d0199e0c5c
gnu: r-biomart: Update to 2.56.0.
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* gnu/packages/bioconductor.scm (r-biomart): Update to 2.56.0.
2023-04-29 20:27:55 +02:00
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gnu: r-biobase: Update to 2.60.0.
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* gnu/packages/bioconductor.scm (r-biobase): Update to 2.60.0.
[native-inputs]: Add r-knitr.
2023-04-29 20:27:55 +02:00
b8c4b8b44f
gnu: r-bamsignals: Update to 1.32.0.
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* gnu/packages/bioconductor.scm (r-bamsignals): Update to 1.32.0.
2023-04-29 20:27:55 +02:00
968878ef27
gnu: r-aroma-light: Update to 3.30.0.
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* gnu/packages/bioconductor.scm (r-aroma-light): Update to 3.30.0.
2023-04-29 20:27:55 +02:00
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gnu: r-annotationhub: Update to 3.8.0.
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* gnu/packages/bioconductor.scm (r-annotationhub): Update to 3.8.0.
2023-04-29 20:27:55 +02:00
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gnu: r-annotationforge: Update to 1.42.0.
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* gnu/packages/bioconductor.scm (r-annotationforge): Update to 1.42.0.
2023-04-29 20:27:55 +02:00
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gnu: r-annotationfilter: Update to 1.24.0.
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* gnu/packages/bioconductor.scm (r-annotationfilter): Update to 1.24.0.
2023-04-29 20:27:55 +02:00
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gnu: r-annotationdbi: Update to 1.62.0.
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* gnu/packages/bioconductor.scm (r-annotationdbi): Update to 1.62.0.
2023-04-29 20:27:55 +02:00
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gnu: r-annotate: Update to 1.78.0.
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* gnu/packages/bioconductor.scm (r-annotate): Update to 1.78.0.
2023-04-29 20:27:55 +02:00
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gnu: r-affxparser: Update to 1.72.0.
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* gnu/packages/bioconductor.scm (r-affxparser): Update to 1.72.0.
2023-04-29 20:27:55 +02:00
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* gnu/packages/bioconductor.scm (r-affyio): Update to 1.70.0.
2023-04-29 20:27:55 +02:00
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gnu: r-affycoretools: Update to 1.72.0.
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* gnu/packages/bioconductor.scm (r-affycoretools): Update to 1.72.0.
2023-04-29 20:27:55 +02:00
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gnu: r-affycontam: Update to 1.58.0.
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* gnu/packages/bioconductor.scm (r-affycontam): Update to 1.58.0.
2023-04-29 20:27:55 +02:00
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gnu: r-affycomp: Update to 1.76.0.
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* gnu/packages/bioconductor.scm (r-affycomp): Update to 1.76.0.
2023-04-29 20:27:55 +02:00
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gnu: r-affy: Update to 1.78.0.
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* gnu/packages/bioconductor.scm (r-affy): Update to 1.78.0.
2023-04-29 20:27:55 +02:00
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gnu: r-italics: Update to 2.60.0.
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* gnu/packages/bioconductor.scm (r-italics): Update to 2.60.0.
2023-04-29 20:27:55 +02:00
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gnu: r-isoformswitchanalyzer: Update to 1.21.0.
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* gnu/packages/bioconductor.scm (r-isoformswitchanalyzer): Update to 1.21.0.
2023-04-29 20:27:54 +02:00
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gnu: r-iranges: Update to 2.34.0.
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* gnu/packages/bioconductor.scm (r-iranges): Update to 2.34.0.
2023-04-29 20:27:54 +02:00
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gnu: r-infercnv: Update to 1.16.0.
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* gnu/packages/bioconductor.scm (r-infercnv): Update to 1.16.0.
2023-04-29 20:27:54 +02:00
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gnu: r-ideoviz: Update to 1.36.0.
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* gnu/packages/bioconductor.scm (r-ideoviz): Update to 1.36.0.
2023-04-29 20:27:54 +02:00
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gnu: r-bluster: Update to 1.10.0.
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* gnu/packages/bioconductor.scm (r-bluster): Update to 1.10.0.
2023-04-29 20:27:54 +02:00
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gnu: r-dss: Update to 2.48.0.
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* gnu/packages/bioconductor.scm (r-dss): Update to 2.48.0.
2023-04-29 20:27:54 +02:00
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gnu: r-drimseq: Update to 1.28.0.
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* gnu/packages/bioconductor.scm (r-drimseq): Update to 1.28.0.
2023-04-29 20:27:54 +02:00
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gnu: r-dmrcate: Update to 2.14.0.
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* gnu/packages/bioconductor.scm (r-dmrcate): Update to 2.14.0.
2023-04-29 20:27:54 +02:00
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gnu: r-derfinderhelper: Update to 1.34.0.
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* gnu/packages/bioconductor.scm (r-derfinderhelper): Update to 1.34.0.
2023-04-29 20:27:54 +02:00
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gnu: r-delayedarray: Update to 0.25.0.
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* gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.25.0.
2023-04-29 20:27:54 +02:00
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gnu: r-deepsnv: Update to 1.46.0.
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* gnu/packages/bioconductor.scm (r-deepsnv): Update to 1.46.0.
2023-04-29 20:27:54 +02:00
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gnu: r-decoupler: Update to 2.6.0.
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* gnu/packages/bioconductor.scm (r-decoupler): Update to 2.6.0.
2023-04-29 20:27:54 +02:00
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gnu: r-deconvr: Update to 1.6.0.
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* gnu/packages/bioconductor.scm (r-deconvr): Update to 1.6.0.
2023-04-29 20:27:54 +02:00
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gnu: r-decontam: Update to 1.20.0.
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* gnu/packages/bioconductor.scm (r-decontam): Update to 1.20.0.
2023-04-29 20:27:54 +02:00
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gnu: r-deconrnaseq: Update to 1.42.0.
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* gnu/packages/bioconductor.scm (r-deconrnaseq): Update to 1.42.0.
2023-04-29 20:27:54 +02:00
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gnu: r-decomptumor2sig: Update to 2.16.0.
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* gnu/packages/bioconductor.scm (r-decomptumor2sig): Update to 2.16.0.
2023-04-29 20:27:54 +02:00
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gnu: r-decipher: Update to 2.28.0.
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* gnu/packages/bioconductor.scm (r-decipher): Update to 2.28.0.
2023-04-29 20:27:54 +02:00
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gnu: r-debcam: Update to 1.18.0.
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* gnu/packages/bioconductor.scm (r-debcam): Update to 1.18.0.
[source]: Delete bundled Java archives.
[arguments]: Add phase 'build-jar; add phase 'strip-jar-timestamps; do a fake
installation and disable tests due to a regression in R 4.3.0.
[inputs]: Replace openjdk with icedtea:jdk; add java-pj.
[native-inputs]: Add zip.
2023-04-29 20:27:17 +02:00
2bf6f659c4
gnu: Add java-pj.
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* gnu/packages/java.scm (java-pj): New variable.
2023-04-29 20:09:33 +02:00
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gnu: r-dearseq: Update to 1.12.0.
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* gnu/packages/bioconductor.scm (r-dearseq): Update to 1.12.0.
2023-04-29 20:09:33 +02:00
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gnu: r-damefinder: Update to 1.12.0.
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* gnu/packages/bioconductor.scm (r-damefinder): Update to 1.12.0.
2023-04-29 20:09:33 +02:00
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gnu: r-dama: Update to 1.72.0.
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* gnu/packages/bioconductor.scm (r-dama): Update to 1.72.0.
2023-04-29 20:09:33 +02:00
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gnu: r-cummerbund: Update to 2.42.0.
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* gnu/packages/bioconductor.scm (r-cummerbund): Update to 2.42.0.
2023-04-29 20:09:33 +02:00
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gnu: r-coverageview: Update to 1.38.0.
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* gnu/packages/bioconductor.scm (r-coverageview): Update to 1.38.0.
2023-04-29 20:09:33 +02:00
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gnu: r-cardelino: Update to 1.2.0.
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* gnu/packages/bioconductor.scm (r-cardelino): Update to 1.2.0.
2023-04-29 20:09:33 +02:00
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gnu: r-breakpointr: Update to 1.18.0.
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* gnu/packages/bioconductor.scm (r-breakpointr): Update to 1.18.0.
