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

Dan Tenenbaum dtenenba at fhcrc.org
Fri Feb 8 05:48:51 CET 2013

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


> Cheers,
> Norman
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