3f03f502ee
gnu: libgda: Do not use the bundled sqlite.
...
* gnu/packages/gnome.scm (libgda)[source]: Add snippet.
[arguments]: Pass "--enable-system-sqlite".
[inputs]: Add SQLITE.
2021-12-04 22:39:46 +01:00
634b46a469
gnu: java-commons-math3: Remove references to %build-inputs.
...
* gnu/packages/java.scm (java-commons-math3)[arguments]: Use a gexp
to remove references to %build-inputs.
2021-12-04 22:07:26 +01:00
ba5cb6456d
gnu: java-commons-collections4: Remove references to %build-inputs.
...
* gnu/packages/java.scm (java-commons-collections4)[arguments]: Use a gexp
to remove references to %build-inputs.
2021-12-04 22:07:17 +01:00
035fec27fc
gnu: java-commons-exec-1.1: Remove references to %build-inputs.
...
* gnu/packages/java.scm (java-commons-exec-1.1)[arguments]: Use a gexp
to remove references to %build-inputs.
2021-12-04 22:07:11 +01:00
5a4ad372ef
gnu: java-commons-exec: Remove references to %build-inputs.
...
* gnu/packages/java.scm (java-commons-exec)[arguments]: Use a gexp to
remove references to %build-inputs.
2021-12-04 22:06:49 +01:00
2aee138485
gnu: maven-components-parent-pom-22: Remove references to %build-inputs.
...
* gnu/packages/maven-parent-pom.scm (maven-components-parent-pom-22)
[arguments]: Use a gexp to remove references to %build-inputs.
2021-12-04 22:06:41 +01:00
d29f14aca2
gnu: java-sonatype-oss-parent-pom-9: Remove references to %build-inputs.
...
* gnu/packages/maven-parent-pom.scm (java-sonatype-oss-parent-pom-9)
[arguments]: Use a gexp to remove references to %build-inputs.
2021-12-04 22:06:23 +01:00
f044ffc1c4
gnu: ocaml4.07-ppx-let: Make 'properties' an alist.
...
The incorrect 'properties' value was introduced in
3649c56a5f
2021-12-04 21:57:27 +01:00
98d2abe523
gnu: sailfish: Remove references to %build-inputs.
...
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use a gexp to remove
references to %build-inputs.
2021-12-04 19:54:28 +01:00
39e2a84f52
gnu: sailfish: Simplify snippet.
...
* gnu/packages/bioinformatics.scm (sailfish)[source]: Remove trailing #T from
snippet.
2021-12-04 19:54:28 +01:00
b0fd09f856
gnu: piranha: Remove references to %build-inputs.
...
* gnu/packages/bioinformatics.scm (piranha)[arguments]: Use gexp to remove
references to %build-inputs.
2021-12-04 19:54:28 +01:00
01d2e2b334
gnu: piranha: Remove trailing #T.
...
* gnu/packages/bioinformatics.scm (piranha)[arguments]: Remove trailing #T
from build phases.
2021-12-04 19:54:28 +01:00
502538c6e4
gnu: emboss: Remove reference to %build-inputs.
...
* gnu/packages/bioinformatics.scm (emboss)[arguments]: Use gexp to remove
reference to %build-inputs.
2021-12-04 19:54:28 +01:00
2657bdc100
gnu: vcftools: Replace references to %outputs.
...
* gnu/packages/bioinformatics.scm (vcftools)[arguments]: Use gexp to remove
references to %outputs.
2021-12-04 19:54:28 +01:00
eec1bdcd9e
gnu: seqan-1: Use gexp for builder.
...
* gnu/packages/bioinformatics.scm (seqan-1)[arguments]: Use a gexp to remove
references to %build-inputs and %outputs.
2021-12-04 19:54:28 +01:00
2c1c75a56c
gnu: seqan-2: Use gexp for builder.
...
* gnu/packages/bioinformatics.scm (seqan-2)[arguments]: Use a gexp to remove
references to %build-inputs and %outputs.
2021-12-04 19:54:28 +01:00
f41576c09f
gnu: sra-tools: Remove references to %build-inputs.
...
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use a gexp instead
of referencing %build-inputs.
2021-12-04 19:54:27 +01:00
f33e490334
gnu: preseq: Remove references to %outputs and %build-inputs.
...
* gnu/packages/bioinformatics.scm (preseq)[arguments]: Replace references to
%outputs and %build-inputs by using a gexp.
2021-12-04 19:54:27 +01:00
8a446f5e41
gnu: preseq: Simplify snippet.
...
* gnu/packages/bioinformatics.scm (preseq)[source]: Simplify snippet.
2021-12-04 19:54:27 +01:00
bd746917a2
gnu: julia-forwarddiff: Disable tests on i686-linux.
...
* gnu/packages/julia-xyz.scm (julia-forwarddiff)[arguments]<#:tests?>:
Conditionally disable tests.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:33 +02:00
82586916be
gnu: julia-geometrybasics: Fix tests on i686-linux.
...
* gnu/packages/julia-xyz (julia-geometrybasics)[arguments]<#:phases>:
Conditionally replace the incorrect type in test suite.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:33 +02:00
eb4f1fcf74
gnu: julia-structarrays: Fix tests on i686-linux.
...
* gnu/packages/julia-xyz.scm (julia-structarrays)[arguments]<#:phases>:
Conditionally replace the incorrect type in the test suite.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:32 +02:00
afd35e8e9c
gnu: julia-mutablearithmetics: Fix tests on i686-linux.
...
* gnu/packages/julia-xyz.scm (julia-mutablearithmetics)[arguments]<#:phases>:
Conditionally disable the failing test.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:32 +02:00
630824a238
gnu: julia-woodburymatrices: Fix tests on i686-linux.
...
* gnu/packages/julia-xyz.scm (julia-woodburymatrices)[arguments]<#:phases>:
Conditionally disable the failing test.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:32 +02:00
828012ed9f
gnu: julia-intervalsets: Fix tests on i686-linux.
...
* gnu/packages/julia-xyz.scm (julia-intervalsets)[arguments]<#:phases>:
Conditionally disable the failing test.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:32 +02:00
29c0410086
gnu: julia-reversediff: Disable tests on i686-linux.
...
* gnu/packages/julia-xyz (julia-reversediff)[arguments]<#:tests?>:
Conditionally disable tests.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:31 +02:00
28d530ea44
gnu: julia-interpolations: Disable tests in i686-linux.
...
* gnu/packages/julia-xyz.scm (julia-interpolations)[arguments]<#:tests?>:
Conditionally disable tests.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:31 +02:00
e3c15b0bfc
gnu: julia-arrayinterface: Disable tests for i686.
...
* gnu/packages/julia-xyz.scm (julia-arrayinterface)[arguments]<#:tests?>:
Conditionally disable tests.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:31 +02:00
7c8e9cbfa9
gnu: julia-mappedarrays: Fix tests on i686-linux.
...
* gnu/packages/julia-xyz.scm (julia-mappedarrays)[arguments]<#:phases>:
Conditionally replace the incorrect type in test suite.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:30 +02:00
dcd7c950c6
gnu: julia-blockarrays: Fix tests on i686-linux.
