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2025-05-12gnu: abc-yosyshq: Update to 0.53.Cayetano Santos
* gnu/packages/fpga.scm (abc-yosyshq): Update to 0.53. Change-Id: I32e4973a26e831c558ab13b2cf7e00bea87637a1 Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com> Reviewed-by: Gabriel Wicki <gabriel@erlikon.ch>
2025-05-12gnu: python-hdlmake: Update to 3.3-1.9338e3e and enable tests.Cayetano Santos
* gnu/packages/fpga.scm (python-hdlmake): Update to 3.3-1.9338e3e. [source]: Update URL. [arguments] <#:tests?>: Delete. [native-inputs]: Add python-pytest. [home-page]: Update URL. Change-Id: Ied124a3ceb22be427c5255b5d139f5f63031e260 Co-authored-by: Maxim Cournoyer <maxim.cournoyer@gmail.com> Reviewed-by: Gabriel Wicki <gabriel@erlikon.ch>
2025-05-12gnu: yosys: Update to 0.53.Cayetano Santos
* gnu/packages/fpga.scm (yosys): Update to 0.53. Change-Id: I7bd53033860ca9bcad367c4360625ac406fbad04 Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com> Reviewed-by: Gabriel Wicki <gabriel@erlikon.ch>
2025-05-12gnu: libinfinity: Fix test.Andreas Enge
* gnu/packages/patches/libinfinity-renew-test-certificate.patch: New file. * gnu/local.mk (dist_patch_DATA): Register patch. * gnu/packages/gobby.scm (source): Add patch. Change-Id: I37fe93799e443d3ecdba5e75fc15b2e183dfb4df
2025-05-12gnu: knot-resolver: Update to 5.7.5. [security fixes]Ashish SHUKLA
* gnu/packages/dns.scm (knot-resolver): Update to 5.7.5. Change-Id: I8e62f61c13a8161fae4fb909fad7b1522d4c3d52 Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2025-05-12gnu: Add ntpsec.Ahmad Draidi
* gnu/packages/ntp.scm: Add use-modules (gnu packages gps), (gnu packages m4), (gnu packages python), (gnu packages python-xyz), (gnu packages time), (guix build-system waf). (ntpsec): New variable. Change-Id: I34704665c338475f146fd1b61979b9e3dd8f23f4 Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2025-05-12gnu: Add pps-tools.Ahmad Draidi
* gnu/packages/time.scm (pps-tools): New variable. Change-Id: I06a10988acbf4dcd684721e1bee6a2d0c6f2dac6 Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2025-05-12linux-container: Do not attempt to lock mounts for ‘guix system container’.Ludovic Courtès
Fixes <https://issues.guix.gnu.org/78356>. * gnu/system/linux-container.scm (container-script): Pass #:lock-mounts? #f to ‘call-with-container’. Reported-by: Rutherther <rutherther@ditigal.xyz> Change-Id: Ie670868147f32baf2c2a94c9c7b1636bc84d0a0a
2025-05-12gnu: r-chromunity: Update to 0.0.2-2.101e30a.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-chromunity): Update to 0.0.2-2.101e30a. [arguments]: Disable one test. Change-Id: I522e993d86cf88914a95c9fb15d933c7af906c41
2025-05-12gnu: Remove r-snapcgh.Ricardo Wurmus
This package has been removed with the release of Bioconductor 3.19, and it now fails to build. * gnu/packages/bioconductor.scm (r-snapcgh): Remove variable. Change-Id: Id4408ea2d17d07913fea359292eb3e5d7329b13d
2025-05-12gnu: pigx-scrnaseq: Use Snakemake 5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace snakemake-7 with snakemake-5. [arguments]: Set HOME. Change-Id: I45257e138c4cf468d179ff35b0c705bc73046052
2025-05-12gnu: pigx-bsseq: Set HOME.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Add phase 'pre-check. Change-Id: Ic88976554e6e7c7955ae9ab4f0232330060446c9
2025-05-12gnu: pigx-chipseq: Set HOME.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-chipseq)[arguments]: Add phase 'pre-check. Change-Id: Ia95db9209b5ea0cb340f9827197bdcc851266961
