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Author SHA1 Message Date
Ricardo Wurmus
673cc29908
gnu: bamutils: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (bamutils)[arguments]: Use gexp.
 2021-12-03 13:56:01 +01:00
Ricardo Wurmus
361e0d9f27
gnu: bamm: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (bamm)[arguments]: Use gexp instead of
%build-inputs.
 2021-12-03 13:56:01 +01:00
Ricardo Wurmus
4f536c4607
gnu: python2-openpyxl: Explicitly build with Python 2. 
* gnu/packages/python-xyz.scm (python2-openpyxl)[arguments]: Add value
for #:python field.
 2021-12-03 13:56:01 +01:00
Ricardo Wurmus
7fb5bfc54f
gnu: python-plastid: Update to 0.5.1. 
* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.5.1.
 2021-12-03 13:56:01 +01:00
Ricardo Wurmus
b7aaf6c418
gnu: ivar: Disable parallel tests. 
* gnu/packages/bioinformatics.scm (ivar)[arguments]: Disable parallel tests.
 2021-12-03 13:48:41 +01:00
Ricardo Wurmus
aa2d5ca02e
gnu: Remove python2-biom-format. 
There are no users of this variant, and the current version of biom-format
does not support Python 2.

* gnu/packages/bioinformatics.scm (python2-biom-format): Remove variable.
(python-biom-format)[properties]: Remove field.
 2021-12-03 13:31:32 +01:00
Ricardo Wurmus
8fa7de386c
gnu: r-flowclust: Add gsl. 
* gnu/packages/bioconductor.scm (r-flowclust)[inputs]: Remove accidentally
committed comment character.
 2021-12-03 13:31:32 +01:00
Mark H Weaver
3e9dc2754e
gnu: icecat: Remove vestigial icecat-78-makeicecat.patch. 
This is a followup to commit a63231003e.

* gnu/packages/patches/icecat-78-makeicecat.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2021-12-03 04:45:15 -05:00
Mathieu Othacehe
c0d9ba22d0
gnu: cuirass: Update to 1.1.0-6.df8837c. 
* gnu/packages/ci.scm (cuirass): Update to 1.1.0-6.df8837c.
 2021-12-03 10:41:37 +01:00
jgart
fcf7e6513c
gnu: python-pandocfilters: Update to 1.5.0. 
* gnu/packages/textutils.scm (python-pandocfilters): Update to 1.5.0.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-03 10:41:37 +01:00
Mark H Weaver
d49e7a592f
gnu: icecat: Fix CVE-2021-43527. 
* gnu/packages/patches/icecat-CVE-2021-43527.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gnuzilla.scm (icecat-source): Apply it.
 2021-12-03 04:37:42 -05:00
Mark H Weaver
080a5de2ee
gnu: nss: Fix CVE-2021-43527 via graft. 
* gnu/packages/patches/nss-CVE-2021-43527.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/nss.scm (nss/fixed): New variable
(nss)[replacement]: New field.
 2021-12-03 04:37:21 -05:00
Ricardo Wurmus
345b341919
gnu: openjdk16: Use MAKE-FILE-WRITABLE. 
* gnu/packages/java.scm (openjdk16)[arguments]: Do not shell out to "chmod".
 2021-12-02 23:58:56 +01:00
Arne Babenhauserheide
68e71fbb17
gnu: Add openjdk17. 
* gnu/packages/java.scm (openjdk17): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2021-12-02 23:58:53 +01:00
Leo Famulari
f697fc267c
doc: Give more details about generating patches with base commit information. 
* doc/contributing.texi (Submitting Patches): Talk more about '--base'.
 2021-12-02 14:31:13 -05:00
Ricardo Wurmus
1f5c1bc024
gnu: python2-decorator: Downgrade to 4.3.0 
* gnu/packages/python-xyz.scm (python2-decorator): Keep at 4.3.0.
(python-decorator)[properties]: Add python2-variant.
 2021-12-02 18:56:29 +01:00
Ricardo Wurmus
a2423c0ca4
gnu: ribodiff: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Remove trailing #T
from build phase.
 2021-12-02 18:32:33 +01:00
Ricardo Wurmus
1123d25830
gnu: ribodiff: Disable broken test. 
* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Add build phase
'disable-plot-test.
 2021-12-02 18:32:10 +01:00
Ricardo Wurmus
f28f5be11d
gnu: python2-statsmodels: Downgrade to 0.9.0. 
* gnu/packages/statistics.scm (python2-statsmodels): Downgrade to 0.9.0.
 2021-12-02 18:31:38 +01:00
Ricardo Wurmus
31d372cd8a
gnu: khmer: Fix build with Python 3.8. 
* gnu/packages/bioinformatics.scm (khmer)[source]: Remove trailing #T.
[arguments]: Remove trailing #T from build phases; add build phase
'python-3.8-compatibility.
 2021-12-02 18:24:31 +01:00
Ricardo Wurmus
32d5fb01f8
gnu: python-biom-format: Update to 2.1.10. 
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.10.
[source]: Simplify snippet.
[arguments]: Add phase 'relax; remove trailing #T from other build phases.
[propagated-inputs]: Add python-anndata; replace python-pandas-0.25 with
python-pandas.
 2021-12-02 18:02:07 +01:00
jgart
fab80c3672
gnu: Add trayer-srg. 
* gnu/packages/wm.scm (trayer-srg): New variable.