...
* gnu/packages/julia-xyz.scm (julia-blockarrays)[arguments]<#:phases>:
Conditionally replace the incorrect type in test suite.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:30 +02:00
557caa4e2c
gnu: julia-lazyarrays: Fix tests on i686-linux.
...
* gnu/packages/julia-xyz.scm (julia-lazyarrays)[arguments]<#:phases>:
Conditionally replace the incorrect type in test suite.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:30 +02:00
dbad333481
gnu: julia-configurations: Fix tests on i686-linux.
...
* gnu/packages/julia-xyz.scm (julia-configurations)[arguments]<#:phases>:
Conditionally replace the incorrect type in test suite.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:30 +02:00
a31a4517b6
gnu: julia-finitedifferences: Fix tests on i686-linux.
...
* gnu/packages/julia-xyz (julia-finitedifferences)[arguments]<#:phases>:
Conditionnally disable the failing test.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:29 +02:00
2a749f34e5
gnu: julia-benchmarktools: Fix tests on i686-linux.
...
* gnu/packages/julia-xyz.scm (julia-benchmarktools)[arguments]<#:phases>:
Conditionnally disable the failing tests.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:29 +02:00
7fee8a46fb
gnu: julia-datastructures: Fix tests on i686-linux.
...
* gnu/packages/julia-xyz.scm (julia-datastructures)[arguments]<#:phases>:
Conditionnally disable the failing test.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:29 +02:00
9112bed608
gnu: libunwind-julia: Fix build on i686-linux.
...
* gnu/packages/julia.scm (libunwind)[origin]<patches>: Add patch.
* gnu/packages/patches/libunwind-julia-fix-GCC10-fno-common.patch: New file.
* gnu/local/mk (dist_patch_DATA): Register it.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:33:30 +02:00
f199427c1b
gnu: emacs-org-roam-bibtex: Update to 0.6.1.
...
* gnu/packages/emacs-xyz.scm (emacs-org-roam-bibtex): Update to 0.6.1.
2021-12-04 16:17:58 +01:00
cc491eab7e
gnu: plink-ng: Enable tests.
...
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Replace 'check phase
to run tests; do not disable tests via arguments.
[native-inputs]: Add diffutils, plink, and python.
2021-12-04 16:00:08 +01:00
e28b8a9cea
gnu: plink-ng: Replace reference to %outputs.
...
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Remove reference to
%outputs by using a gexp.
2021-12-04 15:35:28 +01:00
88bb81b515
gnu: plink: Remove reference to %build-inputs.
...
* gnu/packages/bioinformatics.scm (plink)[arguments]: Use a gexp to replace
reference to %build-inputs.
2021-12-04 15:31:31 +01:00
e920101141
gnu: plink: Remove trailing #T.
...
* gnu/packages/bioinformatics.scm (plink)[arguments]: Remove trailing #T from
build phase.
2021-12-04 15:31:08 +01:00
a4e7475edc
gnu: rsem: Update to 1.3.3.
...
* gnu/packages/bioinformatics.scm (rsem): Update to 1.3.3.
[arguments]: Build with gnu++11 standard; patch sources for compatibility.
2021-12-04 15:27:39 +01:00
c45c909026
gnu: rsem: Remove trailing #T.
...
* gnu/packages/bioinformatics.scm (rsem)[arguments]: Remove trailing #T from
build phases.
2021-12-04 15:26:48 +01:00
5e0bcba57b
gnu: rsem: Remove references to %build-inputs.
...
* gnu/packages/bioinformatics.scm (rsem)[arguments]: Use a gexp.
2021-12-04 15:26:01 +01:00
23975fe27a
gnu: rsem: Remove trailing #T from snippet.
...
* gnu/packages/bioinformatics.scm (rsem)[source]: Remove trailing #T.
2021-12-04 15:25:26 +01:00
cfaf37d10b
gnu: prodigal: Remove reference to %outputs.
...
* gnu/packages/bioinformatics.scm (prodigal)[arguments]: Remove reference to
%outputs by using a gexp.
2021-12-04 15:13:11 +01:00
09ae51f7b8
gnu: prank: Bind INPUTS in 'install phase.
...
* gnu/packages/bioinformatics.scm (prank)[arguments]: Bind INPUTS in 'install
phase to remove references to %build-inputs.
2021-12-04 15:11:28 +01:00
e128839a94
gnu: prank: Remove trailing #T.
...
* gnu/packages/bioinformatics.scm (prank)[arguments]: Remove trailing #T from
build phases.
2021-12-04 15:11:04 +01:00
da70132ee9
gnu: janet: Update to 1.19.0.
...
* gnu/packages/lisp.scm (janet): Update to 1.19.0.
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2021-12-04 13:51:49 +01:00
612fe425b4
gnu: tinmop: Update to 0.9.2.
...
* gnu/packages/web-browsers.scm (tinmop): Update to 0.9.2.
[inputs]: Move nano, openssl and xdg-utils to...
[native-inputs]: ... here. Add automake, autoconf and mandoc. Remove curl
and gnupg.
[arguments]: Add 'fix-configure.ac' phase.
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2021-12-04 13:44:17 +01:00
18a85213ae
gnu: pigx-sars-cov2-ww: Update to 0.0.4.
...
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.4.
[inputs]: Add bbmap, bedtools, fastp, ivar, and r-r-utils.
2021-12-04 12:42:51 +01:00
114eb987cb
gnu: mash: Replace references to %build-inputs.
...
* gnu/packages/bioinformatics.scm (mash)[arguments]: Use a gexp.
2021-12-04 00:32:01 +01:00
22d9097b5e
gnu: mash: Move htslib and capnproto to regular inputs.
...
* gnu/packages/bioinformatics.scm (mash)[native-inputs]: Move htslib and
capnproto from here...
[inputs]: ...to here.
2021-12-04 00:31:20 +01:00
a6b6084649
gnu: mash: Simplify snippet.
...
* gnu/packages/bioinformatics.scm (mash)[snippet]: Simplify.
2021-12-04 00:30:44 +01:00
31409a4af7
gnu: mafft: Remove trailing #T.
...
* gnu/packages/bioinformatics.scm (mafft)[arguments]: Remove trailing #T from
build phase.
2021-12-04 00:22:27 +01:00
630671d2e8
gnu: mafft: Replace references to %build-inputs and %outputs.
...
* gnu/packages/bioinformatics.scm (mafft)[arguments]: Replace references to
%outputs with a gexp; replace reference to %build-inputs in the 'wrap-programs
phase by binding INPUTS.
2021-12-04 00:21:27 +01:00
5cb2920b8d
gnu: jellyfish: Replace reference to %outputs.
...
* gnu/packages/bioinformatics.scm (jellyfish)[arguments]: Use a gexp.
2021-12-04 00:19:08 +01:00
7c2ee27360
gnu: fastp: Replace reference to %outputs.
...
* gnu/packages/bioinformatics.scm (fastp)[arguments]: Use a gexp.
