run KEGGprofile sofware on UNIX server
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@gregory-voisin-945
Last seen 6.3 years ago
Canada

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

 

keggprofile UNIX error exit • 618 views
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