[BioC] affy segmentation fault

[Adaikalavan Ramasamy]

A normal installation procedure for me would be something like :

make clean   # or make distclean if you tried configuring before
./configure --prefix=/home/adai/R
make
make check
make install

There are variants of versions of 'make check' such as 'make check-all'
which are more comprehensive testing (see page 3 of R-admin).

I do not know comprehend the flags and various options. If there is an
error or problem, I usually get my system administrator involved and
failing that I would try R-help mailing which is the more appropriate
place. 

And when you email R-help, please mention some vital information such as
your operating system (and kernel), gcc version, R version. Have you
tried checking R-help or BioC mailing archives ?

BTW, does Ben Bolstad's reply about affy 1.6.0. answer your question ?

 

On Tue, 2004-11-09 at 23:51, Sucheta Tripathy wrote:
> 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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