snapCGH, runBioHMM, Error: segfault from C stack overflow
1
0
Entering edit mode
@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
ADD COMMENT •
0
Entering edit mode
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
ADD COMMENT •
0
Entering edit mode
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
ADD REPLY •
0
Entering edit mode
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
ADD REPLY •
0
Entering edit mode
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
ADD REPLY •
0
Entering edit mode
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
ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 885 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6