snapCGH, runBioHMM, Error: segfault from C stack overflow
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@ivanek-robert-3765
Last seen 10.2 years ago
Dear John, BioC-community, I tried to run the runBioHMM function on my data (Nimblegen HD 2.1 Arrays), however I am always getting the error: "Error: segfault from C stack overflow". What is the reason for that error? Are the data too big? I tried to split the array according the chromosomes but it did not help. Only after splitting the data into small pieces the function run successfully. I preprocessed the data according the snapCGH manual (snapCGHguide.pdf), below is the code that produced the error, object class and sessionInfo. Best Regards Robert -- Robert Ivanek Postdoctoral Fellow Schuebeler Group Friedrich Miescher Institute Maulbeerstrasse 66 4058 Basel / Switzerland Office phone: +41 61 697 6100 ###################################################################### ########## R> SegInfo.BioHMM <- runBioHMM(MA.cgh2) sample is 1 Chromosomes: 1 2 Error: segfault from C stack overflow ###################################################################### ########## R> class(MA.cgh2) [1] "SegList" attr(,"package") [1] "snapCGH" ###################################################################### ########## R> dim(MA.cgh2$M) [1] 1967673 10 ###################################################################### ########## R> MA.cgh2 An object of class "SegList" $state NULL $rpred NULL $prob NULL $M.predicted NULL $dispersion NULL $variance NULL $M.observed a b c d e f g [1,] -0.12942320 0.02683309 -0.10259011 0.22068827 0.1938552 0.09126507 0.08812914 [2,] -0.13219905 0.34312167 0.21092262 0.08040469 -0.2627170 -0.05179436 0.28135520 [3,] 0.07700826 -0.01331928 0.06368898 0.12494860 0.1382679 0.20195685 -0.05675671 [4,] 0.14806237 -0.25316790 -0.10510554 0.01550725 0.2686752 0.16356962 -0.38026647 [5,] 0.22431210 -0.39476064 -0.17044853 -0.29215523 0.1026054 -0.06784313 -0.34597137 h i j [1,] 0.06129606 -0.04129405 -0.13255913 [2,] -0.06176647 0.14915615 0.20095051 [3,] -0.04343744 0.02025154 -0.18170531 [4,] -0.12709857 -0.23220410 -0.39577372 [5,] 0.04878927 -0.12165927 -0.05381614 1967668 more rows ... $genes Block GENE_EXPR_OPTION PROBE_ID POSITION Row Column Status ID Chr Position 2 1 BLOCK1 CHR01FS003044249 3044249 266 3118 BLOCK1 CHR01FS003044249 1 3.044249 4 1 BLOCK1 CHR01FS003090598 3090598 454 3038 BLOCK1 CHR01FS003090598 1 3.090598 7 1 BLOCK1 CHR01FS003090918 3090918 109 3793 BLOCK1 CHR01FS003090918 1 3.090918 9 1 BLOCK1 CHR01FS003091098 3091098 14 3674 BLOCK1 CHR01FS003091098 1 3.091098 10 1 BLOCK1 CHR01FS003091218 3091218 1047 3673 BLOCK1 CHR01FS003091218 1 3.091218 1967668 more rows ... $M a b c d e f g [1,] -0.12942320 0.02683309 -0.10259011 0.22068827 0.1938552 0.09126507 0.08812914 [2,] -0.13219905 0.34312167 0.21092262 0.08040469 -0.2627170 -0.05179436 0.28135520 [3,] 0.07700826 -0.01331928 0.06368898 0.12494860 0.1382679 0.20195685 -0.05675671 [4,] 0.14806237 -0.25316790 -0.10510554 0.01550725 0.2686752 0.16356962 -0.38026647 [5,] 0.22431210 -0.39476064 -0.17044853 -0.29215523 0.1026054 -0.06784313 -0.34597137 h i j [1,] 0.06129606 -0.04129405 -0.13255913 [2,] -0.06176647 0.14915615 0.20095051 [3,] -0.04343744 0.02025154 -0.18170531 [4,] -0.12709857 -0.23220410 -0.39577372 [5,] 0.04878927 -0.12165927 -0.05381614 1967668 more rows ... $design [1] 1 1 1 1 1 1 1 1 1 1 ###################################################################### ########## R> sessionInfo() R version 2.10.1 (2009-12-14) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=C [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] splines stats graphics grDevices utils datasets methods base other attached packages: [1] RMySQL_0.7-4 DBI_0.2-5 snapCGH_1.16.0 aCGH_1.22.0 multtest_2.2.0 survival_2.35-8 cluster_1.12.1 [8] GLAD_2.6.0 DNAcopy_1.20.0 tilingArray_1.24.0 pixmap_0.4-10 Biobase_2.6.1 limma_3.2.2 RColorBrewer_1.0-2 loaded via a namespace (and not attached): [1] affy_1.24.2 affyio_1.14.0 annotate_1.24.1 AnnotationDbi_1.8.1 genefilter_1.28.2 grid_2.10.1 lattice_0.18-3 [8] MASS_7.3-5 preprocessCore_1.8.0 RSQLite_0.8-4 strucchange_1.4-0 tools_2.10.1 vsn_3.14.0 xtable_1.5-6
snapCGH snapCGH • 2.1k views
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Seth Falcon ▴ 150
@seth-falcon-2443
Last seen 10.2 years ago
Hi Robert, On 3/15/10 6:46 AM, Ivanek, Robert wrote: > I tried to run the runBioHMM function on my data (Nimblegen HD 2.1 > Arrays), however I am always getting the error: "Error: segfault from C > stack overflow". You need to provide us with more information so that we can help you. A good start would include: - sessionInfo() - the exact code you are running - more details on the input data. > > What is the reason for that error? Are the data too big? I tried to > split the array according the chromosomes but it did not help. Only > after splitting the data into small pieces the function run > successfully. That does suggest that data size is the issue. Are you able to obtain any details on where the segfault occurs? R-devel includes a fix for an issue in gsub that could cause a stack overflow segfault for long strings. You might try installing latest R-devel, Bioconductor devel packages and see if the problem is reproducible there. > > I preprocessed the data according the snapCGH manual (snapCGHguide.pdf), > below is the code that produced the error, object class and sessionInfo. > Maybe you forgot to copy/paste? + seth
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Hi Seth, OK, I will try it with devel version of R. I thought I copied the information to my previous email but here it is once again: ###################################################################### ########## R> SegInfo.BioHMM <- runBioHMM(MA.cgh2) sample is 1 Chromosomes: 1 2 Error: segfault from C stack overflow ###################################################################### ########## R> class(MA.cgh2) [1] "SegList" attr(,"package") [1] "snapCGH" ###################################################################### ########## R> dim(MA.cgh2$M) [1] 1967673 10 ###################################################################### ########## R> MA.cgh2 An object of class "SegList" $state NULL $rpred NULL $prob NULL $M.predicted NULL $dispersion NULL $variance NULL $M.observed a b c d e f g [1,] -0.12942320 0.02683309 -0.10259011 0.22068827 0.1938552 0.09126507 0.08812914 [2,] -0.13219905 0.34312167 0.21092262 0.08040469 -0.2627170 -0.05179436 0.28135520 [3,] 0.07700826 -0.01331928 0.06368898 0.12494860 0.1382679 0.20195685 -0.05675671 [4,] 0.14806237 -0.25316790 -0.10510554 0.01550725 0.2686752 0.16356962 -0.38026647 [5,] 0.22431210 -0.39476064 -0.17044853 -0.29215523 0.1026054 -0.06784313 -0.34597137 h i j [1,] 0.06129606 -0.04129405 -0.13255913 [2,] -0.06176647 0.14915615 