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

[Norman Pavelka]

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
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel