm (r-regioner): Update to 1.14.0. [propagated-inputs]: Add r-biostrings. Ricardo Wurmus
2018-11-07gnu: r-ruvseq: Update to 1.16.0....* gnu/packages/bioconductor.scm (r-ruvseq): Update to 1.16.0. Ricardo Wurmus
2018-11-07gnu: Add r-biocneighbors....* gnu/packages/bioconductor.scm (r-biocneighbors): New variable. Ricardo Wurmus
2018-11-07gnu: r-dnabarcodes: Update to 1.12.0....* gnu/packages/bioconductor.scm (r-dnabarcodes): Update to 1.12.0. Ricardo Wurmus
2018-11-07gnu: r-inspect: Update to 1.12.0....* gnu/packages/bioconductor.scm (r-inspect): Update to 1.12.0. Ricardo Wurmus
2018-11-07gnu: r-rots: Update to 1.10.0....* gnu/packages/bioconductor.scm (r-rots): Update to 1.10.0. Ricardo Wurmus
2018-11-07gnu: r-glimma: Update to 1.10.0....* gnu/packages/bioconductor.scm (r-glimma): Update to 1.10.0. Ricardo Wurmus
2018-11-07gnu: r-goseq: Update to 1.34.0....* gnu/packages/bioconductor.scm (r-goseq): Update to 1.34.0. Ricardo Wurmus
2018-11-07gnu: r-ctc: Update to 1.56.0....* gnu/packages/bioconductor.scm (r-ctc): Update to 1.56.0. Ricardo Wurmus
2018-11-07gnu: r-genomicinteractions: Update to 1.16.0....* gnu/packages/bioconductor.scm (r-genomicinteractions): Update to 1.16.0. Ricardo Wurmus
2018-11-07gnu: r-interactionset: Update to 1.10.0....* gnu/packages/bioconductor.scm (r-interactionset): Update to 1.10.0. Ricardo Wurmus
2018-11-07gnu: r-riboseqr: Update to 1.16.0....* gnu/packages/bioconductor.scm (r-riboseqr): Update to 1.16.0. Ricardo Wurmus
2018-11-07gnu: r-riboprofiling: Update to 1.12.0....* gnu/packages/bioconductor.scm (r-riboprofiling): Update to 1.12.0. Ricardo Wurmus
2018-11-07gnu: r-ripseeker: Update to 1.22.0....* gnu/packages/bioconductor.scm (r-ripseeker): Update to 1.22.0. Ricardo Wurmus
2018-11-07gnu: r-chipcomp: Update to 1.12.0....* gnu/packages/bioconductor.scm (r-chipcomp): Update to 1.12.0. Ricardo Wurmus
2018-11-07gnu: r-bayseq: Update to 2.16.0....* gnu/packages/bioconductor.scm (r-bayseq): Update to 2.16.0. Ricardo Wurmus
2018-11-07gnu: r-chippeakanno: Update to 3.16.0....* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.16.0. [propagated-inputs]: Remove r-biocinstaller; add r-biocmanager. Ricardo Wurmus
2018-11-07gnu: r-graph: Update to 1.60.0....* gnu/packages/bioconductor.scm (r-graph): Update to 1.60.0. Ricardo Wurmus
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
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