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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KEGGSOAP installation error
3 messages · TEOMB84, 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 -- View this message in context: http://r.789695.n4.nabble.com/KEGGSOAP-installation-error-tp4630053.html Sent from the R help mailing list archive at Nabble.com.
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5 days later
Hi Martin, I've already checked XML library in R but it seems there's no issues regarding it. I've also tried to update all installed R packages and to install several libraries related to libxml2 library in ubuntu, but the problem is still there. I will try to post the same problem in the bioconductor mailing list. Thanks, Matteo -- View this message in context: http://r.789695.n4.nabble.com/KEGGSOAP-installation-error-tp4630053p4630660.html Sent from the R help mailing list archive at Nabble.com.