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Author SHA1 Message Date
Ricardo Wurmus 2bf6f659c4
gnu: Add java-pj.
* gnu/packages/java.scm (java-pj): New variable.
2023-04-29 20:09:33 +02:00
Ricardo Wurmus 4837210129
gnu: r-dearseq: Update to 1.12.0.
* gnu/packages/bioconductor.scm (r-dearseq): Update to 1.12.0.
2023-04-29 20:09:33 +02:00
Ricardo Wurmus 8f93a53a4c
gnu: r-damefinder: Update to 1.12.0.
* gnu/packages/bioconductor.scm (r-damefinder): Update to 1.12.0.
2023-04-29 20:09:33 +02:00
Ricardo Wurmus 01ba2a24d2
gnu: r-dama: Update to 1.72.0.
* gnu/packages/bioconductor.scm (r-dama): Update to 1.72.0.
2023-04-29 20:09:33 +02:00
Ricardo Wurmus 9b305554a3
gnu: r-cummerbund: Update to 2.42.0.
* gnu/packages/bioconductor.scm (r-cummerbund): Update to 2.42.0.
2023-04-29 20:09:33 +02:00
Ricardo Wurmus 6233b26d1d
gnu: r-coverageview: Update to 1.38.0.
* gnu/packages/bioconductor.scm (r-coverageview): Update to 1.38.0.
2023-04-29 20:09:33 +02:00
Ricardo Wurmus f869abfae3
gnu: r-cardelino: Update to 1.2.0.
* gnu/packages/bioconductor.scm (r-cardelino): Update to 1.2.0.
2023-04-29 20:09:33 +02:00
Ricardo Wurmus 084e990d2f
gnu: r-breakpointr: Update to 1.18.0.
* gnu/packages/bioconductor.scm (r-breakpointr): Update to 1.18.0.
2023-04-29 20:09:33 +02:00
Ricardo Wurmus cb191936d8
gnu: r-biocgenerics: Update to 0.46.0.
* gnu/packages/bioconductor.scm (r-biocgenerics): Update to 0.46.0.
2023-04-29 20:09:33 +02:00
Ricardo Wurmus 3b302bdf35
gnu: r-biocversion: Update to 3.17.1.
* gnu/packages/bioconductor.scm (r-biocversion): Update to 3.17.1.
2023-04-29 20:09:33 +02:00
Ricardo Wurmus ae85652e4b
gnu: r-barcodetrackr: Update to 1.8.0.
* gnu/packages/bioconductor.scm (r-barcodetrackr): Update to 1.8.0.
2023-04-29 20:09:33 +02:00
Ricardo Wurmus 41bff44b32
gnu: r-banocc: Update to 1.24.0.
* gnu/packages/bioconductor.scm (r-banocc): Update to 1.24.0.
2023-04-29 20:09:33 +02:00
Ricardo Wurmus c6d14bd6fb
gnu: r-bandits: Update to 1.16.0.
* gnu/packages/bioconductor.scm (r-bandits): Update to 1.16.0.
2023-04-29 20:09:33 +02:00
Ricardo Wurmus 7bce4cdacb
gnu: r-bambu: Update to 3.2.0.
* gnu/packages/bioconductor.scm (r-bambu): Update to 3.2.0.
2023-04-29 20:09:33 +02:00
Ricardo Wurmus 4f4d38cc4d
gnu: r-badregionfinder: Update to 1.28.0.
* gnu/packages/bioconductor.scm (r-badregionfinder): Update to 1.28.0.
2023-04-29 20:09:33 +02:00
Ricardo Wurmus e10c8fe41a
gnu: r-bader: Update to 1.38.0.
* gnu/packages/bioconductor.scm (r-bader): Update to 1.38.0.
2023-04-29 20:09:33 +02:00
Ricardo Wurmus ff5191816e
gnu: r-basespacer: Update to 1.44.0.
* gnu/packages/bioconductor.scm (r-basespacer): Update to 1.44.0.
2023-04-29 20:09:33 +02:00
Ricardo Wurmus bc466e59b8
gnu: r-baalchip: Update to 1.26.0.
* gnu/packages/bioconductor.scm (r-baalchip): Update to 1.26.0.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus 14191d89a7
gnu: r-awst: Update to 1.8.0.
* gnu/packages/bioconductor.scm (r-awst): Update to 1.8.0.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus d12336de7d
gnu: r-awfisher: Update to 1.14.0.
* gnu/packages/bioconductor.scm (r-awfisher): Update to 1.14.0.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus ed2578b585
gnu: r-attract: Update to 1.52.0.
* gnu/packages/bioconductor.scm (r-attract): Update to 1.52.0.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus 36aa29a62f
gnu: r-atsnp: Update to 1.16.0.
* gnu/packages/bioconductor.scm (r-atsnp): Update to 1.16.0.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus 9f61c365a4
gnu: r-atena: Update to 1.6.0.
* gnu/packages/bioconductor.scm (r-atena): Update to 1.6.0.
[propagated-inputs]: Remove r-scales.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus 7751b88692
gnu: r-asset: Update to 2.18.0.
* gnu/packages/bioconductor.scm (r-asset): Update to 2.18.0.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus 32b0da7762
gnu: r-assessorf: Update to 1.18.0.
* gnu/packages/bioconductor.scm (r-assessorf): Update to 1.18.0.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus 0968cf8f55
gnu: r-aspli: Update to 2.10.0.
* gnu/packages/bioconductor.scm (r-aspli): Update to 2.10.0.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus ba469d4674
gnu: r-asics: Update to 2.16.0.
* gnu/packages/bioconductor.scm (r-asics): Update to 2.16.0.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus d3ae3e616e
gnu: r-asgsca: Update to 1.34.0.
* gnu/packages/bioconductor.scm (r-asgsca): Update to 1.34.0.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus e1e75eec31
gnu: r-aseb: Update to 1.44.0.
* gnu/packages/bioconductor.scm (r-aseb): Update to 1.44.0.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus 4a5f8cede6
gnu: r-asafe: Update to 1.26.0.
* gnu/packages/bioconductor.scm (r-asafe): Update to 1.26.0.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus 5329b80aa1
gnu: r-arrayexpress: Update to 1.60.0.
* gnu/packages/bioconductor.scm (r-arrayexpress): Update to 1.60.0.
[propagated-inputs]: Remove r-xml; add r-httr, r-jsonlite, and r-rlang.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus 0e88aa5b07
gnu: r-antiprofiles: Update to 1.40.0.
* gnu/packages/bioconductor.scm (r-antiprofiles): Update to 1.40.0.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus b77e71f07c
gnu: r-annmap: Update to 1.42.0.
* gnu/packages/bioconductor.scm (r-annmap): Update to 1.42.0.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus 18ad546d0a
gnu: r-anf: Update to 1.22.0.
* gnu/packages/bioconductor.scm (r-anf): Update to 1.22.0.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus 099340458b
gnu: r-aneufinder: Update to 1.28.0.
* gnu/packages/bioconductor.scm (r-aneufinder): Update to 1.28.0.
[propagated-inputs]: Remove r-reordercluster.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus 8e5e97293d
gnu: r-altcdfenvs: Update to 2.62.0.
* gnu/packages/bioconductor.scm (r-altcdfenvs): Update to 2.62.0.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus 55f6d75cdb
gnu: r-alpsnmr: Update to 4.2.0.
* gnu/packages/bioconductor.scm (r-alpsnmr): Update to 4.2.0.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus dec3658f6b
gnu: r-alpine: Update to 1.25.0.
* gnu/packages/bioconductor.scm (r-alpine): Update to 1.25.0.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus 19636f0341
gnu: r-alphabeta: Update to 1.14.0.
* gnu/packages/bioconductor.scm (r-alphabeta): Update to 1.14.0.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus 76ffa191be
gnu: r-alevinqc: Update to 1.16.0.
* gnu/packages/bioconductor.scm (r-alevinqc): Update to 1.16.0.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus 769af4fda7
gnu: r-aldex2: Update to 1.32.0.
* gnu/packages/bioconductor.scm (r-aldex2): Update to 1.32.0.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus 87932885ea
gnu: r-anvil: Update to 1.12.0.
* gnu/packages/bioconductor.scm (r-anvil): Update to 1.12.0.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus fd5e94f6df
gnu: r-annotationhubdata: Update to 1.30.0.
* gnu/packages/bioconductor.scm (r-annotationhubdata): Update to 1.30.0.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus 6027d657bd
gnu: r-animalcules: Update to 1.16.0.
* gnu/packages/bioconductor.scm (r-animalcules): Update to 1.16.0.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus 71b23bf5e1
gnu: r-ancombc: Update to 2.2.0.
* gnu/packages/bioconductor.scm (r-ancombc): Update to 2.2.0.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus 1f753b82c1
gnu: r-anaquin: Update to 2.24.0.
* gnu/packages/bioconductor.scm (r-anaquin): Update to 2.24.0.
2023-04-29 20:09:32 +02:00
Ricardo Wurmus ab79d3a4b8
gnu: r-amaretto: Update to 1.16.0.
* gnu/packages/bioconductor.scm (r-amaretto): Update to 1.16.0.
2023-04-29 20:09:31 +02:00
Ricardo Wurmus 4b2295bd4f
gnu: r-amplican: Update to 1.21.0.
* gnu/packages/bioconductor.scm (r-amplican): Update to 1.21.0.
2023-04-29 20:09:31 +02:00
Ricardo Wurmus a49b8d3be0
gnu: r-amountain: Update to 1.26.0.
* gnu/packages/bioconductor.scm (r-amountain): Update to 1.26.0.
2023-04-29 20:09:31 +02:00
Ricardo Wurmus 945ed79525
gnu: r-airpart: Update to 1.8.0.
* gnu/packages/bioconductor.scm (r-airpart): Update to 1.8.0.
2023-04-29 20:09:31 +02:00
Ricardo Wurmus 02a34b10b6
gnu: r-aims: Update to 1.32.0.
* gnu/packages/bioconductor.scm (r-aims): Update to 1.32.0.
2023-04-29 20:09:31 +02:00
Ricardo Wurmus 47024dae6e
gnu: r-agimicrorna: Update to 2.50.0.
