[Bioc-devel] R CMD build not copying PDF vignettes to inst\doc

Norman Pavelka normanpavelka at gmail.com
Wed Feb 13 05:11:19 CET 2013

Hi Dan,

I can see the issue is resolved now! I will update my version of R-devel, too.


On Fri, Feb 8, 2013 at 1:19 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> On Thu, Feb 7, 2013 at 8:48 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>> Hi Norman,
>> On Thu, Feb 7, 2013 at 6:59 PM, Norman Pavelka <normanpavelka at gmail.com> wrote:
>>> Hi,
>>> I am sure many of you may have noticed already, but basically every
>>> package in Bioc-devel that has a vignette (i.e. almost every package)
>>> is currently issuing warnings in R CMD check:
>>> http://www.bioconductor.org/checkResults/2.12/bioc-LATEST/
>>> I ran some tests myself and it appears that in the latest version of
>>> R-devel some changes have been introduced in R CMD build that causes
>>> it not to copy the compiled PDF vignettes to inst\doc. R CMD build
>>> returns only a silent warning such as:
>>> * creating vignettes ... OK
>>> Warning in file.copy(c(vigns$docs, outfiles), doc_dir) :
>>>   problem copying
>>> E:\biocbld\bbs-2.12-bioc\tmpdir\Rtmpq4jjoR\Rbuild93c202b5ca6\plgem\vignettes\plgem.pdf
>>> to inst\doc\plgem.pdf: No such file or directory
>>> R CMD check then issues the following user-visible warning:
>>> * checking package vignettes in 'inst/doc' ... WARNING
>>> Package vignette without corresponding PDF:
>>>    'plgem.Rnw'
>>> Compiling my package from the same source but using the previous
>>> version of R CMD build does not cause any problems, i.e. the vignette
>>> PDF is correctly copied to inst/doc and R CMD check does not issue any
>>> warning.
>>> Should we bring this up to R-Devel mailing list?
>> I'm not sure (checking right now) but I think this was fixed in r61843.
>> The build machines are running r61836. The nightly build is underway
>> but I will update R-devel tomorrow if doing so indeed fixes the
>> problem.
> I can confirm that pdfs are properly copied into source tarballs with
> R-devel r61868.
> I will update to the latest R-devel tomorrow.
> Dan
>> Thanks!
>> Dan
>>> Cheers,
>>> Norman
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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