[R] R-1.6.0 crashing on RedHat6.3

[Peter Dalgaard BSA]

Douglas Grove <dgrove at fhcrc.org> writes:

> > Are you sure that it is 6.3?? To my knowledge, there is nothing
> > between 6.2 and 7.0. What's in /etc/redhat-release ?
> 
> Sorry, I was told it was running 6.3. I just checked and
> it's running 6.2.

OK, so the Fortran problems are there, but the usual symptom of that
is crash-on-load.
 

> > The Fortran in RH6.x was rather badly broken for some packages, but
> > one would expect that you had run into that before. 1.6.0 has a memory
> > leak but it generally affects repeated applications of model fits,
> > rather than big matrices. 
> > 
> > Do you really mean 144x5300 ? (more columns than rows) That's big: The
> > covariance matrix at 5300x5300 will take more than 200 MB (OK, it
> > might only be storing upper or lower triangle.) I tried a matrix like
> > that on a 1.6.1beta system with about 0.75 GB and got an out of memory
> > error. A 144x2500 problem is currently running in
> > 
> >   PID USER     PRI  NI  SIZE  RSS SHARE STAT %CPU %MEM   TIME COMMAND
> > 16111 pd        17   0  207M 163M 18536 R    99.8 65.8   1:58 R.bin
> > 
> > and seems to be staying there....
> 
> Yep, it's 144x5300.  The machine has 2GB of RAM, and this uses about 1.5GB.

Hmm. My half-size toy version conked out with 

> D <- matrix(rnorm(2500*144),ncol=2500)
> library(mva)
> pc.norm <- princomp(D,scores=FALSE)
Error in princomp.default(D, scores = FALSE) : 
        covariance matrix is not non-negative definite

which is a bit odd, but at least it didn't run out of memory. However,
the tolerances seem to require some tweaking!

-- 
   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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