[Bioc-devel] Missing link files in Windows (release and devel)
On 01/17/2018 12:02 PM, Stephanie M. Gogarten wrote:
This sentence seems to indicate that the original format
\link[base]{rbind} should work:
"Because they have been frequently misused, the HTML help system looks
for topic foo in package pkg if it does not find file foo.html."
I looked at the code https://github.com/wch/r-source/blob/89ec1150299f7be62b839d5d5eb46bd9a63653bd/src/library/tools/R/Rd2HTML.R#L377 and for \link[base]{rbind} it seems (a) like the condition is reversed and one would have expected a warning "file link 'rbind' in package 'base' does not exist and so has been treated as a topic" The warning "missing file link" would seem to be intended for \link[base]{foo}. But (b) it's a warning either way, so one needs to correct it. And (c) Leonardo's original code generated a valid link -- as the corrected warning would have indicated, 'rbind' was treated as a 'topic' (i.e., listed as an '\alias{}'), and found in cbind.html. FWIW I debugged this with links <- findHTMLlinks(system.file(package="base")) Rd2HTML("recount/man/geo_characteristics.Rd", Links=links) to generate the HTML with links, and then options(warn=2, error=recover) links <- findHTMLlinks(system.file(package="base")) Rd2HTML("recount/man/geo_characteristics.Rd", Links=links) to get into the debugger and see what was going wrong. I'll follow up on part (a). Martin
On 1/17/18 8:56 AM, James W. MacDonald 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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