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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