GNU bug report logs - #59329
[PATCH 000/444] Update Bioconductor to 3.16

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: guix-patches <at> gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 000/444] Update Bioconductor to 3.16
Date: Thu, 17 Nov 2022 04:55:54 +0100

Hi Ricardo,

Sorry for the delay.  Here some work, not fully polished but the final state
builds.  However, it requires the update of r-ggplot2 -- and this update
breaks the leaf package r-ggtern.

Note that the update of r-ggplot2 is only required by the Bioconductor package
r-fgsea, if I remember correctly.

I marked some patches as DRAFT, because it remains something -- for instance,
refresh recommended the addition of a package but it builds and the tests seem
fine without, so I do not know if it is a false-positive of refresh.

Well, I am rebuilding to see if these updates introduce non-reproducible
packages.  But that's not blocking, IMHO.

Last, I will not spam guix-patches with 444 emails.  Please checkout the
branch wip-bioconductor on:

    https://gitlab.com/zimoun/guix/-/tree/wip-bioconductor

Cheers,
simon



zimoun (444):
  DRAFT update 3.16.
  gnu: Add r-hdo-db.
  DRAFT gnu: r-ggplot2: Update to 3.4.0.
  gnu: r-ggprism: Update to 1.0.4.
  gnu: Add r-biocbaseutils.
  gnu: Add r-rorcid.
  gnu: Add r-gson.
  gnu: r-abarray: Update to 1.66.0.
  gnu: r-absseq: Update to 1.52.0.
  gnu: r-adam: Update to 1.14.0.
  gnu: r-adamgui: Update to 1.14.0.
  gnu: r-adimpute: Update to 1.8.0.
  gnu: r-adsplit: Update to 1.68.0.
  gnu: r-affixcan: Update to 1.16.0.
  gnu: r-affyrnadegradation: Update to 1.44.0.
  gnu: r-agdex: Update to 1.46.0.
  gnu: r-aggregatebiovar: Update to 1.8.0.
  gnu: r-agilp: Update to 3.30.0.
  gnu: r-adductomicsr: Update to 1.14.0.
  gnu: r-agimicrorna: Update to 2.48.0.
  gnu: r-airpart: Update to 1.6.0.
  gnu: r-amountain: Update to 1.24.0.
  gnu: r-amaretto: Update to 1.13.0.
  gnu: r-anaquin: Update to 2.22.0.
  gnu: r-aldex2: Update to 1.30.0.
  gnu: r-aneufinder: Update to 1.26.0.
  gnu: r-anf: Update to 1.20.0.
  gnu: r-annmap: Update to 1.40.0.
  gnu: r-antiprofiles: Update to 1.38.0.
  gnu: r-aseb: Update to 1.42.0.
  gnu: r-asgsca: Update to 1.32.0.
  gnu: r-aspli: Update to 2.8.0.
  gnu: r-assessorf: Update to 1.16.0.
  gnu: r-asset: Update to 2.16.0.
  gnu: r-atena: Update to 1.4.0.
  gnu: r-atsnp: Update to 1.14.0.
  gnu: r-attract: Update to 1.50.0.
  gnu: r-awfisher: Update to 1.12.0.
  gnu: r-awst: Update to 1.6.0.
  gnu: r-baalchip: Update to 1.24.0.
  gnu: r-basespacer: Update to 1.42.0.
  gnu: r-bac: Update to 1.58.0.
  gnu: r-bader: Update to 1.36.0.
  gnu: r-badregionfinder: Update to 1.26.0.
  gnu: r-bambu: Update to 3.0.1.
  gnu: r-bandits: Update to 1.14.0.
  gnu: r-banocc: Update to 1.22.0.
  gnu: r-barcodetrackr: Update to 1.6.0.
  gnu: r-biocversion: Update to 3.16.0.
  gnu: r-biocgenerics: Update to 0.44.0.
  gnu: r-coverageview: Update to 1.36.0.
  gnu: r-cummerbund: Update to 2.40.0.
