[BioC] Building BioC 2.2 with R 2.7.0

Atro Tossavainen atossava at cc.helsinki.fi
Thu May 29 07:49:32 CEST 2008


>    Thanks for all your efforts in trouble shooting.  If I understand, 
> the GO issue is now resolved but genefilter is still problematic.

Yes indeed.

>    Could you try using gcc to compile rather than sunperf?

As the Bioconductor packages are built with whatever was used to compile
R itself, this meant having to compile R from scratch with gcc, which
I wasn't really looking forward to.  However, at the moment, that looks
like the only way I could get a working genefilter going on Solaris/SPARC,
and I also found I could substitute the gcc-compiled genefilter.so for
the Sun Studio generated one in the otherwise Sun Studio generated
install.  While this is far from practical, it at least allowed me to
have a working set of R and Bioconductor for Solaris/SPARC for now.

> >   ld.so.1: /.../R/2.7.0/lib/R/bin/exec/R: fatal: relocation error: file /.../R/2.7.0/lib/R/library/genefilter/libs/genefilter.so: symbol __1cDstdJexceptionG__vtbl_: referenced symbol not found

As far as I can guess, this might mean that g++ was used to compile
something somewhere even though I've specified Sun Studio all along.
I'd need to rebuild all of R once more and log everything to verify.

Atro Tossavainen (Mr.)               / The Institute of Biotechnology at
Systems Analyst, Techno-Amish &     / the University of Helsinki, Finland,
+358-9-19158939  UNIX Dinosaur     / employs me, but my opinions are my own.
< URL : http : / / www . helsinki . fi / %7E atossava / > NO FILE ATTACHMENTS

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