[Bioc-devel] R source code files of package vignettes

[Kasper Daniel Hansen]

To make it even easier you can have a
\SweaveOpts{eval=FALSE}
in your preamble. This sets eval=FALSE to be the default value for all  
chunks.

Kasper

On Jul 28, 2009, at 10:27 , Hervé Pagès wrote:

> Hi Joern,
>
> One possible workaround would be to replace the dummy Rnw file by a
> version of the true vignette where all the code chunks are tagged
> with eval=FALSE. Then you would need to keep in sync 2 versions of the
> same file: the eval=TRUE and the eval=FALSE versions. But that can
> easily be achieved on Unix with a 2 line shell script using the sed
> command.
>
> Cheers,
> H.
>
> Joern Toedling wrote:
>> Dear all,
>> I would welcome your feedback on a small problem regarding vignettes.
>> For the data package ccTutorial, I pre-build the vignettes on my  
>> machine, as
>> building these vignettes takes considerable time. The folder 'inst/ 
>> doc' only
>> contains dummy versions of the two vignettes and a Makefile which  
>> copies the
>> pre-built vignettes from another directory into 'doc' after running  
>> Sweave on
>> the dummy files.
>> I would also like to provide the source code of the pre-built  
>> vignettes
>> in the doc directory (as these are also linked on the BioC package  
>> web page).
>> However, having the *R files copied from the other directory into  
>> doc via use
>> of the Makefile is pointless as it seems that the command Stangle  
>> is run on
>> the dummy vignettes afterwards. So the source code files in the  
>> directory
>> 'doc' only contain the non-relevant source code of the dummy files.  
>> Do you
>> know of a way to avoid having Stangle run on the dummy files? Or is  
>> there
>> another way to copy files afterwards?
>> Cheers,
>> Joern
>> ---
>> Joern Toedling
>> Institut Curie -- U900
>> 26 rue d'Ulm, 75005 Paris, FRANCE
>> Tel. +33 (0)156246926
>> _______________________________________________
>> Bioc-devel at stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> -- 
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
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