[Bioc-devel] Boost as build dependency ?

Patrick Aboyoun paboyoun at fhcrc.org
Tue Feb 17 18:38:23 CET 2009

The BioC build machines does not rely upon an external BOOST library 
installation to build packages. For example, the RBGL BioC package is an 
interface to The Boost Graph Library (BGL) and includes the source code 
for BGL.

I would like to reframe this discussion from one about the build system 
to one about the end users and in particular consumers of the Windows 
and Mac binary packages. Do you want typical Windows and Mac users to 
have the BOOST libraries installed on their system to use the xcms 
package? Even if the build system can build binary packages for xcms 
that rely on external libraries, a typical user may have a hard time 
reconstructing the required components on their machine to use the 
binary packages on bioconductor.org. I was recently reminded of this 
when I was helping Mac users with the Rgraphviz package since it 
dynamically links to the graphviz library. The graphviz installation on 
the build machines is old and hard for others to reproduce so there was 
very little utility to Rgraphviz Mac binary packages out-of-the-box. I 
upgraded graphviz on the Mac build machines, but this is only a partial 
fix since end users still need to match the graphviz installation that 
created the Rgraphviz binary package.


Steffen Neumann wrote:
> Hi,
> to add more input file formats to xcms I'd like 
> to include pwiz into xcms.so
> pwiz has several boost (version >1.36.x) libraries as dependency.
> Shipping and Building the whole boost in the xcms package
> is probably out of question. 
> Are they available on the build machines ?
> I could also try to check for them in the configure,
> and make them linking optional.
> Yours,
> Steffen
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