  gnu: r-dama: Update to 1.70.0.
  gnu: r-damefinder: Update to 1.10.0.
  gnu: r-dearseq: Update to 1.10.0.
  gnu: r-debcam: Update to 1.16.0.
  gnu: r-decipher: Update to 2.26.0.
  gnu: r-deco: Update to 1.13.0.
  gnu: r-decomplexdisease: Update to 1.18.0.
  gnu: r-decomptumor2sig: Update to 2.14.0.
  gnu: r-deconrnaseq: Update to 1.40.0.
  gnu: r-decontam: Update to 1.18.0.
  gnu: r-deconvr: Update to 1.4.0.
  gnu: r-decoupler: Update to 2.4.0.
  gnu: r-deepsnv: Update to 1.44.0.
  gnu: r-delayedarray: Update to 0.24.0.
  gnu: r-derfinderhelper: Update to 1.32.0.
  gnu: r-drimseq: Update to 1.26.0.
  gnu: r-bluster: Update to 1.8.0.
  gnu: r-ideoviz: Update to 1.34.0.
  gnu: r-infercnv: Update to 1.14.0.
  gnu: r-iranges: Update to 2.32.0.
  gnu: r-isoformswitchanalyzer: Update to 1.20.0.
  gnu: r-affy: Update to 1.76.0.
  gnu: r-affycomp: Update to 1.74.0.
  gnu: r-affycompatible: Update to 1.58.0.
  gnu: r-affycontam: Update to 1.56.0.
  gnu: r-affycoretools: Update to 1.70.0.
  gnu: r-affyio: Update to 1.68.0.
  gnu: r-affxparser: Update to 1.70.0.
  gnu: r-annotate: Update to 1.76.0.
  gnu: r-annotationdbi: Update to 1.60.0.
  gnu: r-annotationfilter: Update to 1.22.0.
  gnu: r-annotationforge: Update to 1.40.0.
  gnu: r-annotationhub: Update to 3.6.0.
  gnu: r-aroma-light: Update to 3.28.0.
  gnu: r-bamsignals: Update to 1.30.0.
  gnu: r-biobase: Update to 2.58.0.
  gnu: r-biomart: Update to 2.54.0.
  gnu: r-biocparallel: Update to 1.32.1.
  gnu: r-biostrings: Update to 2.66.0.
  gnu: r-biovizbase: Update to 1.46.0.
  gnu: r-bsgenome: Update to 1.66.1.
  gnu: r-category: Update to 2.64.0.
  gnu: r-chipseeker: Update to 1.34.0.
  gnu: r-chipseq: Update to 1.48.0.
  gnu: r-complexheatmap: Update to 2.14.0.
  gnu: r-copywriter: Update to 2.29.0.
  gnu: r-deseq2: Update to 1.38.1.
  gnu: r-dexseq: Update to 1.44.0.
  gnu: r-diffcyt: Update to 1.18.0.
  gnu: r-dirichletmultinomial: Update to 1.40.0.
  gnu: r-dittoseq: Update to 1.10.0.
  gnu: r-edaseq: Update to 2.32.0.
  gnu: r-edger: Update to 3.40.0.
  gnu: r-ensembldb: Update to 2.22.0.
  gnu: r-fastseg: Update to 1.44.0.
  gnu: r-gage: Update to 2.48.0.
  gnu: r-genefilter: Update to 1.80.0.
  gnu: r-geneoverlap: Update to 1.34.0.
  gnu: r-genomation: Update to 1.30.0.
  gnu: r-genomeinfodb: Update to 1.34.3.
  gnu: r-genomicalignments: Update to 1.34.0.
  gnu: r-genomicfeatures: Update to 1.50.2.
  gnu: r-genomicfiles: Update to 1.34.0.
  gnu: r-genomicranges: Update to 1.50.1.
  gnu: r-gostats: Update to 2.64.0.
  gnu: r-gseabase: Update to 1.60.0.
  gnu: r-hpar: Update to 1.40.0.
  gnu: r-rhtslib: Update to 2.0.0.
  gnu: r-impute: Update to 1.72.1.
  gnu: r-interactivedisplaybase: Update to 1.36.0.
  gnu: r-keggrest: Update to 1.38.0.
  gnu: r-lfa: Update to 1.28.0.
  gnu: r-limma: Update to 3.54.0.
  gnu: r-made4: Update to 1.72.0.
  gnu: r-methylkit: Update to 1.24.0.
  gnu: r-muscat: Update to 1.12.0.
