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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