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117221 Commits (1701b1244d15dc6e8b7b1fe7af5fe26a82a465ba)

Author SHA1 Message Date
Efraim Flashner 1701b1244d
guix: cpu: Add gcc-architecture->micro-architecture-level mapping. 
* guix/cpu.scm (gcc-architecture->micro-architecture-level): New
variable.
 2023-07-12 16:48:28 +03:00
Efraim Flashner 4dd5fa9e76
guix: cpu: Refactor cpu->gcc-architecture. 
* guix/cpu.scm (cpu->gcc-architecture): Refactor to wrap all the x86_64
options inside a common letrec-syntax.
 2023-07-12 16:48:28 +03:00
Efraim Flashner b93057256f
guix: cpu: Rewrite fallback for x86_64 cpu->gcc-architecture. 
* guix/cpu.scm (cpu->gcc-architecture): Adjust the fallback case to use
cpu->micro-architecture-level.
 2023-07-12 16:48:28 +03:00
Efraim Flashner cb0cab2db0
guix: cpu: Add generalized CPU matching. 
* guix/cpu.scm (cpu->micro-architecture-level): New variable.
 2023-07-12 16:48:27 +03:00
Efraim Flashner db6503a6ff
gnu: %gcc-11-x86_64-micro-architectures: Add psabi entries. 
* gnu/packages/gcc.scm (%gcc-11-x86_64-micro-architectures): Add entries
for x86_64-v{1,2,3,4}.
 2023-07-12 16:48:24 +03:00
Ricardo Wurmus f2f27c4952
gnu: r-tcgabiolinks: Update to 2.28.3. 
* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.28.3.
 2023-07-12 14:29:11 +02:00
Ricardo Wurmus 2ef18c24a4
gnu: r-bionero: Update to 1.8.5. 
* 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.
 2023-07-12 14:29:11 +02:00
Ricardo Wurmus cbdaf26d0c
gnu: r-biocthis: Update to 1.10.3. 
* gnu/packages/bioconductor.scm (r-biocthis): Update to 1.10.3.
 2023-07-12 14:29:11 +02:00
Ricardo Wurmus 165a4755a4
gnu: r-basilisk: Update to 1.12.1. 
* gnu/packages/bioconductor.scm (r-basilisk): Update to 1.12.1.
 2023-07-12 14:29:11 +02:00
Ricardo Wurmus bdd11e0229
gnu: r-delayedmatrixstats: Update to 1.22.1. 
* gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.22.1.
 2023-07-12 14:29:11 +02:00
Ricardo Wurmus 5a61307327
gnu: r-sparsematrixstats: Update to 1.12.2. 
* gnu/packages/bioconductor.scm (r-sparsematrixstats): Update to 1.12.2.
 2023-07-12 14:29:11 +02:00
Ricardo Wurmus 72c0125649
gnu: r-fishpond: Update to 2.6.2. 
* gnu/packages/bioconductor.scm (r-fishpond): Update to 2.6.2.
 2023-07-12 14:29:11 +02:00
Ricardo Wurmus 3bfbd6ddd8
gnu: r-bioccheck: Update to 1.36.1. 
* gnu/packages/bioconductor.scm (r-bioccheck): Update to 1.36.1.
 2023-07-12 14:29:11 +02:00
Ricardo Wurmus aada7f3a53
gnu: r-universalmotif: Update to 1.18.1. 
* gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.18.1.
 2023-07-12 14:29:11 +02:00
Ricardo Wurmus e728562cd3
gnu: r-variancepartition: Update to 1.30.2. 
* gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.30.2.
 2023-07-12 14:29:11 +02:00
Ricardo Wurmus c4ea43f75c
gnu: r-variantfiltering: Update to 1.36.1. 
* gnu/packages/bioconductor.scm (r-variantfiltering): Update to 1.36.1.
 2023-07-12 14:29:11 +02:00
Ricardo Wurmus 8637eba2a5
gnu: r-quasr: Update to 1.40.1. 
* gnu/packages/bioconductor.scm (r-quasr): Update to 1.40.1.
 2023-07-12 14:29:11 +02:00
Ricardo Wurmus 1d53aa680e
gnu: r-motifbreakr: Update to 2.14.2. 
* gnu/packages/bioconductor.scm (r-motifbreakr): Update to 2.14.2.
 2023-07-12 14:29:11 +02:00
Ricardo Wurmus a98f8bdcf3
gnu: r-lpsymphony: Update to 1.28.1. 
* gnu/packages/bioconductor.scm (r-lpsymphony): Update to 1.28.1.
[native-inputs]: Add gfortran.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus 0514c45d4a
gnu: r-glmgampoi: Update to 1.12.2. 
* gnu/packages/bioconductor.scm (r-glmgampoi): Update to 1.12.2.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus 75a5504e49
gnu: r-interactionset: Update to 1.28.1. 