2025-05-12gnu: pigx-rnaseq: Set HOME.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase 'pre-check. Change-Id: Ibabfa8f14b8eaec6d25ae72a2cd0f33e6a7d2819
2025-05-12gnu: r-tradeseq: Add missing input.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-tradeseq)[native-inputs]: Add r-delayedmatrixstats. [properties]: Record it in updater-extra-native-inputs. Change-Id: Icc877a48320083d2e5c4987643d52d60c9b11f05
2025-05-12gnu: r-screpertoire: Disable one more test.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-screpertoire)[arguments]: Disable one more test. Change-Id: I9d44fc50137f6e90f69a2e871a375aff192045ae
2025-05-12gnu: r-duckdb: Disable tests.Ricardo Wurmus
* gnu/packages/cran.scm (r-duckdb)[arguments]: Disable tests. Change-Id: I046fe9e9fb34f35c9f2fcaa6bbb726fb4bbfd81c
2025-05-12gnu: r-scdd: Add missing input.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-scdd)[properties]: Record updater-extra-native-inputs. [native-inputs]: Add r-testthat. Change-Id: Ibd0925b94ae82145055a0b2c5d53f38df202b077
2025-05-12gnu: pigx-sars-cov-2: Use Snakemake 7.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-sars-cov-2)[inputs]: Replace snakemake with snakemake-7. Change-Id: I059ea25c0e4a45e42f8f288cd92f548b9684e624
2025-05-12gnu: pigx-scrnaseq: Use Snakemake 7.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace snakemake with snakemake-7. Change-Id: I9b903dba192e862d3b5b6ca4e0018ed88069937d
2025-05-12gnu: pigx-bsseq: Use Snakemake 7.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace snakemake with snakemake-7. Change-Id: If82236f94d46c8e1f7f325e6eaf76f68397218d1
2025-05-12gnu: pigx-chipseq: Use Snakemake 7.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace snakemake with snakemake-7. Change-Id: Ib4d7d95713be3535b44ad10b655cf1a217048121
2025-05-12gnu: pigx-rnaseq: Use Snakemake 7.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace snakemake with snakemake-7. Change-Id: I2ab8af1438b59c3d36951b5901aeb57039b4aafc
2025-05-12gnu: r-automap: Update to 1.1-16.Ricardo Wurmus
* gnu/packages/cran.scm (r-automap): Update to 1.1-16. Change-Id: Id03925a9a292d8761facc8174e4a7baa854209d0
2025-05-12gnu: r-spacefillr: Update to 0.4.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-spacefillr): Update to 0.4.0. Change-Id: I313d740322b991ce5aacaa5d7177d49f2b25bc25
2025-05-12gnu: r-mathjaxr: Update to 1.8-0.Ricardo Wurmus
* gnu/packages/cran.scm (r-mathjaxr): Update to 1.8-0. Change-Id: I1c4286b47602493facbbe72a914319df15b05e86
2025-05-12gnu: r-vgam: Update to 1.1-13.Ricardo Wurmus
* gnu/packages/cran.scm (r-vgam): Update to 1.1-13. Change-Id: Ief01a8634a55b6387e767166a0e146d2d151dbf8
2025-05-12gnu: r-zoltr: Update to 1.0.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-zoltr): Update to 1.0.2. [native-inputs]: Add r-devtools. Change-Id: If358691f354a2d32a79002a7833e57483f63a916
2025-05-12gnu: r-zonebuilder: Update to 0.1.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-zonebuilder): Update to 0.1.0. Change-Id: If5875def520050b5adfa6fe1c6443979a9646b24
2025-05-12gnu: r-paws: Update to 0.9.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-paws): Update to 0.9.0. Change-Id: I4a115b73bfa89ba18c4ee1b4dec4777b383fc35d
2025-05-12gnu: r-paws-compute: Update to 0.9.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-paws-compute): Update to 0.9.0. Change-Id: I41716a54b9fb69fca298d2a516b5461970414caf
2025-05-12gnu: r-paws-storage: Update to 0.9.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-paws-storage): Update to 0.9.0. Change-Id: Iee12b7a726eb1a09729d307a54a55f57acc4b191
