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2021-03-12gnu: r-gostats: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-gostats): Move from here... * gnu/packages/bioconductor.scm (r-gostats): ...to here.
2021-03-12gnu: r-category: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-category): Move from here... * gnu/packages/bioconductor.scm (r-category): ...to here.
2021-03-12gnu: r-gseabase: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-gseabase): Move from here... * gnu/packages/bioconductor.scm (r-gseabase): ...to here.
2021-03-12gnu: r-rbgl: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-rbgl): Move from here... * gnu/packages/bioconductor.scm (r-rbgl): ...to here.
2021-03-12gnu: r-annotationforge: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-annotationforge): Move from here... * gnu/packages/bioconductor.scm (r-annotationforge): ...to here.
2021-03-12gnu: r-dexseq: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-dexseq): Move from here... * gnu/packages/bioconductor.scm (r-dexseq): ...to here.
2021-03-12gnu: r-deseq2: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-deseq2): Move from here... * gnu/packages/bioconductor.scm (r-deseq2): ...to here.
2021-03-12gnu: r-genefilter: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-genefilter): Move from here... * gnu/packages/bioconductor.scm (r-genefilter): ...to here.
2021-03-12gnu: r-bioassayr: Update home page.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bioassayr)[home-page]: Follow permanent redirect.
2021-03-12gnu: r-bioassayr: Update to 1.28.2.zimoun
* gnu/packages/bioconductor.scm (r-bioassayr): Update to 1.28.2.
2021-03-12gnu: r-chemminer: Update to 3.42.2.zimoun
* gnu/packages/bioconductor.scm (r-chemminer): Update to 3.42.2.
2021-03-12gnu: r-circrnaprofiler: Update to 1.4.2.zimoun
* gnu/packages/bioconductor.scm (r-circrnaprofiler): Update to 1.4.2.
2021-03-12gnu: Add r-puniform.Lars-Dominik Braun
* gnu/packages/statistics.scm (r-puniform): New variable.
2021-03-12gnu: Add r-clubsandwich.Lars-Dominik Braun
* gnu/packages/statistics.scm (r-clubsandwich): New variable.
2021-03-12gnu: Add r-quantpsyc.Lars-Dominik Braun
* gnu/packages/statistics.scm (r-quantpsyc): New variable.
2021-03-12gnu: Add r-ez.Lars-Dominik Braun
* gnu/packages/cran.scm (r-ez): New variable.
2021-03-12gnu: Add r-prereg.Lars-Dominik Braun
* gnu/packages/cran.scm (r-prereg): New variable.
2021-03-12gnu: Add python-upsetplot.Ricardo Wurmus
* gnu/packages/python-science.scm (python-upsetplot): New variable.
2021-03-12gnu: Add python-statannot.Ricardo Wurmus
* gnu/packages/python-science.scm (python-statannot): New variable.
2021-03-12gnu: lisp-repl-core-dumper: Update to 0.7.0.Pierre Neidhardt
* gnu/packages/lisp.scm (lisp-repl-core-dumper): Update to 0.7.0.
2021-03-12gnu: snakemake: Update to 5.32.2.Ricardo Wurmus
* gnu/packages/python-xyz.scm (snakemake): Update to 5.32.2. [arguments]: Adjust patch in call-wrapper-not-wrapped-snakemake.
2021-03-12gnu: gnome-shell: Fix CVE-2020-17489.Mark H Weaver
* gnu/packages/patches/gnome-shell-CVE-2020-17489.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/gnome.scm (gnome-shell)[source]: Add patch.
2021-03-12gnu: gnome-shell: Update to 3.34.5.Mark H Weaver
* gnu/packages/gnome.scm (gnome-shell): Update to 3.34.5.
2021-03-12gnu: gvfs: Update to 1.40.2 [security fixes].Mark H Weaver
Includes fixes for CVE-2019-12447, CVE-2019-12448, CVE-2019-12449, and CVE-2019-12795. * gnu/packages/gnome.scm (gvfs): Update to 1.40.2.
2021-03-12gnu: cairo: Fix CVE-2018-19876 and CVE-2020-35492.Mark H Weaver
* gnu/packages/patches/cairo-CVE-2018-19876.patch, gnu/packages/patches/cairo-CVE-2020-35492.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. * gnu/packages/gtk.scm (cairo)[replacement]: New field. (cairo/fixed): New variable. (cairo-xcb): Use package/inherit.
2021-03-12gnu: gdk-pixbuf: Fix CVE-2020-29385.Mark H Weaver
* gnu/packages/patches/gdk-pixbuf-CVE-2020-29385.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/gtk.scm (gdk-pixbuf)[replacement]: New field. (gdk-pixbuf/fixed): New variable. (gdk-pixbuf+svg): Use package/inherit.
