[Bioc-devel] Boost as build dependency ?

[In Response to https://stat.ethz.ch/pipermail/bioc-devel/2009-February/001806.html]

On Tue, 2009-02-17 at 17:51 -0800, Patrick Aboyoun wrote:

I hadn't done a survey of BOOST usage in BioC packages. It does look 
like we have hit critical mass for BOOST usage. Perhaps the developers 
of RBGL, bgx, BGmix and Steffen could get together to make a lightweight 
"RBOOST" package that they could all link to.

I have started an RBOOST package. It's currently living at 
http://msbi.ipb-halle.de/~sneumann/RBOOST.tgz
and contains an untarred boot-1.38.0

R CMD INSTALL RBOOST will build and install the headers 
and a subset of boost libraries into the RBOOST package:

	BOOST_DIRS="--includedir=${R_PACKAGE_DIR}/include --libdir=${R_PACKAGE_DIR}/libs"
	BOOST_LIBS="--with-filesystem --with-iostreams --with-regex --with-system"
	BOOST_CONF="--user-config=user-config.jam --layout=system link=shared"
	$BJAM ${BOOST_CONF} ${BOOST_DIRS} ${BOOST_LIBS} install

The depending packages should have in their DESCRIPTION:

	...
	LinkingTo: RBOOST 
	...

to be able to pick up the headers. Linking is a bit more difficult, 
and I am not sure I got the best way described in:
http://cran.r-project.org/doc/manuals/R-exts.html#Linking-to-other-packages

Currently my src/Makevars contains the following hack, 
although I feel that if I want to make the boost stuff 
optional and more generic, a configure.in would be the way to go:

	RBOOST_DIR=`echo 'library(RBOOST); cat(system.file("libs", package="RBOOST"))' | ${R_HOME}/bin/R --vanilla --no-save --slave`
	RBOOST_LIBS=-L"$(RBOOST_LIB)" \
	            -lboost_filesystem-mt -lboost_iostreams-mt \
	            -lboost_regex-mt -lboost_system-mt

Comments ?

Yours,
Steffen