[Bioc-devel] packages modifying 'library' during R CMD check

Rainer Johannes Johannes.Rainer at eurac.edu
Sat Dec 2 18:56:04 CET 2017

Thanks Val

I'll fix that for `xcms`. Is it enough to fix the devel version, or should we also fix the Bioc 3.6 release version?

cheers, jo

> On 29 Nov 2017, at 15:43, Obenchain, Valerie <Valerie.Obenchain at 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():
> 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
> mammaPrintData
> metagenomeSeq
> MinimumDistance
> multiClust
> oligo
> oligoClasses
> plasFIA
> proFIA
> Rdisop
> RImmPort
> SNPchip
> SRGnet
> triform
> Uniquorn
> VanillaICE
> xcms
> xmapbridge
> Thanks.
> Valerie
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