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2019-12-27gnu: r-topgo: Update to 2.38.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.38.1.
2019-12-27gnu: r-summarizedexperiment: Update to 1.16.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.16.1.
2019-12-27gnu: r-delayedarray: Update to 0.12.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.1.
2019-12-27gnu: r-biocparallel: Update to 1.20.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.20.1.
2019-12-27gnu: r-shortread: Update to 1.44.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.1.
2019-12-27gnu: guix-data-service: Update to 0.0.1-12.f56935a.Christopher Baines
* gnu/packages/web.scm (guix-data-service): Update to 0.0.1-12.f56935a.
2019-12-27doc: Mention "make authenticate".Ludovic Courtès
* doc/contributing.texi (Building from Git): Add instructions to run 'git verify-commit' and 'make authenticate'.
2019-12-27git-authenticate: Keep a local cache of previously-authenticated commits.Ludovic Courtès
A list of already-authenticated commits is kept in ~/.cache/guix/authentication. This speeds up subsequent "make authenticate" invocations. * build-aux/git-authenticate.scm (authenticated-commit-cache-file) (previously-authenticated-commits, cache-authenticated-commit): New procedures. (git-authenticate): Define 'authenticated-commits' and pass it as a third argument to 'commit-difference'. Add call to 'cache-authenticated-commit'. Don't display signing stats when STATS is null.
2019-12-27git: 'commit-difference' takes a list of excluded commits.Ludovic Courtès
* guix/git.scm (commit-closure): Add 'visited' optional parameter. (commit-difference): Add 'excluded' optional parameter; pass second argument to 'commit-closure'. * tests/git.scm ("commit-difference, excluded commits"): New test.
2019-12-27Add 'build-aux/git-authenticate.scm'.Ludovic Courtès
* build-aux/git-authenticate.scm: New file. * Makefile.am (EXTRA_DIST): Add it. (commit_v1_0_1): New variable. (authenticate): New target.
2019-12-27gnu: emacs-org-contrib: Update to 20191226.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-org-contrib): Update to 20191226.
2019-12-27gnu: emacs-org: Update to 9.3.1.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-org): Update to 9.3.1.
2019-12-26gnu: emacs-telega: Update to 0.5.4.Brett Gilio
* 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.
2019-12-26gnu: Add ffmpegthumbs.Hartmut Goebel
* gnu/packages/kde-multimedia.scm (ffmpegthumbs): New variable.
2019-12-26gnu: Add audiocd-kio.Hartmut Goebel
* gnu/packages/kde-multimedia.scm (audiocd-kio): New variable.
2019-12-26gnu: Add libkcompactdisc.Hartmut Goebel
* gnu/packages/kde-multimedia.scm (libkcompactdisc): New variable.
2019-12-26gnu: Add kamoso.Hartmut Goebel
* gnu/packages/kde-multimedia.scm (kamoso): New variable.
2019-12-26gnu: Add elisa.Hartmut Goebel
* gnu/packages/kde-multimedia.scm (elisa): New variable.
2019-12-26gnu: Add kwave.Hartmut Goebel
* gnu/packages/kde-multimedia.scm (kwave): New variable.
2019-12-26gnu: Add kmplayer.Hartmut Goebel
`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.
2019-12-26gnu: Add kmix.Hartmut Goebel
* gnu/packages/kde-multimedia.scm (kmix): New variable.
2019-12-26gnu: Add kaffeine.Hartmut Goebel
* gnu/packages/kde-multimedia.scm (kaffeine): New variable.
2019-12-26gnu: Add libkcddb.Hartmut Goebel
* gnu/packages/kde-multimedia.scm (libkcddb): New variable.
2019-12-26gnu: Add k3b.Hartmut Goebel
* gnu/packages/kde-multimedia.scm (k3b): New variable.
2019-12-26gnu: Add juk.Hartmut Goebel
* gnu/packages/kde-multimedia.scm (juk): New variable.
2019-12-26gnu: Add dragon.Hartmut Goebel
* gnu/packages/kde-multimedia.scm: New file. * gnu/lokal.mk (MODULES): Add it.
2019-12-26gnu: Add audiofile.Hartmut Goebel
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.
2019-12-26gnu: python-fonttools: Update home-page.Riku Viitanen
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>
2019-12-26gnu: i3-gaps: Update source checksum.Marius Bakke
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.
