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* gnu/packages/bioconductor.scm (r-deconvr): Update to 1.6.0.
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* gnu/packages/bioconductor.scm (r-decontam): Update to 1.20.0.
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* gnu/packages/bioconductor.scm (r-deconrnaseq): Update to 1.42.0.
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* gnu/packages/bioconductor.scm (r-decomptumor2sig): Update to 2.16.0.
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* gnu/packages/bioconductor.scm (r-decipher): Update to 2.28.0.
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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.
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* gnu/packages/java.scm (java-pj): New variable.
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* gnu/packages/bioconductor.scm (r-dearseq): Update to 1.12.0.
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* gnu/packages/bioconductor.scm (r-damefinder): Update to 1.12.0.
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* gnu/packages/bioconductor.scm (r-dama): Update to 1.72.0.
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* gnu/packages/bioconductor.scm (r-cummerbund): Update to 2.42.0.
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* gnu/packages/bioconductor.scm (r-coverageview): Update to 1.38.0.
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* gnu/packages/bioconductor.scm (r-cardelino): Update to 1.2.0.
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* gnu/packages/bioconductor.scm (r-breakpointr): Update to 1.18.0.
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* gnu/packages/bioconductor.scm (r-biocgenerics): Update to 0.46.0.
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* gnu/packages/bioconductor.scm (r-biocversion): Update to 3.17.1.
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* gnu/packages/bioconductor.scm (r-barcodetrackr): Update to 1.8.0.
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* gnu/packages/bioconductor.scm (r-banocc): Update to 1.24.0.
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* gnu/packages/bioconductor.scm (r-bandits): Update to 1.16.0.
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* gnu/packages/bioconductor.scm (r-bambu): Update to 3.2.0.
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* gnu/packages/bioconductor.scm (r-badregionfinder): Update to 1.28.0.
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* gnu/packages/bioconductor.scm (r-bader): Update to 1.38.0.
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* gnu/packages/bioconductor.scm (r-basespacer): Update to 1.44.0.
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* gnu/packages/bioconductor.scm (r-baalchip): Update to 1.26.0.
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* gnu/packages/bioconductor.scm (r-awst): Update to 1.8.0.
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* gnu/packages/bioconductor.scm (r-awfisher): Update to 1.14.0.
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* gnu/packages/bioconductor.scm (r-attract): Update to 1.52.0.
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* gnu/packages/bioconductor.scm (r-atsnp): Update to 1.16.0.
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* gnu/packages/bioconductor.scm (r-atena): Update to 1.6.0.
[propagated-inputs]: Remove r-scales.
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* gnu/packages/bioconductor.scm (r-asset): Update to 2.18.0.
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* gnu/packages/bioconductor.scm (r-assessorf): Update to 1.18.0.
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* gnu/packages/bioconductor.scm (r-aspli): Update to 2.10.0.
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* gnu/packages/bioconductor.scm (r-asics): Update to 2.16.0.
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* gnu/packages/bioconductor.scm (r-asgsca): Update to 1.34.0.
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* gnu/packages/bioconductor.scm (r-aseb): Update to 1.44.0.
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* gnu/packages/bioconductor.scm (r-asafe): Update to 1.26.0.
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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.
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* gnu/packages/bioconductor.scm (r-antiprofiles): Update to 1.40.0.
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* gnu/packages/bioconductor.scm (r-annmap): Update to 1.42.0.
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* gnu/packages/bioconductor.scm (r-anf): Update to 1.22.0.
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* gnu/packages/bioconductor.scm (r-aneufinder): Update to 1.28.0.
[propagated-inputs]: Remove r-reordercluster.
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* gnu/packages/bioconductor.scm (r-altcdfenvs): Update to 2.62.0.
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* gnu/packages/bioconductor.scm (r-alpsnmr): Update to 4.2.0.
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* gnu/packages/bioconductor.scm (r-alpine): Update to 1.25.0.
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* gnu/packages/bioconductor.scm (r-alphabeta): Update to 1.14.0.
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* gnu/packages/bioconductor.scm (r-alevinqc): Update to 1.16.0.
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* gnu/packages/bioconductor.scm (r-aldex2): Update to 1.32.0.
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* gnu/packages/bioconductor.scm (r-anvil): Update to 1.12.0.
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* gnu/packages/bioconductor.scm (r-annotationhubdata): Update to 1.30.0.
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* gnu/packages/bioconductor.scm (r-animalcules): Update to 1.16.0.
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