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

Hervé Pagès hpages at fhcrc.org
Tue Jul 28 19:27:50 CEST 2009

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


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
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