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

[Martin Morgan]

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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