* gnu/packages/bioconductor.scm (r-agimicrorna): Update to 2.50.0.
2023-04-29 20:09:31 +02:00
Ricardo Wurmus a8730669b5
gnu: r-adductomicsr: Update to 1.16.0.
* gnu/packages/bioconductor.scm (r-adductomicsr): Update to 1.16.0.
2023-04-29 20:09:31 +02:00
Ricardo Wurmus 89c4664ac7
gnu: r-agilp: Update to 3.32.0.
* gnu/packages/bioconductor.scm (r-agilp): Update to 3.32.0.
2023-04-29 20:09:31 +02:00
Ricardo Wurmus 0174fb6d49
gnu: r-aggregatebiovar: Update to 1.10.0.
* gnu/packages/bioconductor.scm (r-aggregatebiovar): Update to 1.10.0.
2023-04-29 20:09:31 +02:00
Ricardo Wurmus 626b010f1a
gnu: r-agdex: Update to 1.48.0.
* gnu/packages/bioconductor.scm (r-agdex): Update to 1.48.0.
2023-04-29 20:09:31 +02:00
Ricardo Wurmus 9baa783e63
gnu: r-affyrnadegradation: Update to 1.46.0.
* gnu/packages/bioconductor.scm (r-affyrnadegradation): Update to 1.46.0.
2023-04-29 20:09:31 +02:00
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 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
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
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
Ricardo Wurmus 40451d0f2d
gnu: python-google-resumable-media: Add missing input.
* gnu/packages/python-web.scm (python-google-resumable-media)[native-inputs]:
Add python-mock.
2023-04-27 06:53:12 +02:00
Ricardo Wurmus cec543e70f
gnu: python-aws-xray-sdk: Update to 2.12.0.
* gnu/packages/python-web.scm (python-aws-xray-sdk): Update to 2.12.0.
[build-system]: Use pyproject-build-system.
[arguments]: Specify #:test-flags; do not override 'check phase; add
'pre-check phase.
[native-inputs]: Add python-httpx, python-mock, python-pytest-asyncio, and
python-pytest-benchmark.
2023-04-27 06:48:27 +02:00
Ricardo Wurmus e5619147d4
gnu: python-httpx: Update to 0.24.0.
* gnu/packages/python-web.scm (python-httpx): Update to 0.24.0.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom check phase in favor of specifying #:test-flags.
[native-inputs]: Add python-hatchling and python-hatch-fancy-pypi-readme.
(python-httpx-bootstrap)[native-inputs]: Add python-hatchling and
python-hatch-fancy-pypi-readme.
2023-04-27 06:37:23 +02:00
Ricardo Wurmus 3b19fc1801
gnu: python-httpcore: Update to 0.17.0.
* gnu/packages/python-web.scm (python-httpcore): Update to 0.17.0.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom check phase; specify #:test-flags; disable broken
tests.
2023-04-27 06:36:19 +02:00
Ricardo Wurmus f95498c92e
gnu: python-h11: Update to 0.14.0.
* gnu/packages/python-web.scm (python-h11): Update to 0.14.0.
[build-system]: Use pyproject-build-system.
[arguments]: Remove.
2023-04-27 06:35:38 +02:00
Ricardo Wurmus e1ca411852
gnu: python-wsproto: Update to 1.2.0.
* gnu/packages/python-web.scm (python-wsproto): Update to 1.2.0.
[build-system]: Use pyproject-build-system.
[arguments]: Remove.
2023-04-27 06:34:57 +02:00
Ricardo Wurmus bb385f2472
gnu: python-dendropy: Fix build.
* gnu/packages/bioinformatics.scm (python-dendropy)[native-inputs]: Add
python-pytest.
[arguments]: Add phase 'python-compatibility; remove 'skip-broken-tests; add
 #:test-flags; do not delete test files.
[build-system]: Use pyproject-build-system.
2023-04-26 22:53:26 +02:00
Ricardo Wurmus 4ea332cd50
gnu: python-watchgod: Update to 0.8.1.
* gnu/packages/python-xyz.scm (python-watchgod): Update to 0.8.1.
[build-system]: Use pyproject-build-system.
[arguments]: Specify #:test-flags instead of overwriting 'check phase.
[native-inputs]: Add python-anyio.
2023-04-26 22:52:05 +02:00
Ricardo Wurmus 18786ae502
gnu: python-fastjsonschema: Use pyproject-build-system.
* gnu/packages/python-xyz.scm (python-fastjsonschema): Reindent.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom check phase; update comment on why tests are
disabled.
2023-04-26 22:12:32 +02:00
Ricardo Wurmus 182fbbb009
gnu: python-rapidjson: Update to 1.10.
* gnu/packages/python-web.scm (python-rapidjson): Update to 1.10.
[source]: Simplify snippet.
[arguments]: Run tests conditionally; do not delete test files.
2023-04-26 22:11:07 +02:00
Ricardo Wurmus 00cf71df80
gnu: rapidjson: Update to 1.1.0-1.949c771.
* gnu/packages/patches/rapidjson-gcc-compat.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/web.scm (rapidjson): Update to 1.1.0-1.949c771.
[source]: Remove obsolete patch.
2023-04-26 22:09:06 +02:00
Ricardo Wurmus abda97b645
gnu: python-multiprocess: Update to 0.70.14.
* gnu/packages/python-xyz.scm (python-multiprocess): Update to 0.70.14.
[build-system]: Use pyproject-build-system.
[arguments]: Adjust directory containing tests; disable two more tests;
replace check phase instead of deleting and adding it; run tests
conditionally.
2023-04-26 21:33:02 +02:00
Ricardo Wurmus 95fdd862d0
gnu: python-dill: Update to 0.3.6.
* gnu/packages/python-xyz.scm (python-dill): Update to 0.3.6.
[build-system]: Use pyproject-build-system.
[arguments]: Run tests conditionally; drop trailing #T from build phase.
2023-04-26 21:33:02 +02:00
Ricardo Wurmus d12ad4105a
gnu: python-jupyterlab-widgets: Update to 1.1.4.
* gnu/packages/jupyter.scm (python-jupyterlab-widgets): Update to 1.1.4.
[build-system]: Use pyproject-build-system.
2023-04-26 21:33:02 +02:00
Ricardo Wurmus faa4485b52
gnu: python-fire: Add missing input.
* gnu/packages/python-xyz.scm (python-fire)[native-inputs]: Add python-mock.
2023-04-26 21:33:02 +02:00
Liliana Marie Prikler d38bdca344
gnu: gitg: Fix build.
* gnu/packages/patches/gitg-fix-positional-argument.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it here.
* gnu/packages/gnome.scm (gitg)[source]<patches>: Use it here.
2023-04-26 20:52:33 +02:00
Liliana Marie Prikler d7e489d6e0
gnu: gnome-2048: Fix build.
* gnu/packages/patches/gnome-2048-fix-positional-argument.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it here.
* gnu/packages/games.scm (gnome-2048)[source]<patches>: Use it here.
2023-04-26 20:52:32 +02:00
Ricardo Wurmus e86851ccb3
gnu: python-umap-learn: Patch for sklearn/numpy compatibility.
* gnu/packages/machine-learning.scm (python-umap-learn)[arguments]: Add phase
'numpy-compatibility.
2023-04-26 18:34:46 +02:00
Ricardo Wurmus 5bfce83dc4
gnu: python-tables: Build cython files from source.
* gnu/packages/python-xyz.scm (python-tables)[source]: Remove generated C
files.
[arguments]: Remove trailing #T from build phases; use G-expression; override
library directories.
[inputs]: Add c-blosc and lzo.
2023-04-26 17:01:08 +02:00
Ricardo Wurmus 2d883cbd6d
gnu: python-bokeh: Add missing input.
* gnu/packages/python-xyz.scm (python-bokeh)[native-inputs]: Add python-mock.
2023-04-26 16:39:10 +02:00
Ricardo Wurmus 41ba9df6ba
gnu: python-tornado: Run a lot more tests and fix collections.
* gnu/packages/python-web.scm (python-tornado)[arguments]: Do run tests; add
phase 'fix-collections.
2023-04-26 16:11:11 +02:00
Andreas Enge 81ec8eba91
gnu: nikola: Add input.
* gnu/packages/python-xyz.scm (nikola)[propagated-inputs]: Add python-toml.
2023-04-26 15:56:30 +02:00
Sharlatan Hellseher 1f7d1125a3
gnu: cl-mock: Update to 1.1.0-0.01762fd.
* gnu/packages/lisp-xyz.scm (sbcl-cl-mock): Update to 1.1.0-0.01762fd.
  [arguments]: Build cl-mock and cl-mock-basic systems.
  [inputs]: Add sbcl-bordeaux-threads.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2023-04-26 15:08:15 +02:00
Sharlatan Hellseher 8d217f1e22
gnu: cl-fast-ecs: Update to 0.2.2.
* gnu/packages/lisp-xyz.scm (sbcl-cl-fast-ecs): Update to 0.2.2.
  [native-inputs]: Add sbcl-chlorophyll, sbcl-cl-mock.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2023-04-26 15:08:15 +02:00
Sharlatan Hellseher 870f2d40e0
gnu: Add cl-chlorophyll.
* gnu/packages/lisp-xyz.scm (cl-chlorophyll, ecl-chlorophyll,
  sbcl-chlorophyll): New variables.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2023-04-26 15:08:15 +02:00
Artyom Bologov e129321f13
gnu: cl-nclasses: Update to 0.4.0.
gnu/packages/lisp-xyz.scm (sbcl-nclasses): Update to 0.4.0.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2023-04-26 15:08:15 +02:00
Guillaume Le Vaillant 62fed3b874
gnu: flwrap: Update to 1.3.6.
* gnu/packages/radio.scm (flwrap): Update to 1.3.6.
2023-04-26 15:08:15 +02:00
Guillaume Le Vaillant bfbe2a518d
gnu: pdf2djvu: Update to 0.9.19.
* gnu/packages/djvu.scm (pdf2djvu): Update to 0.9.19.
2023-04-26 15:08:15 +02:00
jgart f858704e7c
gnu: xonsh: Add missing input.
Xonsh vim emulation mode/environment variable does not work without this.