  gnu: r-mutationalpatterns: Update to 3.8.0.
  gnu: r-msnbase: Update to 2.24.0.
  gnu: r-msnid: Update to 1.32.0.
  gnu: r-mzid: Update to 1.36.0.
  gnu: r-mzr: Update to 2.32.0.
  gnu: r-organism-dplyr: Update to 1.26.0.
  gnu: r-organismdbi: Update to 1.40.0.
  gnu: r-pcaexplorer: Update to 2.24.0.
  gnu: r-pcamethods: Update to 1.90.0.
  gnu: r-protgenerics: Update to 1.30.0.
  gnu: r-rbgl: Update to 1.74.0.
  gnu: r-rcas: Update to 1.24.0.
  gnu: r-regioner: Update to 1.30.0.
  gnu: r-reportingtools: Update to 2.38.0.
  gnu: r-rhdf5: Update to 2.42.0.
  gnu: r-rhdf5filters: Update to 1.10.0.
  gnu: r-rsamtools: Update to 2.14.0.
  gnu: r-rtracklayer: Update to 1.58.0.
  gnu: r-scannotatr: Update to 1.4.0.
  gnu: r-scdblfinder: Update to 1.12.0.
  gnu: r-scmap: Update to 1.20.0.
  gnu: r-scry: Update to 1.10.0.
  gnu: r-seqlogo: Update to 1.64.0.
  gnu: r-seqpattern: Update to 1.30.0.
  gnu: r-shortread: Update to 1.56.0.
  gnu: r-simplifyenrichment: Update to 1.8.0.
  gnu: r-transcriptr: Update to 1.26.0.
  gnu: r-trajectoryutils: Update to 1.6.0.
  gnu: r-slingshot: Update to 2.6.0.
  gnu: r-stager: Update to 1.20.0.
  gnu: r-stringdb: Update to 2.10.0.
  gnu: r-structuralvariantannotation: Update to 1.13.0.
  gnu: r-summarizedexperiment: Update to 1.28.0.
  gnu: r-sva: Update to 3.46.0.
  gnu: r-systempiper: Update to 2.4.0.
  gnu: r-topgo: Update to 2.50.0.
  gnu: r-tximport: Update to 1.26.0.
  gnu: r-variantannotation: Update to 1.44.0.
  gnu: r-vsn: Update to 3.66.0.
  gnu: r-xina: Update to 1.16.0.
  gnu: r-xmapbridge: Update to 1.56.0.
  gnu: r-xvector: Update to 0.38.0.
  gnu: r-zlibbioc: Update to 1.44.0.
  gnu: r-zellkonverter: Update to 1.8.0.
  gnu: r-geneplotter: Update to 1.76.0.
  gnu: r-oligoclasses: Update to 1.60.0.
  gnu: r-oligo: Update to 1.62.0.
  gnu: r-qvalue: Update to 2.30.0.
  gnu: r-apeglm: Update to 1.20.0.
  gnu: r-greylistchip: Update to 1.30.0.
  gnu: r-diffbind: Update to 3.8.1.
  gnu: r-mbkmeans: Update to 1.14.0.
  gnu: r-multtest: Update to 2.54.0.
  gnu: r-graph: Update to 1.76.0.
  gnu: r-chippeakanno: Update to 3.32.0.
  gnu: r-matrixgenerics: Update to 1.10.0.
  gnu: r-marray: Update to 1.76.0.
  gnu: r-cghbase: Update to 1.58.0.
  gnu: r-cghcall: Update to 2.60.0.
  gnu: r-qdnaseq: Update to 1.34.0.
  gnu: r-bayseq: Update to 2.31.0.
  gnu: r-chipcomp: Update to 1.28.0.
  gnu: r-riboprofiling: Update to 1.28.0.
  gnu: r-riboseqr: Update to 1.32.0.
  gnu: r-interactionset: Update to 1.26.0.
  gnu: r-genomicinteractions: Update to 1.32.0.
  gnu: r-ctc: Update to 1.72.0.
  gnu: r-goseq: Update to 1.50.0.
  gnu: r-glimma: Update to 2.8.0.
  gnu: r-rots: Update to 1.26.0.
  gnu: r-plgem: Update to 1.70.0.
  gnu: r-inspect: Update to 1.28.0.
  gnu: r-dnabarcodes: Update to 1.28.0.
  gnu: r-ruvseq: Update to 1.32.0.
  gnu: r-biocneighbors: Update to 1.16.0.
  gnu: r-scaledmatrix: Update to 1.6.0.
  gnu: r-treeio: Update to 1.22.0.
  gnu: r-ggtree: Update to 3.6.2.
