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

Sun, Oct 20, 2013 10:36 PM

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 
machine.

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 
using

   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.

Thanks
Gordon

PS.  I am running Rtools3.1 with:

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

locale:
[1] LC_COLLATE=English_Australia.1252
[2] LC_CTYPE=English_Australia.1252
[3] LC_MONETARY=English_Australia.1252
[4] LC_NUMERIC=C
[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

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

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