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Notes about issue randomness_in_r_rdb_rds_databases in bookworm

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 'bookworm' known to be affected by this issue:
(the 1/4 most-popular ones (within this issue) are underlined)

reproducible icon 1256 reproducible packages in bookworm/amd64: abind acepack boot car chron cluster codetools date dbi effects fassets fbasics fbonds fcopulae fextremes fgarch fimport fmultivar fnonlinear foreign fportfolio fregression ftrading funitroots gdata gmodels gplots gregmisc gtools hmisc isospec kernsmooth lattice latticeextra littler lme4 lmtest mgcv misc3d mnormt multcomp mvtnorm nlme openturns polspline ppx-derivers quadprog 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-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-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-decoupler r-bioc-degnorm r-bioc-degreport r-bioc-delayedarray r-bioc-delayedmatrixstats r-bioc-demixt 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-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-gviz r-bioc-hdf5array r-bioc-hilbertvis r-bioc-hsmmsinglecell r-bioc-htsfilter r-bioc-hypergraph r-bioc-ihw r-bioc-impute r-bioc-interactivedisplaybase 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-org.hs.eg.db r-bioc-organismdbi r-bioc-pcamethods r-bioc-phyloseq r-bioc-preprocesscore r-bioc-protgenerics r-bioc-purecn r-bioc-pwmenrich r-bioc-qtlizer r-bioc-qusage r-bioc-qvalue r-bioc-rbgl r-bioc-rcpi 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-s4vectors 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-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-actuar r-cran-ade4 r-cran-adegenet r-cran-adegraphics r-cran-adephylo r-cran-admisc r-cran-aer r-cran-afex r-cran-airr r-cran-alakazam r-cran-amap r-cran-amore r-cran-animation r-cran-apcluster r-cran-ape r-cran-aplpack r-cran-argparse r-cran-argparser r-cran-arm r-cran-arsenal r-cran-askpass r-cran-assertive.base r-cran-assertive.sets r-cran-assertthat r-cran-av r-cran-aweek r-cran-backports r-cran-base64enc r-cran-base64url r-cran-batchjobs r-cran-batchtools r-cran-bayesfactor r-cran-bayesfm r-cran-bayesm r-cran-bayesplot r-cran-bayestestr r-cran-bbmisc r-cran-bbmle r-cran-bdgraph r-cran-bdsmatrix r-cran-beeswarm r-cran-bench 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r-cran-drr r-cran-dslabs r-cran-dt r-cran-dtplyr r-cran-dygraphs r-cran-dynamictreecut r-cran-dynlm r-cran-e1071 r-cran-eaf r-cran-earth r-cran-eco r-cran-ecodist r-cran-ecosolver r-cran-effectsize r-cran-egg r-cran-ei r-cran-eipack r-cran-ellipse r-cran-ellipsis r-cran-elliptic r-cran-emdbook r-cran-emmeans r-cran-emoa r-cran-energy r-cran-enrichwith r-cran-epi r-cran-epibasix r-cran-epicalc r-cran-epiestim r-cran-epir r-cran-epitools r-cran-erm r-cran-estimability r-cran-estimatr r-cran-etm r-cran-evaluate r-cran-evd r-cran-exactranktests r-cran-expint r-cran-expm r-cran-extradistr r-cran-factoextra r-cran-factominer r-cran-fail r-cran-fancova r-cran-fansi r-cran-farver r-cran-fastcluster r-cran-fastica r-cran-fastmap r-cran-fastmatch r-cran-fauxpas r-cran-fdrtool r-cran-ff r-cran-ffield r-cran-fftw r-cran-fields r-cran-filehash r-cran-filelock r-cran-findpython r-cran-fingerprint r-cran-fit.models r-cran-fitbitscraper r-cran-fitcoach r-cran-fitdistrplus r-cran-flashclust r-cran-flexmix r-cran-flextable r-cran-fnn r-cran-fontawesome r-cran-fontbitstreamvera r-cran-fontliberation r-cran-fontquiver r-cran-forcats r-cran-foreach r-cran-forecast r-cran-formatr r-cran-formattable r-cran-formula r-cran-fpc r-cran-fracdiff r-cran-freetypeharfbuzz r-cran-fs r-cran-fts r-cran-furrr r-cran-futile.options r-cran-future r-cran-future.apply r-cran-future.batchtools r-cran-g.data r-cran-gam r-cran-gamm4 r-cran-gargle r-cran-gb2 r-cran-gbm r-cran-gbrd r-cran-gbutils r-cran-gclus r-cran-gdtools r-cran-gee r-cran-geepack r-cran-genabel r-cran-genabel.data r-cran-generics r-cran-genetics r-cran-genie r-cran-genieclust r-cran-genoplotr r-cran-geoknife r-cran-geometry r-cran-geosphere r-cran-getopt r-cran-getoptlong r-cran-ggalluvial r-cran-ggally r-cran-gganimate r-cran-ggbeeswarm r-cran-ggdendro r-cran-ggeffects r-cran-ggforce r-cran-ggfortify r-cran-ggm r-cran-ggplot.multistats r-cran-ggplot2 r-cran-ggpubr r-cran-ggraph r-cran-ggrastr r-cran-ggrepel r-cran-ggridges r-cran-ggsci r-cran-ggseqlogo r-cran-ggsignif r-cran-ggtext r-cran-ggthemes r-cran-ggvis r-cran-gh r-cran-git2r r-cran-gitcreds r-cran-glasso r-cran-glmmtmb r-cran-glmnet r-cran-globaloptions r-cran-globals r-cran-glue r-cran-gmaps r-cran-gmm r-cran-gmp r-cran-gnm r-cran-goftest r-cran-googledrive r-cran-googlesheets4 r-cran-googlevis r-cran-goplot r-cran-gower r-cran-gparotation r-cran-graphlayouts r-cran-gridbase r-cran-gridextra r-cran-gridgraphics r-cran-gridsvg r-cran-gridtext r-cran-grimport2 r-cran-gsa r-cran-gsl r-cran-gss r-cran-gstat r-cran-gsubfn r-cran-gtable r-cran-guerry r-cran-gunifrac r-cran-gwidgets r-cran-gwidgetstcltk r-cran-haplo.stats r-cran-hardhat r-cran-hash r-cran-haven r-cran-hdf5r r-cran-heatmaply r-cran-here r-cran-hexbin r-cran-highr r-cran-hms r-cran-hsaur3 r-cran-htmltable r-cran-htmltools r-cran-htmlwidgets r-cran-httpcode r-cran-httpuv r-cran-httr r-cran-httr2 r-cran-huge r-cran-hunspell r-cran-hwriter r-cran-hypergeo r-cran-ica r-cran-ids r-cran-igraph r-cran-incidence r-cran-ini r-cran-inline r-cran-insight r-cran-interp r-cran-intervals r-cran-inum r-cran-ipred r-cran-irace r-cran-irdisplay r-cran-irkernel r-cran-irlba r-cran-iso r-cran-isoband r-cran-isocodes r-cran-isospecr r-cran-isoweek r-cran-iterators r-cran-itertools r-cran-janeaustenr r-cran-jinjar r-cran-jomo r-cran-jpeg r-cran-jquerylib r-cran-jrc r-cran-jsonld r-cran-jsonlite r-cran-kaos r-cran-kedd r-cran-kernelheaping r-cran-kernlab r-cran-keyring r-cran-km.ci r-cran-kmi r-cran-kmsurv r-cran-knn.covertree r-cran-kohonen r-cran-ks r-cran-ksamples r-cran-kutils r-cran-labdsv r-cran-labeling r-cran-laeken r-cran-lamw r-cran-lasso2 r-cran-later r-cran-lava r-cran-lavaan r-cran-lavasearch2 r-cran-lazyeval r-cran-lbfgsb3c r-cran-leaps r-cran-learnbayes r-cran-leiden r-cran-leidenbase r-cran-lexrankr r-cran-lhs r-cran-libcoin r-cran-lifecycle r-cran-linprog r-cran-lintr r-cran-lisreltor r-cran-listenv r-cran-lmertest r-cran-lobstr r-cran-locfit r-cran-logcondens r-cran-logger 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r-cran-rpostgresql r-cran-rprotobuf r-cran-rrcov r-cran-rredlist r-cran-rsample r-cran-rsclient r-cran-rsconnect r-cran-rslurm r-cran-rsolnp r-cran-rspectra r-cran-rsqlite r-cran-rstanarm r-cran-rstantools r-cran-rstatix r-cran-rstudioapi r-cran-rsvd r-cran-rsvg r-cran-rtdists r-cran-rtsne r-cran-rtweet r-cran-runit r-cran-rversions r-cran-rvest r-cran-rwave r-cran-rwiener r-cran-s2 r-cran-sampling r-cran-samr r-cran-satellite r-cran-scales r-cran-scatterd3 r-cran-scattermore r-cran-scatterplot3d r-cran-sctransform r-cran-sdmtools r-cran-segmented r-cran-selectr r-cran-sem r-cran-semplot r-cran-semtools r-cran-sendmailr r-cran-seqinr r-cran-seriation r-cran-seroincidence r-cran-sessioninfo r-cran-setrng r-cran-sets r-cran-seurat r-cran-seuratobject r-cran-sf r-cran-sfsmisc r-cran-sftime r-cran-shades r-cran-shape r-cran-shapes r-cran-shazam r-cran-shiny r-cran-shinybs r-cran-shinycssloaders r-cran-shinydashboard r-cran-shinyfiles r-cran-shinyjs r-cran-shinystan r-cran-shinythemes r-cran-simplermarkdown r-cran-sitmo