Thank you! I will do as you suggested for the documentation. Still unsure as of yet about what to do about the Rd warnings regarding BiocGenerics.
As for motifdb, for now I will just not allow the example to run on windows.. I hope that’s not considered bad form. Thanks, Benjamin > Le 1 janv. 2019 à 22:15, Martin Morgan <mtmorgan.b...@gmail.com> a écrit : > > 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 > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