2019-12-26download: Enable TLS 1.3.Marius Bakke
This reverts commit e4ee84202633636b4c8cef4a332f0c74912a3b23. * guix/build/download.scm (tls-wrap): Dot not disable TLS 1.3.
2019-12-26gnu: gdal: Use HTTPS home page URI.Arun Isaac
* gnu/packages/geo.scm (gdal)[home-page]: Use HTTPS URI.
2019-12-26gnu: gdal: Enable netCDF format driver.Arun Isaac
* gnu/packages/geo.scm (gdal)[inputs]: Add netcdf.
2019-12-26gnu: gdal: Enable GPKG format driver.Arun Isaac
* gnu/packages/geo.scm (gdal)[inputs]: Enable sqlite. [arguments]: Add --with-sqlite3 to #:configure-flags.
2019-12-26gnu: gdal: Enable ODS format driver.Arun Isaac
* gnu/packages/geo.scm (gdal)[inputs]: Add expat. [arguments]: Add --with-expat to #:configure-flags.
2019-12-26gnu: libspatialindex: Update to 1.9.3.Arun Isaac
* gnu/packages/geo.scm (libspatialindex): Update to 1.9.3. [build-system]: Switch to cmake-build-system. [source]: Update URI.
2019-12-26gnu: postgis: Update to 3.0.0.Arun Isaac
* gnu/packages/geo.scm (postgis): Update to 3.0.0. [inputs]: Add json-c and libjpeg-turbo. Replace proj.4 with proj.
2019-12-26gnu: gdal: Update to 3.0.2.Arun Isaac
* gnu/packages/geo.scm (gdal): Update to 3.0.2. [inputs]: Add proj.
2019-12-26gnu: libgeotiff: Update to 1.5.1.Arun Isaac
* 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.
2019-12-26gnu: Add proj.Arun Isaac
* gnu/packages/geo.scm (proj): New variable.
2019-12-26gnu: geos: Update to 3.8.0.Arun Isaac
* gnu/packages/geo.scm (geos): Update to 3.8.0.
2019-12-26gnu: python-pyserial: Update to 3.4.Björn Höfling
* gnu/packages/python-xyz.scm (python-pyserial): Update to 3.4.
2019-12-26gnu: Remove squashfs-tools-next.Ricardo Wurmus
* 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.
2019-12-26gnu: axoloti-patcher-next: Remove commented expression.Ricardo Wurmus
* gnu/packages/axoloti.scm (axoloti-patcher-next)[arguments]: Remove commented substitute* expression.
2019-12-26gnu: guix-data-service: Update to 0.0.1-11.7342280.Christopher Baines
* gnu/packages/web.scm (guix-data-service): Update to 0.0.1-11.7342280.
2019-12-26gnu: mumimu: Remove reference to guile-email.Christopher Baines
The use of guile-email in this package definition seems to cause errors when working with other packages, errors like: error: guile-email: unbound variable I'm not sure why the version of the Guile email package is appropriate here either, but for now just to avoid the problems, inline the current version of the package (and add a comment so this is more obvious). This issue was probably introduced in: c7b2b539802eaa3f969e212c98eb671a1a75e9f3 * gnu/packages/mail.scm (mumimu)[version]: Inline the current value of (package-version guile-email) as a string.
2019-12-26gnu: bluez-alsa: Place dbus configuration in canonical location.Ricardo Wurmus
* gnu/packages/audio.scm (bluez-alsa)[arguments]: Install dbus configuration files to /etc/dbus-1/system.d.
2019-12-26gnu: artanis: Update to 0.4.1.Ricardo Wurmus
* gnu/packages/guile-xyz.scm (artanis): Update to 0.4.1. [inputs]: Add nss; move guile-json-1 and guile-redis from here... [propagated-inputs]: ...to here; add guile-readline. [arguments]: Add phase "patch-references-to-libnss".
2019-12-26gnu: Add zfs.Efraim Flashner
* gnu/packages/file-systems.scm (zfs): New variable.
2019-12-26build-system: linux-module: Add substitutable keyword.Efraim Flashner
* guix/build-system/linux-module.scm (linux-module-build) Add substitutable keyword.
2019-12-26gnu: python-funcparserlib: Fix typo.Nicolas Goaziou
* gnu/packages/python-xyz.scm (python-funcparserlib): Fix typo in description.
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