2021-12-04 00:16:10 +01:00
64aafe4bc5
gnu: java-picard: Replace reference to %build-inputs.
...
* gnu/packages/bioinformatics.scm (java-picard): Use a gexp.
2021-12-04 00:06:43 +01:00
a3b00a21c0
gnu: java-htsjdk: Replace reference to %outputs.
...
* gnu/packages/bioinformatics.scm (java-htsjdk)[arguments]: Use a gexp.
2021-12-04 00:03:54 +01:00
62e0641892
gnu: fxtract: Replace reference to %outputs.
...
* gnu/packages/bioinformatics.scm (fxtract)[arguments]: Use a gexp.
2021-12-04 00:02:20 +01:00
4f03151ca4
gnu: delly: Replace reference to %outputs.
...
* gnu/packages/bioinformatics.scm (delly)[arguments]: Replace reference to
%outputs with a gexp.
2021-12-04 00:00:26 +01:00
3601fcbf65
gnu: libbigwig: Replace reference to %outputs.
...
* gnu/packages/bioinformatics.scm (libbigwig)[arguments]: Replace reference to
%outputs with a gexp.
2021-12-03 23:57:24 +01:00
fd607a9efa
gnu: cd-hit: Replace reference to %outputs.
...
* gnu/packages/bioinformatics.scm (cd-hit)[arguments]: Replace reference to
%outputs with gexp.
2021-12-03 23:56:11 +01:00
c40852a227
gnu: bowtie1: Replace reference to %outputs.
...
* gnu/packages/bioinformatics.scm (bowtie1)[arguments]: Remove reference to
%outputs by using a gexp.
2021-12-03 23:54:10 +01:00
a47a90b900
gnu: bowtie: Remove reference to %outputs.
...
* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Replace reference to
%outputs with a gexp.
2021-12-03 23:52:43 +01:00
f5c38ee45f
gnu: bless: Remove reference to %build-inputs.
...
* gnu/packages/bioinformatics.scm (bless)[arguments]: Replace reference to
%build-inputs with a gexp. Use the dynamic library of zlib while we're at it.
[inputs]: Remove zlib:static.
2021-12-03 23:51:16 +01:00
dd19c8da88
gnu: bless: Remove trailing #T from snippet and build phases.
...
* gnu/packages/bioinformatics.scm (bless)[source, arguments]: Remove all
trailing #Ts.
2021-12-03 23:48:46 +01:00
0e09065460
gnu: bedtools: Remove reference to %outputs.
...
* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use a gexp instead of
referencing %outputs.
2021-12-03 23:36:18 +01:00
a5663a7c8a
gnu: qtltools: Replace references to %build-inputs.
...
* gnu/packages/bioinformatics.scm (qtltools)[arguments]: Use a gexp instead of
referencing %build-inputs.
2021-12-03 23:26:48 +01:00
ce9bfcddb5
gnu: imp: Update to 2.15.0.
...
* gnu/packages/bioinformatics.scm (imp): Update to 2.15.0.
[arguments]: Disable one more test.
2021-12-03 22:29:52 +01:00
dcf857e486
gnu: Add r-fpeek.
...
* gnu/packages/cran.scm (r-fpeek): New variable.
2021-12-03 22:29:40 +01:00
15404ff19b
gnu: emacs: Load package descriptors from packages referenced by subdirs.el
...
* gnu/packages/aux-files/emacs/guix-emacs.el
(guix-emacs--non-core-load-path): New procedure.
(guix-emacs-autoload-packages): Use it here.
(guix-emacs-load-package-descriptors): New procedure.
* gnu/packages/emacs.scm (emacs)[install-site-start]: Install advice to run
‘guix-emacs-load-package-descriptors’.
2021-12-03 21:39:50 +01:00
4baeb72717
gnu: emacs: Make DocView PDF work out of the box.
...
* gnu/packages/emacs.scm (emacs)[patch-program-file-names]: Add patches for
the programs “gs”, “dvipdf”, “ps2pdf” and “pdftotext”.
[inputs]: Add ghostscript and poppler.
2021-12-03 21:39:49 +01:00
f725279cdd
gnu: emacs: Find real GVFS processes.
...
* gnu/packages/emacs.scm (emacs)[#:phases]<patch-program-file-names>: Expand
calls to “tramp-compat-process-running-p” so that Guix wrappers are also
matched.
2021-12-03 21:39:49 +01:00
269baba919
gnu: Add valeronoi.
...
* gnu/packages/engineering.scm (valeronoi): New variable.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-03 21:38:30 +01:00
19528e39bb
gnu: st: Install terminfo files.
...
* gnu/packages/suckless.scm (st)[native-inputs]: Add ncurses.
[make-flags](TERMINFO): New flag.
[phases](inhibit-terminfo-install): Remove phase.
Signed-off-by: Raghav Gururajan <rg@raghavgururajan.name>
2021-12-03 15:27:41 -05:00
170cb4c881
gnu: emacs-org: Preserve version information.
...
* gnu/packages/emacs-xyz.scm (emacs-org)[#:phases]: Prevent install phase from
deleting the version information.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-03 21:14:25 +01:00
85ed37c170
gnu: emacs-consult-notmuch: Update to 0.6.
...
* gnu/packages/emacs-xyz.scm (emacs-consult-notmuch): Update to 0.6.
2021-12-03 19:43:12 +01:00
6557f17000
gnu: emacs-helm: Update to 3.8.2.
...
* gnu/packages/emacs-xyz.scm (emacs-helm): Update to 3.8.2.
2021-12-03 19:41:27 +01:00
a7776d5ac0
gnu: emacs-vertico: Update to 0.17.
...
* gnu/packages/emacs-xyz.scm (emacs-vertico): Update to 0.17.
2021-12-03 19:36:35 +01:00
b8d6e77476
gnu: python-ont-fast5-api: Update to 4.0.0.
...
* gnu/packages/bioinformatics.scm (python-ont-fast5-api): Update to 4.0.0.
[source]: Remove bundled plugin binaries.
[arguments]: Install plugin from inputs.
[inputs]: Add vbz-compression.
[propagated-inputs]: Remove python-six; add python-packaging.
2021-12-03 14:55:38 +01:00
d0aa14a43d
gnu: Add vbz-compression.
...
* gnu/packages/bioinformatics.scm (vbz-compression): New variable.
2021-12-03 14:55:38 +01:00
3354e41c1e
system: vm: Remove the vga argument.
...
* gnu/system/vm.scm (common-qemu-options): Remove the "-vga std" argument that
is the default since QEMU 2.2.
Suggested-by: Attila Lendvai <attila@lendvai.name>
2021-12-03 14:25:57 +01:00
b42bfbdfe5
guix system vm: Add --no-graphic CLI argument.
...
It configures QEMU to use the tty it was started in for IO (as opposed to
opening a separate graphical window). This enables copy-pasting and
scrollback. Exit QEMU with C-a x.
* gnu/system/vm.scm (system-qemu-image/shared-store-script): Also add the
'-nographic' QEMU argument when called with #:graphic? #false.
