Hello,
I try to use KEGGprofile on Unix Server.
Basically, I run this script : http://www.bioconductor.org/packages/release/bioc/vignettes/KEGGprofile/inst/doc/KEGGprofile.R
at the last line of this script : the most interesting line because it draw the map pathway with information.
temp<-plot_pathway(pho_expr,type="bg",bg_col=col,text_col="white",magnify=1.2,species='hsa',database_dir=system.file("extdata",package="KEGGprofile"),pathway_id="04110")
PROBLEM: I have this message and forced the exit to R
*** caught segfault ***
address 0x700001c4f, 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(paste(database_dir, "/", species, pathway_id, ".xml", sep = ""), useInternalNodes = TRUE)
3: parse_XMLfile(pathway_id = pathway_id, species = species, database_dir = database_dir)
4: plot_pathway(pho_expr, type = "bg", bg_col = col, text_col = "white", magnify = 1.2, species = "hsa", database_dir = system.file("extdata", package = "KEGGprofile"), pathway_id = "04110")
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:
--------------------------------------- SessionInfo() R version 3.1.1 (2014-07-10) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods [7] base other attached packages: [1] KEGGprofile_1.8.0 RSQLite_1.0.0 DBI_0.3.1 loaded via a namespace (and not attached): [1] AnnotationDbi_1.28.1 Biobase_2.26.0 BiocGenerics_0.12.0 [4] biomaRt_2.22.0 Biostrings_2.34.0 GenomeInfoDb_1.2.2 [7] httr_0.5 IRanges_2.0.0 KEGG.db_3.0.0 [10] KEGGREST_1.6.0 parallel_3.1.1 png_0.1-7 [13] RCurl_1.95-4.3 S4Vectors_0.4.0 stats4_3.1.1 [16] stringr_0.6.2 TeachingDemos_2.9 XML_3.98-1.1 [19] XVector_0.6.0 zlibbioc_1.12.0
Thanks for your help
greg
