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

[Hervé Pagès]

Kasper Daniel Hansen wrote:
> 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.

That's indeed really good to know :-) Thanks Kasper!

H.

> 
> 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
>>
>> _______________________________________________
>> 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