[R] R on gentoo amd64 (gcc 3.3.3) is unstable

Peter Dalgaard p.dalgaard at biostat.ku.dk
Fri Aug 20 20:05:11 CEST 2004

<ivo_welch-rstat8783 at mailblocks.com> writes:

> dear wizards:
>   FYI: gentoo is a linux meta distribution, which compiles all
> packages. Once running, gentoo is stable on most applications.  (it
> has some problems with system tools, such as grub.)  the compiler is
> gcc 3.3.3.  I do not expect anyone to track down for me why R fails on
> the gentoo amd64+gcc3.3.3 system, but I thought that it would be good
> to put it on the record to save others some time.
> The resulting from-source-compiled R is not stable in this
> combination. R starts up ok, but a couple of commands (a simple linear
> regression) usually result in a Segfault.  this applies both to the R
> provided by gentoo (an old version of 1.9.0) or the latest version
> 1.9.1 which I just pulled down.  in case someone is wondering, the
> debugger backtrace provides
> #0  0x000000000052ac16 in dnrm2_ ()
> #1  0x00000000005185e8 in dqrdc2_ ()
> #2  0x0000000000518db1 in dqrls_ ()
> #3  0x000000000045d5d5 in do_dotCode ()
> #4  0x0000000000472b6b in Rf_eval ()
> ...
> (if any R wizard were to find it useful to try it out for himself, I
> could arrange for machine access, or provide other relevant
> information.  if anyone has compiled R 1.9.1 under amd64 with gcc
> 3.3.3 and found it to be stable, please let me know, too.)

SuSE 9.1 appears quite happy.

> gcc -v
Reading specs from /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/specs
Configured with: ../configure --enable-threads=posix --prefix=/usr
--with-local-prefix=/usr/local --infodir=/usr/share/info
--mandir=/usr/share/man --enable-languages=c,c++,f77,objc,java,ada
--disable-checking --libdir=/usr/lib64 --enable-libgcj
--with-gxx-include-dir=/usr/include/g++ --with-slibdir=/lib64
--with-system-zlib --enable-shared --enable-__cxa_atexit
Thread model: posix
gcc version 3.3.3 (SuSE Linux)

I'd suspect that your blas libs are broken rather than R itself.

   O__  ---- Peter Dalgaard             Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark      Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)             FAX: (+45) 35327907

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