[Bioc-devel] R CMD build not copying PDF vignettes to inst\doc
Hi Dan,
I actually just installed the latest version of R-Devel (r61902) and
used biocLite("plgem") to download and install the latest version of
my package from the server. Although there are no errors or warnings
on the Bioc build/check report, my package still lacks the PDF version
of the vignette. I checked the source tarball in
http://www.bioconductor.org/packages/2.12/bioc/src/contrib/plgem_1.31.1.tar.gz
and in fact cannot see any PDFs in inst/doc. You can also notice the
vignette is not listed anymore in
http://www.bioconductor.org/packages/2.12/bioc/html/plgem.html
I then rebuilt the package from source myself from a freshly
checked-out version from the Bioc-devel repository (plgem version
1.31.1) using R-Devel r61902. I get no errors, no warnings and most
importantly the PDF is being built and included in the tarball
correctly.
So it appears that R-Devel r61868 (the version currenlty on the build
machine) is still not copying the vignette PDF into the package. Could
you please try to update R-Devel to r61902 and see if it solves the
problem?
Thanks!
Norman
P.S.: For full disclosure, I should probably mention that I recently
moved the .Rnw file from inst/doc to /vignettes following the latest R
recommendations, but I am unsure if this has anything to do with the
problem, as the package builds just fine on my machine using the
latest version of R-Devel.
On Wed, Feb 13, 2013 at 12:11 PM, Norman Pavelka
<normanpavelka at gmail.com> wrote:
Hi Dan, I can see the issue is resolved now! I will update my version of R-devel, too. Thanks, Norman 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
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