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" 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". Either that apt solver setup/configuration needs adjusting or the r-bioc-* packages need enhanced minimum version specifiers without manual intervention. My guess is that could be done by making dh-update-R set matching minimum version numbers of the r-bioc-* Build-Depends (and autopkgtest "extra_depends") that match the relevant bioc release of the corresponding packages. --- Everything is built and in installed "experimental". However 24 of the autopkgtests are currently failing: https://qa.debian.org/excuses.php?package=r-bioc-biocgenerics&experimental=1 The autopkgtest failures are all in the "preparing testbed" phase where the resolver is having issues explicitly choosing the new r-bioc-* packages from "experimental" and not the ones from "unstable". Example error message is at https://ci.debian.net/packages/r/r-bioc-biobase/unstable/amd64/49811272/#L619 My understanding is that the autopkgtest testbed apt solver is configured to not pull packages from "experimental" unless the minimum version requires it. Therefore I have been manually adding minimal version numbers (corresponding to the bioc-3.19 release) to the r-bioc-* packages listed as build-deps and copying those to the "Depends" of the binary packages as well, along with the same for the r-bioc-* packages listed in the "extra_depend" section of "debian/tests/autopkgtest-pkg-r.conf" (when present) and copying those to the "Suggests" stanza of the binary package listing in "debian/control". I also guess that the CI/autopkgtest setup isn't resolving the "r-api-bioc-api-3.19" virtual package dependency to the r-bioc-biocgenerics 0.50.0-* package from "experimental". If my other fixes that are in flight don't work, then I will manually add an explicit dependency on "r-bioc-biocgenerics >= 0.50.0" in strategic places. All these extra minimum versions are a lot of work and it seems to defeat the whole purpose of dh-r injecting the dependency on the "r-api-bioc-3.19" virtual package. I'm fairly sure that uploading everything to unstable will remove this issue, but it would be nice to see all the autopkgtests pass before then. On 14/07/2024 18.13, Michael R. Crusoe wrote:
Links for overview (any hints on shorter links would be welcome!): https://buildd.debian.org/status/package.php?p=r-bioc-affxparser%2Cr-bioc-affy%2Cr-bioc-affyio%2Cr-bioc-all%2Cr-bioc-altcdfenvs%2Cr-bioc-annotate%2Cr-bioc-annotationdbi%2Cr-bioc-annotationfilter%2Cr-bioc-annotationhub%2Cr-bioc-aroma.light%2Cr-bioc-arrayexpress%2Cr-bioc-ballgown%2Cr-bioc-basilisk%2Cr-bioc-basilisk.utils%2Cr-bioc-beachmat%2Cr-bioc-biobase%2Cr-bioc-biocbaseutils%2Cr-bioc-bioccheck%2Cr-bioc-biocfilecache%2Cr-bioc-biocgenerics%2Cr-bioc-biocio%2Cr-bioc-biocneighbors%2Cr-bioc-biocparallel%2Cr-bioc-biocsingular%2Cr-bioc-biocstyle%2Cr-bioc-biocversion%2Cr-bioc-biocviews%2Cr-bioc-biomart%2Cr-bioc-biomformat%2Cr-bioc-biostrings%2Cr-bioc-biovizbase%2Cr-bioc-bladderbatch%2Cr-bioc-bluster%2Cr-bioc-bsgenome%2Cr-bioc-bsseq%2Cr-bioc-chemminer%2Cr-bioc-cner%2Cr-bioc-complexheatmap%2Cr-bioc-consensusclusterplus%2Cr-bioc-ctc%2Cr-bioc-cummerbund%2Cr-bioc-dada2%2Cr-bioc-decontam%2Cr-bioc-decoupler%2Cr-bioc-degnorm