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Notes about issue randomness_in_r_rdb_rds_databases in unstable

Identifier: randomness_in_r_rdb_rds_databases
Suites: stretch / buster / unstable / 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 / 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:
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:
Packages in 'unstable' known to be affected by this issue:
(the 1/4 most-popular ones (within this issue) are underlined)

unreproducible icon 22 unreproducible packages in unstable/amd64: gtools openturns r-bioc-genomicfeatures r-bioc-iranges r-bioc-rsamtools r-bioc-shortread r-cran-amelia r-cran-cubature r-cran-diagnosismed r-cran-fastcluster r-cran-futile.logger r-cran-knitr r-cran-lambda.r r-cran-mi r-cran-rinside r-cran-rms r-cran-rredlist r-cran-rsdmx r-cran-runit r-cran-teachingdemos r-cran-tm rgtk2

FTBFS icon 2 FTBFS packages in unstable/amd64: r-bioc-rtracklayer r-cran-randomfields

reproducible icon 451 reproducible packages in unstable/amd64: abind acepack bitops boot cairodevice car chron cluster codetools date dbi dichromat effects fasianoptions fassets fbasics fbonds fcopulae fexoticoptions fextremes fgarch fimport fmultivar fnonlinear foptions foreign fportfolio fregression ftrading funitroots gdata gmodels gplots greenbone-security-assistant gtable hmisc its lattice latticeextra littler lme4 lmtest matchit mgcv misc3d mnormt multcomp mvtnorm nlme permute polspline pvclust quadprog r-bioc-affy r-bioc-affyio r-bioc-altcdfenvs r-bioc-annotate r-bioc-annotationdbi r-bioc-annotationhub r-bioc-aroma.light r-bioc-biobase r-bioc-biocgenerics r-bioc-biocinstaller r-bioc-biocparallel r-bioc-biomart r-bioc-biomformat r-bioc-biostrings r-bioc-biovizbase r-bioc-bsgenome r-bioc-cummerbund r-bioc-deseq2 r-bioc-dnacopy r-bioc-ebseq r-bioc-edger r-bioc-ensembldb r-bioc-genefilter r-bioc-geneplotter r-bioc-genomeinfodb r-bioc-genomicalignments r-bioc-genomicranges r-bioc-go.db r-bioc-graph r-bioc-gviz r-bioc-hilbertvis r-bioc-hypergraph r-bioc-interactivedisplaybase r-bioc-limma r-bioc-makecdfenv r-bioc-metagenomeseq r-bioc-multtest r-bioc-phyloseq r-bioc-preprocesscore r-bioc-qvalue r-bioc-s4vectors r-bioc-savr r-bioc-snpstats r-bioc-summarizedexperiment r-bioc-variantannotation r-bioc-xvector r-cran-ade4 r-cran-adegenet r-cran-adegraphics r-cran-adephylo r-cran-afex r-cran-amore r-cran-ape r-cran-arm r-cran-assertthat r-cran-backports r-cran-base64enc r-cran-batchjobs r-cran-bayesfactor r-cran-bayesm r-cran-bbmisc r-cran-bbmle r-cran-beeswarm r-cran-biasedurn r-cran-bio3d r-cran-blockmodeling r-cran-bms r-cran-bold r-cran-boolnet r-cran-bradleyterry2 r-cran-brew r-cran-brglm r-cran-ca r-cran-cairo r-cran-calibrate r-cran-caret r-cran-catools r-cran-cellranger r-cran-checkmate r-cran-class r-cran-cmprsk r-cran-coda r-cran-coin r-cran-colorspace r-cran-combinat r-cran-contfrac r-cran-conting r-cran-corpcor r-cran-crayon r-cran-crul r-cran-curl r-cran-data.table r-cran-dbitest r-cran-deal r-cran-deldir r-cran-deoptimr r-cran-desolve r-cran-digest r-cran-distory r-cran-domc r-cran-doparallel r-cran-dosefinding r-cran-dosnow r-cran-downloader r-cran-dplyr r-cran-dynlm r-cran-e1071 r-cran-eco r-cran-ecodist r-cran-ellipse r-cran-elliptic r-cran-energy r-cran-epi r-cran-epibasix r-cran-epicalc r-cran-epir r-cran-epitools r-cran-erm r-cran-estimability r-cran-etm r-cran-evaluate r-cran-evd r-cran-expm r-cran-fail r-cran-fastmatch r-cran-fields r-cran-filehash r-cran-fitbitscraper r-cran-fitcoach r-cran-foreach r-cran-formatr r-cran-formula r-cran-futile.options r-cran-future r-cran-gam r-cran-gbm r-cran-geepack r-cran-genabel r-cran-genetics r-cran-getopt r-cran-ggplot2 r-cran-glmnet r-cran-globals r-cran-gmaps r-cran-gnm r-cran-goftest r-cran-googlevis r-cran-gridbase r-cran-gridextra r-cran-gsl r-cran-gss r-cran-haplo.stats r-cran-hdf5 