[R] KEGGSOAP installation error

[Martin Morgan]

On 05/15/2012 03:29 AM, TEOMB84 wrote:
> Hello,
>
> I'm trying to install KEGGSOAP with bioconductor but i'm facing this
> problem:
>
> />  biocLite("KEGGSOAP")

Hi -- ask questions about Bioconductor packages on the Bioconductor 
mailing list.

   http://bioconductor.org/help/mailing-list/

This looks like an error in XML, perhaps your XML package

   biocLite('XML')

and other packages

   biocLite(character())

are out of date?

Martin

> BioC_mirror: http://bioconductor.org
> Using R version 2.15, BiocInstaller version 1.4.4.
> Installing package(s) 'KEGGSOAP'
> trying URL
> 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/KEGGSOAP_1.30.0.tar.gz'
> Content type 'application/x-gzip' length 11324 bytes (11 Kb)
> opened URL
> ==================================================
> downloaded 11 Kb
>
> * installing *source* package ‘KEGGSOAP’ ...
> ** R
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
>
>   *** caught segfault ***
> address 0x500001c4f, 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),     FALSE,
> as.logical(isSchema), as.logical(fullNamespaceInfo),
> as.character(encoding), as.logical(useDotNames), xinclude,     error,
> addFinalizer, PACKAGE = "XML")
>   2: xmlParse(url)
>   3: parseSchemaDoc(fileName)
>   4: processWSDL("http://soap.genome.jp/KEGG.wsdl")
>   5: fun(libname, pkgname)
>   6: doTryCatch(return(expr), name, parentenv, handler)
>   7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
>   8: tryCatchList(expr, classes, parentenv, handlers)
>   9: tryCatch(fun(libname, pkgname), error = identity)
> 10: runHook(".onLoad", env, package.lib, package)
> 11: loadNamespace(package, c(which.lib.loc, lib.loc))
> 12: doTryCatch(return(expr), name, parentenv, handler)
> 13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> 14: tryCatchList(expr, classes, parentenv, handlers)
> 15: tryCatch(expr, error = function(e) {    call<- conditionCall(e)    if
> (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))
> call<- sys.call(-4L)        dcall<- deparse(call)[1L]        prefix<-
> paste("Error 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(dcall, 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(msg[1L]))    if (!silent&&
> identical(getOption("show.error.messages"),         TRUE)) {        cat(msg,
> file = stderr())        .Internal(printDeferredWarnings())    }
> invisible(structure(msg, class = "try-error", condition = e))})
> 16: try({    ns<- loadNamespace(package, c(which.lib.loc, lib.loc))
> dataPath<- file.path(which.lib.loc, package, "data")    env<-
> attachNamespace(ns, pos = pos, dataPath = dataPath,         deps)})
> 17: library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return =
> TRUE)
> 18: withCallingHandlers(expr, packageStartupMessage = function(c)
> invokeRestart("muffleMessage"))
> 19: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib,
> character.only = TRUE, logical.return = TRUE))
> 20: doTryCatch(return(expr), name, parentenv, handler)
> 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> 22: tryCatchList(expr, classes, parentenv, handlers)
> 23: tryCatch(expr, error = function(e) {    call<- conditionCall(e)    if
> (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))
> call<- sys.call(-4L)        dcall<- deparse(call)[1L]        prefix<-
> paste("Error 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(dcall, 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(msg[1L]))    if (!silent&&
> identical(getOption("show.error.messages"),         TRUE)) {        cat(msg,
> file = stderr())        .Internal(printDeferredWarnings())    }
> invisible(structure(msg, class = "try-error", condition = e))})
> 24: try(suppressPackageStartupMessages(library(pkg_name, lib.loc = lib,
> character.only = TRUE, logical.return = TRUE)))
> 25: tools:::.test_load_package("KEGGSOAP", "/usr/local/lib/R/site-library")
> aborting ...
> Segmentation fault/
>
> How can i solve this error?
>
> Thanks in advance,
> Matteo
>
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