r-cran-sjlabelled r-cran-sjmisc r-cran-sjplot r-cran-sjstats r-cran-skimr r-cran-slam r-cran-slider r-cran-smcfcs r-cran-smoother r-cran-sn r-cran-sna r-cran-snakecase r-cran-snowballc r-cran-snowfall r-cran-sodium r-cran-solrium r-cran-sourcetools r-cran-sp r-cran-spacetime r-cran-spam r-cran-sparql r-cran-sparr r-cran-sparsem r-cran-sparsesvd r-cran-spatial r-cran-spatialreg r-cran-spatstat r-cran-spatstat.core r-cran-spatstat.data r-cran-spatstat.explore r-cran-spatstat.geom r-cran-spatstat.linnet r-cran-spatstat.model r-cran-spatstat.sparse r-cran-spatstat.utils r-cran-spc r-cran-spdata r-cran-spdep r-cran-spdl r-cran-spelling r-cran-splines2 r-cran-spp r-cran-sqldf r-cran-squarem r-cran-stable r-cran-stabledist r-cran-stablelearner r-cran-stanheaders r-cran-stars r-cran-statcheck r-cran-statip r-cran-statmod r-cran-statnet.common r-cran-stringdist r-cran-stringi r-cran-stringr r-cran-suppdists r-cran-surveillance r-cran-survey r-cran-survminer r-cran-survmisc r-cran-susier r-cran-svglite r-cran-svmisc r-cran-svunit r-cran-swagger r-cran-sys r-cran-systemfit r-cran-systemfonts r-cran-tcltk2 r-cran-tcr r-cran-tensor r-cran-tensora r-cran-testextra r-cran-testit r-cran-testthat r-cran-textshaping r-cran-tfisher r-cran-tfmpvalue r-cran-tgp r-cran-th.data r-cran-thematic r-cran-themis r-cran-threejs r-cran-tibble r-cran-tidygraph r-cran-tidyr r-cran-tidyselect r-cran-tidytext r-cran-tidyverse r-cran-tiff r-cran-tigger r-cran-tikzdevice r-cran-timechange r-cran-timedate r-cran-timereg r-cran-timeseries r-cran-tinytest r-cran-tinytex r-cran-tmb r-cran-tmvnsim r-cran-tokenizers r-cran-transformr r-cran-treescape r-cran-treespace r-cran-triebeard r-cran-trimcluster r-cran-truncdist r-cran-truncnorm r-cran-tsne r-cran-tsp r-cran-ttr r-cran-tufte r-cran-tzdb r-cran-ucminf r-cran-udunits2 r-cran-unbalanced r-cran-uniqtag r-cran-unitizer r-cran-units r-cran-upsetr r-cran-urlchecker r-cran-urltools r-cran-uroot r-cran-usethis r-cran-utf8 r-cran-uuid r-cran-uwot r-cran-v8 r-cran-vcd r-cran-vcdextra r-cran-vcr r-cran-vctrs r-cran-vdiffr r-cran-vegan r-cran-venndiagram r-cran-vgam r-cran-vim r-cran-vioplot r-cran-vipor r-cran-viridis r-cran-viridislite r-cran-vroom r-cran-waldo r-cran-warp r-cran-waveslim r-cran-wavethresh r-cran-wdi r-cran-webfakes r-cran-webgestaltr r-cran-webmockr r-cran-webshot r-cran-webutils r-cran-wgcna r-cran-whatif r-cran-whisker r-cran-whoami r-cran-wikidataqueryservicer r-cran-wikidatar r-cran-wikipedir r-cran-wikitaxa r-cran-withr r-cran-wk r-cran-wkutils r-cran-wordcloud r-cran-worrms r-cran-xfun r-cran-xml r-cran-xml2 r-cran-xmlparsedata r-cran-xopen r-cran-xslt r-cran-xtable r-cran-xts r-cran-yaml r-cran-zeallot r-cran-zelig r-cran-zeligchoice r-cran-zeligei r-cran-zeligverse r-cran-zip r-other-amsmercury r-other-ascat r-other-chbutils r-other-curvefdp r-other-disgenet2r r-other-iwrlars r-other-kcha-psiplot r-other-mott-happy r-other-nitpick r-other-rajewsky-dropbead r-other-wasabi r-other-x4r r-zoo rcmdr rcpp relimp rgl rglpk rjava rmatrix rmpi rmysql robustbase rodbc rpart rquantlib rserve rsymphony sandwich sm snow strucchange survival tkrplot tseries urca

FTBR icon 32 unreproducible packages in bookworm/amd64: r-base r-bioc-biocparallel r-bioc-genomicfeatures r-bioc-ioniser r-cran-amelia r-cran-cli r-cran-cliapp r-cran-dbitest r-cran-diagnosismed r-cran-dimred r-cran-emayili r-cran-futile.logger r-cran-gert r-cran-gprofiler2 r-cran-knitr r-cran-lambda.r r-cran-parsetools r-cran-quantmod r-cran-r.devices r-cran-repr r-cran-rinside r-cran-rprojroot r-cran-rsdmx r-cran-rstan r-cran-sass r-cran-taxize r-cran-teachingdemos r-cran-tm r-cran-tmvtnorm r-cran-tweenr rcolorbrewer rkward

 

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