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@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@jimmy.harvard.edu | > >+------------------------------------------------------------------ ---------+ > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >