From ripley at stats.ox.ac.uk  Mon Jun  6 18:59:17 2011
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Mon, 6 Jun 2011 17:59:17 +0100 (BST)
Subject: [Rd] Log file of building vignette in RCMD check
In-Reply-To: <4DECFD2E.2030800@statistik.tu-dortmund.de>
References: <1C56F3EE22DF4F458FE02F58B96D4150555EA9FD3B@DJFEXMBX01.djf.agrsci.dk>
	<4DECFD2E.2030800@statistik.tu-dortmund.de>
Message-ID: <alpine.LFD.2.02.1106061755400.15375@gannet.stats.ox.ac.uk>

On Mon, 6 Jun 2011, Uwe Ligges wrote:

>
>
> On 06.06.2011 15:30, Stefan McKinnon H?j-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 H?j-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 All? 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


[Rd] Log file of building vignette in RCMD check
Prof Brian Ripley