[BioC] Building BioC 2.2 with R 2.7.0

[Atro Tossavainen]

Here's the line that generated genefilter.so:

(I'm using Sun's Studio 11 compilers and enabled the use of the sunperf
library while building R.)

CC -G -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -R/opt/SUNWspro/lib/v8plus:/opt/SUNWspro/lib:/opt/SUNWspro/lib/v8plus:/opt/SUNWspro/lib -L/opt/SUNWspro/lib/v8plus -L/opt/SUNWspro/prod/lib/v8plus -L/opt/SUNWspro/lib -L/opt/SUNWspro/prod/lib -L/usr/ccs/lib -lfui -lfai -lfai2 -lfsumai -lfprodai -lfminlai -lfmaxlai -lfminvai -lfmaxvai -lfsu -lsunmath -lmtsk -lm

I think all of the various -R, -L and -l parameters should have been
reduced into "-library=sunperf" above.  It might not be an issue.

I removed the existing genefilter installation and tried building again
simply with biocLite("genefilter"), which resulted in exactly the same
problem.  I also tried building the .so by hand:

CC -G -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -library=sunperf

which resulted in exactly the same problem when loading via

> library(genefilter)
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: survival
Loading required package: splines
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared library '/.../R/2.7.0/lib/R/library/genefilter/libs/genefilter.so':
  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
Error: package/namespace load failed for 'genefilter'

-- 
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.
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