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

[Leonardo Collado Torres]

Thank you Jim! I changed it to \link[Rsamtools:BamFile-class]{BamFile}.

Best,
Leo

On Wed, Jan 17, 2018 at 11:56 AM, James W. MacDonald <jmacdon at uw.edu> wrote:
>
> 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
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