[Bioc-devel] memory not mapped error when installing Bioc 2.13 packages on R 3.0.2
Martin Morgan
mtmorgan at fhcrc.org
Sat Sep 28 18:03:24 CEST 2013
On 09/28/2013 05:19 AM, Nicolas Delhomme wrote:
> 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")
Not a full answer, but the problem seems to come from RCurl, which is called when...
> 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"))
...the initialize method of UCSCTableQuery in rtracklayer.
I'd try
library(BiocInstaller)
biocValid()
to spot any version mis-matches, then start at the bottom with a clean install
of RCurl and then rtracklayer.
Martin
> 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
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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