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.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():
>
> 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
>
>
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