[BioC] affy segmentation fault

[Sucheta Tripathy]

At 04:59 PM 11/9/2004 -0500, Robert Gentleman wrote:
>On Tue, Nov 09, 2004 at 04:46:03PM -0500, Sucheta Tripathy wrote:
> >
> > I know we have been cluttering this mailing list with this question over
> > and again. The reason I want to ask again is after seeing the segmentation
> > fault error, I found it says 340000 KB to be the size it needs.
> >
> > What puzzles me is our memory is way beyond that(almost 5 GB with 10 GB
> > swap memory).
>
>   And as I have said very many times already, it likely has nothing to
>   do with that, but rather that you have a corrupted installation. You
>   almost surely need to recompile R with the correct set of compiler
>   flags for your system and to reinstall the the appropriate
>   packages. I am not sure how I can say this more explicitly, but the
>   problem does not seem to be affy, it seems to be your installation.

I guess at this point if any body else who has done installation and 
compilation with any other flag, shares the flags they have used, I will 
really appreciate that. After digging through the installation instruction, 
I don't find anything other than

$ ./configure
      $ make

with may be a option to prefix path.(where R binaries and libraries should go).

Probably I need help from someone who can point where to find a more 
detailed installation help. I have been also looking at file config.site, 
and most of the default options look fine to me.

If it is just the case of R being corrupted,is no big deal provided we know 
what flags we are using to compile next.

-Sucheta

>   Robert
>
>
> >
> > After trying all the remedies, it still fails. Can anyone suggest if in
> > the source where the exact memory allocation takes place, how much is
> > fixed to be the size. Can we not increase it? Or to begin with which
> > version of affy package has a fix for it.
> >
> > Thanks in advance.
> >
> > Sucheta
> >
> > --
> > Sucheta Tripathy
> > Virginia Bioinformatics Institute Phase-I
> > Washington street.
> > Virginia Tech.
> > Blacksburg,VA 24061-0447
> > phone:(540)231-8138
> > Fax:  (540) 231-2606
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>--
>+---------------------------------------------------------------------------+
>| Robert Gentleman                 phone : (617) 632-5250                   |
>| Associate Professor              fax:   (617)  632-2444                   |
>| Department of Biostatistics      office: M1B20                            |
>| Harvard School of Public Health  email: rgentlem at jimmy.harvard.edu        |
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