0.20095051 [3,] -0.04343744 0.02025154 -0.18170531 [4,] -0.12709857 -0.23220410 -0.39577372 [5,] 0.04878927 -0.12165927 -0.05381614 1967668 more rows ... $genes Block GENE_EXPR_OPTION PROBE_ID POSITION Row Column Status ID Chr Position 2 1 BLOCK1 CHR01FS003044249 3044249 266 3118 BLOCK1 CHR01FS003044249 1 3.044249 4 1 BLOCK1 CHR01FS003090598 3090598 454 3038 BLOCK1 CHR01FS003090598 1 3.090598 7 1 BLOCK1 CHR01FS003090918 3090918 109 3793 BLOCK1 CHR01FS003090918 1 3.090918 9 1 BLOCK1 CHR01FS003091098 3091098 14 3674 BLOCK1 CHR01FS003091098 1 3.091098 10 1 BLOCK1 CHR01FS003091218 3091218 1047 3673 BLOCK1 CHR01FS003091218 1 3.091218 1967668 more rows ... $M a b c d e f g [1,] -0.12942320 0.02683309 -0.10259011 0.22068827 0.1938552 0.09126507 0.08812914 [2,] -0.13219905 0.34312167 0.21092262 0.08040469 -0.2627170 -0.05179436 0.28135520 [3,] 0.07700826 -0.01331928 0.06368898 0.12494860 0.1382679 0.20195685 -0.05675671 [4,] 0.14806237 -0.25316790 -0.10510554 0.01550725 0.2686752 0.16356962 -0.38026647 [5,] 0.22431210 -0.39476064 -0.17044853 -0.29215523 0.1026054 -0.06784313 -0.34597137 h i j [1,] 0.06129606 -0.04129405 -0.13255913 [2,] -0.06176647 0.14915615 0.20095051 [3,] -0.04343744 0.02025154 -0.18170531 [4,] -0.12709857 -0.23220410 -0.39577372 [5,] 0.04878927 -0.12165927 -0.05381614 1967668 more rows ... $design [1] 1 1 1 1 1 1 1 1 1 1 ###################################################################### ########## R> sessionInfo() R version 2.10.1 (2009-12-14) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=C [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] splines stats graphics grDevices utils datasets methods base other attached packages: [1] RMySQL_0.7-4 DBI_0.2-5 snapCGH_1.16.0 aCGH_1.22.0 multtest_2.2.0 survival_2.35-8 cluster_1.12.1 [8] GLAD_2.6.0 DNAcopy_1.20.0 tilingArray_1.24.0 pixmap_0.4-10 Biobase_2.6.1 limma_3.2.2 RColorBrewer_1.0-2 loaded via a namespace (and not attached): [1] affy_1.24.2 affyio_1.14.0 annotate_1.24.1 AnnotationDbi_1.8.1 genefilter_1.28.2 grid_2.10.1 lattice_0.18-3 [8] MASS_7.3-5 preprocessCore_1.8.0 RSQLite_0.8-4 strucchange_1.4-0 tools_2.10.1 vsn_3.14.0 xtable_1.5-6 -----Original Message----- From: Seth Falcon <seth@userprimary.net> To: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] snapCGH, runBioHMM, Error: segfault from C stack overflow Date: Mon, 15 Mar 2010 08:30:55 -0700 Hi Robert, On 3/15/10 6:46 AM, Ivanek, Robert wrote: > I tried to run the runBioHMM function on my data (Nimblegen HD 2.1 > Arrays), however I am always getting the error: "Error: segfault from C > stack overflow". You need to provide us with more information so that we can help you. A good start would include: - sessionInfo() - the exact code you are running - more details on the input data. > > What is the reason for that error? Are the data too big? I tried to > split the array according the chromosomes but it did not help. Only > after splitting the data into small pieces the function run > successfully. That does suggest that data size is the issue. Are you able to obtain any details on where the segfault occurs? R-devel includes a fix for an issue in gsub that could cause a stack overflow segfault for long strings. You might try installing latest R-devel, Bioconductor devel packages and see if the problem is reproducible there. > > I preprocessed the data according the snapCGH manual (snapCGHguide.pdf), > below is the code that produced the error, object class and sessionInfo. > Maybe you forgot to copy/paste? + seth _______________________________________________ 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 -- Robert Ivanek Postdoctoral Fellow Schuebeler Group Friedrich Miescher Institute Maulbeerstrasse 66 4058 Basel / Switzerland Office phone: +41 61 697 6100