* guix/scripts/system.scm (system-derivation-for-action): Propagate
the #:graphic? keyword arg.
(perform-action): Add and propagate the #:graphic? keyword arg.
(show-help): Add --no-graphic CLI arg.
(%options): Process the new --no-graphic CLI arg.
(process-action): Feed in the CLI arg through the #:graphic? keyword arg.
* doc/guix.texi (Invoking guix system): Add example to combine guix system and
invoking the vm start script into one command. Split the description of the
various options into separate paragraphs. Add a paragraph to describe
--no-graphic.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-03 14:18:32 +01:00
5a18cf3604
gnu: cl-coalton: Update to 0.0.1-2.012f6c8.
...
* gnu/packages/lisp-xyz.scm (sbcl-coalton): Update to 0.0.1-2.012f6c8.
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2021-12-03 14:08:14 +01:00
6e0c4a28b9
gnu: cl-float-features: Update to 1.0.0-2.c1f86ae.
...
* gnu/packages/lisp-xyz.scm (sbcl-float-features): Update to 1.0.0-2.c1f86ae.
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2021-12-03 13:59:46 +01:00
6d4f260166
gnu: bamutils: Update to 1.0.14.
...
* gnu/packages/bioinformatics.scm (bamutils): Update to 1.0.14.
[arguments]: Patch DATE for reproducibility; prepare sources of libstatgen.
[native-inputs]: Add sources of libstatgen.
2021-12-03 13:56:02 +01:00
673cc29908
gnu: bamutils: Remove reference to %outputs.
...
* gnu/packages/bioinformatics.scm (bamutils)[arguments]: Use gexp.
2021-12-03 13:56:01 +01:00
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
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
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
b7aaf6c418
gnu: ivar: Disable parallel tests.
...
* gnu/packages/bioinformatics.scm (ivar)[arguments]: Disable parallel tests.
2021-12-03 13:48:41 +01:00
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
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
3e9dc2754e
gnu: icecat: Remove vestigial icecat-78-makeicecat.patch.
...
This is a followup to commit a63231003e
2021-12-03 04:45:15 -05:00
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
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
d49e7a592f
gnu: icecat: Fix CVE-2021-43527.
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* 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
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
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
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
1f5c1bc024
gnu: python2-decorator: Downgrade to 4.3.0
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* 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
a2423c0ca4
gnu: ribodiff: Remove trailing #T.
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* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Remove trailing #T
from build phase.
2021-12-02 18:32:33 +01:00
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
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
31d372cd8a
gnu: khmer: Fix build with Python 3.8.
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* 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
32d5fb01f8
gnu: python-biom-format: Update to 2.1.10.
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* 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
fab80c3672
gnu: Add trayer-srg.
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* 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
28ad55a59d
gnu: pardre: Update to 2.2.5.
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* 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
fc20fad6f7
gnu: pardre: Use C++ bindings for MPI.
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* gnu/packages/bioinformatics.scm (pardre)[inputs]: Replace openmpi with
openmpi-c++.
2021-12-02 15:40:46 +01:00
2d6be35ea2
gnu: Add openmpi-c++.
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* gnu/packages/mpi.scm (openmpi-c++): New variable.
2021-12-02 15:40:45 +01:00
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
2d92b3bbb6
gnu: shotcut: Update to 21.10.31.
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* 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
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
6fc0cfe1b5
gnu: mlt: Update to 7.2.0.
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* 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
e8d5dd5c9b
gnu: ccls: Update to 0.20210330.
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* 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
a4cc1ae446
gnu: guile-udev: Update to 0.2.0
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* 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
e080e35dc1
gnu: glade: Remove dependency on GJS on non-x86_64.
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* 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
689d141cd8
gnu: Remove librsvg@2.50 from the Xfce dependency graph.
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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
d371abbd0f
gnu: librsvg: Add 'librsvg-for-system' procedure.
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* gnu/packages/gnome.scm (librsvg-for-system): New procedure.
2021-12-02 14:59:56 +01:00
8477a6d743
gnu: librsvg: Reintroduce version 2.40.
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* gnu/packages/gnome.scm (librsvg-2.40): New variable.
2021-12-02 14:59:56 +01:00
46b73fd22d
gnu: python-ipython: Update to 7.20.0.
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* gnu/packages/python-xyz.scm (python-ipython): Update to 7.20.0.
2021-12-02 13:42:17 +01:00
5723503f9f
gnu: python-ipython: Remove trailing #T.
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* gnu/packages/python-xyz.scm (python-ipython)[arguments]: Remove trailing #T
from build phases.
2021-12-02 13:42:17 +01:00
923a121751
gnu: yggdrasil: Simplify build phases.
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* 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
d19e646c83
gnu: go-golang-zx2c4-com-wireguard: Fix downloading source.
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* gnu/packages/golang.scm (go-golang-zx2c4-com-wireguard)[source]:
Adjust commit string in git-reference.
2021-12-02 14:13:27 +02:00
e0755470f8
gnu: go-github-com-vividcortex-ewma: Adjust import-path.
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* 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
052f56e5a6
gnu: guix: Update to 8cc099b.
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* gnu/packages/package-management.scm (guix): Update to 8cc099b
2021-12-02 12:52:59 +01:00
a8fff63daa
gnu: Add python-mygene.
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* gnu/packages/bioinformatics.scm (python-mygene): New variable.
2021-12-02 11:57:28 +01:00
b15a525703
gnu: Add python-biothings-client.
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* gnu/packages/bioinformatics.scm (python-biothings-client): New variable.
2021-12-02 11:57:13 +01:00
37c475ebc0
gnu: prinseq: Fix use of SEARCH-INPUT-FILE.
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* gnu/packages/bioinformatics.scm (prinseq)[arguments]: Pass missing argument
to SEARCH-INPUT-FILE.
2021-12-02 11:26:55 +01:00
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
e1cb787870
gnu: python2-matplotlib: Disable sanity-check.
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* gnu/packages/python-xyz.scm (python2-matplotlib)[arguments]: Delete
'sanity-check phase.
2021-12-02 10:30:40 +01:00
a33ca53492
gnu: python2-matplotlib: Remove trailing #T.
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* gnu/packages/python-xyz.scm (python2-matplotlib)[arguments]: Remove
trailing #T from build phase.
2021-12-02 10:29:59 +01:00
c14ab97a03
Revert "gnu: Change source file-name suffix in rust packages."
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This reverts commit 07a80e30a1
2021-12-02 11:10:37 +02:00
e577889828
gnu: tor: Limit test suite adjustments to affected architectures.
...
This is a follow-up to 68d090002a
2021-12-02 11:07:18 +02:00
c2c63a00de
gnu: Add r-scdblfinder.
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* gnu/packages/bioconductor.scm (r-scdblfinder): New variable.
2021-12-02 10:03:07 +01:00
24832d2ebd
gnu: python2-numpy: Delete file that depends on deleted test.
...
This is a follow-up to commit ec4892c742
2021-12-02 09:45:24 +01:00
07a80e30a1
gnu: Change source file-name suffix in rust packages.