* gnu/packages/bioconductor.scm (r-interactionset): Update to 1.28.1.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus 6652f72e13
gnu: r-matrixgenerics: Update to 1.12.2. 
* gnu/packages/bioconductor.scm (r-matrixgenerics): Update to 1.12.2.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus 1b83659902
gnu: r-systempiper: Update to 2.6.3. 
* gnu/packages/bioconductor.scm (r-systempiper): Update to 2.6.3.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus 0a0304ef3a
gnu: r-summarizedexperiment: Update to 1.30.2. 
* gnu/packages/bioconductor.scm (r-summarizedexperiment): Update to 1.30.2.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus 464ad1fd79
gnu: r-maaslin2: Update to 1.14.1. 
* gnu/packages/bioconductor.scm (r-maaslin2): Update to 1.14.1.
[propagated-inputs]: Remove r-lpsymphony; add r-tibble.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus 5588562fb9
gnu: r-limma: Update to 3.56.2. 
* gnu/packages/bioconductor.scm (r-limma): Update to 3.56.2.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus 5db8d3e600
gnu: r-lfa: Update to 2.0.11. 
* gnu/packages/bioconductor.scm (r-lfa): Update to 2.0.11.
[propagated-inputs]: Add r-rspectra.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus 3193a2a04d
gnu: r-genomicfeatures: Update to 1.52.1. 
* gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.52.1.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus 2b62bc3f67
gnu: r-deseq2: Update to 1.40.2. 
* gnu/packages/bioconductor.scm (r-deseq2): Update to 1.40.2.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus 6604189891
gnu: r-biomart: Update to 2.56.1. 
* gnu/packages/bioconductor.scm (r-biomart): Update to 2.56.1.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus 1f0633db11
gnu: r-annotationforge: Update to 1.42.2. 
* gnu/packages/bioconductor.scm (r-annotationforge): Update to 1.42.2.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus c397d6a5e1
gnu: r-genomeinfodb: Update to 1.36.1. 
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.36.1.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus 3c201e1aab
gnu: r-annotationdbi: Update to 1.62.2. 
* gnu/packages/bioconductor.scm (r-annotationdbi): Update to 1.62.2.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus 565d84170a
gnu: r-affy: Update to 1.78.1. 
* gnu/packages/bioconductor.scm (r-affy): Update to 1.78.1.
 2023-07-12 14:29:10 +02:00
Ricardo Wurmus a9d140996c
gnu: r-isoformswitchanalyzer: Update to 2.0.1. 
* 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.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus b864a5956f
gnu: r-iranges: Update to 2.34.1. 
* gnu/packages/bioconductor.scm (r-iranges): Update to 2.34.1.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus 5eaf9f6b83
gnu: r-delayedarray: Update to 0.26.6. 
* gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.26.6.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus 6e83dee12a
gnu: r-bambu: Update to 3.2.5. 
* gnu/packages/bioconductor.scm (r-bambu): Update to 3.2.5.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus f0c82ddced
gnu: r-alevinqc: Update to 1.16.1. 
* gnu/packages/bioconductor.scm (r-alevinqc): Update to 1.16.1.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus 4db85c197b
gnu: r-ancombc: Update to 2.2.1. 
* 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.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus 558637533f
gnu: r-gdsfmt: Update to 1.36.1. 
* gnu/packages/bioconductor.scm (r-gdsfmt): Update to 1.36.1.
[properties]: Tell updater to leave the extra inputs be.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus b4cafa71ae
gnu: Add r-saturn. 
* gnu/packages/bioconductor.scm (r-saturn): New variable.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus 990bac0ea5
gnu: Add r-pfamanalyzer. 
* gnu/packages/bioconductor.scm (r-pfamanalyzer): New variable.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus b10bff65be
gnu: r-mzr: Update to 2.34.1. 
* gnu/packages/bioconductor.scm (r-mzr): Update to 2.34.1.
[properties]: Tell updater to not remove the "boost" input.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus ee50cae529
gnu: r-norm: Update to 1.0-11.1. 
* gnu/packages/statistics.scm (r-norm): Update to 1.0-11.1.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus c141725c65
gnu: r-logspline: Update to 2.1.20. 
* gnu/packages/statistics.scm (r-logspline): Update to 2.1.20.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus 5a1c16fa18
gnu: r-pbapply: Update to 1.7-2. 
* gnu/packages/statistics.scm (r-pbapply): Update to 1.7-2.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus 42c29d9d22
gnu: r-robust: Update to 0.7-2. 
* gnu/packages/statistics.scm (r-robust): Update to 0.7-2.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus 2108aa1975
gnu: r-rrcov: Update to 1.7-4. 
* gnu/packages/statistics.scm (r-rrcov): Update to 1.7-4.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus 387c1fafce
gnu: r-robustbase: Update to 0.99-0. 
* gnu/packages/statistics.scm (r-robustbase): Update to 0.99-0.
 2023-07-12 14:29:08 +02:00