Dear R-help Hi, I'm Won. I try to do microarray normalization by R. I use justRMA function within affy package, got error about segment fault. I don't know why it happen. I attached error below. Please help me. Thank you. Cheers, Won ======================OS : Redhat linux Cpu : intel xeon X5570 Memory : 26Gb & OS : Ubuntu Cpu : intel q6600 Memory : 8Gb ======================Loading required package: Biobase Loading required package: methods Welcome to Bioconductor Vignettes contain introductory material. To view, type 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation("pkgname")'. Loading required package: gcrma Loading required package: preprocessCore Attaching package: 'affyPLM' The following object(s) are masked from 'package:stats': resid, residuals, weights *** caught segfault *** address 0xc609000, cause 'memory not mapped' Traceback: 1: .Call("rma_c_complete", probeintensities$pm, pNList, ngenes, normalize, background, bgversion, verbose, PACKAGE = "affy") 2: just.rma(filenames = l$filenames, phenoData = l$phenoData, description l$description, notes = notes, compress = compress, rm.mask = rm.mask, rm.outliers = rm.outliers, rm.extra = rm.extra, verbose = verbose, normalize = normalize, background = background, bgversion = bgversion, destructive = destructive, cdfname = cdfname) 3: justRMA() aborting ... /var/spool/sge/tachyon1145/job_scripts/477103: line 21: 22829 Segmentation fault /home01/e133ywc/R/R-2.13.0/bin/Rscript /scratch/e133ywc/big/198/198.R -- View this message in context: http://r.789695.n4.nabble.com/cause-memory-not-mapped-tp3593833p3593833.html Sent from the R help mailing list archive at Nabble.com.
You need to ask this question on the Bioconductor mailing list. --------------------------------------------------------------------------- Jeff Newmiller The ..... ..... Go Live... DCN:<jdnewmil@dcn.davis.ca.us> Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/Batteries O.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --------------------------------------------------------------------------- Sent from my phone. Please excuse my brevity. ascendo <ascendo@dongguk.edu> wrote: Dear R-help Hi, I'm Won. I try to do microarray normalization by R. I use justRMA function within affy package, got error about segment fault. I don't know why it happen. I attached error below. Please help me. Thank you. Cheers, Won ======================OS : Redhat linux Cpu : intel xeon X5570 Memory : 26Gb & OS : Ubuntu Cpu : intel q6600 Memory : 8Gb ======================Loading required package: Biobase Loading required package: methods Welcome to Bioconductor Vignettes contain introductory material. To view, type 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation("pkgname")'. Loading required package: gcrma Loading required package: preprocessCore Attaching package: 'affyPLM' The following object(s) are masked from 'package:stats': resid, residuals, weights *** caught segfault *** address 0xc609000, cause 'memory not mapped' Traceback: 1: .Call("rma_c_complete", probeintensities$pm, pNList, ngenes, normalize, background, bgversion, verbose, PACKAGE = "affy") 2: just.rma(filenames = l$filenames, phenoData = l$phenoData, description l$description, notes = notes, compress = compress, rm.mask = rm.mask, rm.outliers = rm.outliers, rm.extra = rm.extra, verbose = verbose, normalize = normalize, background = background, bgversion = bgversion, destructive = destructive, cdfname = cdfname) 3: justRMA() aborting ... /var/spool/sge/tachyon1145/job_scripts/477103: line 21: 22829 Segmentation fault /home01/e133ywc/R/R-2.13.0/bin/Rscript /scratch/e133ywc/big/198/198.R -- View this message in context: http://r.789695.n4.nabble.com/cause-memory-not-mapped-tp3593833p3593833.html Sent from the R help mailing list archive at Nabble.com. _____________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]]
On 06/13/2011 06:23 AM, ascendo wrote:> Dear R-help > > Hi, > > I'm Won. > > I try to do microarray normalization by R. > > I use justRMA function within affy package, got error about segment fault. > > I don't know why it happen. > > I attached error below.Hi Won -- as suggested, post to the Bioconductor mailing list https://stat.ethz.ch/mailman/listinfo/bioconductor Make sure that you've installed and updated your packages following the Bioconductor protocol; problems can arise when package versions are not matched correctly. http://bioconductor.org/install/ You include the output of your script, but not the commands. Include the commands, and include the output of sessionInfo(). If at all possible make the example reproducible, e.g., by using the examples in the package or data provided by the sample data sets. For instance after source('http://bioconductor.org/biocLite.R') biocLite(c("affy", "AffymetrixDataTestFiles")) Run these commands library(affy) library(AffymetrixDataTestFiles) sessionInfo() cel <- system.file("rawData", "FusionSDK_HG-U133A", "HG-U133A", "2.Calvin", "ethan1-1.CEL", package="AffymetrixDataTestFiles") res <- just.rma(cel) which produces > library(affy) > library(AffymetrixDataTestFiles) > sessionInfo() R version 2.12.2 Patched (2011-02-25 r54588) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] AffymetrixDataTestFiles_0.1.2 affy_1.28.0 [3] Biobase_2.10.0 loaded via a namespace (and not attached): [1] affyio_1.18.0 preprocessCore_1.12.0 > cel <- system.file("rawData", "FusionSDK_HG-U133A", "HG-U133A", + "2.Calvin", "ethan1-1.CEL", package="AffymetrixDataTestFiles") > res <- just.rma(cel) Warning message: In just.rma(cel) : Incompatible phenoData object. Created a new one. Martin> > Please help me. > > Thank you. > > Cheers, > > Won > > ======================> OS : Redhat linux > Cpu : intel xeon X5570 > Memory : 26Gb > > & > > OS : Ubuntu > Cpu : intel q6600 > Memory : 8Gb > > ======================> Loading required package: Biobase > Loading required package: methods > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'browseVignettes()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation("pkgname")'. > > Loading required package: gcrma > Loading required package: preprocessCore > > Attaching package: 'affyPLM' > > The following object(s) are masked from 'package:stats': > > resid, residuals, weights > > > *** caught segfault *** > address 0xc609000, cause 'memory not mapped' > > Traceback: > 1: .Call("rma_c_complete", probeintensities$pm, pNList, ngenes, > normalize, background, bgversion, verbose, PACKAGE = "affy") > 2: just.rma(filenames = l$filenames, phenoData = l$phenoData, description > l$description, notes = notes, compress = compress, rm.mask = rm.mask, > rm.outliers = rm.outliers, rm.extra = rm.extra, verbose = verbose, > normalize = normalize, background = background, bgversion = bgversion, > destructive = destructive, cdfname = cdfname) > 3: justRMA() > aborting ... > /var/spool/sge/tachyon1145/job_scripts/477103: line 21: 22829 Segmentation > fault /home01/e133ywc/R/R-2.13.0/bin/Rscript > /scratch/e133ywc/big/198/198.R > > -- > View this message in context: http://r.789695.n4.nabble.com/cause-memory-not-mapped-tp3593833p3593833.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.-- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793