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Author SHA1 Message Date
Efraim Flashner
1e81140cb5
gnu: python-dendropy: Skip additional test. 
* gnu/packages/bioinformatics.scm (python-dendropy)[arguments]: Adjust
custom 'skip-broken-tests phase to skip additional test.
 2021-12-09 22:43:42 +02:00
Ricardo Wurmus
13bc332ed5
gnu: mumi: Update to 0.0.1-6.8a45281. 
* gnu/packages/mail.scm (mumi): Update to 0.0.1-6.8a45281.
[arguments]: Remove trailing #T.
 2021-12-09 19:17:22 +01:00
Ricardo Wurmus
0e8826824c
gnu: python-rich: Remove optional input ipywidgets. 
* gnu/packages/python-xyz.scm (python-rich)[propagated-inputs]: Remove
python-ipywidgets.
 2021-12-09 19:17:21 +01:00
Ricardo Wurmus
4709decb45
gnu: r-minimal: Remove extraneous references. 
* gnu/packages/statistics.scm (r-minimal)[arguments]: Remove references to
native build-time tools.
 2021-12-09 19:17:16 +01:00
Marius Bakke
d974b3f860
gnu: uBlock Origin: Update to 1.39.2. 
* gnu/packages/browser-extensions.scm (ublock-origin): Update to 1.39.2.
 2021-12-09 17:39:29 +01:00
Marius Bakke
4cb5f0daf2
gnu: ungoogled-chromium: Update to 96.0.4664.93-1. 
* gnu/packages/chromium.scm (%chromium-version): Set to 96.0.4664.93.
(%ungoogled-origin, ungoogled-chromium): Update hashes.
 2021-12-09 17:39:29 +01:00
Efraim Flashner
f0cc0e8f30
gnu: imp: Build with default cmake. 
* gnu/packages/bioinformatics.scm (imp)[arguments]: Remove cmake flag.
 2021-12-09 14:39:22 +02:00
Ricardo Wurmus
2648d3207f
gnu: repeat-masker: Update to 4.1.2-p1. 
* gnu/packages/bioinformatics.scm (repeat-masker): Update to 4.1.2-p1.
 2021-12-09 12:10:18 +01:00
Ricardo Wurmus
0bf3c9abaa
gnu: metabat: Update to 2.15. 
* gnu/packages/bioinformatics.scm (metabat): Update to 2.15.
[source]: Remove patch.
[build-system]: Use cmake-build-system.
[arguments]: Adjust to new build system.
* gnu/packages/patches/metabat-fix-compilation.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2021-12-09 11:50:10 +01:00
Ricardo Wurmus
ab445eb4b7
gnu: python2-scikit-learn: Disable one more test. 
* gnu/packages/machine-learning.scm (python2-scikit-learn)[arguments]: Do not
inherit; remove obsolete 'make-files-writable phase; disable one more failing
test in 'check phase.
 2021-12-09 11:17:45 +01:00
Ricardo Wurmus
1c7914009a
gnu: seek: Update to 1-1.196ed4c. 
* gnu/packages/bioinformatics.scm (seek): Update to 1-1.196ed4c.
[source]: Fetch from github.
[build-system]: Use cmake-build-system.
[arguments]: Remove all custom phases; replace 'check phase; disable tests;
set configure flags.
[inputs]: Add apache-thrift:include, apache-thrift:lib, and python.
[native-inputs]: Remove autoconf, automake, and perl; add pkg-config.
 2021-12-09 11:17:45 +01:00
Ricardo Wurmus
4fb363c906
gnu: libsvm: Install header and library. 
* gnu/packages/machine-learning.scm (libsvm)[arguments]: Add build phase
'build-lib; also install header file and shared library in the 'install phase.
 2021-12-09 11:17:45 +01:00
Ricardo Wurmus
26e26bc819
gnu: miso: Update to 0.5.4-1.b714021. 
* gnu/packages/bioinformatics.scm (miso): Update to 0.5.4-1.b714021.
[source]: Fetch via git; simplify snippet.
[inputs]: Replace samtools with samtools-1.2.
[home-page]: Update to new location.
 2021-12-09 11:17:45 +01:00
Ricardo Wurmus
0b8a75cc3a
gnu: Add samtools-1.2. 
* gnu/packages/bioinformatics.scm (samtools-1.2): New variable.
 2021-12-09 11:17:45 +01:00
Ricardo Wurmus
f505f588a7
gnu: Add htslib-for-samtools-1.2. 
* gnu/packages/bioinformatics.scm (htslib-for-samtools-1.2): New variable.
 2021-12-09 11:17:45 +01:00
Ricardo Wurmus
3ebcd637a5
gnu: python2-scipy: Override native inputs. 
* gnu/packages/python-science.scm (python2-scipy)[native-inputs]: Override;
replace gfortran with gfortran-7; add gcc-7.
 2021-12-09 11:17:45 +01:00
Ricardo Wurmus
3cd37c94bd
gnu: python2-matplotlib: Fix mpl_toolkits module. 
* gnu/packages/python-xyz.scm (python2-matplotlib)[arguments]: Add phase
'create-init-file; restore 'sanity-check phase.
 2021-12-09 11:17:45 +01:00
Ricardo Wurmus
b69156ef30
gnu: Add gfortran-7. 
* gnu/packages/gcc.scm (gfortran-7): New variable.
 2021-12-09 11:17:45 +01:00
jgart via Guix-patches via
bfaf6c1801
gnu: emacs-evil-magit: Remove deprecated package. 
* gnu/packages/emacs-xyz.scm (emacs-evil-magit): Delete variable.

evil-magit has been consolidated into evil-collection. The package has been
removed from MELPA since February. See here:
<https://github.com/emacs-evil/evil-magit>.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-09 09:17:35 +01:00
Andrew Tropin
1490e02ea2
gnu: Add emacs-dpd. 
* gnu/packages/emacs-xyz.scm (emacs-dpd): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-09 09:13:33 +01:00
Petr Hodina
479742f195
gnu: valeronoi: Update to 0.1.6. 
* gnu/packages/engineering.scm (valeronoi): Update to 0.1.6.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2021-12-09 09:07:24 +01:00
terramorpha
38ea869b20
gnu: tiramisu: Update to 2.0.20211107. 
* gnu/packages/gnome-xyz.scm (tiramisu): Update to 2.0.20211107.
[native-inputs]: Add vala.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2021-12-08 23:10:25 -05:00
Leo Famulari
37186ec462
gnu: isc-dhcp: Update bundled BIND to 9.11.36 [fixes CVE-2021-25219]. 
* gnu/packages/admin.scm (isc-dhcp)[inputs]:
Update bundled BIND to 9.11.36.

Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
 2021-12-09 01:24:37 +01:00
Tobias Geerinckx-Rice
4ca0e9d5f7
gnu: bind: Update to 9.16.23 [fixes CVE-2021-25218, CVE-2021-25219]. 
* gnu/packages/dns.scm (isc-bind): Update to 9.16.23.
[source]: Add patch.
* gnu/packages/patches/bind-re-add-attr-constructor-priority.patch:
New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2021-12-09 01:24:37 +01:00
Tobias Geerinckx-Rice
e5e307b676
Revert "installer: Make LUKS2 the default format for encrypted devices" 
This reverts commit a82e9f45fd at the
author's request.  We are not quite ready to boot all resulting
systems.

See <https://logs.guix.gnu.org/guix/2021-12-08.log#231815>.
 2021-12-08 23:23:19 +01:00
Ludovic Courtès
95a4965f2d
gnu: python-slepc4py: Update to 3.16.1. 
This is a followup 5b4d1e57b6.

* gnu/packages/maths.scm (slepc-openmpi)[inputs]: Move ARPACK-NG-OPENMPI to...
[propagated-inputs]: ... here.
(python-slepc4py): Update to 3.16.1.
 2021-12-08 23:04:00 +01:00
Ludovic Courtès
fe55ae488b
gnu: python-petsc4py: Update to 3.16.1. 
This is a followup to 07ac13a26a.

