[BioC] warning if pdf of vignette is missing

Manuela Hummel hummel at ibe.med.uni-muenchen.de
Mon Sep 19 09:43:54 CEST 2005

Hi Wolfgang,

thank you for your reply. So this warning should not be the problem - 
but the fact that no vignette can be built...

When I build a zip file everything is normal except that no pdf is created.
When building a tar.gz file there is something strange:

Z:\GlobalAncova>Rcmd build z:/GA_Subversion/GlobalAncova
* checking for file 'z:/GA_Subversion/GlobalAncova/DESCRIPTION' ... OK
* preparing 'z:/GA_Subversion/GlobalAncova':
* creating vignettes ... OK        
* removing junk files
* building 'GlobalAncova_1.2.tar.gz'
tar: GlobalAncova/inst/doc/Rplots.ps: file changed as we read it
tar: Error exit delayed from previous errors

Do you know what can be the reason?

Best regards

Wolfgang Huber schrieb:

> Hi Manuela,
> as far as I understand, you can safely ignore this Warning. It seems 
> there are different opinions around what should constitute a warning, 
> ranging from "look at this interesting factoid" to "here's something 
> that is not acceptable for a bioconductor package", which are not the 
> same.
> However, "R CMD build" should produce the PDF file for the vignette - 
> why does this go wrong? Do have details?
>  Best wishes
>  Wolfgang
> Manuela Hummel wrote:
>> Hello,
>> I am working on building a package under Windows. Everything works 
>> well; only if I do not provide the pdf version of the vignette in the 
>> 'inst/doc' directory I get the following warning when running Rcmd 
>> check:
>> * checking package vignettes in 'inst/doc' ... WARNING
>> Package vignettes without corresponding PDF
>> Also then the pdf is not built with Rcmd build.
>> I have seen on the daily check results page of the development 
>> packages that many packages get this warning.
>> How can I avoid this warning or can I ignore it? Or do I have to 
>> provide the pdf (which is not recommended)?
>> Thank you very much
>> Best regards
>> Manuela Hummel
> -------------------------------------
> Wolfgang Huber
> European Bioinformatics Institute
> European Molecular Biology Laboratory
> Cambridge CB10 1SD
> England
> Phone: +44 1223 494642
> Fax:   +44 1223 494486
> Http:  www.ebi.ac.uk/huber
> -------------------------------------

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