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

Dan Tenenbaum dtenenba at fhcrc.org
Wed Feb 13 07:52:36 CET 2013

Hi Norman,

On Tue, Feb 12, 2013 at 10:35 PM, Norman Pavelka
<normanpavelka at gmail.com> wrote:
> 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 for following up on this.

The problem is not with R--that problem was cleared up. However, we
needed to flush our internal BioC repos in order to force the packages
with vignettes to propagate. I've now done so, so tomorrow's build
(available late morning Seattle time) will contain vignettes with

Thanks again,

> 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

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