* gnu/packages/maths.scm (python-petsc4py): Update to 3.16.1.
 2021-12-08 22:59:44 +01:00
Ludovic Courtès
3b8825421b
gnu: geeqie: Fix X11 error at startup. 
Fixes <https://issues.guix.gnu.org/52089>.
Reported by Maxim Cournoyer <maxim.cournoyer@gmail.com>.
Patch provided by John Kehayias <john.kehayias@protonmail.com>.

* gnu/packages/patches/geeqie-clutter.patch: New file.
* gnu/packages/image-viewers.scm (geeqie)[sources]: Use it.
* gnu/local.mk (dist_patch_DATA): Add it.
 2021-12-08 22:35:03 +01:00
Tobias Geerinckx-Rice
f3af1fb0bc
bash completion: Complete ‘guix shell -f’. 
* etc/completion/bash/guix (_guix_complete): Suggest a file name
following ‘guix shell […] -f’.
 2021-12-08 21:09:55 +01:00
Petr Hodina
0ba4e94e84
gnu: Add realmd. 
* gnu/packages/admin.scm (realmd): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2021-12-08 14:26:39 -05:00
Sarah Morgensen
8ac2d303e4
gnu: go-github-com-alcortesm-tgz: Don't reset gzip timestamps. 
The tgz files are committed test fixtures, so don't reset their timestamps.

* gnu/packages/golang.scm (go-github-com-alcortesm-tgz)[arguments]:
Remove 'make-git-checkout-writable' phase.  Delete 'reset-gzip-timestamps' phase
instead.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2021-12-08 13:35:34 -05:00
Sarah Morgensen
93c7a5103d
gnu: Remove go-gopkg.in-check.v1. 
This package is a duplicate of go-gopkg-in-check-v1 in golang.scm,
has no binaries, and has no dependents, so remove it.

* gnu/packages/check.scm (go-gopkg.in-check.v1): Remove variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2021-12-08 13:35:34 -05:00
Ludovic Courtès
77c8382bb6
gnu: mumps: Allow compilation with GCC 10. 
Following the suggestion at
<https://community.freefem.org/t/compline-on-macos-10-15-6/543>.

* gnu/packages/maths.scm (mumps)[arguments]: In 'configure' phase, add
'-fallow-argument-mismatch' to 'OPTF'.
 2021-12-08 18:56:53 +01:00
Ludovic Courtès
3867cb7885
maint: Don't require unsupported packages such as GNOME on i686-linux. 
* etc/release-manifest.scm (%system-manifest): Filter out PACKAGE when
it doesn't pass 'supported-package?'.
 2021-12-08 18:56:52 +01:00
Ludovic Courtès
49599fab56
services: %desktop-services: Use SDDM rather than GDM on non-x86_64. 
This works around the fact that Rust is currently unavailable in Guix on
platforms other than x86_64-linux:

  https://lists.gnu.org/archive/html/guix-devel/2021-11/msg00197.html

* gnu/services/desktop.scm (desktop-services-for-system): New
procedure.
(%desktop-services): Turn into a macro.
 2021-12-08 18:56:52 +01:00
Ludovic Courtès
24ead149db
system: Mark 'services' field as thunked. 
This allows us to make services dependent on (%current-system), for
example.

* gnu/system.scm (<operating-system>)[services]: Mark as thunked.
 2021-12-08 18:56:47 +01:00
Ludovic Courtès
20e6446a68
gnu: idutils: Fix build with glibc 2.33. 
* gnu/packages/idutils.scm (idutils)[source]: Remove reference to 'gets'
from "lib/stdio.in.h".
 2021-12-08 18:55:58 +01:00
Tobias Geerinckx-Rice
9bac41c2b8
gnu: fzf: Wrap with a compliant find(1). 
* gnu/packages/terminals.scm (fzf)[inputs]: Add findutils.
[arguments]: Wrap the ‘fzf’ executable with its /bin directory in $PATH.