  gnu: r-metapod: Update to 1.6.0.
  gnu: r-biocsingular: Update to 1.14.0.
  gnu: r-destiny: Update to 3.12.0.
  gnu: r-savr: Update to 1.36.0.
  gnu: r-chipexoqual: Update to 1.22.0.
  gnu: r-copynumber: Update to 1.38.0.
  gnu: r-dnacopy: Update to 1.72.0.
  gnu: r-ebseq: Update to 1.38.0.
  gnu: r-karyoploter: Update to 1.24.0.
  gnu: r-lpsymphony: Update to 1.26.0.
  gnu: r-ihw: Update to 1.26.0.
  gnu: r-icobra: Update to 1.26.0.
  gnu: r-residualmatrix: Update to 1.8.0.
  gnu: r-batchelor: Update to 1.14.0.
  gnu: r-mast: Update to 1.24.0.
  gnu: r-monocle: Update to 2.26.0.
  gnu: r-noiseq: Update to 2.42.0.
  gnu: r-scdd: Update to 1.22.0.
  gnu: r-scone: Update to 1.22.0.
  gnu: r-geoquery: Update to 2.66.0.
  gnu: r-illuminaio: Update to 0.40.0.
  gnu: r-siggenes: Update to 1.72.0.
  gnu: r-bumphunter: Update to 1.40.0.
  gnu: r-microbiome: Update to 1.20.0.
  gnu: r-milor: Update to 1.6.0.
  gnu: r-minfi: Update to 1.44.0.
  gnu: r-methylumi: Update to 2.44.0.
  gnu: r-lumi: Update to 2.50.0.
  gnu: r-linnorm: Update to 2.22.0.
  gnu: r-ioniser: Update to 2.22.0.
  gnu: r-tradeseq: Update to 1.12.0.
  gnu: r-varianttools: Update to 1.40.0.
  gnu: r-heatplus: Update to 3.6.0.
  gnu: r-gosemsim: Update to 2.24.0.
  gnu: r-anota: Update to 1.46.0.
  gnu: r-sigpathway: Update to 1.66.0.
  gnu: r-fcscan: Update to 1.12.0.
  gnu: r-fgsea: Update to 1.24.0.
  gnu: r-dose: Update to 3.24.1.
  DRAFT gnu: r-enrichplot: Update to 1.18.0.
  gnu: r-clusterprofiler: Update to 4.6.0.
  gnu: r-clusterexperiment: Update to 2.18.0.
  gnu: r-mlinterfaces: Update to 1.78.0.
  gnu: r-annaffy: Update to 1.70.0.
  gnu: r-a4core: Update to 1.46.0.
  gnu: r-a4classif: Update to 1.46.0.
  gnu: r-a4preproc: Update to 1.46.0.
  gnu: r-a4reporting: Update to 1.46.0.
  gnu: r-a4base: Update to 1.46.0.
  gnu: r-a4: Update to 1.46.0.
  gnu: r-abseqr: Update to 1.16.0.
  gnu: r-bacon: Update to 1.26.0.
  gnu: r-rgadem: Update to 2.46.0.
  gnu: r-motifdb: Update to 1.40.0.
  gnu: r-motifbreakr: Update to 2.12.0.
  gnu: r-motifstack: Update to 1.42.0.
  gnu: r-genomicscores: Update to 2.10.0.
  gnu: r-atacseqqc: Update to 1.22.0.
  gnu: r-gofuncr: Update to 1.18.0.
  gnu: r-annotationtools: Update to 1.72.0.
  gnu: r-allelicimbalance: Update to 1.36.0.
  gnu: r-aucell: Update to 1.20.1.
  gnu: r-ebimage: Update to 4.40.0.
  gnu: r-yamss: Update to 1.24.0.
  gnu: r-gtrellis: Update to 1.30.0.
  gnu: r-somaticsignatures: Update to 2.34.0.
  gnu: r-yapsa: Update to 1.24.0.
  gnu: r-gcrma: Update to 2.70.0.
  gnu: r-quantro: Update to 1.32.0.
  gnu: r-yarn: Update to 1.24.0.
  gnu: r-roar: Update to 1.34.0.
  gnu: r-massspecwavelet: Update to 1.64.0.
  gnu: r-xcms: Update to 3.20.0.
  gnu: r-wppi: Update to 1.6.0.
  gnu: r-wrench: Update to 1.16.0.
  gnu: r-wiggleplotr: Update to 1.22.0.
  gnu: r-widgettools: Update to 1.76.0.
  gnu: r-webbioc: Update to 1.70.0.
  gnu: r-zinbwave: Update to 1.20.0.
  gnu: r-zfpkm: Update to 1.20.0.