r-cran-hexbin r-cran-highr r-cran-htmltable r-cran-htmltools r-cran-htmlwidgets r-cran-httpcode r-cran-httpuv r-cran-httr r-cran-hwriter r-cran-hypergeo r-cran-igraph r-cran-inline r-cran-int64 r-cran-irlba r-cran-isocodes r-cran-iterators r-cran-jsonlite r-cran-kernlab r-cran-labeling r-cran-lavaan r-cran-lazyeval r-cran-learnbayes r-cran-lexrankr r-cran-lhs r-cran-listenv r-cran-logspline r-cran-lpsolve r-cran-lsmeans r-cran-lubridate r-cran-luminescence r-cran-magrittr r-cran-maldiquant r-cran-maldiquantforeign r-cran-mapdata r-cran-mapproj r-cran-maps r-cran-maptools r-cran-maptree r-cran-markdown r-cran-mass r-cran-matrixcalc r-cran-matrixmodels r-cran-matrixstats r-cran-maxlik r-cran-mcmc r-cran-mcmcpack r-cran-medadherence r-cran-memoise r-cran-mfilter r-cran-mime r-cran-miniui r-cran-minpack.lm r-cran-minqa r-cran-misctools r-cran-mixtools r-cran-mlbench r-cran-mlmrev r-cran-mnp r-cran-modelmetrics r-cran-modeltools r-cran-msm r-cran-multicore r-cran-munsell r-cran-mvnormtest r-cran-natserv r-cran-ncdf4 r-cran-nleqslv r-cran-nloptr r-cran-nlp r-cran-nmf r-cran-nnet r-cran-nnls r-cran-numderiv r-cran-nws r-cran-openssl r-cran-optparse r-cran-pbapply r-cran-pbdzmq r-cran-pbivnorm r-cran-pbkrtest r-cran-phangorn r-cran-pheatmap r-cran-phylobase r-cran-pkgkitten r-cran-pkgmaker r-cran-plogr r-cran-plotrix r-cran-plyr r-cran-png r-cran-polyclip r-cran-polycub r-cran-praise r-cran-prettyunits r-cran-princurve r-cran-profilemodel r-cran-progress r-cran-proto r-cran-pscbs r-cran-pscl r-cran-psy r-cran-pwt r-cran-pwt8 r-cran-pwt9 r-cran-qqman r-cran-qtl r-cran-quantreg r-cran-qvcalc r-cran-r.cache r-cran-r.methodss3 r-cran-r.oo r-cran-r.utils r-cran-r6 r-cran-randomforest r-cran-raschsampler r-cran-raster r-cran-rcmdrmisc r-cran-rcpparmadillo r-cran-rcppeigen r-cran-rcppgsl r-cran-rcurl r-cran-readbrukerflexdata r-cran-readmzxmldata r-cran-readxl r-cran-registry r-cran-rematch r-cran-rentrez r-cran-repr r-cran-reshape r-cran-reshape2 r-cran-rglwidget r-cran-ritis r-cran-rjags r-cran-rjson r-cran-rlumshiny r-cran-rncl r-cran-rneos r-cran-rnetcdf r-cran-rnexml r-cran-rngtools r-cran-rniftilib r-cran-rocr r-cran-rotl r-cran-rpostgresql r-cran-rprotobuf r-cran-rsclient r-cran-rsolnp r-cran-rsqlite r-cran-scales r-cran-scatterd3 r-cran-segmented r-cran-sem r-cran-semtools r-cran-sendmailr r-cran-seqinr r-cran-seroincidence r-cran-shape r-cran-shiny r-cran-shinybs r-cran-shinyjs r-cran-slam r-cran-sn r-cran-snowballc r-cran-solrium r-cran-sourcetools r-cran-sp r-cran-spam r-cran-sparsem r-cran-spatial r-cran-spatstat r-cran-spc r-cran-spdep r-cran-stabledist r-cran-statmod r-cran-stringi r-cran-stringr r-cran-surveillance r-cran-survey r-cran-taxize r-cran-tcltk2 r-cran-tensor r-cran-testit r-cran-testthat r-cran-tgp r-cran-tibble r-cran-tidyr r-cran-tikzdevice r-cran-timedate r-cran-timeseries r-cran-treescape r-cran-triebeard r-cran-uuid r-cran-v8 r-cran-vcd r-cran-vcdextra r-cran-vegan r-cran-vgam r-cran-vioplot r-cran-viridis r-cran-wdi r-cran-withr r-cran-xml r-cran-xml2 r-cran-xtable r-cran-xts r-cran-yaml r-omegahat-xmlrpc r-other-amsmercury r-other-curvefdp r-other-iwrlars r-other-mott-happy r-other-nitpick r-zoo rcmdr rcolorbrewer rcpp relimp rggobi rgl rglpk rjava rkward rmatrix rmpi rmysql robustbase rodbc rpart rquantlib rserve rsprng rsymphony sandwich scatterplot3d sm snow strucchange survival tkrplot tseries urca zelig kernsmooth#


Our notes about issues affecting packages are stored in notes.git and are targeted at packages in Debian in 'unstable/amd64' (unless they say otherwise).

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A # sign after the name of a package indicates that a bug is filed against it. Likewise, a + sign indicates there is a patch available, a P means a pending bug while # indicates a closed bug. In cases of several bugs, the symbol is repeated.