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Hi Seth, I tried it with a new version of R and BioConductor but I am still getting the same error. Any ideas? Robert R> SegInfo.BioHMM <- runBioHMM(MA.cgh2) sample is 1 Chromosomes: 1 2 Error: segfault from C stack overflow R> class(MA.cgh2) [1] "SegList" attr(,"package") [1] "snapCGH" R> dim(MA.cgh2$M) [1] 1967673 10 R> MA.cgh2 An object of class "SegList" $state NULL $rpred NULL $prob NULL $M.predicted NULL $dispersion NULL $variance NULL $M.observed a b c d e f g [1,] -0.12942320 0.02683309 -0.10259011 0.22068827 0.1938552 0.09126507 0.08812914 [2,] -0.13219905 0.34312167 0.21092262 0.08040469 -0.2627170 -0.05179436 0.28135520 [3,] 0.07700826 -0.01331928 0.06368898 0.12494860 0.1382679 0.20195685 -0.05675671 [4,] 0.14806237 -0.25316790 -0.10510554 0.01550725 0.2686752 0.16356962 -0.38026647 [5,] 0.22431210 -0.39476064 -0.17044853 -0.29215523 0.1026054 -0.06784313 -0.34597137 h i j [1,] 0.06129606 -0.04129405 -0.13255913 [2,] -0.06176647 0.14915615 0.20095051 [3,] -0.04343744 0.02025154 -0.18170531 [4,] -0.12709857 -0.23220410 -0.39577372 [5,] 0.04878927 -0.12165927 -0.05381614 1967668 more rows ... $genes Block GENE_EXPR_OPTION PROBE_ID POSITION Row Column Status ID Chr Position 2 1 BLOCK1 CHR01FS003044249 3044249 266 3118 BLOCK1 CHR01FS003044249 1 3.044249 4 1 BLOCK1 CHR01FS003090598 3090598 454 3038 BLOCK1 CHR01FS003090598 1 3.090598 7 1 BLOCK1 CHR01FS003090918 3090918 109 3793 BLOCK1 CHR01FS003090918 1 3.090918 9 1 BLOCK1 CHR01FS003091098 3091098 14 3674 BLOCK1 CHR01FS003091098 1 3.091098 10 1 BLOCK1 CHR01FS003091218 3091218 1047 3673 BLOCK1 CHR01FS003091218 1 3.091218 1967668 more rows ... $M a b c d e f g [1,] -0.12942320 0.02683309 -0.10259011 0.22068827 0.1938552 0.09126507 0.08812914 [2,] -0.13219905 0.34312167 0.21092262 0.08040469 -0.2627170 -0.05179436 0.28135520 [3,] 0.07700826 -0.01331928 0.06368898 0.12494860 0.1382679 0.20195685 -0.05675671 [4,] 0.14806237 -0.25316790 -0.10510554 0.01550725 0.2686752 0.16356962 -0.38026647 [5,] 0.22431210 -0.39476064 -0.17044853 -0.29215523 0.1026054 -0.06784313 -0.34597137 h i j [1,] 0.06129606 -0.04129405 -0.13255913 [2,] -0.06176647 0.14915615 0.20095051 [3,] -0.04343744 0.02025154 -0.18170531 [4,] -0.12709857 -0.23220410 -0.39577372 [5,] 0.04878927 -0.12165927 -0.05381614 1967668 more rows ... $design [1] 1 1 1 1 1 1 1 1 1 1 R> sessionInfo() R version 2.11.0 Under development (unstable) (2010-03-14 r51276) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=C [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] splines stats graphics grDevices utils datasets methods base other attached packages: [1] RColorBrewer_1.0-2 snapCGH_1.17.1 aCGH_1.23.0 multtest_2.3.2 survival_2.35-8 cluster_1.12.1 GLAD_2.8.4 [8] DNAcopy_1.21.1 tilingArray_1.25.0 pixmap_0.4-10 Biobase_2.7.5 limma_3.3.12 loaded via a namespace (and not attached): [1] affy_1.25.2 affyio_1.15.2 annotate_1.25.1 AnnotationDbi_1.9.4 DBI_0.2-5 genefilter_1.29.6 grid_2.11.0 [8] lattice_0.18-3 MASS_7.3-5 preprocessCore_1.9.0 RSQLite_0.8-4 strucchange_1.4-0 