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svm in e1071 package segment fault in redhat 7.2

5 messages · jason zhao, Uwe Ligges, David Meyer +1 more

jason zhao
# 
Hi, Guys
I run one simple R script like this
       
library(e1071) 
data(iris)
attach(iris)
model <- svm (Species~., data=iris)

The R version is 1.4.1. The OS is standard redhat 7.2.
Then I got a segmentation fault like this (run through
R CMD BATCH scriptName)
/usr/local/R/lib/R/bin/BATCH: line 54: 28513 Done     
              (    
echo "invisible(options(echo = TRUE))"; cat ${in};
echo "proc.time()" )
     28514 Segmentation fault      | ${R_HOME}/bin/R
${opts} >${out} 2>&1

There is no problem if the R-binary is running redhat
6.2.

Does anyone see this problem?  Is there a workaround
for this?
  
Help is appreciated.

Jason

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Uwe Ligges
#
jason zhao wrote:
Haven't got RedHat 7.2 available, but your example works perfectly on
SuSE 7.3, Solaris 5.7 and WinXP.
So I guess you didn't compile R (or e1071) on your system. 
Maybe there is a small incompatibility with the precompiled version.
I'd suggest to compile R yourself and install e1071 from the sources.

Uwe Ligges
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jason zhao
# 
--- Uwe Ligges <ligges at statistik.uni-dortmund.de>
wrote:
I installed everyting  (the R basic, R-recommended
package and e1071 ) from source.   My test example
worked fine with redhat 6.2, but not redhat 7.2. I
think maybe it is  problem in gcc library or something
in e1071 package. 
Any suggestion
Thanks





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David Meyer
# 
It's almost shurely the broken red-hat gcc (guess you have version 2.96?). Try a
newer release (but they may buggy also, beware).

g.
-d
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Martyn Plummer
# 
I can replicate this bug on Red Hat 7.2.  It seems to be a compiler
problem. Here is the relevant output from gdb

(gdb) frame 2
#2  0x403a2ab6 in SVC_Q::get_Q (this=0xbfffdae0, i=41, len=100) at svm.cpp:1131
1131                    if((start = cache->get_data(i,&data,len)) < len)
(gdb) p cache
$10 = (Cache *) 0x8b083a8
(gdb) p i
$11 = 41
(gdb) p &data
$12 = (Qfloat **) 0xbfffd984
(gdb) p len
$13 = 100
(gdb) frame 1
#1  0x4039d90e in Cache::get_data (this=0x8b083a8, index=146466881, 
    data=0xbfffd984, len=100) at svm.cpp:109
109             if(h->len) lru_delete(h);

The index argument to Cache::get_data is corrupted (should be 41
not 14646881).

I see that Red Hat have released a package for gcc3.  You can
download this from 

ftp://updates.redhat.com/7.2/en/os/i386/

or a mirror near you.  I recommend that you try this.

Martyn
On 11-Mar-2002 jason zhao wrote:
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