R devel - Mar 2009 - Fix for foreign package segfault on Solaris 10 Intel

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

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
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
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