[Bioc-devel] memory not mapped error when installing Bioc 2.13 packages on R 3.0.2
Nicolas Delhomme
delhomme at embl.de
Sat Sep 28 14:19:53 CEST 2013
Hej all!
When trying to install the following packages c("GO.db","org.Hs.eg.db","PFAM.db","AnnotationForge","Category","DESeq2","ReportingTools","rtracklayer","GenomicFeatures","biovizBase","QuasR","VariantAnnotation","gmapR","VariantTools") from Bioc 2.13 on R3.0.2, I'm getting a memory not mapped error.
Below the trace from VariantTools:
* installing *source* package ‘VariantTools’ ...
** R
** inst
** preparing package for lazy loading
Warning: subclass "GIntervalTree" of class "GenomicRanges" is not local and cannot be updated for new inheritance information; consider setClassUnion()
*** caught segfault ***
address 0xcb8, cause 'memory not mapped'
Traceback:
1: .Call("R_curl_easy_init", PACKAGE = "RCurl")
2: getCurlHandle(followLocation = TRUE, ...)
3: .local(.Object, ...)
4: initialize(value, ...)
5: initialize(value, ...)
6: new(ClassDef)
7: doTryCatch(return(expr), name, parentenv, handler)
8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: tryCatchList(expr, classes, parentenv, handlers)
10: tryCatch(new(ClassDef), error = function(e) { value <- ClassDef at prototype class(value) <- ClassDef at className value})
11: tryNew(el(props, i), where)
12: reconcilePropertiesAndPrototype(name, slots, prototype, superClasses, where)
13: makeClassRepresentation(Class, properties, superClasses, prototype, package, validity, access, version, sealed, where = where)
14: setClass("UCSCTableQuery", representation(session = "UCSCSession", track = "characterORNULL", table = "characterORNULL", range = "GRanges", outputType = "characterORNULL", NAMES = "characterORNULL", intersectTrack = "characterORNULL"))
15: eval(expr, envir, enclos)
16: eval(i, envir)
17: sys.source(codeFile, env, keep.source = keep.source)
18: doTryCatch(return(expr), name, parentenv, handler)
19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
20: tryCatchList(expr, classes, parentenv, handlers)
21: 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))})
22: try(sys.source(codeFile, env, keep.source = keep.source))
23: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
24: asNamespace(ns)
25: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
26: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
27: asNamespace(ns)
28: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
29: loadNamespace(package, c(which.lib.loc, lib.loc))
30: doTryCatch(return(expr), name, parentenv, handler)
31: tryCatchOne(expr, names, parentenv, handlers[[1L]])
32: tryCatchList(expr, classes, parentenv, handlers)
33: 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))})
34: try({ ns <- loadNamespace(package, c(which.lib.loc, lib.loc)) env <- attachNamespace(ns, pos = pos, deps)})
35: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc)
36: .getRequiredPackages2(pkgInfo, quietly, lib.loc, useImports)
37: .getRequiredPackages(quietly = TRUE)
38: withCallingHandlers(expr, packageStartupMessage = function(c) invokeRestart("muffleMessage"))
39: suppressPackageStartupMessages(.getRequiredPackages(quietly = TRUE))
40: doTryCatch(return(expr), name, parentenv, handler)
41: tryCatchOne(expr, names, parentenv, handlers[[1L]])
42: tryCatchList(expr, classes, parentenv, handlers)
43: 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))})
44: try({ suppressPackageStartupMessages(.getRequiredPackages(quietly = TRUE)) makeLazyLoading(pkg_name, lib, keep.source = keep.source)})
45: do_install_source(pkg_name, instdir, pkg, desc)
46: do_install(pkg)
47: tools:::.install_packages()
aborting ...
/Users/delhomme/opt/R-3.0.2_SRC/../R-3.0.2/R.framework/Resources/bin/INSTALL: line 34: 63387 Done echo 'tools:::.install_packages()'
63388 Segmentation fault | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args}
The downloaded source packages are in
‘/private/var/folders/Bj/BjnLEfPYGO0TRUgXtHmcOk+++TQ/-Tmp-/RtmpGsioBO/downloaded_packages’
Any idea what could be the reason for this? I'm on MacOSX, but I use MacPort, so it's basically a linux sort of installation.
My sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.11.4
Thanks,
Nico
---------------------------------------------------------------
Nicolas Delhomme
Genome Biology Computational Support
European Molecular Biology Laboratory
Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
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