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Notes about issue randomness_in_r_rdb_rds_databases in experimental

Identifier: randomness_in_r_rdb_rds_databases
Suites: unstable / trixie / bookworm / bullseye / experimental
Description: R creates .rdb files and .rds with some randomness. They are a serialisation of some
sorts, related to lazy loading of modules?
Randomness seems to come from using absolute paths in .rd[bs] files.
.
Is not related to https://bugs.debian.org/774031 / r_base_appends_built_header_to_description_files
.
We have a pending patch to fix most of these (463/478) packages at the time
of writing) upstream in R:
.
https://stat.ethz.ch/pipermail/r-devel/2017-April/074138.html
.
When this is accepted into R upstream, commit 28d4af25 may be
(un-)reverted to remove these packages. In the meantime, please do not
remove this issue, nor mark it as deterministic, nor untag these packages.
.
The remaining ~15 packages are not completely fixed by this patch, so this
issue should remain, even when our upstream patch is accepted. These
packages will need to be investigated and fixed individually, see our blog
post on how to do that:
.
https://reproducible-builds.org/news/2017/05/03/reproduciing-r-packages/
Packages in 'experimental' known to be affected by this issue:
(the 1/4 most-popular ones (within this issue) are underlined)

reproducible icon 152 reproducible packages in experimental/amd64: r-bioc-affxparser r-bioc-affy r-bioc-affyio 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-basilisk r-bioc-basilisk.utils r-bioc-biobase r-bioc-biocbaseutils r-bioc-bioccheck r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocio r-bioc-biocversion r-bioc-biocviews r-bioc-biomart r-bioc-biomformat r-bioc-biostrings r-bioc-biovizbase r-bioc-bladderbatch r-bioc-bsgenome r-bioc-bsseq r-bioc-chemminer r-bioc-cner r-bioc-complexheatmap r-bioc-consensusclusterplus r-bioc-ctc r-bioc-dada2 r-bioc-decoupler r-bioc-degnorm r-bioc-degreport r-bioc-delayedarray r-bioc-delayedmatrixstats 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-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-genomicfiles r-bioc-genomicranges r-bioc-geoquery r-bioc-go.db r-bioc-gosemsim r-bioc-graph r-bioc-grohmm r-bioc-gseabase r-bioc-gsva r-bioc-hdf5array r-bioc-hilbertvis r-bioc-hsmmsinglecell r-bioc-htsfilter r-bioc-hypergraph r-bioc-ihw r-bioc-impute r-bioc-iranges 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-netsam r-bioc-noiseq r-bioc-oligo r-bioc-oligoclasses r-bioc-org.hs.eg.db r-bioc-organismdbi r-bioc-pcamethods r-bioc-pfamanalyzer r-bioc-phyloseq r-bioc-preprocesscore r-bioc-protgenerics r-bioc-purecn r-bioc-pwmenrich r-bioc-qusage r-bioc-qvalue r-bioc-rbgl r-bioc-rcpi r-bioc-residualmatrix r-bioc-rhdf5 r-bioc-rhdf5filters r-bioc-rhdf5lib r-bioc-rhtslib r-bioc-rots r-bioc-rsamtools r-bioc-rtracklayer r-bioc-rwikipathways r-bioc-s4arrays r-bioc-s4vectors r-bioc-saturn 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-snpstats r-bioc-sparsematrixstats 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-tximeta r-bioc-tximport r-bioc-tximportdata r-bioc-variantannotation r-bioc-wrench r-bioc-xvector r-bioc-zlibbioc r-cran-alakazam r-cran-ggm r-cran-mutoss

FTBR icon 5 unreproducible packages in experimental/amd64: r-bioc-ballgown r-bioc-biocparallel r-bioc-genomicfeatures r-bioc-ioniser r-bioc-qtlizer

depwait icon 5 depwait packages in experimental/amd64: r-bioc-beachmat r-bioc-biocsingular r-bioc-dropletutils r-bioc-glmgampoi r-bioc-singler

 

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Last update: 2024-12-03 00:59 UTC