* gnu/packages/shell.scm (xonsh)[inputs]: Add PYTHON-PROMPT-TOOLKIT.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2023-04-26 14:56:55 +02:00
kiasoc5 9d12ce6fa4
gnu: plocate: Update to 1.1.18.
* gnu/packages/search.scm (plocate): Update to 1.1.18.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2023-04-26 14:49:08 +02:00
Nicolas Goaziou 2dc87d8dcf
gnu: emacs-vertico: Update to 1.3.
* gnu/packages/emacs-xyz.scm (emacs-vertico): Update to 1.3.
2023-04-26 14:49:08 +02:00
Christine Lemmer-Webber 3856ca96fc
gnu: Add emacs-lojban.
* gnu/packages/emacs-xyz.scm (emacs-lojban): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2023-04-26 14:49:07 +02:00
zimoun c3509c2148
gnu: valgrind: Update to 3.20.0.
* gnu/packages/valgrind.scm (valgrind): Update to 3.20.0. Remove patch.
[arguments]<phases>: Remove trailing #t.
* gnu/packages/patches/valgrind-enable-arm.patch: Delete file.
* gnu/packages/valgrind.scm (dist_patch_DATA): Unregister patch.

Signed-off-by: Andreas Enge <andreas@enge.fr>
2023-04-26 14:34:23 +02:00
zimoun 50dcd1acd7
gnu: lz4: Remove valgrind from native-inputs.
* gnu/compression.scm (lz4)[native-inputs]: Remove valgrind.
[arguments]<phases>: Remove trailing #t.

