bb5d84a048
gnu: ImageMagick: Fix version number in build configuration of grafted replacement.
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Fixes <https://bugs.gnu.org/47110 >.
This is a followup to commits 852ba914a482e887ba48
2021-03-12 14:41:17 -05:00
a39faf1abd
gnu: OpenSSL: Fix version number in build configuration.
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Fixes <https://bugs.gnu.org/47108 >.
This is a followup to commit 4a8b529ce1
2021-03-12 14:22:21 -05:00
35b3ab8e57
gnu: libtiff: Fix documentation directory name in grafted replacement.
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Fixes <https://bugs.gnu.org/47107 >.
This is a followup to commit 6320700b11
2021-03-12 14:10:31 -05:00
a5a5ec5603
gnu: nushell: Update to 0.28.0.
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* 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.
2021-03-12 16:09:37 +01:00
56613cc619
gnu: Add rust-minus-3.
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* gnu/packages/crates-io.scm (rust-minus-3): New variable.
2021-03-12 16:09:37 +01:00
1fcaac7941
gnu: rust-surf-2: Update to 2.2.0.
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* gnu/packages/crates-io.scm (rust-surf-2): Update to 2.2.0.
2021-03-12 16:09:37 +01:00
7d29bfd567
gnu: rust-http-client-6: Update to 6.3.4.
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* gnu/packages/crates-io.scm (rust-http-client-6): Update to 6.3.4.
2021-03-12 16:09:36 +01:00
10a1ab0d26
gnu: Add rust-async-tls-0.10.
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* gnu/packages/crates-io.scm (rust-async-tls-0.10): New variable.
2021-03-12 16:09:36 +01:00
6fe6ab50bd
gnu: rust-webpki-0.21: Update to 0.21.4.
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* gnu/packages/crates-io.scm (rust-webpki-0.21): Update to 0.21.4.
2021-03-12 16:09:36 +01:00
a7c8060360
gnu: rust-ring-0.16: Update to 0.16.20.
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* gnu/packages/crates-io.scm (rust-ring-0.16): Update to 0.16.20.
[arguments]: Skip tests.
2021-03-12 16:09:35 +01:00
0f0589b8cd
gnu: Add rust-deadpool-0.7.
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* gnu/packages/crates-io.scm (rust-deadpool-0.7): New variable.
2021-03-12 16:09:35 +01:00
b89714b40a
gnu: rust-url-2: Update to 2.2.1.
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* gnu/packages/crates-io.scm (rust-url-2): Update to 2.2.1.
2021-03-12 16:09:09 +01:00
a04aef2430
utils: Use Guile-zlib for gzip compression and decompression.
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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.
2021-03-12 15:59:46 +01:00
97b45977f4
gnu: guile-zlib: Update to 0.1.0.
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* gnu/packages/guile.scm (guile-zlib): Update to 0.1.0.
2021-03-12 15:59:45 +01:00
2e5ac371e7
gnu: Add sbcl-stumpwm-disk.
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* gnu/packages/wm.scm: (sbcl-stumpwm-disk): New variable.
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2021-03-12 15:06:51 +01:00
77ee8af58c
gnu: stumpwm-contrib: Update to 0.0.1-3.a7dc1c.
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* gnu/packages/wm.scm (stumpwm-contrib): Update to 0.0.1-3.a7dc1c.
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2021-03-12 15:06:51 +01:00
a56b331e07
gnu: Add gnuais.
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* gnu/packages/radio.scm (gnuais): New variable.
2021-03-12 15:06:50 +01:00
df6b3c25bb
gnu: r-systempiper: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-systempiper): Move from here...
* gnu/packages/bioconductor.scm (r-systempiper): ...to here.
2021-03-12 14:45:55 +01:00
8957efa8ef
gnu: r-shortread: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-shortread): Move from here...
* gnu/packages/bioconductor.scm (r-shortread): ...to here.
2021-03-12 14:45:54 +01:00
2a97057688
gnu: r-gostats: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-gostats): Move from here...
* gnu/packages/bioconductor.scm (r-gostats): ...to here.
2021-03-12 14:45:54 +01:00
4e7cf96c9f
gnu: r-category: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-category): Move from here...
* gnu/packages/bioconductor.scm (r-category): ...to here.
2021-03-12 14:45:54 +01:00
031fdda47a
gnu: r-gseabase: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-gseabase): Move from here...
* gnu/packages/bioconductor.scm (r-gseabase): ...to here.
