Can you show us the output you get from building foreign, and explain
how it comes to be linked against libavl? I get (SunStudio 12)
cc -xc99 -G -L/opt/csw/lib -o foreign.so R_systat.o Rdbfread.o
Rdbfwrite.o SASxport.o avl.o dbfopen.o file-handle.o format.o init.o
minitab.o pfm-read.o sfm-read.o spss.o stataread.o
and ldd library/foreign/libs/foreign.so reveals no dependencies (and
the R binary is not linked against libavl either).
I can see that linking against libavl could cause problems, but have
no idea why that might be happening.
On Fri, 6 Mar 2009, Jeff Long wrote:
Like a couple of other posters in the past year, I was seeing R 2.8.1
segfault in the foreign package on my Solaris 10 Intel system:
> library(foreign)
*** caught segfault ***
address fe1d5c70, cause 'invalid permissions'
Traceback:
1: .C("spss_init", PACKAGE = "foreign")
2: fun(...)
This happened whether I built with gcc3, gcc4, or SunStudio 12.
Using pstack I found that the code was crashing in avl_create(). Using truss
I found that identically named functions in the Solaris /lib/libavl.so.1
library were being used instead of the AVL functions provided in avl.c in the
foreign package. To verify, I replaced all of the "avl_" and "AVL_" patterns
in foreign/src/*.[ch] with "ravl_" and "RAVL_" respectively. Once I made this
change, loading the foreign package caused no further problems.
An alternative workaround was a hack involving symlinks and LD_LIBRARY_PATH,
but that was not satisfactory. Since the foreign avl functions are
incompatible with the ones provided by the standard Sun library, this
approach has other potential gotchas.
FYI.
Jeff
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Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
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