Signed-off-by: Andreas Enge <andreas@enge.fr>
2023-04-26 14:34:08 +02:00
Ricardo Wurmus 399e1b8e01
gnu: python-ipykernel: Fix build.
* gnu/packages/python-xyz.scm (python-ipykernel)[build-system]: Use
pyproject-build-system.
[arguments]: Use pyproject-build-system modules; add build phase
'hide-zmq-deprecation-warnings.
2023-04-26 13:33:30 +02:00
Ricardo Wurmus 4ef9fbcc35
gnu: python-jupyter-client: Disable one test.
* gnu/packages/python-xyz.scm (python-jupyter-client)[arguments]: Begrudgingly
disable one failing test, because there is no information on why it fails.
2023-04-26 11:44:45 +02:00
Ricardo Wurmus cc79caccee
gnu: python-jupyter-client-bootstrap: Hide zmq deprecation warning.
* gnu/packages/python-xyz.scm (python-jupyter-client-bootstrap)[arguments]:
Add phase 'hide-zmq-deprecation-warning.
2023-04-26 11:44:45 +02:00
Ricardo Wurmus 358428c1ec
gnu: python-jupyter-client-bootstrap: Use pyproject-build-system.
* gnu/packages/python-xyz.scm (python-jupyter-client-bootstrap)[build-system]:
Use pyproject-build-system.
2023-04-26 11:44:45 +02:00
Ricardo Wurmus 5409ae48af
gnu: python-distributed: Fix build.
* gnu/packages/python-science.scm (python-distributed)[build-system]: Use
pyproject-build-system.
[arguments]: Hide deprecation warnings from tornado, because they break almost
all tests; disable three more tests.
2023-04-26 11:17:41 +02:00
Efraim Flashner 2bf96f2d9e
gnu: cppcheck: Update to 2.10.3.
* gnu/packages/check.scm (cppcheck): Update to 2.10.3.
[home-page]: Update to new home-page.
2023-04-26 10:51:52 +03:00
Efraim Flashner 8720e22fd0
gnu: cppcheck: Skip failing test.
* gnu/packages/patches/check.scm (cppcheck)[source]: Add patch.
* gnu/packages/patches/cppcheck-disable-char-signedness-test.patch: New
file.
* gnu/local.mk (dist_patch_DATA): Register it.
2023-04-26 10:51:44 +03:00
Andreas Enge ff4e463ddc
gnu: graphviz: Remove version 2.38.
This is a follow-up to commit 370cb92eaa .

