On Wed, Nov 29, 2017 at 9:43 AM, Obenchain, Valerie < valerie.obench...@roswellpark.org> wrote:
> Hi developers, > > Several Bioconductor packages have been flagged as modifying 'library' > during R CMD check. Thanks to Tomas Kalibera for identifying these. > > Behavior falls roughly into 3 categories: > > 1) installing/updating packages: > > Some packages call biocLite(), install.packages(), update.packages() or > the devtools equivalent in code accessible from examples or vignettes. This > modifies packages in .libPaths() which is a problem for reproducibility. > The user is expecting a snapshot of particular package(s) and this behavior > changes versions out from under them. > > 2) writing to disk instead of tempfile(): > For some cases where longer-than-R-session storage is needed, there may be a use for the rappdirs package: https://CRAN.R-project.org/package=rappdirs <https://cran.r-project.org/package=rappdirs> Sean > > Packages that write result or intermediate files to disk are in danger of > overwriting the user's carefully created local files. In some cases, the > setwd() is modified such that the files are written out in the library when > the package is installed, e.g., > > setwd(system.file("extra", package="DiffBind")) > > 3) RUnit summary file: > > RUnit has an option to output results to "unitTests/reportSummary.txt" > which is written to the installation tree of a package. Because the output > summarizes test results, which one presumably wants to see after the R > process has ended, using tempdir() or tempfile() may not be appropriate. > Possibly the file should be written to the .Rcheck directory. We aren't > sure how to best handle this situation yet - Tomas may have some guidance > eventually. > > > Tomas ran CRAN+BIOC check with read-only "library" directory to prevent > installation and updates of packages during tests. The packages below > failed their tests as they tried to write to "library". If you are a > maintainer of one of these please visit this link for details on the exact > failure: > > https://github.com/kalibera/rlibwrite > > agilp > alpine > annmap > BadRegionFinder > BBCAnalyzer > BeadDataPackR > CoverageView > crlmm > DiffBind > geneRxCluster > GeneticsPed > LOLA > mammaPrintData > metagenomeSeq > MinimumDistance > mQTL.NMR > multiClust > oligo > oligoClasses > PAA > plasFIA > proFIA > RCAS > Rdisop > RImmPort > SIMAT > SNPchip > SRGnet > triform > Uniquorn > VanillaICE > xcms > XDE > xmapbridge > > Thanks. > Valerie > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Sean Davis, MD, PhD Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda, MD 20892 https://seandavi.github.io/ https://twitter.com/seandavis12 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
