On 01/08/2024 10.56, Michael R. Crusoe wrote:
August 1st update Summary: there is a benefit to testing in experimental, but forcing the installation of the matching bioc-3.19 packages during the autopkgtests is requiring too much manual work. Things that would help for next time (and help opening wishlist bugs about these would be appreciated!): 1. SalsaCI needs to be manually configured to use the "experimental" distribution for building and testing; it would be great if SalsaCI automatically enabled the "experimental" distribution when the branch name is "debian/experimental"
According to https://salsa.debian.org/salsa-ci-team/pipeline/#changing-the-debian-release , the release is pulled from "debian/changelog" ; so maybe this complaint is void. While looking to confirm that, I can't find a single r-bioc-* SalsaCI autokpgktest job that truly succeeded due to our use of "skip-not-installable" and its inability to resolve the "r-api-bioc-3.19" virtual package from "experimental".
2. "experimental psuedo-excuses" (via ci.debian.net / autokpkgtest) seem to struggle resolving the "r-api-bioc-3.19" virtual package dependency and using that as a reason to install from "experimental" over "unstable".
Another way this could be fixed is if "dh-r" expanded the "r-api-bioc-N.NN" in "${R:Depends}" for r-bioc-* packages to include the specific minimum version of r-bioc-biocgenerics as an alternative. For example: "r-api-bioc-3.19 | r-bioc-biocgenerics (>= 0.50.0)". Thought this seems to remove some of the benefits of using the "r-api-bioc-N.NN" virtual package
To add to my wishlist:
3. autopkgtest gains a "Architecture: 64-bit" or equivalent feature. Currently we specify the "skip-not-installable" restriction instead of manually listing the 64-bit architectures we care about, but "skip-not-installable" hides a lot of real errors; so that might deserve rethinking.
Updated build URL:
https://buildd.debian.org/status/package.php?p=r-bioc-affxparser,r-bioc-affy,r-bioc-affyio,r-bioc-alabaster.base,r-bioc-alabaster.matrix,r-bioc-alabaster.ranges,r-bioc-alabaster.sce,r-bioc-alabaster.schemas,r-bioc-alabaster.se,r-bioc-all,r-bioc-altcdfenvs,r-bioc-annotate,r-bioc-annotationdbi,r-bioc-annotationfilter,r-bioc-annotationhub,r-bioc-aroma.light,r-bioc-arrayexpress,r-bioc-ballgown,r-bioc-basilisk,r-bioc-basilisk.utils,r-bioc-beachmat,r-bioc-biobase,r-bioc-biocbaseutils,r-bioc-bioccheck,r-bioc-biocfilecache,r-bioc-biocgenerics,r-bioc-biocio,r-bioc-biocneighbors,r-bioc-biocparallel,r-bioc-biocsingular,r-bioc-biocstyle,r-bioc-biocversion,r-bioc-biocviews,r-bioc-biomart,r-bioc-biomformat,r-bioc-biostrings,r-bioc-biovizbase,r-bioc-bladderbatch,r-bioc-bluster,r-bioc-bsgenome,r-bioc-bsseq,r-bioc-chemminer,r-bioc-cner,r-bioc-complexheatmap,r-bioc-consensusclusterplus,r-bioc-ctc,r-bioc-cummerbund,r-bioc-dada2,r-bioc-decontam,r-bioc-decoupler,r-bioc-degnorm,r-bioc-degreport,r-bioc-delayedarray,r-bioc-delayedmatrixstats,r-bioc-demixt,r-bioc-densvis,r-bioc-deseq,r-bioc-deseq2,r-bioc-destiny,r-bioc-dexseq,r-bioc-dir.expiry,r-bioc-dirichletmultinomial,r-bioc-dnacopy,r-bioc-drimseq,r-bioc-dropletutils,r-bioc-dss,r-bioc-dupradar,r-bioc-ebseq,r-bioc-edaseq,r-bioc-edger,r-bioc-eir,r-bioc-ensembldb,r-bioc-experimenthub,r-bioc-fishpond,r-bioc-fmcsr,r-bioc-genefilter,r-bioc-genelendatabase,r-bioc-geneplotter,r-bioc-genomeinfodb,r-bioc-genomeinfodbdata,r-bioc-genomicalignments,r-bioc-genomicfeatures,r-bioc-genomicfiles,r-bioc-genomicranges,r-bioc-geoquery,r-bioc-ggbio,r-bioc-glmgampoi,r-bioc-go.db,r-bioc-gosemsim,r-bioc-goseq,r-bioc-graph,r-bioc-grohmm,r-bioc-gseabase,r-bioc-gsva,r-bioc-gsvadata,r-bioc-gviz,r-bioc-gypsum,r-bioc-hdf5array,r-bioc-hgu95a.db,r-bioc-hilbertvis,r-bioc-hsmmsinglecell,r-bioc-htsfilter,r-bioc-hypergraph,r-bioc-ihw,r-bioc-impute,r-bioc-interactivedisplaybase,r-bioc-ioniser,r-bioc-iranges,r-bioc-isoformswitchanalyzer,r-bioc-keggrest,r-bioc-limma,r-bioc-lpsymphony,r-bioc-makecdfenv,r-bioc-matrixgenerics,r-bioc-megadepth,r-bioc-mergeomics,r-bioc-metagenomeseq,r-bioc-metapod,r-bioc-mofa,r-bioc-monocle,r-bioc-multiassayexperiment,r-bioc-multtest,r-bioc-mutationalpatterns,r-bioc-nanostringqcpro,r-bioc-netsam,r-bioc-noiseq,r-bioc-oligo,r-bioc-oligoclasses,r-bioc-organismdbi,r-bioc-org.hs.eg.db,r-bioc-pcamethods,r-bioc-pfamanalyzer,r-bioc-phyloseq,r-bioc-preprocesscore,r-bioc-progeny,r-bioc-protgenerics,r-bioc-purecn,r-bioc-pwalign,r-bioc-pwmenrich,r-bioc-qtlizer,r-bioc-qusage,r-bioc-qvalue,r-bioc-rbgl,r-bioc-rcpi,r-bioc-rcwl,r-bioc-residualmatrix,r-bioc-rgsepd,r-bioc-rhdf5,r-bioc-rhdf5filters,r-bioc-rhdf5lib,r-bioc-rhtslib,r-bioc-rots,r-bioc-rsamtools,r-bioc-rsubread,r-bioc-rtracklayer,r-bioc-rwikipathways,r-bioc-s4arrays,r-bioc-s4vectors,r-bioc-saturn,r-bioc-savr,r-bioc-scaledmatrix,r-bioc-scater,r-bioc-scran,r-bioc-scrnaseq,r-bioc-scuttle,r-bioc-seqlogo,r-bioc-shortread,r-bioc-singlecellexperiment,r-bioc-singler,r-bioc-snpstats,r-bioc-sparsearray,r-bioc-sparsematrixstats,r-bioc-spatialexperiment,r-bioc-stringdb,r-bioc-structuralvariantannotation,r-bioc-summarizedexperiment,r-bioc-sva,r-bioc-tcgabiolinks,r-bioc-tcgabiolinksgui.data,r-bioc-tfbstools,r-bioc-titancna,r-bioc-txdbmaker,r-bioc-tximeta,r-bioc-tximport,r-bioc-tximportdata,r-bioc-ucsc.utils,r-bioc-variantannotation,r-bioc-wrench,r-bioc-xvector,r-bioc-zlibbioc&suite=experimental
Updated QA URL:
https://qa.debian.org/developer.php?packages=r-bioc-affxparser%20r-bioc-affy%20r-bioc-affyio%20r-bioc-alabaster.base%20r-bioc-alabaster.matrix%20r-bioc-alabaster.ranges%20r-bioc-alabaster.sce%20r-bioc-alabaster.schemas%20r-bioc-alabaster.se%20r-bioc-all%20r-bioc-altcdfenvs%20r-bioc-annotate%20r-bioc-annotationdbi%20r-bioc-annotationfilter%20r-bioc-annotationhub%20r-bioc-aroma.light%20r-bioc-arrayexpress%20r-bioc-ballgown%20r-bioc-basilisk%20r-bioc-basilisk.utils%20r-bioc-beachmat%20r-bioc-biobase%20r-bioc-biocbaseutils%20r-bioc-bioccheck%20r-bioc-biocfilecache%20r-bioc-biocgenerics%20r-bioc-biocio%20r-bioc-biocneighbors%20r-bioc-biocparallel%20r-bioc-biocsingular%20r-bioc-biocstyle%20r-bioc-biocversion%20r-bioc-biocviews%20r-bioc-biomart%20r-bioc-biomformat%