[Rd] Log file of building vignette in RCMD check

Prof Brian Ripley ripley at stats.ox.ac.uk
Mon Jun 6 18:59:17 CEST 2011

On Mon, 6 Jun 2011, Uwe Ligges wrote:

> On 06.06.2011 15:30, Stefan McKinnon Høj-Edwards wrote:
>> Hello,
>> I am trying to run "RCMD check" on a package. It performs OK, with the 
>> exception of a single warning:
>> * checking package vignettes in 'inst/doc' ... WARNING
>> Package vignette(s) without corresponding PDF:
>>     AnnotationFuncsUserguide.Rnw
> R CMD build should build the vignettes. If it did not succeed, see its output 
> for details.

You can also use tools::buildVignettes to do it manually.  But R CMD 
check is reporting that you failed to do it at all: it is not the job 
of R CMD check and the PDF of the vignette should be in the 
tarball/directory you supply to be checked.

> Uwe Ligges
>> As I understand the problem, the vignette is not built. However, I have no 
>> problems in doing so manually.
>> How do I fix this problem? I cannot find any logs for building the 
>> vignette, however the output from building the pdf-file of the manual is 
>> found in the .Rcheck folder.
>> On a similar note, as my vignette includes a biblio, I have to run "latex" 
>> twice to get the citations referenced properly with a number. Is this an 
>> issue? How can I work around it? (The package is submitted to BioC, so 
>> there might be other rules there?)

It indicates that you failed to use the tools we provided, R CMD 
build, tools::buildVignettes() and tools::texi2dvi().

>> Thank you in advanced.
>> Yours sincerely,
>> Stefan McKinnon Høj-Edwards     Dept. of Genetics and Biotechnology
>> PhD student                     Faculty of Agricultural Sciences
>> stefan.hoj-edwards at agrsci.dk    Aarhus University
>> Tel.: +45 8999 1291             Blichers Allé 20, Postboks 50
>> Web: www.iysik.com              DK-8830 Tjele
>>                                  Tel.: +45 8999 1900
>>                                  Web: www.agrsci.au.dk

Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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