2023-04-29 20:09:33 +02:00
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gnu: r-biocgenerics: Update to 0.46.0.
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* gnu/packages/bioconductor.scm (r-biocgenerics): Update to 0.46.0.
2023-04-29 20:09:33 +02:00
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gnu: r-biocversion: Update to 3.17.1.
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* gnu/packages/bioconductor.scm (r-biocversion): Update to 3.17.1.
2023-04-29 20:09:33 +02:00
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gnu: r-barcodetrackr: Update to 1.8.0.
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* gnu/packages/bioconductor.scm (r-barcodetrackr): Update to 1.8.0.
2023-04-29 20:09:33 +02:00
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gnu: r-banocc: Update to 1.24.0.
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* gnu/packages/bioconductor.scm (r-banocc): Update to 1.24.0.
2023-04-29 20:09:33 +02:00
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gnu: r-bandits: Update to 1.16.0.
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* gnu/packages/bioconductor.scm (r-bandits): Update to 1.16.0.
2023-04-29 20:09:33 +02:00
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gnu: r-bambu: Update to 3.2.0.
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* gnu/packages/bioconductor.scm (r-bambu): Update to 3.2.0.
2023-04-29 20:09:33 +02:00
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gnu: r-badregionfinder: Update to 1.28.0.
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* gnu/packages/bioconductor.scm (r-badregionfinder): Update to 1.28.0.
2023-04-29 20:09:33 +02:00
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gnu: r-bader: Update to 1.38.0.
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* gnu/packages/bioconductor.scm (r-bader): Update to 1.38.0.
2023-04-29 20:09:33 +02:00
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gnu: r-basespacer: Update to 1.44.0.
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* gnu/packages/bioconductor.scm (r-basespacer): Update to 1.44.0.
2023-04-29 20:09:33 +02:00
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gnu: r-baalchip: Update to 1.26.0.
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* gnu/packages/bioconductor.scm (r-baalchip): Update to 1.26.0.
2023-04-29 20:09:32 +02:00
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gnu: r-awst: Update to 1.8.0.
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* gnu/packages/bioconductor.scm (r-awst): Update to 1.8.0.
2023-04-29 20:09:32 +02:00
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gnu: r-awfisher: Update to 1.14.0.
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* gnu/packages/bioconductor.scm (r-awfisher): Update to 1.14.0.
2023-04-29 20:09:32 +02:00
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gnu: r-attract: Update to 1.52.0.
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* gnu/packages/bioconductor.scm (r-attract): Update to 1.52.0.
2023-04-29 20:09:32 +02:00
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gnu: r-atsnp: Update to 1.16.0.
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* gnu/packages/bioconductor.scm (r-atsnp): Update to 1.16.0.
2023-04-29 20:09:32 +02:00
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gnu: r-atena: Update to 1.6.0.
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* gnu/packages/bioconductor.scm (r-atena): Update to 1.6.0.
[propagated-inputs]: Remove r-scales.
2023-04-29 20:09:32 +02:00
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gnu: r-asset: Update to 2.18.0.
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* gnu/packages/bioconductor.scm (r-asset): Update to 2.18.0.
2023-04-29 20:09:32 +02:00
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gnu: r-assessorf: Update to 1.18.0.
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* gnu/packages/bioconductor.scm (r-assessorf): Update to 1.18.0.
2023-04-29 20:09:32 +02:00
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gnu: r-aspli: Update to 2.10.0.
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* gnu/packages/bioconductor.scm (r-aspli): Update to 2.10.0.
2023-04-29 20:09:32 +02:00
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gnu: r-asics: Update to 2.16.0.
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* gnu/packages/bioconductor.scm (r-asics): Update to 2.16.0.
2023-04-29 20:09:32 +02:00
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gnu: r-asgsca: Update to 1.34.0.
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* gnu/packages/bioconductor.scm (r-asgsca): Update to 1.34.0.
2023-04-29 20:09:32 +02:00
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gnu: r-aseb: Update to 1.44.0.
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* gnu/packages/bioconductor.scm (r-aseb): Update to 1.44.0.
2023-04-29 20:09:32 +02:00
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gnu: r-asafe: Update to 1.26.0.
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* gnu/packages/bioconductor.scm (r-asafe): Update to 1.26.0.
2023-04-29 20:09:32 +02:00
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gnu: r-arrayexpress: Update to 1.60.0.
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* 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
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gnu: r-antiprofiles: Update to 1.40.0.
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* gnu/packages/bioconductor.scm (r-antiprofiles): Update to 1.40.0.
2023-04-29 20:09:32 +02:00
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gnu: r-annmap: Update to 1.42.0.
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* gnu/packages/bioconductor.scm (r-annmap): Update to 1.42.0.
2023-04-29 20:09:32 +02:00
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gnu: r-anf: Update to 1.22.0.
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* gnu/packages/bioconductor.scm (r-anf): Update to 1.22.0.
2023-04-29 20:09:32 +02:00
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gnu: r-aneufinder: Update to 1.28.0.
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* gnu/packages/bioconductor.scm (r-aneufinder): Update to 1.28.0.
[propagated-inputs]: Remove r-reordercluster.
2023-04-29 20:09:32 +02:00
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gnu: r-altcdfenvs: Update to 2.62.0.
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* gnu/packages/bioconductor.scm (r-altcdfenvs): Update to 2.62.0.
2023-04-29 20:09:32 +02:00
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gnu: r-alpsnmr: Update to 4.2.0.
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* gnu/packages/bioconductor.scm (r-alpsnmr): Update to 4.2.0.
2023-04-29 20:09:32 +02:00
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gnu: r-alpine: Update to 1.25.0.
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* gnu/packages/bioconductor.scm (r-alpine): Update to 1.25.0.
2023-04-29 20:09:32 +02:00
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gnu: r-alphabeta: Update to 1.14.0.
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* gnu/packages/bioconductor.scm (r-alphabeta): Update to 1.14.0.
2023-04-29 20:09:32 +02:00
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gnu: r-alevinqc: Update to 1.16.0.
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* gnu/packages/bioconductor.scm (r-alevinqc): Update to 1.16.0.
2023-04-29 20:09:32 +02:00
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gnu: r-aldex2: Update to 1.32.0.
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* gnu/packages/bioconductor.scm (r-aldex2): Update to 1.32.0.
2023-04-29 20:09:32 +02:00
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gnu: r-anvil: Update to 1.12.0.
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* gnu/packages/bioconductor.scm (r-anvil): Update to 1.12.0.
2023-04-29 20:09:32 +02:00
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gnu: r-annotationhubdata: Update to 1.30.0.
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* gnu/packages/bioconductor.scm (r-annotationhubdata): Update to 1.30.0.
2023-04-29 20:09:32 +02:00
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gnu: r-animalcules: Update to 1.16.0.
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* gnu/packages/bioconductor.scm (r-animalcules): Update to 1.16.0.
2023-04-29 20:09:32 +02:00
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gnu: r-ancombc: Update to 2.2.0.
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* gnu/packages/bioconductor.scm (r-ancombc): Update to 2.2.0.
2023-04-29 20:09:32 +02:00
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gnu: r-anaquin: Update to 2.24.0.
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* gnu/packages/bioconductor.scm (r-anaquin): Update to 2.24.0.
2023-04-29 20:09:32 +02:00
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gnu: r-amaretto: Update to 1.16.0.
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* gnu/packages/bioconductor.scm (r-amaretto): Update to 1.16.0.
2023-04-29 20:09:31 +02:00
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gnu: r-amplican: Update to 1.21.0.
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* gnu/packages/bioconductor.scm (r-amplican): Update to 1.21.0.
2023-04-29 20:09:31 +02:00
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gnu: r-amountain: Update to 1.26.0.
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* gnu/packages/bioconductor.scm (r-amountain): Update to 1.26.0.
2023-04-29 20:09:31 +02:00
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gnu: r-airpart: Update to 1.8.0.
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* gnu/packages/bioconductor.scm (r-airpart): Update to 1.8.0.
2023-04-29 20:09:31 +02:00
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gnu: r-aims: Update to 1.32.0.
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* gnu/packages/bioconductor.scm (r-aims): Update to 1.32.0.
2023-04-29 20:09:31 +02:00
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gnu: r-agimicrorna: Update to 2.50.0.
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* gnu/packages/bioconductor.scm (r-agimicrorna): Update to 2.50.0.
2023-04-29 20:09:31 +02:00
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* gnu/packages/bioconductor.scm (r-adductomicsr): Update to 1.16.0.
2023-04-29 20:09:31 +02:00
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gnu: r-agilp: Update to 3.32.0.
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* gnu/packages/bioconductor.scm (r-agilp): Update to 3.32.0.
2023-04-29 20:09:31 +02:00
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gnu: r-aggregatebiovar: Update to 1.10.0.
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* gnu/packages/bioconductor.scm (r-aggregatebiovar): Update to 1.10.0.
2023-04-29 20:09:31 +02:00
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gnu: r-agdex: Update to 1.48.0.
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* gnu/packages/bioconductor.scm (r-agdex): Update to 1.48.0.
2023-04-29 20:09:31 +02:00
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gnu: r-affyrnadegradation: Update to 1.46.0.
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* gnu/packages/bioconductor.scm (r-affyrnadegradation): Update to 1.46.0.
2023-04-29 20:09:31 +02:00
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gnu: r-affyplm: Update to 1.76.0.
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* gnu/packages/bioconductor.scm (r-affyplm): Update to 1.76.0.
2023-04-29 20:09:31 +02:00
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gnu: r-affylmgui: Update to 1.74.0.
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* gnu/packages/bioconductor.scm (r-affylmgui): Update to 1.74.0.
2023-04-29 20:09:31 +02:00
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gnu: r-affyilm: Update to 1.52.0.
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* gnu/packages/bioconductor.scm (r-affyilm): Update to 1.52.0.
2023-04-29 20:09:31 +02:00
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gnu: r-affixcan: Update to 1.18.0.
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* gnu/packages/bioconductor.scm (r-affixcan): Update to 1.18.0.
2023-04-29 20:09:31 +02:00
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gnu: r-adsplit: Update to 1.70.0.
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* gnu/packages/bioconductor.scm (r-adsplit): Update to 1.70.0.
2023-04-29 20:09:31 +02:00
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gnu: r-adimpute: Update to 1.10.0.
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* gnu/packages/bioconductor.scm (r-adimpute): Update to 1.10.0.
2023-04-29 20:09:31 +02:00
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gnu: r-adamgui: Update to 1.16.0.
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* gnu/packages/bioconductor.scm (r-adamgui): Update to 1.16.0.
2023-04-29 20:09:31 +02:00
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gnu: r-adam: Update to 1.16.0.
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* gnu/packages/bioconductor.scm (r-adam): Update to 1.16.0.
2023-04-29 20:09:31 +02:00
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gnu: r-adacgh2: Update to 2.40.0.
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* gnu/packages/bioconductor.scm (r-adacgh2): Update to 2.40.0.
2023-04-29 20:09:31 +02:00
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gnu: r-absseq: Update to 1.54.0.
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* gnu/packages/bioconductor.scm (r-absseq): Update to 1.54.0.
2023-04-29 20:09:31 +02:00
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gnu: r-abarray: Update to 1.68.0.
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* gnu/packages/bioconductor.scm (r-abarray): Update to 1.68.0.
2023-04-29 20:09:31 +02:00
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gnu: r-missmethyl: Update to 1.34.0.
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* gnu/packages/bioconductor.scm (r-missmethyl): Update to 1.34.0.
2023-04-29 20:09:31 +02:00
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gnu: r-shiny: Update to 1.7.4.
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* gnu/packages/cran.scm (r-shiny): Update to 1.7.4.
2023-04-29 20:09:31 +02:00
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gnu: r-glimma: Update to 2.10.0.
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* 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
9619504c81
gnu: r-reportingtools: Update to 2.39.0.
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* 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
91204fc357
gnu: Add r-densvis.
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* gnu/packages/bioconductor.scm (r-densvis): New variable.
2023-04-29 20:09:31 +02:00
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
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
4884ee6dd4
gnu: libexpected: Update to 1.1.0.
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* 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
8a8bd15bfa
gnu: fwupd: Update to 1.8.14.
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* 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
87ba11eff1
gnu: maven-embedder: Fix build.