Co-authored-by: Disseminate Dissent <disseminatedissent@protonmail.com>
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-02 15:44:31 +01:00
Ricardo Wurmus
28ad55a59d
gnu: pardre: Update to 2.2.5. 
* gnu/packages/bioinformatics.scm (pardre): Update to 2.2.5.
[arguments]: Remove trailing #T and update comment about tests.
 2021-12-02 15:40:46 +01:00
Ricardo Wurmus
fc20fad6f7
gnu: pardre: Use C++ bindings for MPI. 
* gnu/packages/bioinformatics.scm (pardre)[inputs]: Replace openmpi with
openmpi-c++.
 2021-12-02 15:40:46 +01:00
Ricardo Wurmus
2d6be35ea2
gnu: Add openmpi-c++. 
* gnu/packages/mpi.scm (openmpi-c++): New variable.
 2021-12-02 15:40:45 +01:00
Liliana Marie Prikler
df4f960cb8
gnu: Add libconfini. 
* gnu/packages/cpp.scm (libconfini): New variable.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-02 15:38:17 +01:00
Vinicius Monego
2d92b3bbb6
gnu: shotcut: Update to 21.10.31. 
* gnu/packages/video.scm (shotcut): Update to 21.10.31.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-02 15:29:33 +01:00
Vinicius Monego
82e5a1b4c3
gnu: kdenlive: Update to 21.08.3. 
* gnu/packages/kde.scm (kdenlive): Update to 21.08.3.
[arguments]: Pass "-DBUILD_TESTING=off" to #:configure-flags as tests are
currently disabled.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-02 15:29:33 +01:00
Vinicius Monego
6fc0cfe1b5
gnu: mlt: Update to 7.2.0. 
* gnu/packages/video.scm (mlt): Update to 7.2.0.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-02 15:29:33 +01:00
jgart
e8d5dd5c9b
gnu: ccls: Update to 0.20210330. 
* gnu/packages/cpp.scm (ccls): Update to 0.20210330.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-02 15:26:05 +01:00
Artyom V. Poptsov
a4cc1ae446
gnu: guile-udev: Update to 0.2.0 
* gnu/packages/guile-xyz.scm (guile-udev): Update to 0.2.0.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-12-02 15:05:28 +01:00
Ludovic Courtès
e080e35dc1
gnu: glade: Remove dependency on GJS on non-x86_64. 
* gnu/packages/gnome.scm (glade3)[arguments]: Add optional
'skip-gjs-test' phase.
[native-inputs]: Provide GJS only when 'target-x86-64?'.
 2021-12-02 14:59:57 +01:00
Ludovic Courtès
689d141cd8
gnu: Remove librsvg@2.50 from the Xfce dependency graph. 
This allows us to build Xfce on non-x86_64 platforms.

