Hi Thomas, On 11-10-04 12:24 PM, Benilton Carvalho wrote: > What's your *complete* output of sessionInfo()? And is it reproducible > with any public data? > > b > > On 4 October 2011 20:17, Thomas H. Hampton > <thomas.h.hampton at="" dartmouth.edu=""> wrote: >> >> Ideas? >> >>> sessionInfo() >> R version 2.13.0 (2011-04-13) >> Platform: x86_64-redhat-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 >> >> >> >> library(oligo) >> library(pd.hugene.1.0.st.v1) >> >> exonCELs<- list.celfiles(full.names = TRUE) >> affyExonFS<- read.celfiles(exonCELs) >> exonCore<- rma(affyExonFS, target = "core") >> >> Leads to this: >> >> Welcome to oligo version 1.16.2 >> =================================================================== ============= >>> library(pd.hugene.1.0.st.v1) >> Loading required package: RSQLite >> Loading required package: DBI >>> >>> exonCELs<- list.celfiles(full.names = TRUE) >>> affyExonFS<- read.celfiles(exonCELs) >> Platform design info loaded. >> Reading in : ./MD01.CEL >> Reading in : ./MD02.CEL >> Reading in : ./MD03.CEL >> Reading in : ./MD04.CEL >> Reading in : ./MD05.CEL >> Reading in : ./MD06.CEL >> Reading in : ./MD07.CEL >> Reading in : ./MD08.CEL >> Reading in : ./MD09.CEL >> Reading in : ./MD10.CEL >> Reading in : ./MD11.CEL >> Reading in : ./MD12.CEL FWIW, it will be more informative for Benilton if you call sessionInfo() here, that is, just before the call that causes the crash. Thanks! H. >>> exonCore<- rma(affyExonFS, target = "core") >> Background correcting >> >> *** caught segfault *** >> address 0x2addb000, cause 'memory not mapped' >> >> Traceback: >> 1: .Call("rma_c_complete_copy", pmMat, pnVec, nPn, normalize, background, bgversion, verbose, PACKAGE = "oligo") >> 2: basicRMA(pms, pnVec, normalize, background) >> 3: .local(object, ...) >> 4: rma(affyExonFS, target = "core") >> 5: rma(affyExonFS, target = "core") >> >> Possible actions: >> 1: abort (with core dump, if enabled) >> 2: normal R exit >> 3: exit R without saving workspace >> 4: exit R saving workspace >> Selection: >> >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319