[Bioc-devel] IMPORTANT inst/doc/*Rnw to vignettes/

Martin Morgan mtmorgan at fhcrc.org
Fri Oct 18 23:58:52 CEST 2013

Bioconductor developers,

Thank you for your contributions to our last release, with a total of 749 
packages! This is a great resource for the bioninformatics community.

No good deed goes unpunished. The 'devel' version of R no longer builds 
vignettes in the inst/doc directory. Vignette sources (.Rnw or perhaps .Rmd 
files) must be in the vignettes/ directory. There's a lot of work to be done to 
make this happen, and we'd really like your help with this. Here's one recipe 
for the neccessary changes, illustrtated with Biobase

1. Find the url of your package in the devel version of the Bioconductor svn 
repository, e.g., for Biobase


2. Make a clean check-out of the source into a directory where `Biobase' does 
not already exist

    svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase

3. Re-name the inst/doc directory. Using svn rename preserves the commit history

    svn rename Biobase/inst/doc Biobase/vignettes

4. Increase the least significant part of the package version number in 
Biobase/DESCRIPTION. I changed Biobase from 2.23.0 to 2.23.1.

5. Build the package, using the latest devel version of R

    R CMD build Biobase

6. Check that the built version contains .Rnw, .R, and .pdf files in the 
inst/doc directory, e.g.,

    tar tzf Biobase_2.23.1.tar.gz |grep inst/doc

7. Make sure the built package passes R CMD check

    R CMD check Biobase_2.23.1.tar.gz

8. Review and check in your changes

    svn st Biobase
    svn diff Biobase/DESCRIPTION
    svn ci

This will work for many cases, but if you have problems please do not hesitate 
to bring up issues on the mailing list.

If things go smoothly, you might wish to follow the instructions in the 
BiocStyle vignette


for creating vignettes with a consistent look-and-feel. The text is wider, for 
instance, so code generally formats better, and packages are easily linked to 
their 'landing page' on the Bioconductor web site

Please don't hesitate to ask if there are any questions, and thanks in advance 
for your continued effort to support the project.

Computational Biology / Fred Hutchinson Cancer Research Center
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PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

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