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

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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