* gnu/packages/graphviz.scm: Drop imported modules.
(graphviz-2.38): Remove package.
2023-04-26 09:40:16 +02:00
Ludovic Courtès 8093c6ba21
gnu: lcov: Update to 1.16.
* gnu/packages/code.scm (lcov): Update to 1.16.
2023-04-25 23:43:05 +02:00
Ludovic Courtès 9fcd51280f
gnu: perl-io-compress: Update to 2.204.
* gnu/packages/perl-compression.scm (perl-io-compress): Update to 2.204.
2023-04-25 23:43:05 +02:00
Ludovic Courtès 70acf8b23a
gnu: perl-compress-raw-bzip2: Update to 2.204.
* gnu/packages/perl-compression.scm (perl-compress-raw-bzip2): Update to
2.204.
2023-04-25 23:43:05 +02:00
Ludovic Courtès 6ea4228442
gnu: perl-compress-raw-zlib: Update to 2.204.
* gnu/packages/perl-compression.scm (perl-compress-raw-zlib): Update to
2.204.
[arguments]: Remove.
2023-04-25 23:43:05 +02:00
Efraim Flashner e287a0e402
gnu: gnutls: Don't embed a phase inside another phase.
* gnu/packages/tls.scm (gnutls)[arguments]: Adjust powerpc-linux phase
'increase-test-timeout to not be embedded inside another phase.
2023-04-25 23:32:17 +03:00
Efraim Flashner ccf64b6a8b
gnu: mpdevil: Add missing input.
* gnu/packages/mpd.scm (mpdevil)[native-inputs]: Add gettext-minimal.
2023-04-25 23:08:45 +03:00
Efraim Flashner aeda325cf1
gnu: presage: Build with c++-14.
* gnu/packages/fcitx.scm (presage)[arguments]: Adjust configure-flags to
use c++-14 cor CFLAGS and CXXFLAGS.
2023-04-25 23:01:56 +03:00
Efraim Flashner 97323e5262
gnu: libpst: Fix python detection.
* gnu/packages/mail.scm (libpst)[arguments]: Add a phase to detect newer
versions of python3.
[native-inputs]: Add autoconf, automake, gettext-minimal, libool.
2023-04-25 22:52:29 +03:00
Ricardo Wurmus 72b1c9713b
gnu: perl-data-dumper: Update to 2.183.
* gnu/packages/perl.scm (perl-data-dumper): Update to 2.183.
2023-04-25 21:18:36 +02:00
Ricardo Wurmus 4598928a90
gnu: cwltool: Use pyproject-build-system.
"setup.py install is deprecated. Use build and pip and other standards-based
tools."  It then falls back to attempting to install packages via pip.

* gnu/packages/bioinformatics.scm (cwltool)[build-system]: Use
pyproject-build-system.
2023-04-25 21:18:36 +02:00
Ricardo Wurmus 92a903499b
gnu: python-schema-salad: Use pyproject-build-system.
The python-build-system fails with "setuptools.installer is
deprecated. Requirements should be satisfied by a PEP 517 installer."  This,
in turn, causes all Python packages to be ignored and "pip install" to be
invoked for them.

* gnu/packages/bioinformatics.scm (python-schema-salad)[build-system]: Use
pyproject-build-system.
2023-04-25 21:18:35 +02:00
Liliana Marie Prikler 2ec69787aa
gnu: gfeeds: Add missing gettext-minimal.
* gnu/packages/syndication.scm (gfeeds)[inputs]: Add gettext-minimal.
2023-04-25 21:09:13 +02:00
Liliana Marie Prikler 30a252760f
gnu: syndication-domination: Update to 1.0-1-7592032.
* gnu/packages/syndication.scm (syndication-domination): Update to
1.0-1-7592032.
2023-04-25 21:09:13 +02:00
Liliana Marie Prikler ff777165cb
gnu: evolution: Update to 3.46.4.
* gnu/packages/gnome.scm (evolution): Update to 3.46.4.
2023-04-25 21:09:13 +02:00
Liliana Marie Prikler 916df2b9eb
gnu: evolution-data-server: Update to 3.46.4.
* gnu/packages/gnome.scm (evolution-data-server): Update to 3.46.4.
2023-04-25 21:09:12 +02:00
Ricardo Wurmus 5a1b246736
gnu: adapterremoval: Update to 2.3.3.
* gnu/packages/bioinformatics.scm (adapterremoval): Update to 2.3.3.
[arguments]: Simplify.
[inputs]: Reformat.
2023-04-25 19:46:29 +02:00
Efraim Flashner d67b8788b3
gnu: ocaml-lwt: Add ocaml4.07 variant.
* gnu/packages/ocaml.scm (ocaml-lwt)[properties]: New field.
(ocaml4.07-lwt): New variable.
2023-04-25 20:42:22 +03:00
Efraim Flashner 52f6ccef82
gnu: perl-crypt-openssl-rsa: Update to 0.33.
* gnu/packages/tls.scm (perl-crypt-openssl-rsa): Update to 0.33.
2023-04-25 20:42:22 +03:00
Ricardo Wurmus fc80efe1a0
gnu: bedtools-2.18: Fix build.
* gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Fix operators in
'compatibility phase.
2023-04-25 19:41:05 +02:00
Ricardo Wurmus f2e90d6f43
gnu: hisat: Build with GCC 10.
* gnu/packages/bioinformatics.scm (hisat)[native-inputs]: Add gcc-10.
2023-04-25 19:30:43 +02:00
Ricardo Wurmus 0a4fa99b39
gnu: kallisto: Update to 0.48.0.
* gnu/packages/bioinformatics.scm (kallisto): Update to 0.48.0.
[arguments]: Remove trailing #T from build phase.
2023-04-25 19:28:42 +02:00
Ricardo Wurmus 7ae5325bf1
gnu: bpp-core: Build with GCC 10.
* gnu/packages/bioinformatics.scm (bpp-core)[native-inputs]: Add gcc-10.
2023-04-25 19:12:57 +02:00
Ricardo Wurmus 2c09cc19e6
gnu: vcflib: Update to 1.0.9.
* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.9.
[source]: Update snippet.
[inputs]: Add curl, pybind11, and wfa2-lib.
[arguments]: Adjust and reformat.
2023-04-25 19:10:19 +02:00
Ricardo Wurmus 4ad51f5914
gnu: tabixpp: Update to 1.1.2.
* gnu/packages/bioinformatics.scm (tabixpp): Update to 1.1.2.
[source]: Simplify snippet.
[inputs]: Add curl.
[arguments]: Simplify and reformat.
2023-04-25 19:10:19 +02:00
Ricardo Wurmus 8664c6230e
gnu: Add wfa2-lib.
* gnu/packages/bioinformatics.scm (wfa2-lib): New variable.
2023-04-25 19:10:18 +02:00
Josselin Poiret 8c5ba69d6e
gnu: biber: Fix build with new Perl.
* gnu/packages/patches/biber-adapt-perl-5.36.patch: Backport patch from
upstream's 760e6e4ec08a3097f7e6136331541a7b8c1c9df7.
* gnu/packages/tex.scm (biber): Use it.
* gnu/local.mk (dist_patch_DATA): Register it.

