[Bioc-devel] Boost as build dependency ?
rgentlem at fhcrc.org
Wed Feb 18 02:54:36 CET 2009
On Tue, Feb 17, 2009 at 5:33 PM, Hervé Pagès <hpages at fhcrc.org> 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++
> 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.
that seems like a good idea,
> Patrick Aboyoun wrote:
>> 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
>> 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:
>>> to add more input file formats to xcms I'd like to include pwiz into
>>> 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.
>>> Bioc-devel at stat.math.ethz.ch mailing list
>> Bioc-devel at stat.math.ethz.ch mailing list
> Hervé Pagès
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> P.O. Box 19024
> Seattle, WA 98109-1024
> E-mail: hpages at fhcrc.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
> Bioc-devel at stat.math.ethz.ch mailing list
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
rgentlem at fhcrc.org
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