Closed YiweiNiu closed 5 months 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
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:
Here were the session info:
Do you know how to solve this? Thanks! Yiwei Niu