tools_2.11.0 vsn_3.15.1 [15] xtable_1.5-6 -----Original Message----- From: Ivanek, Robert <robert.ivanek@fmi.ch> To: Seth Falcon <seth at="" userprimary.net=""> Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] snapCGH, runBioHMM, Error: segfault from C stack overflow Date: Mon, 15 Mar 2010 17:06:35 +0100 Hi Seth, OK, I will try it with devel version of R. I thought I copied the information to my previous email but here it is once again: ###################################################################### ########## R> SegInfo.BioHMM <- runBioHMM(MA.cgh2) sample is 1 Chromosomes: 1 2 Error: segfault from C stack overflow ###################################################################### ########## R> class(MA.cgh2) [1] "SegList" attr(,"package") [1] "snapCGH" ###################################################################### ########## R> dim(MA.cgh2$M) [1] 1967673 10 ###################################################################### ########## R> MA.cgh2 An object of class "SegList" $state NULL $rpred NULL $prob NULL $M.predicted NULL $dispersion NULL $variance NULL $M.observed a b c d e f g [1,] -0.12942320 0.02683309 -0.10259011 0.22068827 0.1938552 0.09126507 0.08812914 [2,] -0.13219905 0.34312167 0.21092262 0.08040469 -0.2627170 -0.05179436 0.28135520 [3,] 0.07700826 -0.01331928 0.06368898 0.12494860 0.1382679 0.20195685 -0.05675671 [4,] 0.14806237 -0.25316790 -0.10510554 0.01550725 0.2686752 0.16356962 -0.38026647 [5,] 0.22431210 -0.39476064 -0.17044853 -0.29215523 0.1026054 -0.06784313 -0.34597137 h i j [1,] 0.06129606 -0.04129405 -0.13255913 [2,] -0.06176647 0.14915615 0.20095051 [3,] -0.04343744 0.02025154 -0.18170531 [4,] -0.12709857 -0.23220410 -0.39577372 [5,] 0.04878927 -0.12165927 -0.05381614 1967668 more rows ... $genes Block GENE_EXPR_OPTION PROBE_ID POSITION Row Column Status ID Chr Position 2 1 BLOCK1 CHR01FS003044249 3044249 266 3118 BLOCK1 CHR01FS003044249 1 3.044249 4 1 BLOCK1 CHR01FS003090598 3090598 454 3038 BLOCK1 CHR01FS003090598 1 3.090598 7 1 BLOCK1 CHR01FS003090918 3090918 109 3793 BLOCK1 CHR01FS003090918 1 3.090918 9 1 BLOCK1 CHR01FS003091098 3091098 14 3674 BLOCK1 CHR01FS003091098 1 3.091098 10 1 BLOCK1 CHR01FS003091218 3091218 1047 3673 BLOCK1 CHR01FS003091218 1 3.091218 1967668 more rows ... $M a b c d e f g [1,] -0.12942320 0.02683309 -0.10259011 0.22068827 0.1938552 0.09126507 0.08812914 [2,] -0.13219905 0.34312167 0.21092262 0.08040469 -0.2627170 -0.05179436 0.28135520 [3,] 0.07700826 -0.01331928 0.06368898 0.12494860 0.1382679 0.20195685 -0.05675671 [4,] 0.14806237 -0.25316790 -0.10510554 0.01550725 0.2686752 0.16356962 -0.38026647 [5,] 0.22431210 -0.39476064 -0.17044853 -0.29215523 0.1026054 -0.06784313 -0.34597137 h i j [1,] 0.06129606 -0.04129405 -0.13255913 [2,] -0.06176647 0.14915615 0.20095051 [3,] -0.04343744 0.02025154 -0.18170531 [4,] -0.12709857 -0.23220410 -0.39577372 [5,] 0.04878927 -0.12165927 -0.05381614 1967668 more rows ... $design [1] 1 1 1 1 1 1 1 1 1 1 ###################################################################### ########## R> sessionInfo() R version 2.10.1 (2009-12-14) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=C [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] splines stats graphics grDevices utils datasets methods base other attached packages: [1] RMySQL_0.7-4 DBI_0.2-5 snapCGH_1.16.0 aCGH_1.22.0 multtest_2.2.0 survival_2.35-8 cluster_1.12.1 [8] GLAD_2.6.0 