On 14/07/2024 18.05, Andreas Tille wrote:
Hi Michael, Am Sun, Jul 14, 2024 at 05:09:51PM +0200 schrieb Michael R. Crusoe:Am Sat, Jul 13, 2024 at 02:04:52PM +0200 schrieb Michael R. Crusoe:Then I'll cycle through the architecture dependent packages, doing a `ssh mirror.ftp-master.debian.org "dak rm --rdep-check --no-action r-bioc-$NAME"` check and adding the `architecture-is-64-bit` build-dep only when there are no no-bioc packages that would be affected.Luckily I thought about this a little bit and realized I can do a single query about the removals. ssh mirror.ftp-master.debian.org "dak rm --architecture=armel,armhf,i386 --no-arch-all-rdeps --binary-only --partial --rdep-check --no-action $(tr '\n' ' ' < ~/debian/bioc-3.19/packaged-any)" # where ~/debian/bioc-3.19/packaged-any is a list of packages I made that contain "Architecture: any" in their debian/control files The following non-bioc-3.19 packages would also need their 32-bit builds removed: r-bioc-deseq # not part of bioconductor since 3.13 r-cran-nmf # build-dep on r-bioc-biobase r-cran-restfulr # build-dep on r-bioc-s4vectors r-cran-samr # build-dep on r-bioc-impute r-cran-wgcna # build-dep on r-bioc-impute, r-bioc-preprocesscore, r-bioc-go.db, r-bioc-annotationdbi Adding the 5 packages above to the `dak rm` query doesn't reveal any other issues, BUT removing 32-bit builds of any r-cran-* packages is not yet part of the agreement.This sounds all very sensible! If I was not yet convinced that it was a good idea to run for DPL I think this is a good outcome to deal with those tasks automatically. ;-P
:-D
So I'll add the build-dep on "architecture-is-64-bit" to these 76 packages and "extra_restrictions=skip-not-installable" to debian/tests/autopkgtest-pkg-r.conf in all the r-bioc-* packages.ACK.
Done!
The commands I used:
for pkg in $(cat bioc-3.19/packaged-any-subset) ; do sed -i "/Build-Depends:/a\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ architecture-is-64-bit," ${pkg}/debian/control ; done
for pkg in $(cat bioc-3.19/packaged-any-subset) ; do echo ${pkg}; cd ${pkg}; printf "/^ -- Michael/--a\n * d/control: Skip building on 32-bit systems.\n.\nw\nq\n" | ed debian/changelog; debcommit -a ; cd .. ; done
for pkg in $(cat bioc-3.19/packaged-all) ; do cd ${pkg}; mkdir -p debian/tests ; echo extra_restrictions=skip-not-installable >> debian/tests/autopkgtest-pkg-r.conf ; git add debian/tests/autopkgtest-pkg-r.conf ; cd .. ; done
for pkg in $(cat bioc-3.19/packaged-all) ; do echo ${pkg}; cd ${pkg}; printf "/^ -- Michael/--a\n * d/tests/autopkgtest-pkg-r.conf: skip on 32-bit architectures.\n.\nw\nq\n" | ed debian/changelog; debcommit -a ; cd .. ; done
And then I'll start the uploads to "experimental".
In progress!
for pkg in $(cat bioc-3.19/packaged) ; do echo ${pkg}; cd ${pkg} ; git clean -fdx ; gbp tag --debian-branch=debian/experimental ; gbp buildpackage -S -d --git-debian-branch=debian/experimental ; debrelease -S --dput && gbp push --debian-branch=debian/experimental || echo problem: ${pkg}; cd .. ; done
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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