2025-05-12gnu: r-paws-database: Update to 0.9.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-paws-database): Update to 0.9.0. Change-Id: I5bf56853d9984abece401cc7909d4e8db5138b5a
2025-05-12gnu: r-paws-networking: Update to 0.9.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-paws-networking): Update to 0.9.0. Change-Id: I364ee0d82cfaf9706d980f6119db00296016328c
2025-05-12gnu: r-paws-management: Update to 0.9.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-paws-management): Update to 0.9.0. Change-Id: Ie87d855a601fc1146c34cebc4ff30cfd68b3f745
2025-05-12gnu: r-paws-machine-learning: Update to 0.9.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-paws-machine-learning): Update to 0.9.0. Change-Id: I321de81ad18bf8d9919c25c6c97a180816e04d3a
2025-05-12gnu: r-paws-analytics: Update to 0.9.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-paws-analytics): Update to 0.9.0. Change-Id: If0e0c6f51ac8d1ea787e14165c4ff513022355ff
2025-05-12gnu: r-paws-security-identity: Update to 0.9.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-paws-security-identity): Update to 0.9.0. Change-Id: I4ae29cb687826150c9da708e42c357919b1fb659
2025-05-12gnu: r-paws-application-integration: Update to 0.9.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-paws-application-integration): Update to 0.9.0. Change-Id: Id85247e94a1854019ca57beb584b790f593a0eb1
2025-05-12gnu: r-paws-end-user-computing: Update to 0.9.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-paws-end-user-computing): Update to 0.9.0. Change-Id: Id316b69b2e4d8acbe6e6aa8c7dc5d306075d2a0a
2025-05-12gnu: r-paws-developer-tools: Update to 0.9.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-paws-developer-tools): Update to 0.9.0. Change-Id: Ibf2875c0b0d37a6f544019a85be3a8e69f4b7ba2
2025-05-12gnu: r-paws-cost-management: Update to 0.9.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-paws-cost-management): Update to 0.9.0. Change-Id: I4f1930d8b25b6aaa79b79c8f30b5faf85a988c62
2025-05-12gnu: r-paws-customer-engagement: Update to 0.9.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-paws-customer-engagement): Update to 0.9.0. Change-Id: I24d9cf5c0185db68762a896e088732717d7e4e66
2025-05-12gnu: r-distributionutils: Update to 0.6-2.Ricardo Wurmus
* gnu/packages/cran.scm (r-distributionutils): Update to 0.6-2. [native-inputs]: Remove r-runit. Change-Id: I4489889d9da20f86b923db6e45207add66423e58
2025-05-12gnu: r-tzdb: Update to 0.5.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-tzdb): Update to 0.5.0. Change-Id: Id6e369f5686195fe612370d8cf6190b25a86a562
2025-05-12gnu: r-hypergeo: Update to 1.2-14.Ricardo Wurmus
* gnu/packages/cran.scm (r-hypergeo): Update to 1.2-14. Change-Id: I045413eec8897dcf901e2a46fdd44472162dec3a
2025-05-12gnu: r-rjsonio: Update to 2.0.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-rjsonio): Update to 2.0.0. Change-Id: I4016e18784dea414edb579745d6734cd44d3888c
2025-05-12gnu: r-qpdf: Update to 1.3.5.Ricardo Wurmus
* gnu/packages/cran.scm (r-qpdf): Update to 1.3.5. Change-Id: I171e4c4402eac438b4301c8107c79b8ed7826e72
2025-05-12gnu: r-qdapregex: Update to 0.7.10.Ricardo Wurmus
* gnu/packages/cran.scm (r-qdapregex): Update to 0.7.10. Change-Id: I7b623c55a197a4b9be48d64e550a84589a785243
2025-05-12gnu: r-ragg: Update to 1.4.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-ragg): Update to 1.4.0. Change-Id: I911fb0bd40c0b9502a1ea3e711c0d94d95d2e390
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