* gnu/packages/gstreamer.scm (gst-plugins-good)[inputs]: Use
'librsvg-for-system' instead of 'librsvg'.
* gnu/packages/gtk.scm (guile-rsvg)[inputs]: Likewise.
* gnu/packages/xfce.scm (xfce4-xkb-plugin)[inputs]: Likewise.
 2021-12-02 14:59:57 +01:00
Ludovic Courtès
d371abbd0f
gnu: librsvg: Add 'librsvg-for-system' procedure. 
* gnu/packages/gnome.scm (librsvg-for-system): New procedure.
 2021-12-02 14:59:56 +01:00
Ludovic Courtès
8477a6d743
gnu: librsvg: Reintroduce version 2.40. 
* gnu/packages/gnome.scm (librsvg-2.40): New variable.
 2021-12-02 14:59:56 +01:00
Ricardo Wurmus
46b73fd22d
gnu: python-ipython: Update to 7.20.0. 
* gnu/packages/python-xyz.scm (python-ipython): Update to 7.20.0.
 2021-12-02 13:42:17 +01:00
Ricardo Wurmus
5723503f9f
gnu: python-ipython: Remove trailing #T. 
* gnu/packages/python-xyz.scm (python-ipython)[arguments]: Remove trailing #T
from build phases.
 2021-12-02 13:42:17 +01:00
Efraim Flashner
923a121751
gnu: yggdrasil: Simplify build phases. 
* gnu/packages/networking.scm (yggdrasil)[arguments]: Rewrite custom
'build phase reusing go-build-system 'build phase. Remove custom
'install phase.
 2021-12-02 14:28:06 +02:00
Efraim Flashner
d19e646c83
gnu: go-golang-zx2c4-com-wireguard: Fix downloading source. 
* gnu/packages/golang.scm (go-golang-zx2c4-com-wireguard)[source]:
Adjust commit string in git-reference.
 2021-12-02 14:13:27 +02:00
Efraim Flashner
e0755470f8
gnu: go-github-com-vividcortex-ewma: Adjust import-path. 
* gnu/packages/golang.scm (go-github-com-vividcortex-ewma)[arguments]:
Adjust import-path to location other go packages expect it to be.
 2021-12-02 14:12:31 +02:00
Ludovic Courtès
052f56e5a6
gnu: guix: Update to 8cc099b. 
* gnu/packages/package-management.scm (guix): Update to 8cc099b.
 2021-12-02 12:52:59 +01:00
Ricardo Wurmus
a8fff63daa
gnu: Add python-mygene. 
* gnu/packages/bioinformatics.scm (python-mygene): New variable.
 2021-12-02 11:57:28 +01:00
Ricardo Wurmus
b15a525703
gnu: Add python-biothings-client. 
* gnu/packages/bioinformatics.scm (python-biothings-client): New variable.
 2021-12-02 11:57:13 +01:00
Ricardo Wurmus
37c475ebc0
gnu: prinseq: Fix use of SEARCH-INPUT-FILE. 
* gnu/packages/bioinformatics.scm (prinseq)[arguments]: Pass missing argument
to SEARCH-INPUT-FILE.
 2021-12-02 11:26:55 +01:00
Ricardo Wurmus
f1fd313e48
gnu: gnome-shell: Do not wrap in LD_LIBRARY_PATH. 
Fixes <https://bugs.gnu.org/37123>.

* gnu/packages/gnome.scm (gnome-shell)[arguments]: Remove LD_LIBRARY_PATH from
wrapper.
 2021-12-02 10:52:45 +01:00
Ricardo Wurmus
e1cb787870
gnu: python2-matplotlib: Disable sanity-check. 
* gnu/packages/python-xyz.scm (python2-matplotlib)[arguments]: Delete
'sanity-check phase.
 2021-12-02 10:30:40 +01:00
Ricardo Wurmus
a33ca53492
gnu: python2-matplotlib: Remove trailing #T. 
* gnu/packages/python-xyz.scm (python2-matplotlib)[arguments]: Remove
trailing #T from build phase.
 2021-12-02 10:29:59 +01:00
Efraim Flashner
c14ab97a03
Revert "gnu: Change source file-name suffix in rust packages." 
This reverts commit 07a80e30a1.

This commit affects rust crates that are inputs to librsvg, which causes
many packages to be rebuilt.
 2021-12-02 11:10:37 +02:00
Efraim Flashner
e577889828
gnu: tor: Limit test suite adjustments to affected architectures. 
This is a follow-up to 68d090002a.

* gnu/packages/tor.scm (tor)[arguments]: Only add custom
'adjust-test-suite phase on aarch64, powerpc32.
 2021-12-02 11:07:18 +02:00
Ricardo Wurmus
c2c63a00de
gnu: Add r-scdblfinder. 
* gnu/packages/bioconductor.scm (r-scdblfinder): New variable.
 2021-12-02 10:03:07 +01:00