...
* gnu/packages/rust-apps.scm (rust-cbindgen)[source]: Change source
file-name suffix from '.crate' to '.tar.gz'.
* gnu/packages/crates-graphics.scm (rust-ansi-term-0.12): Likewise.
(rust-ansi-term-0.11): Likewise.
(rust-rgb-0.8): Likewise.
* gnu/packages/crates-io.scm (rust-adler32-1): Likewise.
(rust-antidote-1): Likewise.
(rust-atty-0.2): Likewise.
(rust-autocfg-0.1): Likewise.
(rust-backtrace-sys-0.1): Likewise.
(rust-base-x-0.2): Likewise.
(rust-bencher-0.1): Likewise.
(rust-bitflags-1): Likewise.
(rust-blas-sys-0.7): Likewise.
(rust-cargon-0.0): Likewise.
(rust-cblas-sys-0.1): Likewise.
(rust-cc-1): Likewise.
(rust-cfg-if-0.1): Likewise.
(rust-clang-sys-0.26): Likewise.
(rust-clap-2): Likewise.
(rust-clicolors-control-1): Likewise.
(rust-cloudabi-0.1): Likewise.
(rust-cloudabi-0.0): Likewise.
(rust-cmake-0.1): Likewise.
(rust-compiler-builtins-0.1): Likewise.
(rust-constant-time-eq-0.1): Likewise.
(rust-core-foundation-sys-0.6): Likewise.
(rust-data-encoding-2): Likewise.
(rust-defmac-0.2): Likewise.
(rust-defmac-0.1): Likewise.
(rust-dirs-1): Likewise.
(rust-discard-1): Likewise.
(rust-doc-comment-0.3): Likewise.
(rust-dtoa-0.4): Likewise.
(rust-dtoa-0.2): Likewise.
(rust-fallible-iterator-0.2): Likewise.
(rust-filetime-0.2): Likewise.
(rust-findshlibs-0.5): Likewise.
(rust-fixedbitset-0.2): Likewise.
(rust-fixedbitset-0.1): Likewise.
(rust-fnv-1): Likewise.
(rust-foreign-types-shared-0.2): Likewise.
(rust-fs-extra-1): Likewise.
(rust-fuchsia-cprng-0.1): Likewise.
(rust-fuchsia-zircon-0.3): Likewise.
(rust-fuchsia-zircon-sys-0.3): Likewise.
(rust-futures-0.1): Likewise.
(rust-futures-core-preview-0.3): Likewise.
(rust-futures-cpupool-0.1): Likewise.
(rust-futures-io-preview-0.3): Likewise.
(rust-futures-sink-preview-0.3): Likewise.
(rust-getopts-0.2): Likewise.
(rust-glob-0.3): Likewise.
(rust-glob-0.2): Likewise.
(rust-heapsize-0.4): Likewise.
(rust-heapsize-0.3): Likewise.
(rust-heapsize-plugin-0.1): Likewise.
(rust-heck-0.3): Likewise.
(rust-hex-0.3): Likewise.
(rust-hex-0.2): Likewise.
(rust-hostname-0.1): Likewise.
(rust-iovec-0.1): Likewise.
(rust-itoa-0.4): Likewise.
(rust-itoa-0.1): Likewise.
(rust-json-0.11): Likewise.
(rust-kernel32-sys-0.2): Likewise.
(rust-language-tags-0.2): Likewise.
(rust-lazy-static-1): Likewise.
(rust-libloading-0.5): Likewise.
(rust-lock-api-0.1): Likewise.
(rust-log-0.4): Likewise.
(rust-maplit-1): Likewise.
(rust-matches-0.1): Likewise.
(rust-matrixmultiply-0.2): Likewise.
(rust-matrixmultiply-0.1): Likewise.
(rust-md5-0.7): Likewise.
(rust-md5-0.6): Likewise.
(rust-memmap-0.7): Likewise.
(rust-memmap-0.6): Likewise.
(rust-mime-0.3): Likewise.
(rust-miniz-oxide-0.3): Likewise.
(rust-miniz-sys-0.1): Likewise.
(rust-miow-0.3): Likewise.
(rust-miow-0.2): Likewise.
(rust-modifier-0.1): Likewise.
(rust-net2-0.2): Likewise.
(rust-nodrop-0.1): Likewise.
(rust-nodrop-union-0.1): Likewise.
(rust-num-traits-0.1): Likewise.
(rust-numtoa-0.1): Likewise.
(rust-openssl-probe-0.1): Likewise.
(rust-owning-ref-0.4): Likewise.
(rust-parity-wasm-0.40): Likewise.
(rust-peeking-take-while-0.1): Likewise.
(rust-percent-encoding-2): Likewise.
(rust-percent-encoding-1): Likewise.
(rust-permutohedron-0.2): Likewise.
(rust-pico-sys-0.0): Likewise.
(rust-pkg-config-0.3): Likewise.
(rust-plain-0.2): Likewise.
(rust-plugin-0.2): Likewise.
(rust-pocket-resources-0.3): Likewise.
(rust-ppv-lite86-0.2): Likewise.
(rust-proc-macro2-1): Likewise.
(rust-quick-error-2): Likewise.
(rust-quick-error-1): Likewise.
(rust-quote-1): Likewise.
(rust-rand-0.7): Likewise.
(rust-rand-0.6): Likewise.
(rust-rand-0.3): Likewise.
(rust-rand-chacha-0.1): Likewise.
(rust-rand-core-0.4): Likewise.
(rust-rand-core-0.3): Likewise.
(rust-rand-hc-0.2): Likewise.
(rust-rand-hc-0.1): Likewise.
(rust-rand-isaac-0.1): Likewise.
(rust-rand-jitter-0.1): Likewise.
(rust-rand-os-0.1): Likewise.
(rust-rand-pcg-0.3): Likewise.
(rust-rand-pcg-0.2): Likewise.
(rust-rand-pcg-0.1): Likewise.
(rust-rand-xorshift-0.1): Likewise.
(rust-rawpointer-0.2): Likewise.
(rust-rawpointer-0.1): Likewise.
(rust-rdrand-0.4): Likewise.
(rust-redox-syscall-0.1): Likewise.
(rust-redox-termios-0.1): Likewise.
(rust-resolv-conf-0.6): Likewise.
(rust-rustc-demangle-0.1): Likewise.
(rust-rustc-serialize-0.3): Likewise.
(rust-rustc-std-workspace-core-1): Likewise.
(rust-ryu-1): Likewise.
(rust-safemem-0.3): Likewise.
(rust-same-file-1): Likewise.
(rust-schannel-0.1): Likewise.
(rust-scoped-threadpool-0.1): Likewise.
(rust-scoped-tls-1): Likewise.
(rust-scoped-tls-0.1): Likewise.
(rust-scopeguard-1): Likewise.
(rust-scopeguard-0.3): Likewise.
(rust-security-framework-sys-0.3): Likewise.
(rust-semver-parser-0.9): Likewise.
(rust-semver-parser-0.7): Likewise.
