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Author SHA1 Message Date
Ricardo Wurmus 78b3727b60
gnu: r-affyplm: Update to 1.76.0. 
* gnu/packages/bioconductor.scm (r-affyplm): Update to 1.76.0.
 2023-04-29 20:09:31 +02:00
Ricardo Wurmus f862832e36
gnu: r-affylmgui: Update to 1.74.0. 
* gnu/packages/bioconductor.scm (r-affylmgui): Update to 1.74.0.
 2023-04-29 20:09:31 +02:00
Ricardo Wurmus 99e827e67c
gnu: r-affyilm: Update to 1.52.0. 
* gnu/packages/bioconductor.scm (r-affyilm): Update to 1.52.0.
 2023-04-29 20:09:31 +02:00
Ricardo Wurmus 457938bbb0
gnu: r-affixcan: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-affixcan): Update to 1.18.0.
 2023-04-29 20:09:31 +02:00
Ricardo Wurmus 624498f085
gnu: r-adsplit: Update to 1.70.0. 
* gnu/packages/bioconductor.scm (r-adsplit): Update to 1.70.0.
 2023-04-29 20:09:31 +02:00
Ricardo Wurmus 4690ee5805
gnu: r-adimpute: Update to 1.10.0. 
* gnu/packages/bioconductor.scm (r-adimpute): Update to 1.10.0.
 2023-04-29 20:09:31 +02:00
Ricardo Wurmus bf29af41c9
gnu: r-adamgui: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-adamgui): Update to 1.16.0.
 2023-04-29 20:09:31 +02:00
Ricardo Wurmus 02c3985ecf
gnu: r-adam: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-adam): Update to 1.16.0.
 2023-04-29 20:09:31 +02:00
Ricardo Wurmus 331bb1ea91
gnu: r-adacgh2: Update to 2.40.0. 
* gnu/packages/bioconductor.scm (r-adacgh2): Update to 2.40.0.
 2023-04-29 20:09:31 +02:00
Ricardo Wurmus ef9b160820
gnu: r-absseq: Update to 1.54.0. 
* gnu/packages/bioconductor.scm (r-absseq): Update to 1.54.0.
 2023-04-29 20:09:31 +02:00
Ricardo Wurmus da4fbf5604
gnu: r-abarray: Update to 1.68.0. 
* gnu/packages/bioconductor.scm (r-abarray): Update to 1.68.0.
 2023-04-29 20:09:31 +02:00
Ricardo Wurmus 06986a86ad
gnu: r-missmethyl: Update to 1.34.0. 
* gnu/packages/bioconductor.scm (r-missmethyl): Update to 1.34.0.
 2023-04-29 20:09:31 +02:00
Ricardo Wurmus d6acf4de78
gnu: r-shiny: Update to 1.7.4. 
* gnu/packages/cran.scm (r-shiny): Update to 1.7.4.
 2023-04-29 20:09:31 +02:00
Ricardo Wurmus 9b03d78000
gnu: r-glimma: Update to 2.10.0. 
* gnu/packages/bioconductor.scm (r-glimma): Update to 2.10.0.
[source]: Delete minified JavaScript files.
[arguments]: Add 'process-javascript phase.
[native-inputs]: Add esbuild.
 2023-04-29 20:09:31 +02:00
Ricardo Wurmus 9619504c81
gnu: r-reportingtools: Update to 2.39.0. 
* gnu/packages/bioconductor.scm (r-reportingtools): Update to 2.39.0.
[source]: Delete minified JavaScript files.
[arguments]: Add 'process-javascript phase.
[native-inputs]: Add source code for jquery 1.8.0.
 2023-04-29 20:09:31 +02:00
Ricardo Wurmus 91204fc357
gnu: Add r-densvis. 
* gnu/packages/bioconductor.scm (r-densvis): New variable.
 2023-04-29 20:09:31 +02:00
Ricardo Wurmus 90f67705f5
import/cran: Translate from xml2 to libxml2. 
* guix/import/cran.scm (transform-sysname): Add translation from xml2 to
libxml2.
 2023-04-29 20:09:30 +02:00
Ricardo Wurmus 2f53d9cce9
import/cran: Add "unix" to list of invalid packages. 
* guix/import/cran.scm (invalid-packages): Add "unix".
 2023-04-29 20:09:30 +02:00
Ricardo Wurmus 921ee8789d
gnu: r-with-tests: Update to 4.3.0. 
* gnu/packages/statistics.scm (r-with-tests): Update to 4.3.0.
[arguments]: Move 'set-timezone before 'configure.
 2023-04-29 20:09:30 +02:00
Ricardo Wurmus ec52655ce6
guix: Upgrade to Bioconductor 3.16. 
* guix/build-system/r.scm (bioconductor-uri): Bump Bioconductor version to
3.17.