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* 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
1a93ff9a8b
gnu: maven-core-bootstrap: Fix build.
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* 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
3d2ce30f6b
gnu: maven-resolver-provider: Fix build.
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* 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
04f9ac0cfa
gnu: maven-model-builder: Fix build.
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* 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
c0a0cec87f
gnu: maven-settings-builder: Fix build.
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* 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
06277d8070
gnu: Fix supercollider.
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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
aecc6e7058
gnu: dovecot: Fix build.
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* 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
e42117bfc9
gnu: mumble: Update to 1.4.287, fix build.
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* gnu/packages/telephony.scm (mumble): Update to 1.4.287.
[inputs]: Use openssl-1.1.
2023-04-28 08:56:48 +08:00
7193b8f9fd
gnu: python-ipy: Update to 1.01.
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* gnu/packages/networking.scm (python-ipy): Update to 1.01.
2023-04-28 08:36:37 +08:00
b8b3af93da
gnu: ncdu-1: Update to 1.18.1.
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* gnu/packages/ncdu.scm (ncdu-1): Update to 1.18.1.
2023-04-27 22:19:10 +03:00
4d42fbd371
gnu: sleef: Adjust inputs.
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* 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
ecb4f4d015
gnu: gloo: Use OpenSSL 1.1.
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* gnu/packages/machine-learning.scm (gloo)[inputs]: Use openssl-1.1 instead of
openssl.
2023-04-27 20:58:26 +02:00
688d99282b
gnu: yubico-piv-tool: Update to 2.3.1.
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* 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
d59b4764f3
gnu: Add cl-prompter.
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* gnu/packages/lisp-xyz.scm (cl-prompter, ecl-prompter, sbcl-prompter): New variables.
2023-04-27 17:50:38 +02:00
297805b1f8
gnu: python-docutils-0.15: Add missing input.
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* gnu/packages/python-xyz.scm (python-docutils-0.15)[native-inputs]: Add
python-setuptools-57.
2023-04-27 16:32:47 +02:00
5775bbdd4b
gnu: gdcm: Disable dependent tests.
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* 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
fa685c87ea
gnu: freebayes: Update to 1.3.7.
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* 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
133957f7bb
gnu: vcflib: Use libwfa2.pc.
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* 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
479f2558fe
gnu: wfa2-lib: Install pkg-config file.
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* gnu/packages/bioinformatics.scm (wfa2-lib)[arguments]: Install libwfa2.pc.
2023-04-27 11:37:36 +02:00
9d82c475a3
gnu: express: Adjust bamtools location.
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* 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
f196b3b7a5
gnu: python-tinycss2: Simplify.
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* gnu/packages/python-web.scm (python-tinycss2)[build-system]: Use
pyproject-build-system.
[arguments]: Remove.
2023-04-27 09:11:05 +02:00
0dc7f773fd
gnu: python-openapi-core: Add missing input.
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* 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
d8fe2e4735
gnu: libwebsockets: Update to 4.3.2.
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* 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
db19e30673
gnu: python-google-cloud-storage: Add missing input.
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* gnu/packages/python-web.scm (python-google-cloud-storage)[native-inputs]:
Add python-mock.
2023-04-27 06:53:37 +02:00
40451d0f2d
gnu: python-google-resumable-media: Add missing input.
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* gnu/packages/python-web.scm (python-google-resumable-media)[native-inputs]:
Add python-mock.
2023-04-27 06:53:12 +02:00
cec543e70f
gnu: python-aws-xray-sdk: Update to 2.12.0.
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* 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
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
3b19fc1801
gnu: python-httpcore: Update to 0.17.0.
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* 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
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
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
bb385f2472
gnu: python-dendropy: Fix build.
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* 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
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
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
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
00cf71df80
gnu: rapidjson: Update to 1.1.0-1.949c771.
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* 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
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
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
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
faa4485b52
gnu: python-fire: Add missing input.
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* gnu/packages/python-xyz.scm (python-fire)[native-inputs]: Add python-mock.
2023-04-26 21:33:02 +02:00
Ricardo Wurmus
Liliana Marie Prikler
Josselin Poiret
Aleksandr Vityazev
Gabriel Wicki
宋文武
Efraim Flashner
Pierre Neidhardt