[BioC] snapCGH, runBioHMM, Error: segfault from C stack overflow

[Ivanek, Robert]

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