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

[Martin Morgan]

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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>>
>>
> 
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