[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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