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@prototype class(value) <- ClassDef@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.delho...@embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel