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* gnu: Add aws-c-cal.Greg Hogan2021-03-12
| | | | | | | | * gnu/packages/c.scm (aws-c-cal): New variable. * gnu/packages/patches/aws-c-cal-cmake-prefix.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: aws-checksums: Build as shared library.Greg Hogan2021-03-12
| | | | | | * gnu/packages/c.scm (aws-checksums)[arguments]: Build as shared library. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: aws-c-common: Update to 0.5.2.Greg Hogan2021-03-12
| | | | | | | * gnu/packages/c.scm (aws-c-common): Update to 0.5.2. [arguments]: Build as shared library. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: ImageMagick: Fix version number in build configuration of grafted ↵Leo Famulari2021-03-12
| | | | | | | | | | | | replacement. Fixes <https://bugs.gnu.org/47110>. This is a followup to commits 852ba914a43da0977d4f53b53da7039cdd6706b2 and 82e887ba48c2ba91b17aa9b6b17501e3e0ef4aef. * gnu/packages/imagemagick.scm (imagemagick/fixed)[name, arguments]: New fields.
* gnu: OpenSSL: Fix version number in build configuration.Leo Famulari2021-03-12
| | | | | | | | Fixes <https://bugs.gnu.org/47108>. This is a followup to commit 4a8b529ce15ddc69a9dd701e450fc85a0ed65910. * gnu/packages/tls.scm (openssl/fixed)[arguments]: New field.
* gnu: libtiff: Fix documentation directory name in grafted replacement.Leo Famulari2021-03-12
| | | | | | | | Fixes <https://bugs.gnu.org/47107>. This is a followup to commit 6320700b114f09c09fbe613e2032abe077d28583. * gnu/packages/image.scm (libtiff/fixed)[name, arguments]: New fields.
* gnu: nushell: Update to 0.28.0.Nicolas Goaziou2021-03-12
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/shells.scm (nushell): (rust-nu-cli-0.28): (rust-nu-command-0.28): (rust-nu-data-0.28): (rust-nu-engine-0.28): (rust-nu-errors-0.28): (rust-nu-json-0.28): (rust-nu-plugin-0.28): (rust-nu-plugin-binaryview-0.28): (rust-nu-plugin-chart-0.28): (rust-nu-plugin-fetch-0.28): (rust-nu-plugin-from-sqlite-0.28): (rust-nu-plugin-inc-0.28): (rust-nu-plugin-match-0.28): (rust-nu-plugin-post-0.28): (rust-nu-plugin-ps-0.28): (rust-nu-plugin-s3-0.28): (rust-nu-plugin-sys-0.28): (rust-nu-plugin-textview-0.28): (rust-nu-plugin-to-bson-0.28): (rust-nu-plugin-to-sqlite-0.28): (rust-nu-plugin-tree-0.28): (rust-nu-plugin-xpath-0.28): (rust-nu-protocol-0.28): (rust-nu-source-0.28): (rust-nu-stream-0.28): (rust-nu-test-support-0.28): (rust-nu-value-ext-0.28): Update to 0.28.0. (rust-nu-ansi-term-0.28): New variable.
* gnu: Add rust-minus-3.Nicolas Goaziou2021-03-12
| | | | * gnu/packages/crates-io.scm (rust-minus-3): New variable.
* gnu: rust-surf-2: Update to 2.2.0.Nicolas Goaziou2021-03-12
| | | | * gnu/packages/crates-io.scm (rust-surf-2): Update to 2.2.0.
* gnu: rust-http-client-6: Update to 6.3.4.Nicolas Goaziou2021-03-12
| | | | * gnu/packages/crates-io.scm (rust-http-client-6): Update to 6.3.4.
* gnu: Add rust-async-tls-0.10.Nicolas Goaziou2021-03-12
| | | | * gnu/packages/crates-io.scm (rust-async-tls-0.10): New variable.
