affy segmentation fault
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@sucheta-tripathy-987
Last seen 9.6 years ago
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). 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
affy affy • 1.1k views
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@adaikalavan-ramasamy-675
Last seen 9.6 years ago
I just checked the mailing archives. You sent 2 mails in Novembers (excluding this) and 2 in October but none of them talk about segmentation fault error. Perhaps you can explain who "we" are or better yet state the problem or link to past mail (perhaps from https://stat.ethz.ch/pipermail/bioconductor/). Start from a clean R session and see if you can repeat the problem. Next, reduce the number of arrays till you find out how many arrays your machine can handle. Try just.rma or just.gcrma. Also search the mailing archives. These are all guesses. Note that although 5 GB is available to a machine, there might be a limit to how much each process/user can have access to. Speak to your system administrator about any such limitation. Regards, Adai On Tue, 2004-11-09 at 21:46, 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). > > 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
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Ben Bolstad ★ 1.1k
@ben-bolstad-93
Last seen 9.6 years ago
Please wait for the next version of the affy package 1.6.0 which should appear on the web in a few days. It has the requisite fix to deal with your soybean arrays. Ben On Tue, 2004-11-09 at 13:46, 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). > > 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 -- Ben Bolstad <bolstad@stat.berkeley.edu> http://www.stat.berkeley.edu/~bolstad
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@sucheta-tripathy-987
Last seen 9.6 years ago
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 | >+-------------------------------------------------------------------- -------+
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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 >
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