[Bioc-devel] Missing link files in Windows (release and devel)

[James W. MacDonald]

On Wed, Jan 17, 2018 at 11:38 AM, Leonardo Collado Torres <lcollado at 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.morgan at 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'
> >>
> >> _______________________________________________
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> >>
> >
> >
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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