(rust-serde-derive-1): Likewise.
(rust-shlex-1): Likewise.
(rust-shlex-0.1): Likewise.
(rust-slab-0.4): Likewise.
(rust-socket2-0.3): Likewise.
(rust-sourcefile-0.1): Likewise.
(rust-spin-0.5): Likewise.
(rust-stacker-0.1): Likewise.
(rust-static-assertions-1): Likewise.
(rust-static-assertions-0.3): Likewise.
(rust-stdweb-internal-runtime-0.1): Likewise.
(rust-stdweb-internal-test-macro-0.1): Likewise.
(rust-streaming-stats-0.2): Likewise.
(rust-strsim-0.9): Likewise.
(rust-strsim-0.8): Likewise.
(rust-synstructure-test-traits-0.1): Likewise.
(rust-tar-0.4): Likewise.
(rust-tempdir-0.3): Likewise.
(rust-tempfile-3): Likewise.
(rust-term-0.4): Likewise.
(rust-term-0.2): Likewise.
(rust-termcolor-1): Likewise.
(rust-termion-1): Likewise.
(rust-termios-0.3): Likewise.
(rust-thread-id-3): Likewise.
(rust-thread-local-1): Likewise.
(rust-thread-local-0.3): Likewise.
(rust-threadpool-1): Likewise.
(rust-time-0.1): Likewise.
(rust-tokio-mock-task-0.1): Likewise.
(rust-toml-0.5): Likewise.
(rust-tracing-core-0.1): Likewise.
(rust-traitobject-0.1): Likewise.
(rust-try-from-0.3): Likewise.
(rust-try-lock-0.2): Likewise.
(rust-typeable-0.1): Likewise.
(rust-typemap-0.3): Likewise.
(rust-typenum-1): Likewise.
(rust-ucd-trie-0.1): Likewise.
(rust-ucd-util-0.1): Likewise.
(rust-unicode-xid-0.2): Likewise.
(rust-unicode-xid-0.1): Likewise.
(rust-unreachable-1): Likewise.
(rust-unsafe-any-0.4): Likewise.
(rust-untrusted-0.7): Likewise.
(rust-vcpkg-0.2): Likewise.
(rust-vec-map-0.8): Likewise.
(rust-version-check-0.9): Likewise.
(rust-version-check-0.1): Likewise.
(rust-void-1): Likewise.
(rust-wasi-0.5): Likewise.
(rust-wasm-bindgen-shared-0.2): Likewise.
(rust-wasm-bindgen-test-macro-0.2): Likewise.
(rust-widestring-0.4): Likewise.
(rust-winapi-0.3): Likewise.
(rust-winapi-0.2): Likewise.
(rust-winapi-build-0.1): Likewise.
(rust-winapi-util-0.1): Likewise.
(rust-wincolor-1): Likewise.
(rust-winutil-0.1): Likewise.
(rust-ws2-32-sys-0.2): Likewise.
(rust-xattr-0.2): Likewise.
(rust-xdg-2): Likewise.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-02 10:24:17 +02:00
bef86fed3e
Revert "gnu: godot: Update to 3.4."
...
This reverts commit dd4365efa1https://debbugs.gnu.org/cgi/bugreport.cgi?bug=52233#20
2021-12-02 01:27:12 -05:00
934a246409
gnu: cl-tooter: Update to 1.0.0-3.ec97bee.
...
* gnu/packages/lisp-xyz.scm (cl-tooter): Update to 1.0.0-3.ec97bee.
Signed-off-by: Leo Famulari <leo@famulari.name>
2021-12-02 00:12:58 -05:00
e9e2204897
gnu: cl-i18n: Update to 0.5.1-1.4216fe9.
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* gnu/packages/lisp-xyz.scm (cl-i18n): Update to 0.5.1-1.4216fe9.
Signed-off-by: Leo Famulari <leo@famulari.name>
2021-12-02 00:12:57 -05:00
dd4365efa1
gnu: godot: Update to 3.4.
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* gnu/packages/game-development.scm (godot): Update to 3.4.
[source]: Add new bundled dependencies to the origin snippet.
Signed-off-by: Leo Famulari <leo@famulari.name>
2021-12-02 00:02:47 -05:00
ec4892c742
gnu: python2-numpy: Do not inherit native-inputs.
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* gnu/packages/python-xyz.scm (python2-numpy)[native-inputs]: Do not inherit
from Python 3 variant; use only python2-cython, python2-pytest, and gfortran.
[arguments]: Add phase 'delete-failing-test.
2021-12-02 01:20:43 +01:00
7a171235af
gnu: linux-libre 4.19: Update to 4.19.219.
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* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.219.
(linux-libre-4.19-pristine-source): Update hash.
2021-12-01 18:43:05 -05:00
6f18f35297
gnu: linux-libre 5.4: Update to 5.4.163.
...
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.163.
(linux-libre-5.4-pristine-source): Update hash.
2021-12-01 18:43:05 -05:00
f01588736c
gnu: linux-libre 5.10: Update to 5.10.83.
...
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.83.
(linux-libre-5.10-pristine-source): Update hash.
2021-12-01 18:43:05 -05:00
c3ec5eaa75
gnu: linux-libre: Update to 5.15.6.
...
* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.6.
(linux-libre-5.15-pristine-source): Update hash.
2021-12-01 18:43:02 -05:00
d53679c531
gnu: Remove couger.
...
This package has been moved to the Guix Past channel.
* gnu/packages/bioinformatics.scm (couger): Remove variable.
2021-12-02 00:32:12 +01:00
cd40978a4b
gnu: randomjungle: Fix compatibility errors.
...
* gnu/packages/machine-learning.scm (randomjungle)[arguments]: Add build phase
'fix-compatibility-errors to patch type errors.
2021-12-02 00:32:12 +01:00
36f18626a9
gnu: petsc-{complex,openmpi,complex-openmpi}: Use gexps.
...
This is a followup to 07ac13a26a
2021-12-01 23:30:15 +01:00
725d35aa9a
gnu: scalapack: Update to 2.1.0.
...
* gnu/packages/maths.scm (scalapack): Update to 2.1.0.
[source]: Remove "scalapack-blacs-mpi-deprecations.patch" and add
"scalapack-gcc-10-compilation.patch".
[arguments]: Add 'skip-faulty-test' phase.
* gnu/packages/patches/scalapack-blacs-mpi-deprecations.patch: Remove.
* gnu/packages/patches/scalapack-gcc-10-compilation.patch: New file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
2021-12-01 23:30:15 +01:00
a63231003e
gnu: icecat: Remove leftovers of release 78.
...
No longer required as icedove is now based on the 91 branch.
* gnu/packages/gnuzilla.scm (mozilla-78-compare-locales): Remove.
(all-mozilla-78-locales): Remove.
(%icecat-78-version): Remove.
(icecat-78-source): Remove.
2021-12-01 22:07:00 +01:00
52cb5cf5b8
gnu: icedove: Update to 91.3.2.
...
