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