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

Dan Tenenbaum dtenenba at fhcrc.org
Fri Feb 8 06:19:20 CET 2013

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.

> Thanks!
> Dan
>> Cheers,
>> Norman
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
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