  gnu: r-rbowtie2: Update to 2.4.0.
  gnu: r-progeny: Update to 1.20.0.
  gnu: r-arrmnormalization: Update to 1.38.0.
  gnu: r-biocfilecache: Update to 2.6.0.
  gnu: r-iclusterplus: Update to 1.34.0.
  gnu: r-rbowtie: Update to 1.38.0.
  gnu: r-sgseq: Update to 1.32.0.
  gnu: r-rhisat2: Update to 1.14.0.
  gnu: r-quasr: Update to 1.38.0.
  gnu: r-rqc: Update to 1.32.0.
  gnu: r-birewire: Update to 3.30.0.
  gnu: r-multidataset: Update to 1.26.0.
  DRAFT gnu: r-ropls: Update to 1.30.0.
  gnu: r-biosigner: Update to 1.26.0.
  gnu: r-annotatr: Update to 1.24.0.
  gnu: r-rsubread: Update to 2.12.0.
  gnu: r-consensusclusterplus: Update to 1.62.0.
  gnu: r-cytolib: Update to 2.10.0.
  gnu: r-flowcore: Update to 2.10.0.
  gnu: r-flowmeans: Update to 1.58.0.
  gnu: r-ncdfflow: Update to 2.44.0.
  gnu: r-ggcyto: Update to 1.26.0.
  gnu: r-flowviz: Update to 1.62.0.
  gnu: r-flowclust: Update to 3.36.0.
  gnu: r-rprotobuflib: Update to 2.10.0.
  gnu: r-flowworkspace: Update to 4.10.0.
  gnu: r-flowstats: Update to 4.10.0.
  gnu: r-opencyto: Update to 2.10.0.
  gnu: r-cytoml: Update to 2.10.0.
  gnu: r-flowsom: Update to 2.6.0.
  gnu: r-mixomics: Update to 6.22.0.
  gnu: r-depecher: Update to 1.14.0.
  gnu: r-rcistarget: Update to 1.17.0.
  gnu: r-chicago: Update to 1.26.0.
  gnu: r-cicero: Update to 1.16.0.
  gnu: r-circrnaprofiler: Update to 1.12.0.
  gnu: r-genie3: Update to 1.20.0.
  gnu: r-roc: Update to 1.74.0.
  gnu: r-watermelon: Update to 2.4.0.
  gnu: r-gdsfmt: Update to 1.34.0.
  gnu: r-bigmelon: Update to 1.24.0.
  gnu: r-seqbias: Update to 1.46.0.
  gnu: r-reqon: Update to 1.44.0.
  gnu: r-wavcluster: Update to 2.32.0.
  gnu: r-variantfiltering: Update to 1.34.0.
  gnu: r-variancepartition: Update to 1.28.0.
  gnu: r-htqpcr: Update to 1.52.0.
  gnu: r-unifiedwmwqpcr: Update to 1.34.0.
  gnu: r-universalmotif: Update to 1.16.0.
  gnu: r-ace: Update to 1.16.0.
  gnu: r-acgh: Update to 1.76.0.
  gnu: r-acme: Update to 2.54.0.
  gnu: r-acde: Update to 1.28.0.
  gnu: r-bgmix: Update to 1.58.0.
  gnu: r-bgx: Update to 1.64.0.
  gnu: r-bhc: Update to 1.50.0.
  gnu: r-bicare: Update to 1.56.0.
  gnu: r-bifet: Update to 1.18.0.
  gnu: r-rsbml: Update to 2.56.0.
  gnu: r-hypergraph: Update to 1.70.0.
  gnu: r-hyperdraw: Update to 1.50.0.
  gnu: r-biggr: Update to 1.34.0.
  gnu: r-bigpint: Update to 1.14.0.
  gnu: r-chemminer: Update to 3.50.0.
  gnu: r-fmcsr: Update to 1.40.0.
  gnu: r-bioassayr: Update to 1.36.0.
  gnu: r-biobroom: Update to 1.30.0.
  gnu: r-graphite: Update to 1.44.0.
  gnu: r-reactomepa: Update to 1.42.0.
  gnu: r-ebarrays: Update to 2.62.0.
  gnu: r-bioccheck: Update to 1.34.0.
  gnu: r-biocgraph: Update to 1.60.0.
  gnu: r-biocstyle: Update to 2.26.0.
  gnu: r-biocviews: Update to 1.66.0.
  gnu: r-experimenthub: Update to 2.6.0.
  gnu: r-grohmm: Update to 1.32.0.
  gnu: r-multiassayexperiment: Update to 1.24.0.
  gnu: r-bioconcotk: Update to 1.18.0.
  gnu: r-biocor: Update to 1.22.0.