DNAcopy_1.20.0 tilingArray_1.24.0 pixmap_0.4-10 Biobase_2.6.1 limma_3.2.2 RColorBrewer_1.0-2 loaded via a namespace (and not attached): [1] affy_1.24.2 affyio_1.14.0 annotate_1.24.1 AnnotationDbi_1.8.1 genefilter_1.28.2 grid_2.10.1 lattice_0.18-3 [8] MASS_7.3-5 preprocessCore_1.8.0 RSQLite_0.8-4 strucchange_1.4-0 tools_2.10.1 vsn_3.14.0 xtable_1.5-6 -----Original Message----- From: Seth Falcon <seth@userprimary.net> To: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] snapCGH, runBioHMM, Error: segfault from C stack overflow Date: Mon, 15 Mar 2010 08:30:55 -0700 Hi Robert, On 3/15/10 6:46 AM, Ivanek, Robert wrote: > I tried to run the runBioHMM function on my data (Nimblegen HD 2.1 > Arrays), however I am always getting the error: "Error: segfault from C > stack overflow". You need to provide us with more information so that we can help you. A good start would include: - sessionInfo() - the exact code you are running - more details on the input data. > > What is the reason for that error? Are the data too big? I tried to > split the array according the chromosomes but it did not help. Only > after splitting the data into small pieces the function run > successfully. That does suggest that data size is the issue. Are you able to obtain any details on where the segfault occurs? R-devel includes a fix for an issue in gsub that could cause a stack overflow segfault for long strings. You might try installing latest R-devel, Bioconductor devel packages and see if the problem is reproducible there. > > I preprocessed the data according the snapCGH manual (snapCGHguide.pdf), > below is the code that produced the error, object class and sessionInfo. > Maybe you forgot to copy/paste? + seth _______________________________________________ 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 -- Robert Ivanek Postdoctoral Fellow Schuebeler Group Friedrich Miescher Institute Maulbeerstrasse 66 4058 Basel / Switzerland Office phone: +41 61 697 6100
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On 3/16/10 3:39 AM, Ivanek, Robert wrote: > Hi Seth, > > I tried it with a new version of R and BioConductor but I am still > getting the same error. > Any ideas? Can you make your MA.cgh2 object available (you could use a service like http://drop.io/) to share an rda file created using save(MA.cgh2, file="MA.cgh2.rda", compress=TRUE). If you send me a URL in private mail, I will see if I can reproduce the issue and investigate further. + seth -- Seth Falcon Bioconductor Core Team | FHCRC
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On 3/16/10 9:15 AM, Seth Falcon wrote: > On 3/16/10 3:39 AM, Ivanek, Robert wrote: >> Hi Seth, >> >> I tried it with a new version of R and BioConductor but I am still >> getting the same error. >> Any ideas? > > Can you make your MA.cgh2 object available (you could use a service like > http://drop.io/) to share an rda file created using save(MA.cgh2, > file="MA.cgh2.rda", compress=TRUE). > > If you send me a URL in private mail, I will see if I can reproduce the > issue and investigate further. A brief update: Robert made a version of the data available and the error is reproducible and seems to be coming from code within the snapCGH package. The package's maintainer has been notified off-list with some additional debugging details. + seth -- Seth Falcon Bioconductor Core Team | FHCRC
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