The warnings below can be understood by a careful reading of
https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Cross_002dreferences
You use \link[pkg]{foo} and the docs say that foo is the name of the html file
where you would like to link. DNAStringSet is documented in the html file
XStringSet-class, so your links would be
\link[Biostrings:XStringSet-class]{DNAStringSet}. But actually this is just
making work for yourself, and it is more straight-forward to just use
\link{DNAStringSet}; R then does the necessary bookkeeping.
The error, later, looks like a problem loading 32-bit motifdb; I'm not sure
that I have anything immediately helpful to provide...
Martin
On 12/31/18, 1:30 PM, "Bioc-devel on behalf of Benjamin Tremblay"
<bioc-devel-boun...@r-project.org on behalf of b2tre...@uwaterloo.ca> wrote:
Hi,
I recently pushed a bug fix to the devel and release branches of my package
(universalmotif). The updated package in my GitHub repository
(https://github.com/bjmt/universalmotif
<https://github.com/bjmt/universalmotif>) passed all checks with no errors or
warnings on linux in travis CI, and on windows in appveyor
(https://ci.appveyor.com/project/bjmt/universalmotif
<https://ci.appveyor.com/project/bjmt/universalmotif>). It also passed both mac
and linux checks on the Bioc machines. The windows Bioc machine failed the
check however, and I am not quite sure as to why
(http://bioconductor.org/checkResults/release/bioc-LATEST/universalmotif/tokay1-checksrc.html
<http://bioconductor.org/checkResults/release/bioc-LATEST/universalmotif/tokay1-checksrc.html>).
The following warning occurred:
* checking whether package 'universalmotif' can be installed ... WARNING
Found the following significant warnings:
Rd warning:
C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaWjzyP/R.INSTALL3dcce5dc9/universalmotif/man/ArabidopsisPromoters.Rd:7:
file link 'DNAStringSet' in package 'Biostrings' does not exist and so has
been treated as a topic
Rd warning:
C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaWjzyP/R.INSTALL3dcce5dc9/universalmotif/man/create_motif.Rd:124:
file link 'DNAStringSet-class' in package 'Biostrings' does not exist and so
has been treated as a topic
Rd warning:
C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaWjzyP/R.INSTALL3dcce5dc9/universalmotif/man/create_motif.Rd:126:
file link 'RNAStringSet-class' in package 'Biostrings' does not exist and so
has been treated as a topic
… etc
There was also an error for the i386 arch:
** running examples for arch 'i386' ... ERROR
Running examples in 'universalmotif-Ex.R' failed
Though the error message was not informative and did not reveal why the
example failed.
At this point I am at a loss as to what to do. Not only is this warning and
error specific to windows, it is specific to the Bioc windows machine. This
situation also occurred during package submission (though the errors/warnings
were slightly different), but my reviewer OK’d it regardless. At this point, I
would like to ask if there is some flaw in my package which I should fix to
allow it to pass the check? Or is there a problem specific to the Bioc windows
machine?
Thank you,
Benjamin Tremblay
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