[Bioc-devel] Error in Bioc windows check report

Benjamin Tremblay b2trembl@y @ending from uw@terloo@c@
Thu Jan 3 20:06:06 CET 2019

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.



> Le 1 janv. 2019 à 22:15, Martin Morgan <mtmorgan.bioc using 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-bounces using r-project.org on behalf of b2trembl using 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]]
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