[Bioc-devel] CXX on liverpool/lemming

Martin Morgan mtmorgan at fhcrc.org
Mon Oct 15 23:15:44 CEST 2007

"Steffen Neumann (on the road)" <sneumann at ipb-halle.de> writes:

> On Sun, 2007-10-14 at 16:13 -0700, Martin Morgan wrote:
>> Kasper Daniel Hansen <khansen at stat.berkeley.edu> writes:
> ...
>> But this is a detail that you shouldn't have to worry about. As on any
>> platform, you can / should discover the correct compiler by asking R
>> (R CMD config CXX). 
> This is only the information for R compile time. 
> If I have a binary installation, my current development 
> environment could be different. Granted, for c++ 
> compilers should match down to the version number.

On windows there's really only one supported tool chain. On other
platforms your configure could test for a defined CXX env. variable. R
consults R_HOME/etc/Makeconf for source packages without configure
scripts and so I think assumes close similarity between compile time
and current environments.

>> which I guess just means a little more work figuring out where that
>> lims library is.
> Actually, libims is sitting below the Rdisop/src/imslib folder,
> and is compiled via the Makevars Makefile. Afterwards I copy the 
> libims.dll into the Rdisop/src directory.
> On Unix both Rdisop.so and libims.so are picked up during install 
> and copied to site-library/Rdisop/libs/ 
> The same mechanism under Windows copies only Rdisop.dll over.
> Any hint which shared objects are used during R CMD INSTALL ?
> I tried to locate the script or Makefile snippet responsible for this,
> but failed miserably :-(

The paradigm seems to be along the lines of (from the rsbml package
configure.win, copying an external dll into the package)


mkdir $DPKG/libs
cp $LIBSBML_PATH/bin/*.dll $DPKG/libs

DPKG is defined in R_HOME/src/gnuwin32/MakePkg (which seems to be
driving the installation), and is the directory where the package is
being built for installation.

I feel a little uncertain answering these questions definitively; you
might try asking on the R-devel list where you'll tap into a deeper
pool of experience (the original question, about lemming / liverpool,
were very appropriate for the bioc-devel list). Others on the current
list might feel free to chip in, too.


> Thanks for any hints, 
> Yours,
> Steffen
> -- 
> IPB Halle                    AG Massenspektrometrie & Bioinformatik
> Dr. Steffen Neumann          http://www.IPB-Halle.DE
> Weinberg 3                   http://msbi.bic-gh.de
> 06120 Halle                  New Phone number !
>                              Tel. +49 (0) 345 5582 - 1470
> sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409

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