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2019-12-27gnu: r-inspect: Update to 1.16.1.•••* gnu/packages/bioconductor.scm (r-inspect): Update to 1.16.1. [propagated-inputs]: Add r-gdata. Ricardo Wurmus
2019-12-27gnu: r-multiassayexperiment: Update to 1.12.1.•••* gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.12.1. Ricardo Wurmus
2019-12-27gnu: r-rgadem: Update to 2.34.1.•••* gnu/packages/bioconductor.scm (r-rgadem): Update to 2.34.1. [propagated-inputs]: Add r-genomicranges. Ricardo Wurmus
2019-12-27gnu: r-clusterprofiler: Update to 3.14.2.•••* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 3.14.2. Ricardo Wurmus
2019-12-27gnu: r-enrichplot: Update to 1.6.1.•••* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.6.1. Ricardo Wurmus
2019-12-27gnu: r-biocsingular: Update to 1.2.1.•••* gnu/packages/bioconductor.scm (r-biocsingular): Update to 1.2.1. Ricardo Wurmus
2019-12-27gnu: r-affycoretools: Update to 1.58.3.•••* gnu/packages/bioconductor.scm (r-affycoretools): Update to 1.58.3. Ricardo Wurmus
2019-12-27gnu: r-car: Update to 3.0-6.•••* gnu/packages/statistics.scm (r-car): Update to 3.0-6. Ricardo Wurmus
2019-12-27gnu: r-robust: Update to 0.4-18.2.•••* gnu/packages/statistics.scm (r-robust): Update to 0.4-18.2. Ricardo Wurmus
2019-12-27gnu: r-bigmemory: Update to 4.5.36.•••* gnu/packages/statistics.scm (r-bigmemory): Update to 4.5.36. Ricardo Wurmus
2019-12-27gnu: r-foreign: Update to 0.8-74.•••* gnu/packages/statistics.scm (r-foreign): Update to 0.8-74. Ricardo Wurmus
2019-12-27gnu: r-slam: Update to 0.1-47.•••* gnu/packages/cran.scm (r-slam): Update to 0.1-47. Ricardo Wurmus
2019-12-27gnu: r-bibtex: Update to 0.4.2.1.•••* gnu/packages/cran.scm (r-bibtex): Update to 0.4.2.1. Ricardo Wurmus
2019-12-27gnu: r-topgo: Update to 2.38.1.•••* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.38.1. Ricardo Wurmus
2019-12-27gnu: r-summarizedexperiment: Update to 1.16.1.•••* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.16.1. Ricardo Wurmus
2019-12-27gnu: r-delayedarray: Update to 0.12.1.•••* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.1. Ricardo Wurmus
2019-12-27gnu: r-biocparallel: Update to 1.20.1.•••* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.20.1. Ricardo Wurmus
2019-12-27gnu: r-shortread: Update to 1.44.1.•••* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.1. Ricardo Wurmus
2019-12-27gnu: guix-data-service: Update to 0.0.1-12.f56935a.•••* gnu/packages/web.scm (guix-data-service): Update to 0.0.1-12.f56935a. Christopher Baines
2019-12-27gnu: emacs-org-contrib: Update to 20191226.•••* gnu/packages/emacs-xyz.scm (emacs-org-contrib): Update to 20191226. Nicolas Goaziou
2019-12-27gnu: emacs-org: Update to 9.3.1.•••* gnu/packages/emacs-xyz.scm (emacs-org): Update to 9.3.1. Nicolas Goaziou
2019-12-26gnu: emacs-telega: Update to 0.5.4.•••* gnu/packages/emacs-xyz.scm (emacs-telega): Update to 0.5.4. [arguments]: Working around imagemagick and svg is no longer needed. [native-inputs]: Replace emacs-minimal with emacs. This is needed because bytecompilation requires fringe-bitmap support. Brett Gilio
2019-12-26gnu: Add ffmpegthumbs.•••* gnu/packages/kde-multimedia.scm (ffmpegthumbs): New variable. Hartmut Goebel
2019-12-26gnu: Add audiocd-kio.•••* gnu/packages/kde-multimedia.scm (audiocd-kio): New variable. Hartmut Goebel
2019-12-26gnu: Add libkcompactdisc.•••* gnu/packages/kde-multimedia.scm (libkcompactdisc): New variable. Hartmut Goebel
2019-12-26gnu: Add kamoso.•••* gnu/packages/kde-multimedia.scm (kamoso): New variable. Hartmut Goebel
2019-12-26gnu: Add elisa.•••* gnu/packages/kde-multimedia.scm (elisa): New variable. Hartmut Goebel
2019-12-26gnu: Add kwave.•••* gnu/packages/kde-multimedia.scm (kwave): New variable. Hartmut Goebel
2019-12-26gnu: Add kmplayer.•••`guix lint` reports two CVEs, both are unrelated: - CVE-2018-5200: for vendor "pandora" and some 4.2.2.x version - CVE-2019-9133: windows only (I assume it it alsow relates to the "pandora" vendor, since the version the CVE refers to as "solving the issue" does not exist at KDE.) * gnu/packages/kde-multimedia.scm (kmplayer): New variable. * gnu/packages/patches/kmplayer-aarch64.patch, gnu/packages/patches/kmplayer-upstream_Fix-build-with-Qt-5.9.patch: New files. * gnu/local.mk: Add them. Hartmut Goebel
2019-12-26gnu: Add kmix.•••* gnu/packages/kde-multimedia.scm (kmix): New variable. Hartmut Goebel
2019-12-26gnu: Add kaffeine.•••* gnu/packages/kde-multimedia.scm (kaffeine): New variable. Hartmut Goebel
