affxparser::readCdfHeader() core dumps

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Neelanjan Mukherjee ▴ 20

@neelanjan-mukherjee-3870

Last seen 11.3 years ago

I get a core dump and am not sure why. Any help would be greatly appreciated. Neel > library("AffymetrixDataTestFiles") > pathname <- "annotationData/chipTypes/Test3/1.XDA/Test3.CDF" > pathname <- system.file(pathname, package="AffymetrixDataTestFiles") > stopifnot(file.exists(pathname)) > print(pathname) [1] "/Users/Neel/Library/R/2.10/library/AffymetrixDataTestFiles/annota tionData/chipTypes/Test3/1.XDA/Test3.CDF" > library("affxparser") > hdr <- readCdfHeader(pathname) *** caught segfault *** address 0xfffffffc, cause 'memory not mapped' Traceback: 1: .Call("R_affx_get_cdf_file_header", filename, PACKAGE = "affxparser") 2: readCdfHeader(pathname) 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:

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ADD COMMENT • link 16.0 years ago Neelanjan Mukherjee ▴ 20

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Neelanjan Mukherjee ▴ 20

@neelanjan-mukherjee-3870

Last seen 11.3 years ago

Sorry, I forgot to include the sessinInfo: > sessionInfo() R version 2.10.1 (2009-12-14) i386-apple-darwin8.11.1 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base > library("AffymetrixDataTestFiles") > pathname <- "annotationData/chipTypes/Test3/1.XDA/Test3.CDF" > pathname <- system.file(pathname, package="AffymetrixDataTestFiles") > stopifnot(file.exists(pathname)) > print(pathname) [1] "/Users/Neel/Library/R/2.10/library/AffymetrixDataTestFiles/annota tionData/chipTypes/Test3/1.XDA/Test3.CDF" > library("affxparser") > hdr <- readCdfHeader(pathname) *** caught segfault *** address 0xfffffffc, cause 'memory not mapped' Traceback: 1: .Call("R_affx_get_cdf_file_header", filename, PACKAGE = "affxparser") 2: readCdfHeader(pathname) 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]]

ADD COMMENT • link 16.0 years ago Neelanjan Mukherjee ▴ 20

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Hi Neelan I could not reproduce this, using R-2.10 patched on OS X Snow Leopard, using Apple's gcc 4.2. This might be something specific to your platform, so please give us the following information * The full output of sessionInfo (you are missing the package versions in the output below) * Details on how you installed affxparser (I assume using biocLite, but please tell me) * The output (from R) of options("pkgType") * What OS X platform are you on (Tiger, Leopard, Snow Leopard) and how did you install R (using the CRAN binary I assume, but please confirm) * What is the output of the following command run in the Terminal (assuming that R starts the R version you are using) `R CMD config CXX` --version (these are "backticks" on a US keyboard they are typically the upper left hand key (shared with ~)) Kasper On Jan 5, 2010, at 8:44 AM, Neelanjan Mukherjee wrote: > Sorry, I forgot to include the sessinInfo: > >> sessionInfo() > R version 2.10.1 (2009-12-14) > i386-apple-darwin8.11.1 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base >> library("AffymetrixDataTestFiles") >> pathname <- "annotationData/chipTypes/Test3/1.XDA/Test3.CDF" >> pathname <- system.file(pathname, package="AffymetrixDataTestFiles") >> stopifnot(file.exists(pathname)) >> print(pathname) > [1] "/Users/Neel/Library/R/2.10/library/AffymetrixDataTestFiles/anno tationData/chipTypes/Test3/1.XDA/Test3.CDF" >> library("affxparser") >> hdr <- readCdfHeader(pathname) > > *** caught segfault *** > address 0xfffffffc, cause 'memory not mapped' > > Traceback: > 1: .Call("R_affx_get_cdf_file_header", filename, PACKAGE = "affxparser") > 2: readCdfHeader(pathname) > > 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 stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

ADD REPLY • link 16.0 years ago Kasper Daniel Hansen ★ 6.5k

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This issue was solved by re-installing R (off-list correspondence). Kasper On Jan 5, 2010, at 12:43 PM, Kasper Daniel Hansen wrote: > Hi Neelan > > I could not reproduce this, using R-2.10 patched on OS X Snow Leopard, using Apple's gcc 4.2. > > This might be something specific to your platform, so please give us the following information > * The full output of sessionInfo (you are missing the package versions in the output below) > * Details on how you installed affxparser (I assume using biocLite, but please tell me) > * The output (from R) of options("pkgType") > * What OS X platform are you on (Tiger, Leopard, Snow Leopard) and how did you install R (using the CRAN binary I assume, but please confirm) > * What is the output of the following command run in the Terminal (assuming that R starts the R version you are using) > > `R CMD config CXX` --version > > (these are "backticks" on a US keyboard they are typically the upper left hand key (shared with ~)) > > Kasper > > On Jan 5, 2010, at 8:44 AM, Neelanjan Mukherjee wrote: > >> Sorry, I forgot to include the sessinInfo: >> >>> sessionInfo() >> R version 2.10.1 (2009-12-14) >> i386-apple-darwin8.11.1 >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >>> library("AffymetrixDataTestFiles") >>> pathname <- "annotationData/chipTypes/Test3/1.XDA/Test3.CDF" >>> pathname <- system.file(pathname, package="AffymetrixDataTestFiles") >>> stopifnot(file.exists(pathname)) >>> print(pathname) >> [1] "/Users/Neel/Library/R/2.10/library/AffymetrixDataTestFiles/ann otationData/chipTypes/Test3/1.XDA/Test3.CDF" >>> library("affxparser") >>> hdr <- readCdfHeader(pathname) >> >> *** caught segfault *** >> address 0xfffffffc, cause 'memory not mapped' >> >> Traceback: >> 1: .Call("R_affx_get_cdf_file_header", filename, PACKAGE = "affxparser") >> 2: readCdfHeader(pathname) >> >> 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 stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

ADD REPLY • link 16.0 years ago Kasper Daniel Hansen ★ 6.5k

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