[Bioc-devel] R-3.0.2 and vignettes that should not be built

Ramon Diaz-Uriarte rdiaz02 at gmail.com
Tue Sep 17 13:09:13 CEST 2013

Dear All,

Suppose a package contains a vignette that is built quickly
(small.Rnw) and another that takes a long time (big.Rnw). 
We want to provide both the source and the PDF for both, but on routine
CMD build we only want to build the short one (the PDF for the long one
having been pre-generated).

This issue has come up before in this list and I think one suggested
solution (see thread started by Kasper Daniel Hansen on 2012-06-12:
https://stat.ethz.ch/pipermail/bioc-devel/2012-June/003446.html) was

- place small.Rnw (and small.bib) under /vignettes
- place big.Rnw AND big.pdf under /inst/doc

When we execute(d) (as BioC does)

R CMD build --keep-empty-dirs --no-resave-data source

the PDF for small would be created (and placed under /inst/doc in
source.tar.gz) and big.* would also be placed under /inst/doc. This has
worked just fine for me up to now. 

Now, however, with R-3.0.2 (downloaded this morning; svn rev 63937), the
build does not place big.pdf under /inst/doc in the tar.gz. Thus,
we get a warning when we run CMD check 

Package vignette without corresponding PDF/HTML:

What is the recommended way of dealing with this? Should this question be
moved to R-devel (I asked here because an identical question was dealt
with in this list).



Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina 
Universidad Autónoma de Madrid 
Arzobispo Morcillo, 4
28029 Madrid

Phone: +34-91-497-2412

Email: rdiaz02 at gmail.com
       ramon.diaz at iib.uam.es


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