The profile folder moved from `~/.icedove` to `~/.thunderbird`. You may
need to migrate (copy) your profile over.
* gnu/packages/gnuzilla.scm (icedove): Update to 91.3.2.
[source]: Switch back to icecat-source.
[arguments]: `obj-x86_64-pc-linux-gnu` folder is now generated during
build, so it can't deleted in front. Remove surounding `'` from
MOZ_DEDICATED_PROFILES to follow source code. MOZ_APP_BASENAME and
MOZ_APP_DISPLAYNAME are no longer set in `comm/mail/confvars.sh`. Update
path of `customizeToolbar.js`.
Delete `'bootstrap` phase and no longer set AUTOCONF variable as the
autoconf build part was removed. Set MACH_USE_SYSTEM_PYTHON and
MOZ_APP_NAME, the latter is the binary name.
`--enable-calendar` flag got removed. Use bundled NSS until
core-updates merge.
[inputs]: Update to `icu4c-69` and `nspr-4.32`. Use bundled NSS for now.
[native-inputs]: Switch to comm-esr91 branch. Remove autoconf, add m4.
Update rust and cargo to 1.51. Use `rust-cbindgen-0.19`.
2021-12-01 22:07:00 +01:00
f1a2e90409
gnu: Add nspr@4.32.
...
Required for icecat/icedove 91.
* gnu/packages/nss.scm (nspr-4.32): New variable.
2021-12-01 22:06:54 +01:00
d7d7b57965
gnu: emacs-citar: Remove unnecessary input.
...
* gnu/packages/emacs-xyz.scm (emacs-citar)[propagated-inputs]: Remove emacs-helm-bibtex.
2021-12-01 22:00:45 +01:00
2b08cc968b
gnu: bullet: Update to 3.17.
...
* gnu/packages/game-development.scm (bullet): Update to 3.17.
[arguments]<#:configure-flags>: Disable access to third-party libs.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-01 21:54:41 +01:00
d64b78ef0c
installer: parted: Use the swap-space record.
...
* gnu/installer/parted.scm (user-partitions->configuration): Use the
swap-space record.
2021-12-01 20:59:06 +01:00
05c747ea6b
tests: install: Use the swap-space record.
...
This fixes the following error:
In gnu/services/base.scm:
2228:56 4 (_ #<<uuid> type: dce bv: #vu8(17 17 17 17 34 34 51 51 …>)
In gnu/build/file-systems.scm:
239:13 3 (swap-space->flags-bit-mask #<<uuid> type: dce bv: #vu8…>)
In ice-9/boot-9.scm:
1685:16 2 (raise-exception _ #:continuable? _)
1685:16 1 (raise-exception _ #:continuable? _)
1685:16 0 (raise-exception _ #:continuable? _)
ice-9/boot-9.scm:1685:16: In procedure raise-exception:
In procedure swap-space-priority: Wrong type argument: #<<uuid> type: dce bv: #vu8(17 17 17 17 34 34 51 51 68 68 18 52 86 120 154 188)>
* gnu/tests/install.scm (installation-target-os-for-gui-tests): Use the
swap-space record.
2021-12-01 19:23:12 +01:00
c7c4f80881
gnu: Update Trezor support.
...
* gnu/packages/patches/python-trezor-agent-fix-argv0.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Apply previous removal.
* gnu/packages/finance.scm (python-trezor-agent): Update to 0.14.4.
[source]: Remove now useless patch.
(python-mnemonic): Update to 0.20.
(python-trezor): Update to 0.12.4
(trezor-agent): Update to 0.11.0-1.
[source]: Add file-name field.
[arguments]: Remove trailing #T in phases.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-01 18:05:26 +01:00
508200d66a
gnu: python-daemon: Update to 2.3.0.
...
* gnu/packages/python-xyz.scm (python-daemon): Update to 2.3.0.
[native-inputs]: Add python-coverage and python-twine.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-01 17:58:33 +01:00
8cc099b425
gnu: openssh: Add support for ecdsa-sk, ed25519-sk ssh keys.
...
* gnu/packages/ssh.scm (openssh)[inputs]: Add LIBFIDO2.
[arguments]: Pass "--with-security-key-builtin".
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-12-01 17:53:27 +01:00
3aaef047a6
gnu: Add libfido2.
...
* gnu/packages/security-token.scm (libfido2): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-12-01 17:53:27 +01:00
083a710cbb
gnu: Add libcbor.
...
* gnu/packages/compression.scm (libcbor): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-12-01 17:53:27 +01:00
b5d0029771
gnu: Add vim-nerdtree.
...
* gnu/packages/vim.scm (vim-nerdtree): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-12-01 17:53:27 +01:00
a955e4d7f6
gnu: Add smplayer.
...
* gnu/packages/video.scm (smplayer): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-12-01 17:51:38 +01:00
5ff34d596d
gnu: Add python-codespell.
...
* gnu/packages/python-xyz.scm (python-codespell): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-12-01 17:51:37 +01:00
a82e9f45fd
installer: Make LUKS2 the default format for encrypted devices
...
* gnu/installer/parted.scm (luks-format-and-open): Change it.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-12-01 17:51:37 +01:00
adce91a3ec
gnu: system: Add LUKS2 support for the root file system.
...
* gnu/bootloader/grub.scm (grub-configuration-file): Add 'insmod
luks2'.
* gnu/system/mapped-devices.scm (open-luks-device): Create
'/run/cryptsetup/' directory.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-12-01 17:51:37 +01:00
1a0696e0a6
gnu: sdrangel: Add missing input.
...
QtQuick is required by some runtime features.
* gnu/packages/radio.scm (sdrangel)[inputs]: Add qtquickcontrols2.
2021-12-01 17:30:45 +01:00
e7ead42383
gnu: python-language-server: Add deprecated alias.
...
* gnu/packages/python-xyz.scm (python-language-server): New variable.
Add deprecated alias for package removed in the parent commit.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-01 17:13:41 +01:00
7907ddbc3a
gnu: Add python-lsp-server.
...
* gnu/packages/python-xyz.scm (python-language-server): Delete variable.
* gnu/packages/python-xyz.scm (python-lsp-server): New variable.
Removes deprecated python-language-server package and adds maintained
fork.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-01 17:13:27 +01:00
0c3acb247a
gnu: python-lsp-jsonrpc: Add deprecated alias.
...
* gnu/packages/python-xyz.scm (python-jsonrpc-server): New variable.
Add deprecated alias for package removed in the parent commit.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-01 17:13:10 +01:00
869c7d6703
gnu: Add python-lsp-jsonrpc.
...
* gnu/packages/python-xyz.scm (python-jsonrpc-server): Delete variable.
* gnu/packages/python-xyz.scm (python-lsp-jsonrpc): New variable.
Removes deprecated python-jsonrpc-server package and adds maintained
fork.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-01 17:12:58 +01:00
46e030764d
gnu: python-jedi: Update to 0.18.1.
...
* gnu/packages/python-xyz.scm (python-jedi): Update to 0.18.1.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-01 17:12:31 +01:00
6b29c3c735
gnu: python2-jedi: Remove package.
