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

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.

Thanks!
Dan

Cheers,
Norman