2019-12-26gnu: Add libkcddb.•••* gnu/packages/kde-multimedia.scm (libkcddb): New variable. Hartmut Goebel
2019-12-26gnu: Add k3b.•••* gnu/packages/kde-multimedia.scm (k3b): New variable. Hartmut Goebel
2019-12-26gnu: Add juk.•••* gnu/packages/kde-multimedia.scm (juk): New variable. Hartmut Goebel
2019-12-26gnu: Add dragon.•••* gnu/packages/kde-multimedia.scm: New file. * gnu/lokal.mk (MODULES): Add it. Hartmut Goebel
2019-12-26gnu: Add audiofile.•••Patches should fix all CVEs reported by `guix lint`: CVE-2015-7747; CVE-2017-6827, CVE-2017-6828, CVE-2017-6829, CVE-2017-6830, CVE-2017-6831, CVE-2017-6832, CVE-2017-6833, CVE-2017-6834, CVE-2017-6835, CVE-2017-6836, CVE-2017-6837, CVE-2017-6838, CVE-2017-6839; CVE-2018-13440; CVE-2018-17095 Since the patches do not reference to CVEs, it's a bit hard to tell which patch actually closes which CVE. Debian reports all these to be closed by the patches below and NixPkgs provides references. * gnu/packages/audio.scm (audiofile): New variable. * gnu/packages/patches/audiofile-fix-datatypes-in-tests.patch, gnu/packages/patches/audiofile-fix-sign-conversion.patch, gnu/packages/patches/audiofile-CVE-2015-7747.patch, gnu/packages/patches/audiofile-CVE-2018-13440.patch, gnu/packages/patches/audiofile-CVE-2018-17095.patch, gnu/packages/patches/audiofile-Check-the-number-of-coefficients.patch, gnu/packages/patches/audiofile-Fail-on-error-in-parseFormat.patch, gnu/packages/patches/audiofile-Fix-index-overflow-in-IMA.cpp.patch, gnu/packages/patches/audiofile-Fix-multiply-overflow-sfconvert.patch, gnu/packages/patches/audiofile-Fix-overflow-in-MSADPCM-decodeSam.patch, gnu/packages/patches/audiofile-division-by-zero-BlockCodec-runPull.patch, gnu/packages/patches/audiofile-hurd.patch, gnu/packages/patches/audiofile-signature-of-multiplyCheckOverflow.patch: New files. * gnu/local.mk: Add them. Hartmut Goebel
2019-12-26gnu: python-fonttools: Update home-page.•••https://github.com/behdad/fonttools permanently redirects to https://github.com/fonttools/fonttools. * gnu/packages/python-xyz.scm (python-fonttools)[home-page]: Change to current. Signed-off-by: Marius Bakke <mbakke@fastmail.com> Riku Viitanen
2019-12-26gnu: i3-gaps: Update source checksum.•••Fixes <https://bugs.gnu.org/38739>. This is a follow-up to commit 88c9408070280db51d1a0e604b9ec77f1611ab3c. * gnu/packages/wm.scm (i3-gaps)[source](sha256): Change to the correct hash. [build-system]: Remove field, because it is superfluous. Marius Bakke
2019-12-26gnu: gdal: Use HTTPS home page URI.•••* gnu/packages/geo.scm (gdal)[home-page]: Use HTTPS URI. Arun Isaac
2019-12-26gnu: gdal: Enable netCDF format driver.•••* gnu/packages/geo.scm (gdal)[inputs]: Add netcdf. Arun Isaac
2019-12-26gnu: gdal: Enable GPKG format driver.•••* gnu/packages/geo.scm (gdal)[inputs]: Enable sqlite. [arguments]: Add --with-sqlite3 to #:configure-flags. Arun Isaac
2019-12-26gnu: gdal: Enable ODS format driver.•••* gnu/packages/geo.scm (gdal)[inputs]: Add expat. [arguments]: Add --with-expat to #:configure-flags. Arun Isaac
2019-12-26gnu: libspatialindex: Update to 1.9.3.•••* gnu/packages/geo.scm (libspatialindex): Update to 1.9.3. [build-system]: Switch to cmake-build-system. [source]: Update URI. Arun Isaac
2019-12-26gnu: postgis: Update to 3.0.0.•••* gnu/packages/geo.scm (postgis): Update to 3.0.0. [inputs]: Add json-c and libjpeg-turbo. Replace proj.4 with proj. Arun Isaac
2019-12-26gnu: gdal: Update to 3.0.2.•••* gnu/packages/geo.scm (gdal): Update to 3.0.2. [inputs]: Add proj. Arun Isaac
2019-12-26gnu: libgeotiff: Update to 1.5.1.•••* gnu/packages/patches/libgeotiff-adapt-test-script-for-proj-6.2.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/geo.scm (libgeotiff): Update to 1.5.1. [inputs]: Replace proj.4 with proj. [sources]: Add libgeotiff-adapt-test-script-for-proj-6.2.patch to patches. Arun Isaac
2019-12-26gnu: Add proj.•••* gnu/packages/geo.scm (proj): New variable. Arun Isaac
2019-12-26gnu: geos: Update to 3.8.0.•••* gnu/packages/geo.scm (geos): Update to 3.8.0. Arun Isaac
2019-12-26gnu: python-pyserial: Update to 3.4.•••* gnu/packages/python-xyz.scm (python-pyserial): Update to 3.4. Björn Höfling
2019-12-26gnu: Remove squashfs-tools-next.•••* gnu/packages/compression.scm (squashfs-tools-next): Remove variable. * guix/scripts/pack.scm (squashfs-image, guix-pack): Use squashfs-tools. * tests/pack.scm: Use squashfs-tools. Ricardo Wurmus
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