Signed-off-by: Andreas Enge <andreas@enge.fr>
2023-04-25 18:42:22 +02:00
Vivien Kraus 74038cf66e
gnu: gcc: Do not build gcov on MinGW.
* gnu/packages/gcc.scm (gcc-configure-flags-for-triplet): Disable gcov when
targetting mingw.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2023-04-25 17:20:19 +02:00
Nicolas Graves 7f0fbd0463
gnu: nerd-dictation: Add package variants.
* gnu/packages/machine-learning.scm (nerd-dictation)[inputs]: Remove.
(nerd-dictation-gexp): New procedure.
(nerd-dictation/xdotool, nerd-dictation/sox-xdotool)
(nerd-dictation/sox-ydotool, nerd-dictation/sox-wtype): New variables

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-04-25 17:19:21 +02:00
Bruno Victal 9be1ee6a49
services: tor: Deprecate 'tor-hidden-service' procedure.
Due to (now renamed) 'hidden-service' record type not being exported, the only
way Onion services (formely hidden services) could have worked is through the
now deprecated 'tor-hidden-service' procedure.

This commit updates the Tor service documentation, corrects some inconsistently
named accessors in <tor-configuration> record-type, renames and refactors
tor-hidden-service-configuration to tor-onion-service-configuration using
define-configuration and also exports it, allowing Onion services to be
configured directly within a <tor-configuration> record.
Lastly, it also deprecates the 'tor-hidden-service' procedure.

* doc/guix.texi (Networking Services): Substitute mentions of “Hidden services”
with “Onion Services”. Add a Tor Onion service configuration example.
Document <tor-onion-service-configuration>. Remove mention of
'tor-hidden-service' procedure.
* gnu/services/networking.scm: Export tor-configuration-tor,
tor-configuration-config-file, tor-configuration-hidden-services,
tor-configuration-socks-socket-type, tor-configuration-control-socket-path,
tor-onion-service-configuration, tor-onion-service-configuration?,
tor-onion-service-configuration-name, tor-onion-service-configuration-mapping.
(<tor-configuration>)[control-socket?]: Rename accessor.
(<hidden-service>): Replace with …
(<tor-onion-service-configuration>): … this.
(tor-configuration->torrc): Update record-type name.
(tor-activation): Ditto.
(tor-hidden-service-type): Remove variable.
(tor-hidden-service): Deprecate procedure.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-04-25 17:19:21 +02:00
Lars-Dominik Braun c354a345b9
gnu: ghc-8.10: Avoid testsuite timeouts on i686.
* gnu/packages/haskell.scm (ghc-8.10)[arguments]: Add new phase
'skip-failing-tests-i686-cuirass.
2023-04-25 16:54:57 +02:00
Ricardo Wurmus 3a37e3ecd8
gnu: lofreq: Set file timestamps to 1980s.
This keeps Python from complaining: "ZIP does not support timestamps before
1980".

* gnu/packages/bioinformatics.scm (lofreq)[arguments]: Add build phase
'set-source-file-times-to-1980.
2023-04-25 16:17:49 +02:00
Ricardo Wurmus 0ad4a4d155
gnu: lofreq: Drop input labels.
* gnu/packages/bioinformatics.scm (lofreq)[inputs]: Drop package labels.
2023-04-25 16:17:49 +02:00
Ricardo Wurmus 1fca85cd88
gnu: ivar: Update to 1.4.2.
* gnu/packages/bioinformatics.scm (ivar): Update to 1.4.2.
[arguments]: Remove -Werror flag.
2023-04-25 16:17:49 +02:00
Ricardo Wurmus f69f346289
gnu: propeller-gcc-4: Use MODIFY-INPUTS.
* gnu/packages/embedded.scm (propeller-gcc-4)[native-inputs]: Use
MODIFY-INPUTS and drop package label.
2023-04-25 16:17:49 +02:00
Ricardo Wurmus b9162199b3
gnu: propeller-gcc-4: Use G-expression.
* gnu/packages/embedded.scm (propeller-gcc-4)[arguments]: Use G-expression
because the parent GCC package uses them too.
2023-04-25 16:17:49 +02:00
Andreas Enge b380fbca88
gnu: trurl: Correct inputs.
* gnu/packages/curl.scm (trurl): Replace non-existant input curl-7.84.0 by
curl, which is version 7.85.0.
2023-04-25 15:21:05 +02:00
Andreas Enge c919bfefd9
Merge remote-tracking branch 'origin/master' into core-updates 2023-04-25 15:19:29 +02:00
Lars-Dominik Braun 472706ae2f
gnu: python-asyncssh: Update to 2.13.1.
Includes fix for python-cryptography>=39 disallowing SHA-1 signatures,
which caused the testsuite to fail.

