[Bioc-devel] Error in Bioc windows check report

[Benjamin Tremblay]

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
	[[alternative HTML version deleted]]