[R] R_alloc problem (Mac OSX)

From: Dan Kelley <Dan.Kelley_at_Dal.Ca>
Date: Tue 14 Mar 2006 - 06:09:58 EST


Hello. I'm having difficulties getting R_alloc() to work.

The test platform is a 64-bit Mac running R 2.2.1 installed via a .dmg file obtained from the R site. Details are given below, in a level of detail that I hope is appropriate. My eye was particularly drawn to line #2 in the gdb 'where' output, but line #1 seems sensible so I may just be displaying my ignorance by drawing attention to this.

Q: Can anyone advise as to how I should proceed?

$ R --version
R 2.2.1 (2005-12-20).
Copyright (C) 2005 R Development Core Team

$ gcc -g -o test5 test5.c -I/library/Frameworks/R.framework/Versions/ 2.2/Resources/include/ -L/library/Frameworks/R.framework/Versions/2.2/ Resources/lib/ -lR -lm
/usr/bin/ld: warning multiple definitions of symbol _signgam /library/Frameworks/R.framework/Versions/2.2/Resources/lib//libR.dylib
(lgamma.lo) definition of _signgam
/usr/lib/gcc/powerpc-apple-darwin8/4.0.0/../../../libm.dylib
(gamma9.o) definition of _signgam

$ gdb test5
GNU gdb 6.1-20040303 (Apple version gdb-413) (Wed May 18 10:17:02 GMT 2005)
Copyright 2004 Free Software Foundation, Inc. GDB is free software, covered by the GNU General Public License, and you are
welcome to change it and/or distribute copies of it under certain conditions.
Type "show copying" to see the conditions. There is absolutely no warranty for GDB. Type "show warranty" for details.
This GDB was configured as "powerpc-apple-darwin"...Reading symbols for shared libraries .... done

(gdb) run

Starting program: /Users/kelley/src/R-from-fortran/test5 Reading symbols for shared libraries .........+ done about to call R_alloc(1,4)

Program received signal EXC_BAD_ACCESS, Could not access memory. Reason: KERN_PROTECTION_FAILURE at address: 0x0000000c GetNewPage (node_class=1) at ../../../../R-2.2.1/src/main/memory.c:622 622 ../../../../R-2.2.1/src/main/memory.c: No such file or directory.

         in ../../../../R-2.2.1/src/main/memory.c
(gdb) where

#0 GetNewPage (node_class=1) at ../../../../R-2.2.1/src/main/ memory.c:622
#1 0x00293d38 in Rf_allocVector (type=9, length=4) at ../../../../ R-2.2.1/src/main/memory.c:1918
#2 0x002932e8 in R_alloc (nelem=25167368, eltsize=1996) at ../../../../R-2.2.1/src/main/memory.c:1604 #3 0x00002ad0 in main () at test5.c:8
(gdb) list

617 in ../../../../R-2.2.1/src/main/memory.c
(gdb) file test5

Load new symbol table from "/Users/kelley/src/R-from-fortran/test5"?
(y or n) y

Reading symbols from /Users/kelley/src/R-from-fortran/test5...done.
(gdb) list

1       #include <stdio.h>
2       #include <R.h>
3       int main()
4       {
5               int *t;
6               long int n = 1;
7               printf("about to call R_alloc(%d,%d)\n",n,sizeof(int));
8               t = (int *) R_alloc(n, sizeof(int));
9               printf("done\n");
10              return(0);

(gdb) src/R-from-fortran/
Dan E. Kelley, Associate Professor                phone:(902)494-1694
Oceanography Department, Dalhousie University       fax:(902)494-2885
Halifax, Nova Scotia                         mailto:Dan.Kelley@Dal.CA
Canada B3H 4J1 http://www.phys.ocean.dal.ca/~kelley/Kelley_Dan.html

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https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Tue Mar 14 06:30:02 2006

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