2021-03-12gnu: java-openjfx-graphics: Install native libraries.Ricardo Wurmus
* gnu/packages/java.scm (java-openjfx-graphics)[arguments]: Add phase copy-missing-file and build-native. [native-inputs]: Add missing source file.
2021-03-12gnu: glib: Fix CVE-2021-28153.Mark H Weaver
* gnu/packages/patches/glib-CVE-2021-28153.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/glib.scm (glib/fixed): Add the new patch.
2021-03-11gnu: certbot, python-acme: Update to 1.13.0.Leo Famulari
* gnu/packages/tls.scm (python-acme): Update to 1.13.0. [native-inputs]: Remove python-mock. [propagated-inputs]: Remove python-six. (certbot): Update to 1.13.0. [propagated-inputs]: Remove python-six. [arguments]: Remove 'build-documentation' phase.
2021-03-11gnu: git-annex: Update to 8.20210310.Kyle Meyer
* gnu/packages/haskell-apps.scm (git-annex): Update to 8.20210310. Signed-off-by: Leo Famulari <leo@famulari.name>
2021-03-11gnu: linux-libre 4.4: Update to 4.4.261.Leo Famulari
* gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.261. (linux-libre-4.4-pristine-source): Update hash.
2021-03-11gnu: linux-libre 4.9: Update to 4.9.261.Leo Famulari
* gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.261. (linux-libre-4.9-pristine-source): Update hash.
2021-03-11gnu: linux-libre 4.14: Update to 4.14.225.Leo Famulari
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.225. (linux-libre-4.14-pristine-source): Update hash.
2021-03-11gnu: linux-libre 4.19: Update to 4.19.180.Leo Famulari
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.180. (linux-libre-4.19-pristine-source): Update hash.
2021-03-11gnu: linux-libre 5.4: Update to 5.4.105.Leo Famulari
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.105. (linux-libre-5.4-pristine-source): Update hash.
2021-03-11gnu: linux-libre 5.10: Update to 5.10.23.Leo Famulari
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.23. (linux-libre-5.10-pristine-source): Update hash.
2021-03-11gnu: linux-libre: Update to 5.11.6.Leo Famulari
* gnu/packages/linux.scm (linux-libre-5.11-version): Update to 5.11.6. (linux-libre-5.11-pristine-source): Update hash.
2021-03-11gnu: guile-curl: Update to 0.9.Xinglu Chen
* gnu/packages/curl.scm (guile-curl): Update to 0.9. [#:phases]: Update path to module. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-03-11gnu: wireshark: Update to 3.4.4.Tobias Geerinckx-Rice
* gnu/packages/networking.scm (wireshark): Update to 3.4.4.
2021-03-11gnu: hangups: Update to 0.4.13.Tobias Geerinckx-Rice
* gnu/packages/messaging.scm (hangups): Update to 0.4.13.
2021-03-11gnu: fmt: Update to 7.1.3.Greg Hogan
* gnu/packages/pretty-print.scm (fmt): Update to 7.1.3. Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
2021-03-11gnu: btrfs-progs: Update to 5.11.Tobias Geerinckx-Rice
* gnu/packages/linux.scm (btrfs-progs): Update to 5.11.
2021-03-11gnu: libdatrie: Update to 0.2.13.Tobias Geerinckx-Rice
* gnu/packages/gtk.scm (libdatrie): Update to 0.2.13.
2021-03-11gnu: libinih: Update to 53.Tobias Geerinckx-Rice
* gnu/packages/linux.scm (libinih): Update to 53.
2021-03-11gnu: flatpak: Update to 1.10.2 [fixes CVE-2021-21381].Léo Le Bouter
* gnu/packages/package-management.scm (flatpak): Update to 1.10.2.
2021-03-11gnu: mongodb: Update comment about package license.Efraim Flashner
* gnu/packages/databases.scm (mongodb): Adjust the comment about the licensing status of the package, there are still older branches receiving updates under the AGPL license.
2021-03-11Revert "Revert "gnu: mongodb: Update to 3.4.24 [security fixes].""Efraim Flashner
This reverts commit feff80cec3c97a3df2c20d300be12d67f79d4f22. I was mistaken, there are still branches of mongodb which are still licensed under the AGPL3
2021-03-11gnu: Add computable-reals.Pierre Neidhardt
* gnu/packages/lisp-xyz.scm (cl-computable-reals, ecl-computable-reals, sbcl-computable-reals): New variables.
2021-03-11gnu: Add python-praw.Raghav Gururajan
* gnu/packages/python-web.scm (python-raw): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-03-11gnu: Add python-prawcore.Raghav Gururajan
* gnu/packages/python-web.scm (python-prawcore): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
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