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

Gordon K Smyth smyth at wehi.EDU.AU
Mon Oct 21 07:36:11 CEST 2013

Hi Martin,

Thanks for the heads-up.  I think I've made the changes necessary, but am 
having trouble confirming whether the changes are correct on a Windows 

Could you tell me hows Bioconductor builds the Windows binaries of 
Bioconductor packages?

To see how things work, I am playing around with Biobase on svn.  I can 
build Biobase from the svn source including the pdfs of the vignettes 

   R CMD build Biobase

on my Windows machine.  This gives me a tar.gz file of Biobase with an 
inst/doc directory containing Rnws and pdfs of all the vignettes.  This 
shows that my LaTeX etc is working fine.

However when I run

   R CMD INSTALL --build Biobase

which is the recommended way to install a package under Windows, I get a 
zip file containing no sign of any vignette.  In fact there is no doc or 
inst or vignette directory in the zip file.

What else do I need to do to install the package from source with the 
vignettes build under Windows?

No doubt the answer is somewhere in one of the R manuals (writing R 
extensions or admin and installation perhaps) but I cannot find it.


PS.  I am running Rtools3.1 with:

> sessionInfo()
R Under development (unstable) (2013-10-18 r64076)
Platform: i386-w64-mingw32/i386 (32-bit)

[1] LC_COLLATE=English_Australia.1252
[2] LC_CTYPE=English_Australia.1252
[3] LC_MONETARY=English_Australia.1252
[5] LC_TIME=English_Australia.1252

attached base packages:
[1] parallel  stats     graphics  grDevices utils
[6] datasets  methods   base

other attached packages:
[1] Biobase_2.23.1     BiocGenerics_0.9.0

> Date: Fri, 18 Oct 2013 14:58:52 -0700
> From: Martin Morgan <mtmorgan at fhcrc.org>
> To: "bioc-devel at r-project.org" <bioc-devel at r-project.org>
> Subject: [Bioc-devel] IMPORTANT inst/doc/*Rnw to vignettes/
> 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
>    https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/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
> http://bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/LatexStyle.pdf
> 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.
> Martin
> -- 
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793

The information in this email is confidential and intend...{{dropped:4}}

More information about the Bioc-devel mailing list