Addresses <https://issues.guix.gnu.org/52372>.
 2021-12-08 18:13:48 +01:00
Efraim Flashner
a59abcb350
gnu: libtorrent-rasterbar: Build with default cmake. 
* gnu/packages/bittorrent.scm (libtorrent-rasterbar)[arguments]: Remove
cmake flag.
 2021-12-08 17:36:35 +02:00
Ricardo Wurmus
00ae87c41a
gnu: tadbit: Update to 1.0.1-1.5c4c1dd. 
* gnu/packages/bioinformatics.scm (tadbit): Update to 1.0.1-1.5c4c1dd.
[arguments]: Remove trailing #T from build phases; pass -fcommon to test
binaries; run tests conditionally.
 2021-12-08 16:32:37 +01:00
Ricardo Wurmus
7f4d25f86e
gnu: python2-sphinx: Remove websupport test. 
* gnu/packages/sphinx.scm (python2-sphinx)[arguments]: Remove websupport test
file.
 2021-12-08 16:13:08 +01:00
Ricardo Wurmus
68619cad28
gnu: python2-sphinxcontrib-websupport: Downgrade to 1.1.2. 
* gnu/packages/sphinx.scm (python2-sphinxcontrib-websupport): Downgrade to
1.1.2.
[arguments]: Override; delete 'sanity-check phase.
[propagated-inputs]: Override and add python2-six.
(python-sphinxcontrib-websupport)[properties]: Record python2-variant.
 2021-12-08 16:13:08 +01:00
Ricardo Wurmus
a4a7c78f68
gnu: python2-jinja2: Downgrade to 2.11.3 
* gnu/packages/python-xyz.scm (python2-jinja2): Downgrade to the last version
supporting Python 2.
(python-jinja2)[properties]: Record python2-variant.
 2021-12-08 16:13:08 +01:00
Tobias Geerinckx-Rice
852ad65bd4
gnu: fastboot: Fix ‘--version’ output. 
* gnu/packages/android.scm (fastboot)[arguments]: Replace broken
‘git rev-parse’ shell command with the actual package VERSION.

Reported by kwjc on #guix.
 2021-12-08 15:42:33 +01:00
Zhu Zihao
5573d98f81
gnu: rtl8821ce-linux-module: Update to 0.0.0-4-ca204c6. 
Fixes compatibility with linux-libre@5.15:

  […]/source/core/rtw_br_ext.c:20:11: fatal error: net/ipx.h:
  No such file or directory
    #include <net/ipx.h>
             ^~~~~~~~~~~
  compilation terminated.

* gnu/packages/linux.scm (rtl8821ce-linux-module):
Update to 0.0.0-4-ca204c6.

Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
 2021-12-08 15:42:33 +01:00
Ricardo Wurmus
14ed9b049e
gnu: python2-markupsafe: Downgrade to 1.1.1. 
* gnu/packages/python-xyz.scm (python2-markupsafe): Downgrade to 1.1.1,
because that's the last version to support Python 2.
 2021-12-08 14:43:38 +01:00
Ricardo Wurmus
c8060055de
gnu: ocaml-mcl: Add -fcommon to compiler flags. 
* gnu/packages/machine-learning.scm (ocaml-mcl)[arguments]: Add -fcommon.
 2021-12-08 14:31:54 +01:00
Ricardo Wurmus
b835d10d61
gnu: paml: Pass -fcommon to compiler. 
* gnu/packages/bioinformatics.scm (paml)[arguments]: Set CFLAGS.
 2021-12-08 14:31:54 +01:00
Ricardo Wurmus
2157d82ed3
gnu: paml: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (paml)[arguments]: Remove trailing #T from
build phases.
 2021-12-08 14:31:54 +01:00
Ricardo Wurmus
76b39f03d2
gnu: sambamba: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (sambamba)[arguments]: Remove trailing #T
from build phases.
 2021-12-08 14:31:54 +01:00