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jason zhao

2002-Mar-11 19:55 UTC

[R] svm in e1071 package segment fault in redhat 7.2

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

2002-Mar-11 21:20 UTC

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[R] svm in e1071 package segment fault in redhat 7.2

jason zhao wrote:> 
> 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?
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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Martyn Plummer

2002-Mar-12 10:44 UTC

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[R] svm in e1071 package segment fault in redhat 7.2

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:> 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-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !)  To: r-help-request at
stat.math.ethz.ch
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jason zhao

2002-Mar-13 14:36 UTC

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[R] svm in e1071 package segment fault in redhat 7.2

I installed gcc3. Both gcc(2.96) and 3.0.4 are in my
system right now. How can you configure R compiler
with gcc3 instead of gcc(2.96)?
Thanks

jason 

--- Prof Brian D Ripley <ripley at stats.ox.ac.uk>
wrote:> It works for me under RH7.2, using gcc 3.0.4.
> 
> Did you use a released version of gcc?  (Hint `2.96'
> is a figment of
> RedHat's imagination.)  Linux distros love putting
> out snapshot software
> (often ancient snapshots).
> 
> 
> On Mon, 11 Mar 2002, jason zhao wrote:
> 
> >
> > --- Uwe Ligges <ligges at statistik.uni-dortmund.de>
> > wrote:
> > > jason zhao wrote:
> > > >
> > > > 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?
> > >
> > > 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
> > 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
> >
> >
> >
> >
> >
> > __________________________________________________
> >
> >
> >
> >
>
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-> > r-help mailing list -- Read
> http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
> > Send "info", "help", or "[un]subscribe"
> > (in the "body", not the subject !)  To:
> r-help-request at stat.math.ethz.ch
> >
>
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._> >
> 
> -- 
> 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
> 272860 (secr)
> Oxford OX1 3TG, UK                Fax:  +44 1865
> 272595
> 

__________________________________________________



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ripley@stats.ox.ac.uk

2002-Mar-13 15:02 UTC

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[R] svm in e1071 package segment fault in redhat 7.2

On Wed, 13 Mar 2002, jason zhao wrote:
> I installed gcc3. Both gcc(2.96) and 3.0.4 are in my
> system right now. How can you configure R compiler
> with gcc3 instead of gcc(2.96)?
This is all in the R-admin manual.

Just put gcc3 first in your path, if it is called gcc, or set CC=gcc3
(and FC and CXX, I guess) in config.site.

-- 
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 272860 (secr)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
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