  gnu: r-biocpkgtools: Update to 1.16.0.
  gnu: r-biocset: Update to 1.12.0.
  gnu: r-biocworkflowtools: Update to 1.24.0.
  gnu: r-biodist: Update to 1.70.0.
  gnu: r-pcatools: Update to 2.10.0.
  DRAFT gnu: r-rgreat: Update to 2.0.1.
  gnu: r-m3c: Update to 1.20.0.
  gnu: r-icens: Update to 1.70.0.
  gnu: r-preprocesscore: Update to 1.60.0.
  gnu: r-s4vectors: Update to 0.36.0.
  gnu: r-rgraphviz: Update to 2.42.0.
  gnu: r-fishpond: Update to 2.4.0.
  gnu: r-fithic: Update to 1.24.0.
  gnu: r-hitc: Update to 1.42.0.
  gnu: r-hdf5array: Update to 1.26.0.
  gnu: r-rhdf5lib: Update to 1.20.0.
  gnu: r-beachmat: Update to 2.14.0.
  gnu: r-cner: Update to 1.34.0.
  gnu: r-tfbstools: Update to 1.36.0.
  gnu: r-maftools: Update to 2.14.0.
  gnu: r-motifmatchr: Update to 1.20.0.
  gnu: r-chromvar: Update to 1.20.0.
  gnu: r-singlecellexperiment: Update to 1.20.0.
  gnu: r-singler: Update to 2.0.0.
  gnu: r-scuttle: Update to 1.8.0.
  gnu: r-scater: Update to 1.26.1.
  gnu: r-scran: Update to 1.26.0.
  gnu: r-sparsematrixstats: Update to 1.10.0.
  gnu: r-delayedmatrixstats: Update to 1.20.0.
  gnu: r-mscoreutils: Update to 1.10.0.
  gnu: r-msfeatures: Update to 1.6.0.
  gnu: r-biocio: Update to 1.8.0.
  gnu: r-msmseda: Update to 1.36.0.
  gnu: r-msmstests: Update to 1.36.0.
  gnu: r-catalyst: Update to 1.22.0.
  gnu: r-erma: Update to 1.14.0.
  gnu: r-ggbio: Update to 1.46.0.
  gnu: r-gviz: Update to 1.42.0.
  gnu: r-gwascat: Update to 2.30.0.
  gnu: r-kegggraph: Update to 1.58.0.
  gnu: r-ldblock: Update to 1.28.0.
  gnu: r-pathview: Update to 1.38.0.
  gnu: r-snpstats: Update to 1.48.0.
  gnu: r-chromstar: Update to 1.24.0.
  gnu: r-guitar: Update to 2.14.0.
  gnu: r-ballgown: Update to 2.30.0.
  gnu: r-megadepth: Update to 1.8.0.
  gnu: r-beclear: Update to 2.14.0.
  gnu: r-bgeecall: Update to 1.14.0.
  gnu: r-bgeedb: Update to 2.24.0.
  gnu: r-biobtreer: Update to 1.10.0.
  gnu: r-minet: Update to 3.56.0.
  gnu: r-genetclassifier: Update to 1.38.0.
  gnu: r-dir-expiry: Update to 1.6.0.
  gnu: r-basilisk-utils: Update to 1.10.0.
  gnu: r-basilisk: Update to 1.10.2.
  gnu: r-biocthis: Update to 1.8.1.
  gnu: r-biocdockermanager: Update to 1.10.0.
  gnu: r-biodb: Update to 1.6.0.
  gnu: r-biomformat: Update to 1.26.0.
  gnu: r-mvcclass: Update to 1.72.0.
  gnu: r-biomvcclass: Update to 1.66.0.
  gnu: r-biomvrcns: Update to 1.38.0.
  gnu: r-bionero: Update to 1.6.0.
  gnu: r-bionet: Update to 1.58.0.
  gnu: r-bionetstat: Update to 1.18.0.
  gnu: r-bioqc: Update to 1.26.0.
  gnu: r-biotip: Update to 1.12.0.
  gnu: r-biotmle: Update to 1.22.0.
  gnu: r-bsseq: Update to 1.34.0.
  gnu: r-dada2: Update to 1.26.0.
  gnu: r-dmrseq: Update to 1.18.0.
  gnu: r-omicade4: Update to 1.38.0.
  gnu: r-omnipathr: Update to 3.5.25.
  gnu: r-biscuiteer: Update to 1.12.0.
  gnu: r-tcgabiolinks: Update to 2.25.3.
  gnu: r-tricycle: Update to 1.6.0.
  gnu: r-tximeta: Update to 1.16.0.
  gnu: r-phyloseq: Update to 1.42.0.

