[BioC] bug report in pathview
Martin Morgan
mtmorgan at fhcrc.org
Fri Sep 6 18:16:24 CEST 2013
On 09/05/2013 06:44 PM, shang [guest] wrote:
>
> there is a segment fault when using the pathview package data analysis in redhat el 5 64bit server, the error report as,
> -------------------------------------------------------
> Only KEGG ortholog gene ID is supported, make sure it looks like "K01488"!
>
> *** caught segfault ***
> address 0x3300000000, cause 'memory not mapped'
>
> Traceback:
> 1: .Call("RS_XML_ParseTree", as.character(file), handlers, as.logical(ignoreBla nks), as.logical(replaceEntities), as.logical(asText), as.logical(trim), as.logical(validate), as.logical(getDTD), as.logical(isURL), as.logical(add AttributeNamespaces), as.logical(useInternalNodes), as.logical(isHTML), as.l ogical(isSchema), as.logical(fullNamespaceInfo), as.character(encoding), as.
> logical(useDotNames), xinclude, error, addFinalizer, as.integer(options), as .logical(parentFirst), PACKAGE = "XML")
> 2: xmlTreeParse(file, getDTD = FALSE)
this looks like a bug in the XML package. Is there a way that you can reduce
your script (I don't think pathview.R is from the package?) to a reproducible
example that others can run?
Martin
> 3: parseKGML2(file)
> 4: parseKGML2Graph2(xml.file, genes = F, expand = expand.node, split.group = sp lit.group)
> 5: doTryCatch(return(expr), name, parentenv, handler)
> 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> 7: tryCatchList(expr, classes, parentenv, handlers)
> 8: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is. null(call)) { if (identical(call[[1L]], quote(doTryCatch))) c all <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("E rror in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") +
> nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcal l, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(ms g[1L])) if (!silent && identical(getOption("show.error.messages"), TR
> UE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings() ) } invisible(structure(msg, class = "try-error", condition = e))})
> 9: try(parseKGML2Graph2(xml.file, genes = F, expand = expand.node, split.gr oup = split.group), silent = T)
> 10: pathview(gene.data = d[, 1], pathway.id = "04075", species = "ko", kegg. native = FALSE)
> 11: eval(expr, envir, enclos)
> 12: eval(ei, envir)
> 13: withVisible(eval(ei, envir))
> 14: source("pathview.R")
> --------------------------------------------------------
> is any tell me how to cover it, we have test it on the lastest version of R 3.0.1-patched 2013-09-06 version and I have restall it ad hoc as well as update from 2.15
> all version report the same bug, very thanks
>
> -- output of sessionInfo():
>
> version 3.0.1 Patched (2013-09-05 r63850)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=zh_CN.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] parallel stats graphics grDevices utils datasets methods
> [8] base
>
> other attached packages:
> [1] pathview_1.1.6 org.Hs.eg.db_2.9.0 RSQLite_0.11.4
> [4] DBI_0.2-7 AnnotationDbi_1.23.18 Biobase_2.21.6
> [7] BiocGenerics_0.7.4 KEGGgraph_1.17.0 graph_1.39.3
> [10] XML_3.98-1.1
>
> loaded via a namespace (and not attached):
> [1] Biostrings_2.29.15 digest_0.6.3 grid_3.0.1 httr_0.2
> [5] IRanges_1.19.29 KEGGREST_1.1.1 png_0.1-6 RCurl_1.95-4.1
> [9] Rgraphviz_2.5.4 stats4_3.0.1 stringr_0.6.2 tools_3.0.1
> [13] XVector_0.1.0
>
>
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