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Author SHA1 Message Date
zimoun d769b10714
gnu: r-dexseq: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-dexseq): Move from here...
* gnu/packages/bioconductor.scm (r-dexseq): ...to here.
 2021-03-12 14:45:53 +01:00
zimoun 373545855d
gnu: r-deseq2: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-deseq2): Move from here...
* gnu/packages/bioconductor.scm (r-deseq2): ...to here.
 2021-03-12 14:45:53 +01:00
zimoun a35ea5fed9
gnu: r-genefilter: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genefilter): Move from here...
* gnu/packages/bioconductor.scm (r-genefilter): ...to here.
 2021-03-12 14:45:53 +01:00
Ricardo Wurmus 323aec6ad9
gnu: r-bioassayr: Update home page. 
* gnu/packages/bioconductor.scm (r-bioassayr)[home-page]: Follow permanent
redirect.
 2021-03-12 14:41:15 +01:00
zimoun 2528cad451
gnu: r-bioassayr: Update to 1.28.2. 
* gnu/packages/bioconductor.scm (r-bioassayr): Update to 1.28.2.
 2021-03-12 14:41:14 +01:00
zimoun 8c8d365ca3
gnu: r-chemminer: Update to 3.42.2. 
* gnu/packages/bioconductor.scm (r-chemminer): Update to 3.42.2.
 2021-03-12 14:41:14 +01:00
zimoun 4f617bfb8e
gnu: r-circrnaprofiler: Update to 1.4.2. 
* gnu/packages/bioconductor.scm (r-circrnaprofiler): Update to 1.4.2.
 2021-03-12 14:41:14 +01:00
Lars-Dominik Braun 8a8e8198ec
gnu: Add r-puniform. 
* gnu/packages/statistics.scm (r-puniform): New variable.
 2021-03-12 14:34:22 +01:00
Lars-Dominik Braun 28df54d776
gnu: Add r-clubsandwich. 
* gnu/packages/statistics.scm (r-clubsandwich): New variable.
 2021-03-12 14:34:20 +01:00
Lars-Dominik Braun 3a82f1fba2
gnu: Add r-quantpsyc. 
* gnu/packages/statistics.scm (r-quantpsyc): New variable.
 2021-03-12 14:34:19 +01:00
Lars-Dominik Braun 23bfd152c2
gnu: Add r-ez. 
* gnu/packages/cran.scm (r-ez): New variable.
 2021-03-12 14:34:18 +01:00
Lars-Dominik Braun 8a51be3cdd
gnu: Add r-prereg. 
* gnu/packages/cran.scm (r-prereg): New variable.
 2021-03-12 14:34:14 +01:00
Ricardo Wurmus 456355c253
gnu: Add python-upsetplot. 
* gnu/packages/python-science.scm (python-upsetplot): New variable.
 2021-03-12 13:56:12 +01:00
Ricardo Wurmus 4d0fdde344
gnu: Add python-statannot. 
* gnu/packages/python-science.scm (python-statannot): New variable.
 2021-03-12 13:35:02 +01:00
Pierre Neidhardt 5fa4814b4f
gnu: lisp-repl-core-dumper: Update to 0.7.0. 
* gnu/packages/lisp.scm (lisp-repl-core-dumper): Update to 0.7.0.
 2021-03-12 13:09:36 +01:00
Ricardo Wurmus ddc1cddded
gnu: snakemake: Update to 5.32.2. 
* gnu/packages/python-xyz.scm (snakemake): Update to 5.32.2.
[arguments]: Adjust patch in call-wrapper-not-wrapped-snakemake.
 2021-03-12 13:03:33 +01:00
Mark H Weaver 825cc7e0d4
gnu: gnome-shell: Fix CVE-2020-17489. 
* 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.
 2021-03-12 06:08:33 -05:00
Mark H Weaver db7c3410d5
gnu: gnome-shell: Update to 3.34.5. 
* gnu/packages/gnome.scm (gnome-shell): Update to 3.34.5.
 2021-03-12 06:08:33 -05:00
Mark H Weaver f5e1909d9f
gnu: gvfs: Update to 1.40.2 [security fixes]. 
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.
 2021-03-12 06:08:33 -05:00
Mark H Weaver bc16eacc99
gnu: cairo: Fix CVE-2018-19876 and CVE-2020-35492. 
* 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.
 2021-03-12 06:08:33 -05:00
Mark H Weaver 453e101fc3
gnu: gdk-pixbuf: Fix CVE-2020-29385. 
* 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.
 2021-03-12 06:08:32 -05:00
Ricardo Wurmus 57853d69fe
gnu: java-openjfx-graphics: Install native libraries. 
* gnu/packages/java.scm (java-openjfx-graphics)[arguments]: Add phase
copy-missing-file and build-native.
[native-inputs]: Add missing source file.
 2021-03-12 10:32:13 +01:00
Mark H Weaver 5a06b83fc9
gnu: glib: Fix CVE-2021-28153. 
* 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.
 2021-03-12 01:44:26 -05:00
Leo Famulari c3a7537396
gnu: certbot, python-acme: Update to 1.13.0. 
* 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.
 2021-03-11 21:41:47 -05:00
Kyle Meyer 09c05fde52
gnu: git-annex: Update to 8.20210310. 
* gnu/packages/haskell-apps.scm (git-annex): Update to 8.20210310.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2021-03-11 18:06:39 -05:00
Leo Famulari df632e3225
gnu: linux-libre 4.4: Update to 4.4.261. 
* gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.261.
(linux-libre-4.4-pristine-source): Update hash.
 2021-03-11 18:06:39 -05:00
Leo Famulari 2c5aff6160
gnu: linux-libre 4.9: Update to 4.9.261. 
* gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.261.
(linux-libre-4.9-pristine-source): Update hash.
 2021-03-11 18:06:39 -05:00
Leo Famulari 0988cbaeab
gnu: linux-libre 4.14: Update to 4.14.225. 
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.225.
(linux-libre-4.14-pristine-source): Update hash.
 2021-03-11 18:06:39 -05:00
Leo Famulari 129db4f104
gnu: linux-libre 4.19: Update to 4.19.180. 
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.180.
(linux-libre-4.19-pristine-source): Update hash.
 2021-03-11 18:06:39 -05:00
Leo Famulari a4905b424e
gnu: linux-libre 5.4: Update to 5.4.105. 
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.105.
(linux-libre-5.4-pristine-source): Update hash.
 2021-03-11 18:06:38 -05:00
Leo Famulari 234aa6c964
gnu: linux-libre 5.10: Update to 5.10.23. 
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.23.
(linux-libre-5.10-pristine-source): Update hash.
 2021-03-11 18:06:38 -05:00
Leo Famulari c39d8a11c0
gnu: linux-libre: Update to 5.11.6. 
* gnu/packages/linux.scm (linux-libre-5.11-version): Update to 5.11.6.
(linux-libre-5.11-pristine-source): Update hash.
 2021-03-11 18:06:38 -05:00
Xinglu Chen 42d5efc001
gnu: guile-curl: Update to 0.9. 
* gnu/packages/curl.scm (guile-curl): Update to 0.9.
[#:phases]: Update path to module.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-03-11 23:22:04 +01:00
zimoun f1c4df15c3
time-machine: Fail when unrecognized option. 
* guix/scripts/time-machine (parse-args): Fail when unrecognized option.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2021-03-11 23:19:53 +01:00
Ludovic Courtès b168acae2a
download: 'tls-wrap' returns an unbuffered custom port. 
Partly fixes <https://bugs.gnu.org/46967>.

