[R] KEGGSOAP installation error

TEOMB84 matteo.barcella at unimi.it
Tue May 15 12:29:53 CEST 2012


Hello,

I'm trying to install KEGGSOAP with bioconductor but i'm facing this
problem:

/> biocLite("KEGGSOAP")
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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