* gnu/packages/ssh.scm (python-asyncssh): Update to 2.13.1.
2023-04-25 14:27:14 +02:00
Efraim Flashner 0daa747de2
gnu: alacritty: Patch reference to xdg-open.
* gnu/packages/terminals.scm (alacritty)[arguments]: Add a phase to add
an absolute reference to xdg-open.
[inputs]: Add xdg-utils.
2023-04-25 14:06:14 +03:00
Nicolas Goaziou 95787ffaa2
gnu: emacs-eshell-syntax-highlighting: Update to 0.5.
* gnu/packages/emacs-xyz.scm (emacs-eshell-syntax-highlighting): Update to 0.5.
2023-04-25 11:47:52 +02:00
Nicolas Goaziou c9c4fea7c5
gnu: nethack: Update to 3.6.7.
* gnu/packages/games.scm (nethack): Update to 3.6.7.
2023-04-25 11:47:51 +02:00
Sharlatan Hellseher 11f078a1fb
gnu: Add trurl.
* gnu/packages/curl.scm (trurl): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2023-04-25 11:47:51 +02:00
Nicolas Goaziou 26cdc7be84
gnu: emacs-auctex: Update to 13.2.0.
* gnu/packages/emacs-xyz.scm (emacs-auctex): Update to 13.2.0.
2023-04-25 11:47:51 +02:00
Joseph LaFreniere af3daff5ea
gnu: Add emacs-xonsh-mode.
* gnu/packages/emacs-xyz.scm (emacs-xonsh-mode): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2023-04-25 11:47:51 +02:00
Ricardo Wurmus ce0bdceb49
gnu: python-importlib-resources: Update to 5.12.0.
* gnu/packages/python-xyz.scm (python-importlib-resources): Update to 5.12.0.
[build-system]: Use pyproject-build-system.
[arguments]: Add phase to avoid "pip install".
[native-inputs]: Remove python-toml; add python-flake8, python-pytest,
python-pytest-black, python-pytest-checkdocs, python-pytest-cov,
python-pytest-enabler, python-pytest-flake8, python-pytest-mypy, and
python-setuptools-57.
[propagated-inputs]: Add python-zipp.
2023-04-25 11:32:10 +02:00
Christopher Baines 8a5b6d5382
gnu: guix-build-coordinator: Update to 0-79.6a4e827.
* gnu/packages/package-management.scm (guix-build-coordinator): Update to
0-79.6a4e827.
2023-04-25 10:25:55 +01:00
Antero Mejr a50f0dc5ca
gnu: schismtracker: Update to 20221201.
* gnu/packages/music.scm (schismtracker): Update to 20221201.
[source]: Convert snippet to gexp.
[arguments]: Convert to gexp, add configure flags for FLAC and Wayland
support.
[inputs]: Remove libx11, libxext, and sdl; add flac and sdl2.

Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-04-25 10:25:55 +01:00
Lars-Dominik Braun 54771a5b6a
gnu: python-anyio: Upgrade to 3.6.2.
* gnu/packages/python-xyz.scm (python-anyio): Upgrade to 3.6.2.
2023-04-25 11:08:32 +02:00
Lars-Dominik Braun e619750d00
Revert "gnu: python-pytest-trio: Update to 0.8.0."
Not compatible with python-trio 0.8.

This reverts commit 27a4bfbd07.
2023-04-25 11:08:30 +02:00
Lars-Dominik Braun 27e1451891
gnu: python-trio: Downgrade to 0.21.
Version 0.22 deprecates MultiError, which trips up testsuites of
dependents. python-anyio for instance is explicitly not compatible with >=
0.22, so stick to an older release.

* gnu/packages/python-xyz.scm (python-trio): Downgrade to 0.21.
[arguments]: Disable failing test.
2023-04-25 11:08:29 +02:00
Pierre Neidhardt ffb7ea6b63
gnu: sbcl-serapeum: Update to 20230423.
* gnu/packages/lisp-xyz.scm (sbcl-serapeum): Update to 20230423.
2023-04-25 10:44:16 +02:00
Pierre Neidhardt 2ebe270927
gnu: sbcl-njson: Update to 1.0.0.
* gnu/packages/lisp-xyz.scm (sbcl-njson): Update to 1.0.0.
2023-04-25 10:37:13 +02:00
Efraim Flashner 08c63aac53
gnu: slimevolley: Build with gcc-7.
* gnu/packages/games.scm (slimevolley)[native-inputs]: Add gcc-7.
2023-04-25 10:32:46 +03:00
Ricardo Wurmus 8495069bed
gnu: scribus: Fix build with latest poppler.
* gnu/packages/patches/scribus-1.5.8-poppler-22.03.0.patch,
gnu/packages/patches/scribus-1.5.8-poppler-22.04.0.patch,
gnu/packages/patches/scribus-1.5.8-poppler-22.09.0.patch,
gnu/packages/patches/scribus-1.5.8-poppler-22.2.0-1.patch,
gnu/packages/patches/scribus-1.5.8-poppler-22.2.0-2.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/scribus.scm (scribus)[source]: Add patches.
[arguments]: Enable WANT_CPP17 option.
2023-04-25 06:17:16 +02:00
Maxim Cournoyer 7fc2c442c8
gnu: gnucash: Update help installation prefix.
The help installation prefix was changed upstream to match the XDG 'help-spec'
specification (see:
https://www.freedesktop.org/wiki/Specifications/help-spec/).

* gnu/packages/gnucash.scm (gnucash) [arguments]: Adjust install-docs phase.
2023-04-24 23:35:47 -04:00
Maxim Cournoyer 971f00f237
gnu: python-tlsh: Fix build.
* gnu/packages/python-xyz.scm (python-tlsh) [build-system]: Switch to
python-build-system.
[arguments]: Remove #:out-of-source.  Remove install phase override.  Add a
configure, chdir and adjust the check phase override.
[inputs]: Delete field.
[native-inputs]: New field.
2023-04-24 21:31:56 -04:00
Maxim Cournoyer c9f82d57eb
gnu: sicp: Fix build.
* gnu/packages/scheme.scm (sicp) [build-system]: Use copy-build-system.
[native-inputs]: Remove source input.
[arguments]: Remove #:modules and #:builder arguments.  Add #:install-plan and
 #:phases arguments.  Patch out obsolete call.
2023-04-24 20:58:37 -04:00