* guix/build/download.scm (tls-wrap)[unbuffered]: New procedure.
Pass the result of 'make-custom-binary-input/output-port' to
'unbuffered'.
 2021-03-11 23:19:52 +01:00
Ludovic Courtès 279d932b1c
download: 'tls-wrap' avoids intermediate buffer. 
* guix/build/download.scm (tls-wrap)[read!]: Read straight into BV
instead of calling 'get-bytevector-some' and 'unget-bytevector'.
 2021-03-11 23:19:52 +01:00
Tobias Geerinckx-Rice ebd5000263
gnu: wireshark: Update to 3.4.4. 
* gnu/packages/networking.scm (wireshark): Update to 3.4.4.
 2021-03-11 23:11:58 +01:00
Tobias Geerinckx-Rice d3e2ad740f
gnu: hangups: Update to 0.4.13. 
* gnu/packages/messaging.scm (hangups): Update to 0.4.13.
 2021-03-11 23:11:58 +01:00
Greg Hogan 47093ca4cd
gnu: fmt: Update to 7.1.3. 
* gnu/packages/pretty-print.scm (fmt): Update to 7.1.3.

Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
 2021-03-11 23:11:58 +01:00
Tobias Geerinckx-Rice c518925391
gnu: btrfs-progs: Update to 5.11. 
* gnu/packages/linux.scm (btrfs-progs): Update to 5.11.
 2021-03-11 23:11:58 +01:00
Tobias Geerinckx-Rice 8a9d3e9420
gnu: libdatrie: Update to 0.2.13. 
* gnu/packages/gtk.scm (libdatrie): Update to 0.2.13.
 2021-03-11 23:11:58 +01:00
Tobias Geerinckx-Rice ed6900f974
gnu: libinih: Update to 53. 
* gnu/packages/linux.scm (libinih): Update to 53.
 2021-03-11 23:11:57 +01:00
Léo Le Bouter 0aaac779d4
gnu: flatpak: Update to 1.10.2 [fixes CVE-2021-21381]. 
* gnu/packages/package-management.scm (flatpak): Update to 1.10.2.
 2021-03-11 22:58:05 +01:00
Efraim Flashner aa983626a2
gnu: mongodb: Update comment about package license. 
* 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.
 2021-03-11 23:26:01 +02:00
Efraim Flashner 2f9132e2e0
Revert "Revert "gnu: mongodb: Update to 3.4.24 [security fixes]."" 
This reverts commit feff80cec3.

I was mistaken, there are still branches of mongodb which are still
licensed under the AGPL3
 2021-03-11 23:23:00 +02:00
Pierre Neidhardt 6dda223631
gnu: Add computable-reals. 
* gnu/packages/lisp-xyz.scm (cl-computable-reals, ecl-computable-reals,
sbcl-computable-reals): New variables.
 2021-03-11 21:11:51 +01:00
Raghav Gururajan 340e6dd51b
gnu: Add python-praw. 
* gnu/packages/python-web.scm (python-raw): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-03-11 20:48:05 +02:00
Raghav Gururajan 532fc2fbaf
gnu: Add python-prawcore. 
* gnu/packages/python-web.scm (python-prawcore): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-03-11 20:48:03 +02:00
Raghav Gururajan cfa564bcef
gnu: Add python-testfixtures. 
* gnu/packages/python-check.scm (python-testfixtures): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-03-11 20:48:01 +02:00
Raghav Gururajan ce2637c003
gnu: Add python-betamax-serializers. 
* gnu/packages/python-web.scm (python-betamax-serializers): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-03-11 20:47:55 +02:00