20r-bioc-biostrings%20r-bioc-biovizbase%20r-bioc-bladderbatch%20r-bioc-bluster%20r-bioc-bsgenome%20r-bioc-bsseq%20r-bioc-chemminer%20r-bioc-cner%20r-bioc-complexheatmap%20r-bioc-consensusclusterplus%20r-bioc-ctc%20r-bioc-cummerbund%20r-bioc-dada2%20r-bioc-decontam%20r-bioc-decoupler%20r-bioc-degnorm%20r-bioc-degreport%20r-bioc-delayedarray%20r-bioc-delayedmatrixstats%20r-bioc-demixt%20r-bioc-densvis%20r-bioc-deseq%20r-bioc-deseq2%20r-bioc-destiny%20r-bioc-dexseq%20r-bioc-dir.expiry%20r-bioc-dirichletmultinomial%20r-bioc-dnacopy%20r-bioc-drimseq%20r-bioc-dropletutils%20r-bioc-dss%20r-bioc-dupradar%20r-bioc-ebseq%20r-bioc-edaseq%20r-bioc-edger%20r-bioc-eir%20r-bioc-ensembldb%20r-bioc-experimenthub%20r-bioc-fishpond%20r-bioc-fmcsr%20r-bioc-genefilter%20r-bioc-genelendatabase%20r-bioc-geneplotter%20r-bioc-genomeinfodb%20r-bioc-genomeinfodbdata%20r-bioc-genomicalignments%20r-bioc-genomicfeatures%20r-bioc-genomicfiles%20r-bioc-genomicranges%20r-bioc-geoquery%20r-bioc-ggbio%20r-bioc-glmgampoi%20r-bioc-go.db%20r-bioc-gosemsim%20r-bioc-goseq%20r-bioc-graph%20r-bioc-grohmm%20r-bioc-gseabase%20r-bioc-gsva%20r-bioc-gsvadata%20r-bioc-gviz%20r-bioc-gypsum%20r-bioc-hdf5array%20r-bioc-hgu95a.db%20r-bioc-hilbertvis%20r-bioc-hsmmsinglecell%20r-bioc-htsfilter%20r-bioc-hypergraph%20r-bioc-ihw%20r-bioc-impute%20r-bioc-interactivedisplaybase%20r-bioc-ioniser%20r-bioc-iranges%20r-bioc-isoformswitchanalyzer%20r-bioc-keggrest%20r-bioc-limma%20r-bioc-lpsymphony%20r-bioc-makecdfenv%20r-bioc-matrixgenerics%20r-bioc-megadepth%20r-bioc-mergeomics%20r-bioc-metagenomeseq%20r-bioc-metapod%20r-bioc-mofa%20r-bioc-monocle%20r-bioc-multiassayexperiment%20r-bioc-multtest%20r-bioc-mutationalpatterns%20r-bioc-nanostringqcpro%20r-bioc-netsam%20r-bioc-noiseq%20r-bioc-oligo%20r-bioc-oligoclasses%20r-bioc-organismdbi%20r-bioc-org.hs.eg.db%20r-bioc-pcamethods%20r-bioc-pfamanalyzer%20r-bioc-phyloseq%20r-bioc-preprocesscore%20r-bioc-progeny%20r-bioc-protgenerics%20r-bioc-purecn%20r-bioc-pwalign%20r-bioc-pwmenrich%20r-bioc-qtlizer%20r-bioc-qusage%20r-bioc-qvalue%20r-bioc-rbgl%20r-bioc-rcpi%20r-bioc-rcwl%20r-bioc-residualmatrix%20r-bioc-rgsepd%20r-bioc-rhdf5%20r-bioc-rhdf5filters%20r-bioc-rhdf5lib%20r-bioc-rhtslib%20r-bioc-rots%20r-bioc-rsamtools%20r-bioc-rsubread%20r-bioc-rtracklayer%20r-bioc-rwikipathways%20r-bioc-s4arrays%20r-bioc-s4vectors%20r-bioc-saturn%20r-bioc-savr%20r-bioc-scaledmatrix%20r-bioc-scater%20r-bioc-scran%20r-bioc-scrnaseq%20r-bioc-scuttle%20r-bioc-seqlogo%20r-bioc-shortread%20r-bioc-singlecellexperiment%20r-bioc-singler%20r-bioc-snpstats%20r-bioc-sparsearray%20r-bioc-sparsematrixstats%20r-bioc-spatialexperiment%20r-bioc-stringdb%20r-bioc-structuralvariantannotation%20r-bioc-summarizedexperiment%20r-bioc-sva%20r-bioc-tcgabiolinks%20r-bioc-tcgabiolinksgui.data%20r-bioc-tfbstools%20r-bioc-titancna%20r-bioc-txdbmaker%20r-bioc-tximeta%20r-bioc-tximport%20r-bioc-tximportdata%20r-bioc-ucsc.utils%20r-bioc-variantannotation%20r-bioc-wrench%20r-bioc-xvector%20r-bioc-zlibbioc
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