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2023-07-13Merge branch 'master' into emacs-team emacs-teamLiliana Marie Prikler
2023-07-13gnu: libleak: Update to 0.3.6.fanquake
* gnu/packages/debug.scm (libleak): Update to 0.3.6.
2023-07-12gnu: Add r-numbat.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-numbat): New variable.
2023-07-12gnu: Add r-bpcells.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bpcells): New variable.
2023-07-12gnu: nyxt: Update to 3.4.0.Andre A. Gomes
* gnu/packages/web-browsers.scm (nyxt): Update to 3.4.0. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2023-07-12gnu: strace: Update to 6.4.Michael Ford
* gnu/packages/linux.scm (strace): Update to 6.4. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2023-07-12transformations: Allow tuning go packages.Efraim Flashner
* guix/transformations.scm (build-system-with-tuning-compiler): When checking if a microarchitecture is supported by the compiler, also check if it is a go compiler which supports that psabi. Add a phase after 'setup-go-environment to set the go microarchitecture.
2023-07-12gnu: go: Add CPU tuning targets.Efraim Flashner
* gnu/packages/golang.scm (go-1.17)[properties]: New field. (%go-1.17-arm-micro-architectures, %go-1.17-powerpc64le-micro-architectures, %go-1.18-x86_64-micro-architectures): New variables. (go-1.18)[properties]: New field.
2023-07-12guix: cpu: Add gcc-architecture->micro-architecture-level mapping.Efraim Flashner
* guix/cpu.scm (gcc-architecture->micro-architecture-level): New variable.
2023-07-12guix: cpu: Refactor cpu->gcc-architecture.Efraim Flashner
* guix/cpu.scm (cpu->gcc-architecture): Refactor to wrap all the x86_64 options inside a common letrec-syntax.
2023-07-12guix: cpu: Rewrite fallback for x86_64 cpu->gcc-architecture.Efraim Flashner
* guix/cpu.scm (cpu->gcc-architecture): Adjust the fallback case to use cpu->micro-architecture-level.
2023-07-12guix: cpu: Add generalized CPU matching.Efraim Flashner
* guix/cpu.scm (cpu->micro-architecture-level): New variable.
2023-07-12gnu: %gcc-11-x86_64-micro-architectures: Add psabi entries.Efraim Flashner
* gnu/packages/gcc.scm (%gcc-11-x86_64-micro-architectures): Add entries for x86_64-v{1,2,3,4}.
2023-07-12gnu: r-tcgabiolinks: Update to 2.28.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.28.3.
2023-07-12gnu: r-bionero: Update to 1.8.5.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bionero): Update to 1.8.5. [propagated-inputs]: Remove r-ggnewscale and r-networkd3; add r-ggdendro and r-rlang.
2023-07-12gnu: r-biocthis: Update to 1.10.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocthis): Update to 1.10.3.
2023-07-12gnu: r-basilisk: Update to 1.12.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-basilisk): Update to 1.12.1.
2023-07-12gnu: r-delayedmatrixstats: Update to 1.22.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.22.1.
2023-07-12gnu: r-sparsematrixstats: Update to 1.12.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-sparsematrixstats): Update to 1.12.2.
2023-07-12gnu: r-fishpond: Update to 2.6.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-fishpond): Update to 2.6.2.
2023-07-12gnu: r-bioccheck: Update to 1.36.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bioccheck): Update to 1.36.1.
2023-07-12gnu: r-universalmotif: Update to 1.18.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.18.1.
2023-07-12gnu: r-variancepartition: Update to 1.30.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.30.2.
2023-07-12gnu: r-variantfiltering: Update to 1.36.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-variantfiltering): Update to 1.36.1.
2023-07-12gnu: r-quasr: Update to 1.40.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-quasr): Update to 1.40.1.
2023-07-12gnu: r-motifbreakr: Update to 2.14.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-motifbreakr): Update to 2.14.2.
2023-07-12gnu: r-lpsymphony: Update to 1.28.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-lpsymphony): Update to 1.28.1. [native-inputs]: Add gfortran.
2023-07-12gnu: r-glmgampoi: Update to 1.12.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-glmgampoi): Update to 1.12.2.
2023-07-12gnu: r-interactionset: Update to 1.28.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-interactionset): Update to 1.28.1.
2023-07-12gnu: r-matrixgenerics: Update to 1.12.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-matrixgenerics): Update to 1.12.2.
2023-07-12gnu: r-systempiper: Update to 2.6.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-systempiper): Update to 2.6.3.
2023-07-12gnu: r-summarizedexperiment: Update to 1.30.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-summarizedexperiment): Update to 1.30.2.
2023-07-12gnu: r-maaslin2: Update to 1.14.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-maaslin2): Update to 1.14.1. [propagated-inputs]: Remove r-lpsymphony; add r-tibble.
2023-07-12gnu: r-limma: Update to 3.56.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-limma): Update to 3.56.2.
2023-07-12gnu: r-lfa: Update to 2.0.11.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-lfa): Update to 2.0.11. [propagated-inputs]: Add r-rspectra.
2023-07-12gnu: r-genomicfeatures: Update to 1.52.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.52.1.
2023-07-12gnu: r-deseq2: Update to 1.40.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-deseq2): Update to 1.40.2.
2023-07-12gnu: r-biomart: Update to 2.56.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biomart): Update to 2.56.1.
2023-07-12gnu: r-annotationforge: Update to 1.42.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-annotationforge): Update to 1.42.2.
2023-07-12gnu: r-genomeinfodb: Update to 1.36.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.36.1.
2023-07-12gnu: r-annotationdbi: Update to 1.62.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-annotationdbi): Update to 1.62.2.
2023-07-12gnu: r-affy: Update to 1.78.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-affy): Update to 1.78.1.
2023-07-12gnu: r-isoformswitchanalyzer: Update to 2.0.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-isoformswitchanalyzer): Update to 2.0.1. [propagated-inputs]: Remove r-drimseq; add r-biocparallel, r-pfamanalyzer, r-s4vectors, r-saturn, r-summarizedexperiment, r-sva, and r-tidyr.
2023-07-12gnu: r-iranges: Update to 2.34.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-iranges): Update to 2.34.1.
2023-07-12gnu: r-delayedarray: Update to 0.26.6.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.26.6.
2023-07-12gnu: r-bambu: Update to 3.2.5.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bambu): Update to 3.2.5.
2023-07-12gnu: r-alevinqc: Update to 1.16.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-alevinqc): Update to 1.16.1.
2023-07-12gnu: r-ancombc: Update to 2.2.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ancombc): Update to 2.2.1. [propagated-inputs]: Remove r-dplyr, r-emmeans, r-magrittr, r-rlang, r-rngtools, r-tibble, and r-tidyr; add r-gtools, r-matrix, and r-multcomp.
2023-07-12gnu: r-gdsfmt: Update to 1.36.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-gdsfmt): Update to 1.36.1. [properties]: Tell updater to leave the extra inputs be.
2023-07-12gnu: Add r-saturn.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-saturn): New variable.
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