2021-03-12 14:45:54 +01:00
f44079bc21
gnu: r-rbgl: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-rbgl): Move from here...
* gnu/packages/bioconductor.scm (r-rbgl): ...to here.
2021-03-12 14:45:54 +01:00
ff92c2873c
gnu: r-annotationforge: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-annotationforge): Move from here...
* gnu/packages/bioconductor.scm (r-annotationforge): ...to here.
2021-03-12 14:45:53 +01:00
d769b10714
gnu: r-dexseq: Move to (gnu packages bioconductor).
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* 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
373545855d
gnu: r-deseq2: Move to (gnu packages bioconductor).
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* 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
a35ea5fed9
gnu: r-genefilter: Move to (gnu packages bioconductor).
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* 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
323aec6ad9
gnu: r-bioassayr: Update home page.
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* gnu/packages/bioconductor.scm (r-bioassayr)[home-page]: Follow permanent
redirect.
2021-03-12 14:41:15 +01:00
2528cad451
gnu: r-bioassayr: Update to 1.28.2.
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* gnu/packages/bioconductor.scm (r-bioassayr): Update to 1.28.2.
2021-03-12 14:41:14 +01:00
8c8d365ca3
gnu: r-chemminer: Update to 3.42.2.
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* gnu/packages/bioconductor.scm (r-chemminer): Update to 3.42.2.
2021-03-12 14:41:14 +01:00
4f617bfb8e
gnu: r-circrnaprofiler: Update to 1.4.2.
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* gnu/packages/bioconductor.scm (r-circrnaprofiler): Update to 1.4.2.
2021-03-12 14:41:14 +01:00
8a8e8198ec
gnu: Add r-puniform.
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* gnu/packages/statistics.scm (r-puniform): New variable.
2021-03-12 14:34:22 +01:00
28df54d776
gnu: Add r-clubsandwich.
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* gnu/packages/statistics.scm (r-clubsandwich): New variable.
2021-03-12 14:34:20 +01:00
3a82f1fba2
gnu: Add r-quantpsyc.
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* gnu/packages/statistics.scm (r-quantpsyc): New variable.
2021-03-12 14:34:19 +01:00
23bfd152c2
gnu: Add r-ez.
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* gnu/packages/cran.scm (r-ez): New variable.
2021-03-12 14:34:18 +01:00
8a51be3cdd
gnu: Add r-prereg.
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* gnu/packages/cran.scm (r-prereg): New variable.
2021-03-12 14:34:14 +01:00
456355c253
gnu: Add python-upsetplot.
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* gnu/packages/python-science.scm (python-upsetplot): New variable.
2021-03-12 13:56:12 +01:00
4d0fdde344
gnu: Add python-statannot.
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* gnu/packages/python-science.scm (python-statannot): New variable.
2021-03-12 13:35:02 +01:00
5fa4814b4f
gnu: lisp-repl-core-dumper: Update to 0.7.0.
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* gnu/packages/lisp.scm (lisp-repl-core-dumper): Update to 0.7.0.
2021-03-12 13:09:36 +01:00
ddc1cddded
gnu: snakemake: Update to 5.32.2.
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* 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
825cc7e0d4
gnu: gnome-shell: Fix CVE-2020-17489.
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* 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
db7c3410d5
gnu: gnome-shell: Update to 3.34.5.
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* gnu/packages/gnome.scm (gnome-shell): Update to 3.34.5.
2021-03-12 06:08:33 -05:00
f5e1909d9f
gnu: gvfs: Update to 1.40.2 [security fixes].
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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
bc16eacc99
gnu: cairo: Fix CVE-2018-19876 and CVE-2020-35492.
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* 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
453e101fc3
gnu: gdk-pixbuf: Fix CVE-2020-29385.
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* 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
57853d69fe
gnu: java-openjfx-graphics: Install native libraries.
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* 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
5a06b83fc9
gnu: glib: Fix CVE-2021-28153.
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* 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
c3a7537396
gnu: certbot, python-acme: Update to 1.13.0.
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* 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
09c05fde52
gnu: git-annex: Update to 8.20210310.
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* 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
df632e3225
gnu: linux-libre 4.4: Update to 4.4.261.
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* 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
Nicolas Goaziou
Ludovic Courtès
Sharlatan Hellseher
Guillaume Le Vaillant
zimoun
Ricardo Wurmus
Lars-Dominik Braun
Pierre Neidhardt
Mark H Weaver
Kyle Meyer