...
* gnu/packages/python-xyz.scm (python2-jedi): Delete variable.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-01 17:10:34 +01:00
c56e9033f5
gnu: python-parso: Update to 0.8.2.
...
* gnu/packages/python-xyz.scm (python-parso): Update to 0.8.2.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-01 17:10:18 +01:00
d9956e9383
gnu: yggdrasil: Update to 0.4.1.
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* gnu/packages/networking.scm (yggdrasil): Update to 0.4.1.
* gnu/packages/patches/yggdrasil-extra-config.patch: Update for new version.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2021-12-01 17:03:34 +01:00
f3b2af2147
gnu: yggdrasil: Update to 0.4.0.
...
* gnu/packages/patches/yggdrasil-extra-config.patch: Update patch.
* gnu/packages/networking.scm (yggdrasil): Update to 0.4.0.
[arguments]: Also install genkeys.
[propagated-inputs]: Remove go-github-com-cheggaaa-pb; add go-golang-org-x-sys,
go-github-com-mattn-go-runewidth, go-github-com-mattn-go-isatty,
go-github-com-fatih-color, go-github-com-cheggaaa-pb-v3,
go-github-com-vividcortex-ewma, and go-github-com-arceliar-ironwood.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2021-12-01 17:03:34 +01:00
dee3e337b6
gnu: Add go-github-com-arceliar-ironwood.
...
* gnu/packages/golang.scm (go-github-com-arceliar-ironwood): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2021-12-01 17:03:34 +01:00
7e4b418733
gnu: Rename go-github-com-cheggaaa-pb to go-github-com-cheggaaa-pb-v3.
...
* gnu/packages/golang.scm (go-github-com-cheggaaa-pb): Rename this variable...
(go-github-com-cheggaaa-pb-v3): ...to this variable.
(go-github-com-cheggaaa-pb): New variable for deprecated package.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2021-12-01 17:03:34 +01:00
b7e774a828
gnu: go-github-com-cheggaaa-pb: Update to 3.0.8.
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* gnu/packages/golang.scm (go-github-com-cheggaaa-pb): Update to 3.0.8.
[arguments]: Disable tests; update import path.
[native-inputs]: Move go-github-com-mattn-go-isatty from here...
[propagated-inputs]: ...to here; add go-github-com-vividcortex-ewma and
go-github-com-rivo-uniseg.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2021-12-01 17:03:34 +01:00
660062a65b
gnu: Add go-github-com-mattn-go-runewidth.
...
* gnu/packages/golang.scm (go-github-com-mattn-go-runewidth): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2021-12-01 17:03:34 +01:00
f3861469b6
gnu: Add go-github-com-rivo-uniseg.
...
* gnu/packages/golang.scm (go-github-com-rivo-uniseg): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2021-12-01 17:03:34 +01:00
b3a9d079b8
gnu: Add go-github-com-vividcortex-ewma.
...
* gnu/packages/golang.scm (go-github-com-vividcortex-ewma): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2021-12-01 17:03:34 +01:00
5ca0042116
gnu: Add python-mrkd.
...
* gnu/packages/python-xyz.scm (python-mrkd): New variable.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-01 16:40:49 +01:00
0a9edd23ca
gnu: telescope: Update to 0.6.1.
...
* gnu/packages/web-browsers.scm (telescope): Update to 0.6.1.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-01 16:36:39 +01:00
8e7e839c98
gnu: cl-unix-opts: Update to 0.1.7-1.0e61f34.
...
* gnu/packages/lisp-xyz.scm (sbcl-unix-opts): Update to 0.1.7-1.0e61f34.
[source]: Fetch using commit instead of old tag.
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2021-12-01 13:26:29 +01:00
0da9ae01a8
gnu: cl-croatoan: Update to 0.0.1-4.cf87513.
...
* gnu/packages/lisp-xyz.scm (sbcl-croatoan): Update to 0.0.1-4.cf87513.
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2021-12-01 13:16:01 +01:00
dc438820c3
gnu: Add julia-millboard.
...
* gnu/packages/julia-xyz.scm (julia-millboard): New variable.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-01 14:08:46 +02:00
f303eaa31b
gnu: Add julia-jive.
...
* gnu/packages/julia-xyz.scm (julia-jive): New variable.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-01 14:08:46 +02:00
2eca48e310
gnu: Add julia-softglobalscope.
...
* gnu/packages/julay-xyz.scm (julia-softglobalscope): New variable.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-01 14:08:46 +02:00
ce6ea46d40
gnu: Add dynaconf.
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* gnu/packages/python-xyz.scm (dynaconf): New variable.
* gnu/packages/patches/dynaconf-Unvendor-dependencies.patch: New file.
* local.mk (dist_patch_DATA): Register it.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-01 13:58:07 +02:00
f8b1215874
gnu: Add python-dotenv-0.13.0.
...
* gnu/packages/python-xyz.scm (python-dotenv-0.13.0): New variable.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-01 13:58:04 +02:00
1e8ad167f6
gnu: python-dotenv: Run test suite.
...
* gnu/packages/python-xyz.scm (python-dotenv)[arguments]: Add custom
'check phase.
2021-12-01 13:58:04 +02:00
a8d62aea22
gnu: Add python-dotenv.
...
* gnu/packages/python-xyz.scm (python-dotenv): New variable.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-01 13:57:59 +02:00
124d76c5c2
gnu: python2-numpydoc: Update to 0.9.1.
...
* gnu/packages/python-xyz.scm (python2-numpydoc): Update to 0.9.1; do not
inherit from Python 3 variant.
2021-12-01 11:39:58 +01:00
38d648655b
gnu: python-numpydoc: Update to 1.1.0.
...
* gnu/packages/python-xyz.scm (python-numpydoc): Update to 1.1.0.
[arguments]: Override 'check phase to run tests.
[native-inputs]: Remove python-nose; add python-matplotlib, python-pytest, and
python-pytest-cov.
2021-12-01 11:39:58 +01:00
6367c92c6e
gnu: Add python-mwparserfromhell.
...
* gnu/packages/python-web.scm (python-mwparserfromhell): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2021-12-01 11:22:42 +01:00
619e0627a6
gnu: ruby-mocha: Update to 1.13.0.
...
* gnu/packages/ruby.scm (ruby-mocha): Update to 1.13.0.
[home-page]: Update to new location.
2021-12-01 11:39:14 +02:00
Ludovic Courtès
Julien Lepiller
Ricardo Wurmus
zimoun
Nicolas Goaziou
jgart
cage
Liliana Marie Prikler
phodina
Morgan Smith
Mathieu Othacehe
Attila Lendvai
Charles
Mark H Weaver
Arne Babenhauserheide
Vinicius Monego
Artyom V. Poptsov
Efraim Flashner
Z572
Leo Famulari
Andy Tai
Jonathan Brielmaier
Ahmad Jarara
Foo Chuan Wei
Felix Gruber
Josselin Poiret
Guillaume Le Vaillant
jgart via Guix-patches via
raingloom
Giacomo Leidi
Alice BRENON