[Bioc-devel] Boost as build dependency ?

Patrick Aboyoun paboyoun at fhcrc.org
Wed Feb 18 02:51:23 CET 2009

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.


Hervé Pagès wrote:
> 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++
> code.
> 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.
> H.
> 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
>>> _______________________________________________
>>> Bioc-devel at stat.math.ethz.ch mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> _______________________________________________
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