* guix/import/cran.scm (%bioconductor-version): Same.
 2023-04-29 20:09:30 +02:00
Ricardo Wurmus cb8d080349
import/pypi: Generate packages using pyproject-build-system. 
* guix/import/pypi.scm (make-pypi-sexp): Generate PACKAGE expression where the
value for the BUILD-SYSTEM field is PYPROJECT-BUILD-SYSTEM instead of
PYTHON-BUILD-SYSTEM.
 2023-04-29 20:09:30 +02:00
Liliana Marie Prikler 3676e312aa
gnu: libpotassco: Unbundle catch. 
This patch incidentally fixes a build failure caused by the bundled catch.

* gnu/packages/potassco.scm (libpotassco)[source]: Unbundle catch.
[native-inputs]: Add catch2-1.
 2023-04-29 10:28:39 +02:00
Josselin Poiret 4884ee6dd4
gnu: libexpected: Update to 1.1.0. 
* gnu/packages/patches/libexpected-use-provided-catch2.patch: Add new patch.
* gnu/packages/patches/libexpected-nofetch.patch: Remove unused patch.
* gnu/local.mk (dist_patch_DATA): Register changes.
* gnu/packages/cpp.scm (libexpected): Update to 1.1.0, and use new patch.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-04-28 21:13:36 +02:00
Josselin Poiret 8a8bd15bfa
gnu: fwupd: Update to 1.8.14. 
* gnu/packages/firmware.scm (fwupd): Update to 1.8.14.  Also, change two
files' timestamp because they are zipped up by Python.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-04-28 21:04:03 +02:00
Aleksandr Vityazev 87ba11eff1
gnu: maven-embedder: Fix build. 
* gnu/packages/maven (maven-embedder)[arguments]:
Add the'add-sisu-shebang phase after unpack.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-04-28 21:02:54 +02:00
Aleksandr Vityazev 1a93ff9a8b
gnu: maven-core-bootstrap: Fix build. 
* gnu/packages/maven (maven-core-bootstrap)[arguments]:
Add the'add-sisu-shebang phase after unpack.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-04-28 21:02:54 +02:00
Aleksandr Vityazev 3d2ce30f6b
gnu: maven-resolver-provider: Fix build. 
* gnu/packages/maven (maven-resolver-provider)[arguments]:
Add the'add-sisu-shebang phase after unpack.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-04-28 21:02:54 +02:00
Aleksandr Vityazev 04f9ac0cfa
gnu: maven-model-builder: Fix build. 
* gnu/packages/maven (maven-model-builder)[arguments]:
Add the'add-sisu-shebang phase after unpack.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-04-28 21:02:54 +02:00
Aleksandr Vityazev c0a0cec87f
gnu: maven-settings-builder: Fix build. 
* gnu/packages/maven (maven-settings-builder)[arguments]:
Add the'add-sisu-shebang phase after unpack.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-04-28 21:02:54 +02:00
Gabriel Wicki 06277d8070
gnu: Fix supercollider. 
Message-Id: <f67786eb958a65ba778f67a8f443fa3d24293438.1682453413.git.gabriel@erlikon.ch>
From: Gabriel Wicki <gabriel@erlikon.ch>
Date: Tue, 25 Apr 2023 22:03:03 +0200
Subject: [PATCH 1/2] gnu: Fix supercollider.

* gnu/packages/audio.scm (supercollider): Fix the build.
[configure-flags] Re-enable DLIBSCSYNTH.
[phases] New phase fix-struct-SOUNDFILE-tag.
[inputs] Add ruby and python to appease the build process.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-04-28 19:52:41 +02:00
Josselin Poiret ee88acc6e2
tests: guix-graph.sh: Fix expected path from emacs to libffi. 
* tests/guix-graph.sh: Change the expected path from emacs to libffi.  `guix
graph --path` outputs only one possible path, and the one it outputs for this
case has changed.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-04-28 19:50:39 +02:00
Josselin Poiret 5c26e69118
tests: guix-build.sh: Don't use hidden gcc for transformation tests. 
* tests/guix-build.sh: Do not try to rewrite gcc, it is hidden and so will not
be rewritten, as per eee95b5a87.  Instead, try
to build grep with coreutils rewritten to hello.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-04-28 19:50:36 +02:00
宋文武 aecc6e7058
gnu: dovecot: Fix build. 
* gnu/packages/mail.scm (dovecot)[source]: Add patch for OpenSSL v3.
* gnu/packages/patches/dovecot-opensslv3.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2023-04-28 09:33:03 +08:00
宋文武 e42117bfc9
gnu: mumble: Update to 1.4.287, fix build. 
* gnu/packages/telephony.scm (mumble): Update to 1.4.287.
[inputs]: Use openssl-1.1.