 gnu/packages/bioconductor.scm | 1860 +++++++++++++++++----------------
 gnu/packages/cran.scm         |   52 +-
 gnu/packages/statistics.scm   |    9 +-
 guix/build-system/r.scm       |    2 +-
 guix/import/cran.scm          |    4 +-
 5 files changed, 1031 insertions(+), 896 deletions(-)

-- 
2.38.1

Message #8 received at 59329 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 59329 <at> debbugs.gnu.org
Cc: rekado <at> elephly.net
Subject: Re: [bug#59329] [PATCH 000/444] Update Bioconductor to 3.16
Date: Thu, 17 Nov 2022 11:03:36 +0100

Hi,

On Thu, 17 Nov 2022 at 04:55, zimoun <zimon.toutoune <at> gmail.com> wrote:

> Well, I am rebuilding to see if these updates introduce non-reproducible
> packages.  But that's not blocking, IMHO.

The only non-reproducible packages is r-omnipathr but it was not before
the update.


Cheers,
simon

Message #13 received at 59329-done <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 59329-done <at> debbugs.gnu.org
Cc: rekado <at> elephly.net
Subject: Re: bug#59329: [PATCH 000/444] Update Bioconductor to 3.16
Date: Fri, 25 Nov 2022 10:15:27 +0100

Hi,

Thanks Ricardo!

Merged starting at f4a7ccc976a8974803ed4b0bfe72af0bd44a9773, closing.

Cheers,
simon

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