[BioC] snapCGH, runBioHMM, Error: segfault from C stack overflow
Ivanek, Robert
robert.ivanek at fmi.ch
Tue Mar 16 11:39:48 CET 2010
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 ...
$design
[1] 1 1 1 1 1 1 1 1 1 1
R> sessionInfo()
R version 2.11.0 Under development (unstable) (2010-03-14 r51276)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
LC_MONETARY=C
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] splines stats graphics grDevices utils datasets methods
base
other attached packages:
[1] RColorBrewer_1.0-2 snapCGH_1.17.1 aCGH_1.23.0
multtest_2.3.2 survival_2.35-8 cluster_1.12.1
GLAD_2.8.4
[8] DNAcopy_1.21.1 tilingArray_1.25.0 pixmap_0.4-10
Biobase_2.7.5 limma_3.3.12
loaded via a namespace (and not attached):
[1] affy_1.25.2 affyio_1.15.2 annotate_1.25.1
AnnotationDbi_1.9.4 DBI_0.2-5 genefilter_1.29.6
grid_2.11.0
[8] lattice_0.18-3 MASS_7.3-5 preprocessCore_1.9.0
RSQLite_0.8-4 strucchange_1.4-0 tools_2.11.0
vsn_3.15.1
[15] xtable_1.5-6
-----Original Message-----
From: Ivanek, Robert <robert.ivanek at fmi.ch>
To: Seth Falcon <seth at userprimary.net>
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] snapCGH, runBioHMM, Error: segfault from C stack
overflow
Date: Mon, 15 Mar 2010 17:06:35 +0100
Hi Seth,
OK, I will try it with devel version of R.
I thought I copied the information to my previous email but here it is
once again:
################################################################################
R> SegInfo.BioHMM <- runBioHMM(MA.cgh2)
sample is 1 Chromosomes: 1 2 Error: segfault from C stack
overflow
################################################################################
R> class(MA.cgh2)
[1] "SegList"
attr(,"package")
[1] "snapCGH"
################################################################################
R> dim(MA.cgh2$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 at 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
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Robert Ivanek
Postdoctoral Fellow Schuebeler Group
Friedrich Miescher Institute
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