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

[Stephanie M. Gogarten]

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."


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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>>>>
>>>
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> 
> 
>