* gnu: rust-webpki-0.21: Update to 0.21.4.Nicolas Goaziou2021-03-12
| | | | * gnu/packages/crates-io.scm (rust-webpki-0.21): Update to 0.21.4.
* gnu: rust-ring-0.16: Update to 0.16.20.Nicolas Goaziou2021-03-12
| | | | | * gnu/packages/crates-io.scm (rust-ring-0.16): Update to 0.16.20. [arguments]: Skip tests.
* gnu: Add rust-deadpool-0.7.Nicolas Goaziou2021-03-12
| | | | * gnu/packages/crates-io.scm (rust-deadpool-0.7): New variable.
* gnu: rust-url-2: Update to 2.2.1.Nicolas Goaziou2021-03-12
| | | | * gnu/packages/crates-io.scm (rust-url-2): Update to 2.2.1.
* utils: Use Guile-zlib for gzip compression and decompression.Ludovic Courtès2021-03-12
| | | | | | | | | | 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.
* gnu: guile-zlib: Update to 0.1.0.Ludovic Courtès2021-03-12
| | | | * gnu/packages/guile.scm (guile-zlib): Update to 0.1.0.
* gnu: Add sbcl-stumpwm-disk.Sharlatan Hellseher2021-03-12
| | | | | | * gnu/packages/wm.scm: (sbcl-stumpwm-disk): New variable. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
* gnu: stumpwm-contrib: Update to 0.0.1-3.a7dc1c.Sharlatan Hellseher2021-03-12
| | | | | | * gnu/packages/wm.scm (stumpwm-contrib): Update to 0.0.1-3.a7dc1c. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
* gnu: Add gnuais.Guillaume Le Vaillant2021-03-12
| | | | * gnu/packages/radio.scm (gnuais): New variable.
* gnu: r-systempiper: Move to (gnu packages bioconductor).zimoun2021-03-12
| | | | | * gnu/packages/bioinformatics.scm (r-systempiper): Move from here... * gnu/packages/bioconductor.scm (r-systempiper): ...to here.
* gnu: r-shortread: Move to (gnu packages bioconductor).zimoun2021-03-12
| | | | | * gnu/packages/bioinformatics.scm (r-shortread): Move from here... * gnu/packages/bioconductor.scm (r-shortread): ...to here.
* gnu: r-gostats: Move to (gnu packages bioconductor).zimoun2021-03-12
| | | | | * gnu/packages/bioinformatics.scm (r-gostats): Move from here... * gnu/packages/bioconductor.scm (r-gostats): ...to here.
* gnu: r-category: Move to (gnu packages bioconductor).zimoun2021-03-12
| | | | | * gnu/packages/bioinformatics.scm (r-category): Move from here... * gnu/packages/bioconductor.scm (r-category): ...to here.
* gnu: r-gseabase: Move to (gnu packages bioconductor).zimoun2021-03-12
| | | | | * gnu/packages/bioinformatics.scm (r-gseabase): Move from here... * gnu/packages/bioconductor.scm (r-gseabase): ...to here.
* gnu: r-rbgl: Move to (gnu packages bioconductor).zimoun2021-03-12
| | | | | * gnu/packages/bioinformatics.scm (r-rbgl): Move from here... * gnu/packages/bioconductor.scm (r-rbgl): ...to here.
* gnu: r-annotationforge: Move to (gnu packages bioconductor).zimoun2021-03-12
| | | | | * gnu/packages/bioinformatics.scm (r-annotationforge): Move from here... * gnu/packages/bioconductor.scm (r-annotationforge): ...to here.
* gnu: r-dexseq: Move to (gnu packages bioconductor).zimoun2021-03-12
| | | | | * gnu/packages/bioinformatics.scm (r-dexseq): Move from here... * gnu/packages/bioconductor.scm (r-dexseq): ...to here.