%2Cr-bioc-degreport%2Cr-bioc-delayedarray%2Cr-bioc-delayedmatrixstats%2Cr-bioc-demixt%2Cr-bioc-densvis%2Cr-bioc-deseq2%2Cr-bioc-destiny%2Cr-bioc-dexseq%2Cr-bioc-dir.expiry%2Cr-bioc-dirichletmultinomial%2Cr-bioc-dnacopy%2Cr-bioc-drimseq%2Cr-bioc-dropletutils%2Cr-bioc-dss%2Cr-bioc-dupradar%2Cr-bioc-ebseq%2Cr-bioc-edaseq%2Cr-bioc-edger%2Cr-bioc-eir%2Cr-bioc-ensembldb%2Cr-bioc-experimenthub%2Cr-bioc-fishpond%2Cr-bioc-fmcsr%2Cr-bioc-genefilter%2Cr-bioc-genelendatabase%2Cr-bioc-geneplotter%2Cr-bioc-genomeinfodb%2Cr-bioc-genomeinfodbdata%2Cr-bioc-genomicalignments%2Cr-bioc-genomicfeatures%2Cr-bioc-genomicfiles%2Cr-bioc-genomicranges%2Cr-bioc-geoquery%2Cr-bioc-ggbio%2Cr-bioc-glmgampoi%2Cr-bioc-go.db%2Cr-bioc-gosemsim%2Cr-bioc-goseq%2Cr-bioc-graph%2Cr-bioc-grohmm%2Cr-bioc-gseabase%2Cr-bioc-gsva%2Cr-bioc-gviz%2Cr-bioc-hdf5array%2Cr-bioc-hilbertvis%2Cr-bioc-hsmmsinglecell%2Cr-bioc-htsfilter%2Cr-bioc-hypergraph%2Cr-bioc-ihw%2Cr-bioc-impute%2Cr-bioc-interactivedisplaybase%2Cr-bioc-ioniser%2Cr-bioc-iranges%2Cr-bioc-isoformswitchanalyzer%2Cr-bioc-keggrest%2Cr-bioc-limma%2Cr-bioc-lpsymphony%2Cr-bioc-makecdfenv%2Cr-bioc-matrixgenerics%2Cr-bioc-megadepth%2Cr-bioc-mergeomics%2Cr-bioc-metagenomeseq%2Cr-bioc-metapod%2Cr-bioc-monocle%2Cr-bioc-multiassayexperiment%2Cr-bioc-multtest%2Cr-bioc-mutationalpatterns%2Cr-bioc-netsam%2Cr-bioc-noiseq%2Cr-bioc-oligo%2Cr-bioc-oligoclasses%2Cr-bioc-organismdbi%2Cr-bioc-org.hs.eg.db%2Cr-bioc-pcamethods%2Cr-bioc-pfamanalyzer%2Cr-bioc-phyloseq%2Cr-bioc-preprocesscore%2Cr-bioc-progeny%2Cr-bioc-protgenerics%2Cr-bioc-purecn%2Cr-bioc-pwmenrich%2Cr-bioc-qtlizer%2Cr-bioc-qusage%2Cr-bioc-qvalue%2Cr-bioc-rbgl%2Cr-bioc-rcpi%2Cr-bioc-rcwl%2Cr-bioc-residualmatrix%2Cr-bioc-rgsepd%2Cr-bioc-rhdf5%2Cr-bioc-rhdf5filters%2Cr-bioc-rhdf5lib%2Cr-bioc-rhtslib%2Cr-bioc-rots%2Cr-bioc-rsamtools%2Cr-bioc-rsubread%2Cr-bioc-rtracklayer%2Cr-bioc-rwikipathways%2Cr-bioc-s4arrays%2Cr-bioc-s4vectors%2Cr-bioc-saturn%2Cr-bioc-scaledmatrix%2Cr-bioc-scater%2Cr-bioc-scran%2Cr-bioc-scrnaseq%2Cr-bioc-scuttle%2Cr-bioc-seqlogo%2Cr-bioc-shortread%2Cr-bioc-singlecellexperiment%2Cr-bioc-singler%2Cr-bioc-snpstats%2Cr-bioc-sparsearray%2Cr-bioc-sparsematrixstats%2Cr-bioc-stringdb%2Cr-bioc-structuralvariantannotation%2Cr-bioc-summarizedexperiment%2Cr-bioc-sva%2Cr-bioc-tcgabiolinks%2Cr-bioc-tcgabiolinksgui.data%2Cr-bioc-tfbstools%2Cr-bioc-titancna%2Cr-bioc-tximeta%2Cr-bioc-tximport%2Cr-bioc-tximportdata%2Cr-bioc-variantannotation%2Cr-bioc-wrench%2Cr-bioc-xvector%2Cr-bioc-zlibbioc&suite=experimental https://qa.debian.org/developer.php?packages=r-bioc-affxparser%20r-bioc-affy%20r-bioc-affyio%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-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-gviz%20r-bioc-hdf5array%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-monocle%20r-bioc-multiassayexperiment%20r-bioc-multtest%20r-bioc-mutationalpatterns%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-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-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-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-tximeta%20r-bioc-tximport%20r-bioc-tximportdata%20r-bioc-variantannotation%20r-bioc-wrench%20r-bioc-xvector%20r-bioc-zlibbioc
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