[Bioc-devel] Boost as build dependency ?

Hervé Pagès hpages at fhcrc.org
Wed Feb 18 02:33:16 CET 2009

Hi Steffen, Patrick,

Note that Boost is a very peculiar library in the sense that most
modules are header-only i.e. they are entirely made of .hpp files.
The 3 packages in Bioconductor that include Boost (RBGL, bgx and BGmix)
only "use" a few modules. The way they "use" these modules is by
including a few .hpp files from these modules into their own C++
Steffen, if you are about to do the same in xcms, that's fine but
then we would have 4 BioC packages that ship their own
boostIncl.tar.gz (or parts of it). Maybe a better approach would
be to put boostIncl.tar.gz in a BioC package of its own and have
the client packages use the "LinkingTo:" feature?
Note that this infrastructure package would be easy to make and
to maintain as it would be made of .hpp files only, all of them in
the inst/include folder, so there would be nothing to compile,
no R code, no NAMESPACE and no man page.


Patrick Aboyoun wrote:
> Steffen,
> 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.
> Patrick
> 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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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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