 2023-04-28 08:56:48 +08:00
宋文武 7193b8f9fd
gnu: python-ipy: Update to 1.01. 
* gnu/packages/networking.scm (python-ipy): Update to 1.01.
 2023-04-28 08:36:37 +08:00
Efraim Flashner b8b3af93da
gnu: ncdu-1: Update to 1.18.1. 
* gnu/packages/ncdu.scm (ncdu-1): Update to 1.18.1.
 2023-04-27 22:19:10 +03:00
Ricardo Wurmus 4d42fbd371
gnu: sleef: Adjust inputs. 
* gnu/packages/maths.scm (sleef)[inputs]: Replace openssl with openssl-1.1;
remove mpfr.
[arguments]: Remove custom phase 'make-git-checkout-writable; use G-expression
for configure-flags.
 2023-04-27 21:07:15 +02:00
Ricardo Wurmus ecb4f4d015
gnu: gloo: Use OpenSSL 1.1. 
* gnu/packages/machine-learning.scm (gloo)[inputs]: Use openssl-1.1 instead of
openssl.
 2023-04-27 20:58:26 +02:00
Ricardo Wurmus 688d99282b
gnu: yubico-piv-tool: Update to 2.3.1. 
* gnu/packages/security-token.scm (yubico-piv-tool): Update to 2.3.1.
[source]: Fetch from Github repository.
[build-system]: Use cmake-build-system.
 2023-04-27 20:55:25 +02:00
Pierre Neidhardt d59b4764f3
gnu: Add cl-prompter. 
* gnu/packages/lisp-xyz.scm (cl-prompter, ecl-prompter, sbcl-prompter): New variables.
 2023-04-27 17:50:38 +02:00
Ricardo Wurmus 297805b1f8
gnu: python-docutils-0.15: Add missing input. 
* gnu/packages/python-xyz.scm (python-docutils-0.15)[native-inputs]: Add
python-setuptools-57.
 2023-04-27 16:32:47 +02:00
Ricardo Wurmus 5775bbdd4b
gnu: gdcm: Disable dependent tests. 
* gnu/packages/bioinformatics.scm (gdcm)[arguments]: Disable tests that depend
on the output of a disabled test.
 2023-04-27 16:23:22 +02:00
Ricardo Wurmus fa685c87ea
gnu: freebayes: Update to 1.3.7. 
* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.7.
[arguments]: Do not use "grep -P" in tests; drop trailing #T.
 2023-04-27 11:40:09 +02:00
Ricardo Wurmus 133957f7bb
gnu: vcflib: Use libwfa2.pc. 
* gnu/packages/bioinformatics.scm (vcflib)[source]: Use pkg-config to look for
libwfa2.
[inputs]: Move wfa2-lib from here...
[propagated-inputs]: ...to here.
[arguments]: Drop WFA_LINK_LIBRARIES option; fix typo in build phase name;
patch IntervalTree.h includes; add libwfa2 to pkg-config file.
 2023-04-27 11:38:16 +02:00
Ricardo Wurmus 479f2558fe
gnu: wfa2-lib: Install pkg-config file. 
* gnu/packages/bioinformatics.scm (wfa2-lib)[arguments]: Install libwfa2.pc.
 2023-04-27 11:37:36 +02:00
Ricardo Wurmus 9d82c475a3
gnu: express: Adjust bamtools location. 
* gnu/packages/bioinformatics.scm (express)[arguments]: Modify location of
libbamtools.so in 'use-shared-boost-libs-and-set-bamtools-paths; drop trailing
 #T.
 2023-04-27 09:25:26 +02:00
Ricardo Wurmus f196b3b7a5
gnu: python-tinycss2: Simplify. 
* gnu/packages/python-web.scm (python-tinycss2)[build-system]: Use
pyproject-build-system.
[arguments]: Remove.
 2023-04-27 09:11:05 +02:00
Ricardo Wurmus 0dc7f773fd
gnu: python-openapi-core: Add missing input. 
* gnu/packages/python-web.scm (python-openapi-core)[build-system]: Use
pyproject-build-system.
[arguments]: Do not override 'check phase; specify #:test-flags.
[native-inputs]: Add python-mock.
 2023-04-27 08:43:29 +02:00
Ricardo Wurmus d8fe2e4735
gnu: libwebsockets: Update to 4.3.2. 
* gnu/packages/web.scm (libwebsockets): Update to 4.3.2.
[arguments]: Remove.
[source]: Use GIT-FILE-NAME.
 2023-04-27 08:06:13 +02:00
Ricardo Wurmus db19e30673
gnu: python-google-cloud-storage: Add missing input. 
* gnu/packages/python-web.scm (python-google-cloud-storage)[native-inputs]:
Add python-mock.
 2023-04-27 06:53:37 +02:00