Simon-Coetzee / motifBreakR

A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.
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caught segfault when using plotMB #9

Closed YiweiNiu closed 5 months ago

YiweiNiu commented 7 years ago

Hi,

I'm trying with the doc (http://www.bioconductor.org/packages/release/bioc/vignettes/motifbreakR/inst/doc/motifbreakR-vignette.html), but I got error when using plotMB. Here were the error messages:

 *** caught segfault ***
address 0x3900000000, cause 'memory not mapped'

Traceback:
 1: .Call("RS_XML_ParseTree", as.character(file), handlers, as.logical(ignoreBlanks),     as.logical(replaceEntities), as.logical(asText), as.logical(trim),     as.logical(validate), as.logical(getDTD), as.logical(isURL),     as.logical(addAttributeNamespaces), as.logical(useInternalNodes),     as.logical(isHTML), as.logical(isSchema), as.logical(fullNamespaceInfo),     as.character(encoding), as.logical(useDotNames), xinclude,     error, addFinalizer, as.integer(options), as.logical(parentFirst),     PACKAGE = "XML")
 2: xmlTreeParse(rgmlFile, ...)
 3: readPicture(paste(psfilename, ".xml", sep = ""))
 4: coloredSymbols(ncha, font, colset, rname, fontsize)
 5: motifStack::plotMotifLogo(pfms[[n - i + 1]], motifName = pfms[[n -     i + 1]]@name, p = rep(0.25, 4), xlab = NA)
 6: plotMotifLogoStack.2(pwms, ncex = 1)
 7: plotMB(results = res, rsid = "chr11:64125443:C:T", effect = "strong")

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

Here were the session info:

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.6 (Final)

locale:
 [1] LC_CTYPE=zh_CN.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=zh_CN.UTF-8        LC_COLLATE=zh_CN.UTF-8    
 [5] LC_MONETARY=zh_CN.UTF-8    LC_MESSAGES=zh_CN.UTF-8   
 [7] LC_PAPER=zh_CN.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
 [1] stats4    parallel  grid      stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg19_1.4.0      
 [2] SNPlocs.Hsapiens.dbSNP142.GRCh37_0.99.5
 [3] BSgenome_1.42.0                        
 [4] rtracklayer_1.34.2                     
 [5] GenomicRanges_1.26.4                   
 [6] GenomeInfoDb_1.10.3                    
 [7] motifbreakR_1.4.0                      
 [8] MotifDb_1.16.1                         
 [9] Biostrings_2.42.1                      
[10] XVector_0.14.1                         
[11] IRanges_2.8.2                          
[12] S4Vectors_0.12.2                       
[13] BiocGenerics_0.20.0                    

loaded via a namespace (and not attached):
 [1] httr_1.3.1                    Biobase_2.34.0               
 [3] motifStack_1.18.0             bit64_0.9-7                  
 [5] AnnotationHub_2.6.5           splines_3.3.2                
 [7] shiny_1.0.5                   Formula_1.2-2                
 [9] interactiveDisplayBase_1.12.0 latticeExtra_0.6-28          
[11] blob_1.1.0                    Rsamtools_1.26.2             
[13] yaml_2.1.14                   rGADEM_2.22.0                
[15] RSQLite_2.0                   backports_1.1.0              
[17] lattice_0.20-35               biovizBase_1.22.0            
[19] digest_0.6.12                 RColorBrewer_1.1-2           
[21] checkmate_1.8.3               colorspace_1.3-2             
[23] httpuv_1.3.5                  htmltools_0.3.6              
[25] Matrix_1.2-11                 plyr_1.8.4                   
[27] XML_3.98-1.9                  biomaRt_2.30.0               
[29] zlibbioc_1.20.0               xtable_1.8-2                 
[31] scales_0.5.0                  BiocParallel_1.8.2           
[33] htmlTable_1.9                 tibble_1.3.4                 
[35] ggplot2_2.2.1                 SummarizedExperiment_1.4.0   
[37] GenomicFeatures_1.26.4        TFMPvalue_0.0.6              
[39] nnet_7.3-12                   Gviz_1.18.2                  
[41] lazyeval_0.2.0                mime_0.5                     
[43] survival_2.41-3               magrittr_1.5                 
[45] memoise_1.1.0                 foreign_0.8-69               
[47] BiocInstaller_1.24.0          grImport_0.9-0               
[49] tools_3.3.2                   data.table_1.10.4            
[51] matrixStats_0.52.2            stringr_1.2.0                
[53] munsell_0.4.3                 cluster_2.0.6                
[55] AnnotationDbi_1.36.2          ensembldb_1.6.2              
[57] compiler_3.3.2                ade4_1.7-8                   
[59] rlang_0.1.2                   RCurl_1.95-4.8               
[61] dichromat_2.0-0               VariantAnnotation_1.20.3     
[63] htmlwidgets_0.9               MotIV_1.30.0                 
[65] bitops_1.0-6                  base64enc_0.1-3              
[67] gtable_0.2.0                  DBI_0.7                      
[69] R6_2.2.2                      GenomicAlignments_1.10.1     
[71] gridExtra_2.2.1               knitr_1.17                   
[73] seqLogo_1.40.0                bit_1.1-12                   
[75] Hmisc_4.0-3                   stringi_1.1.5                
[77] Rcpp_0.12.12                  rpart_4.1-11                 
[79] acepack_1.4.1

Do you know how to solve this? Thanks! Yiwei Niu