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2018-11-07gnu: r-ffbase: Update to 0.12.7.•••* gnu/packages/cran.scm (r-ffbase): Update to 0.12.7. Ricardo Wurmus
2018-11-07gnu: r-pkgload: Update to 1.0.2.•••* gnu/packages/cran.scm (r-pkgload): Update to 1.0.2. Ricardo Wurmus
2018-11-07gnu: r-ps: Update to 1.2.1.•••* gnu/packages/cran.scm (r-ps): Update to 1.2.1. Ricardo Wurmus
2018-11-07gnu: r-rgraphviz: Update to 2.26.0.•••* gnu/packages/graph.scm (r-rgraphviz): Update to 2.26.0. Ricardo Wurmus
2018-11-07gnu: Add hdf5-1.10.•••* gnu/packages/maths.scm (hdf5-1.10): New variable. Ricardo Wurmus
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
2018-11-06install: 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
2018-11-06gnu: 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
2018-11-06gnu: 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
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