On Wed, Jan 17, 2018 at 11:38 AM, Leonardo Collado Torres <lcoll...@jhu.edu> wrote:
> Thanks Martin! I just finished fixing the links in all my packages > using the \link[base:cbind]{rbind} syntax. One of them did seem a bit > weird to me: > > Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqyL54j/R. > INSTALL22cc280d642c/derfinder/man/loadCoverage.Rd:15: > missing file link 'BamFile' > > As far as I can tell, shouldn't \link[Rsamtools:BamFile]{BamFile} be > the same as \link[Rsamtools]{BamFile} ? On my mac the help page is > called BamFile, but maybe the html file on Windows has a different > name. > On both my Linux and Windows boxes it's BamFile-class. Jim > Best, > Leo > > On Tue, Jan 16, 2018 at 4:58 PM, Martin Morgan > <martin.mor...@roswellpark.org> wrote: > > > > > > On 01/16/2018 10:37 AM, Leonardo Collado Torres wrote: > >> > >> Hi, > >> > >> I have been seen warnings in several of my packages on both release > >> and devel only in the Windows build machines in relation to missing > >> link files. Is this something that I can address from my side or a > >> more widespread issue? If it matters, I use roxygen2 for making my Rd > >> files. > > > > > > taking the first example > > > > > > https://cran.r-project.org/doc/manuals/r-release/R-exts. > html#Cross_002dreferences > > > > "There are two other forms of optional argument specified as > \link[pkg]{foo} and \link[pkg:bar]{foo} to link to the package pkg, to > files foo.html and bar.html respectively. These are rarely needed,... > > > > You have \link[base]{rbind} so R is looking for rbind.html. The file is > actually cbind.html so \link[base:cbind]{rbind}. I don't know why the error > is only on Windows, perhaps because html manuals are only generated on > Windows? > > > > I guess the 'These are rarely needed,...' part of the manual might be > informative. > > > > Martin > > > > > >> Best, > >> Leonardo > >> > >> Examples: > >> > >> Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi4zjs1/R. > INSTALL2e746d54e04/recount/man/geo_characteristics.Rd:17: > >> missing file link 'rbind' > >> > >> Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2NQKYR/R. > INSTALL21702e4399f/regionReport/man/derfinderReport.Rd:46: > >> missing file link 'plotIdeogram' > >> > >> Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQtPk8B/R. > INSTALL17382396f82/derfinder/man/analyzeChr.Rd:54: > >> missing file link 'TxDb.Hsapiens.UCSC.hg19.knownGene' > >> Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQtPk8B/R. > INSTALL17382396f82/derfinder/man/annotateRegions.Rd:49: > >> missing file link 'countOverlaps' > >> > >> _______________________________________________ > >> Bioc-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >> > > > > > > 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. > > > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel