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2021-03-12gnu: Add rust-minus-3.Nicolas Goaziou
* gnu/packages/crates-io.scm (rust-minus-3): New variable.
2021-03-12gnu: rust-surf-2: Update to 2.2.0.Nicolas Goaziou
* gnu/packages/crates-io.scm (rust-surf-2): Update to 2.2.0.
2021-03-12gnu: rust-http-client-6: Update to 6.3.4.Nicolas Goaziou
* gnu/packages/crates-io.scm (rust-http-client-6): Update to 6.3.4.
2021-03-12gnu: Add rust-async-tls-0.10.Nicolas Goaziou
* gnu/packages/crates-io.scm (rust-async-tls-0.10): New variable.
2021-03-12gnu: rust-webpki-0.21: Update to 0.21.4.Nicolas Goaziou
* gnu/packages/crates-io.scm (rust-webpki-0.21): Update to 0.21.4.
2021-03-12gnu: rust-ring-0.16: Update to 0.16.20.Nicolas Goaziou
* gnu/packages/crates-io.scm (rust-ring-0.16): Update to 0.16.20. [arguments]: Skip tests.
2021-03-12gnu: Add rust-deadpool-0.7.Nicolas Goaziou
* gnu/packages/crates-io.scm (rust-deadpool-0.7): New variable.
2021-03-12gnu: rust-url-2: Update to 2.2.1.Nicolas Goaziou
* gnu/packages/crates-io.scm (rust-url-2): Update to 2.2.1.
2021-03-12utils: Use Guile-zlib for gzip compression and decompression.Ludovic Courtès
Fixes <https://bugs.gnu.org/46967>. * guix/utils.scm (decompressed-port): Call 'make-zlib-input-port' instead of invoking %GZIP. (compressed-output-port): Call 'make-zlib-output-port' instead of invoking %GZIP. * doc/guix.texi (Requirements): Require Guile-zlib >= 0.1.0.
2021-03-12gnu: guile-zlib: Update to 0.1.0.Ludovic Courtès
* gnu/packages/guile.scm (guile-zlib): Update to 0.1.0.
2021-03-12gnu: Add sbcl-stumpwm-disk.Sharlatan Hellseher
* gnu/packages/wm.scm: (sbcl-stumpwm-disk): New variable. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2021-03-12gnu: stumpwm-contrib: Update to 0.0.1-3.a7dc1c.Sharlatan Hellseher
* gnu/packages/wm.scm (stumpwm-contrib): Update to 0.0.1-3.a7dc1c. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2021-03-12gnu: Add gnuais.Guillaume Le Vaillant
* gnu/packages/radio.scm (gnuais): New variable.
2021-03-12gnu: r-systempiper: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-systempiper): Move from here... * gnu/packages/bioconductor.scm (r-systempiper): ...to here.
2021-03-12gnu: r-shortread: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-shortread): Move from here... * gnu/packages/bioconductor.scm (r-shortread): ...to here.
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.
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