Question: rGADEM caught segfault
gravatar for vgms3311
4 months ago by
vgms33110 wrote:


I have the following problem running rGADEM on my fasta file.

Any advice would be greatly appreciated

I tried this code on Bio-Linux and Mac OS X Elcapitan.

These sessioninfo() follows the command lines.

Best regards,





> T_ac.seqs <- readDNAStringSet("chippeakanno/T_ac.fa", "fasta")

> T_ac.motif <- GADEM(T_ac.seqs, verbose = 1, genome = Hsapiens)

*** Start C Programm ***


 *** caught segfault ***

address 0x1509e6eb4, cause 'memory not mapped'



 1: .Call("GADEM_Analysis", sequenceFasta, Lengthfasta, accession,     as.logical(verbose), numWordGroup, numTop3mer, numTop4mer,     numTop5mer, numGeneration, populationSize, pValue, eValue,     extTrim, minSpaceWidth, maxSpaceWidth, useChIPscore, numEM,     fEM, widthWt, fullScan, slideWinPWM, stopCriterion, numBackgSets,     weightType, bFileName, Spwm, minSites, maskR, nmotifs)

 2: GADEM(T_ac.seqs, verbose = 1, genome = Hsapiens)


Possible actions:

1: abort (with core dump, if enabled)

2: normal R exit

3: exit R without saving workspace

4: exit R saving workspace





> sessionInfo()

R version 3.2.0 (2015-04-16)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: Ubuntu 14.04.5 LTS



 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C             

 [3] LC_TIME=ja_JP.UTF-8        LC_COLLATE=en_US.UTF-8   


 [7] LC_PAPER=ja_JP.UTF-8       LC_NAME=C                

 [9] LC_ADDRESS=C               LC_TELEPHONE=C           



attached base packages:

 [1] grid      stats4    parallel  stats     graphics  grDevices utils   

 [8] datasets  methods   base    


other attached packages:

 [1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 rGADEM_2.16.0                    

 [3] seqLogo_1.34.0                    BSgenome_1.36.3                 

 [5] rtracklayer_1.28.10               GenomicRanges_1.20.8            

 [7] GenomeInfoDb_1.4.3                Biostrings_2.36.4               

 [9] XVector_0.8.0                     IRanges_2.2.9                   

[11] S4Vectors_0.6.6                   BiocGenerics_0.14.0             


loaded via a namespace (and not attached):

 [1] XML_3.98-1.2            Rsamtools_1.20.5        bitops_1.0-6          

 [4] GenomicAlignments_1.4.2 futile.options_1.0.0    zlibbioc_1.14.0       

 [7] futile.logger_1.4.3     lambda.r_1.1.9          BiocParallel_1.2.22   

[10] tools_3.2.0             RCurl_1.95-4.6




> sessionInfo()

R version 3.4.1 (2017-06-30)

Platform: x86_64-apple-darwin15.6.0 (64-bit)

Running under: OS X El Capitan 10.11.6


Matrix products: default

BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib

LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib



[1] ja_JP.UTF-8/ja_JP.UTF-8/ja_JP.UTF-8/C/ja_JP.UTF-8/ja_JP.UTF-8


attached base packages:

 [1] grid      stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base    


other attached packages:

 [1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 rGADEM_2.24.0                     seqLogo_1.42.0                    BSgenome_1.44.1                 

 [5] rtracklayer_1.36.4                GenomicRanges_1.28.4              GenomeInfoDb_1.12.2               Biostrings_2.44.2               

 [9] XVector_0.16.0                    IRanges_2.10.2                    S4Vectors_0.14.3                  BiocGenerics_0.22.0             


loaded via a namespace (and not attached):

 [1] zlibbioc_1.22.0            GenomicAlignments_1.12.2   BiocParallel_1.10.1        lattice_0.20-35            tools_3.4.1              

 [6] SummarizedExperiment_1.6.3 Biobase_2.36.2             matrixStats_0.52.2         Matrix_1.2-11              GenomeInfoDbData_0.99.0  

[11] bitops_1.0-6               RCurl_1.95-4.8             DelayedArray_0.2.7         compiler_3.4.1             Rsamtools_1.28.0         

[16] XML_3.98-1.9

ADD COMMENTlink modified 4 months ago • written 4 months ago by vgms33110
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