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
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]]
_______________________________________________
[email protected] mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