* gnu: r-deseq2: Move to (gnu packages bioconductor).zimoun2021-03-12
| | | | | * gnu/packages/bioinformatics.scm (r-deseq2): Move from here... * gnu/packages/bioconductor.scm (r-deseq2): ...to here.
* gnu: r-genefilter: Move to (gnu packages bioconductor).zimoun2021-03-12
| | | | | * gnu/packages/bioinformatics.scm (r-genefilter): Move from here... * gnu/packages/bioconductor.scm (r-genefilter): ...to here.
* gnu: r-bioassayr: Update home page.Ricardo Wurmus2021-03-12
| | | | | * gnu/packages/bioconductor.scm (r-bioassayr)[home-page]: Follow permanent redirect.
* gnu: r-bioassayr: Update to 1.28.2.zimoun2021-03-12
| | | | * gnu/packages/bioconductor.scm (r-bioassayr): Update to 1.28.2.
* gnu: r-chemminer: Update to 3.42.2.zimoun2021-03-12
| | | | * gnu/packages/bioconductor.scm (r-chemminer): Update to 3.42.2.
* gnu: r-circrnaprofiler: Update to 1.4.2.zimoun2021-03-12
| | | | * gnu/packages/bioconductor.scm (r-circrnaprofiler): Update to 1.4.2.
* gnu: Add r-puniform.Lars-Dominik Braun2021-03-12
| | | | * gnu/packages/statistics.scm (r-puniform): New variable.
* gnu: Add r-clubsandwich.Lars-Dominik Braun2021-03-12
| | | | * gnu/packages/statistics.scm (r-clubsandwich): New variable.
* gnu: Add r-quantpsyc.Lars-Dominik Braun2021-03-12
| | | | * gnu/packages/statistics.scm (r-quantpsyc): New variable.
* gnu: Add r-ez.Lars-Dominik Braun2021-03-12
| | | | * gnu/packages/cran.scm (r-ez): New variable.
* gnu: Add r-prereg.Lars-Dominik Braun2021-03-12
| | | | * gnu/packages/cran.scm (r-prereg): New variable.
* gnu: Add python-upsetplot.Ricardo Wurmus2021-03-12
| | | | * gnu/packages/python-science.scm (python-upsetplot): New variable.
* gnu: Add python-statannot.Ricardo Wurmus2021-03-12
| | | | * gnu/packages/python-science.scm (python-statannot): New variable.
* gnu: lisp-repl-core-dumper: Update to 0.7.0.Pierre Neidhardt2021-03-12
| | | | * gnu/packages/lisp.scm (lisp-repl-core-dumper): Update to 0.7.0.
* gnu: snakemake: Update to 5.32.2.Ricardo Wurmus2021-03-12
| | | | | * gnu/packages/python-xyz.scm (snakemake): Update to 5.32.2. [arguments]: Adjust patch in call-wrapper-not-wrapped-snakemake.
* gnu: gnome-shell: Fix CVE-2020-17489.Mark H Weaver2021-03-12
| | | | | | * 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.
* gnu: gnome-shell: Update to 3.34.5.Mark H Weaver2021-03-12
| | | | * gnu/packages/gnome.scm (gnome-shell): Update to 3.34.5.
* gnu: gvfs: Update to 1.40.2 [security fixes].Mark H Weaver2021-03-12
| | | | | | | 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.
* gnu: cairo: Fix CVE-2018-19876 and CVE-2020-35492.Mark H Weaver2021-03-12
| | | | | | | | | * 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.
* gnu: gdk-pixbuf: Fix CVE-2020-29385.Mark H Weaver2021-03-12
| | | | | | | | * 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.
* gnu: java-openjfx-graphics: Install native libraries.Ricardo Wurmus2021-03-12
| | | | | | * gnu/packages/java.scm (java-openjfx-graphics)[arguments]: Add phase copy-missing-file and build-native. [native-inputs]: Add missing source file.
* gnu: glib: Fix CVE-2021-28153.Mark H Weaver2021-03-12
| | | | | | * 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.
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