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Question: BiocParallel fatal error
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4.1 years ago by
Guest User12k
Guest User12k wrote:
Hi, I am trying to run the package SimRAD which has a bunch of dependencies - one of which required me to update to R 3.1. I'm now getting a fatal error when trying to load BiocParallel and was hoping someone might be able to direct me how to fix this. Thanks, Rebecca -- output of sessionInfo(): > library(SimRAD) Loading required package: Biostrings Loading required package: BiocGenerics Loading required package: parallel Attaching package: ???BiocGenerics??? The following objects are masked from ???package:parallel???: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from ???package:stats???: xtabs The following objects are masked from ???package:base???: anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist Loading required package: IRanges Loading required package: XVector Loading required package: ShortRead Loading required package: BiocParallel *** caught segfault *** address 0x18, cause 'memory not mapped' Traceback: 1: dyn.load(file, DLLpath = DLLpath, ...) 2: library.dynam(lib, package, package.lib) 3: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 4: asNamespace(ns) 5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 6: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 7: asNamespace(ns) 8: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 9: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 10: asNamespace(ns) 11: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 12: loadNamespace(package, c(which.lib.loc, lib.loc)) 13: doTryCatch(return(expr), name, parentenv, handler) 14: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15: tryCatchList(expr, classes, parentenv, handlers) 16: 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))}) 17: try({ ns <- loadNamespace(package, c(which.lib.loc, lib.loc)) env <- attachNamespace(ns, pos = pos, deps)}) 18: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) 19: .getRequiredPackages2(pkgInfo, quietly = quietly) 20: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) 21: .getRequiredPackages2(pkgInfo, quietly = quietly) 22: library(SimRAD) -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink modified 4.1 years ago by Martin Morgan ♦♦ 21k • written 4.1 years ago by Guest User12k
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4.1 years ago by
Martin Morgan ♦♦ 21k
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Martin Morgan ♦♦ 21k wrote:
On 05/26/2014 07:44 PM, Rebecca [guest] wrote: > Hi, > > I am trying to run the package SimRAD which has a bunch of dependencies - one of which required me to update to R 3.1. I'm now getting a fatal error when trying to load BiocParallel and was hoping someone might be able to direct me how to fix this. > Hi Rebecca -- segfaults are caused by problems in C or other compiled code, but BiocParallel does not have any C code -- it's likely from one of the dependencies or other packages being loaded. I'd try first to make sure that your installation is approximately correct, running the commands source("http://bioconductor.org/biocLite.R") BiocInstaller::biocValid() and making sure that no packages are out-of-date or too new for your installation. The most likely candidates are shared libraries loaded by BiocParallel's dependencies, including BBmisc, RSQLite, digest, Rcpp, and plyr; you could try loading each of these in turn. What is your operating system? i.e., provide the output of sessionInfo() (mine is below). If you're on Linux or Mac, from the command line you can likely $ R -d gdb You'll be in a debugger; start R with (gdb) run and then > library(BiocParallel) when the segfault occurs you'll be back in the debugger, and the output of (gdb) where would be helpful Hope that helps to track down the problem Martin > sessionInfo() R version 3.1.0 Patched (2014-05-21 r65707) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] SimRAD_0.94 ShortRead_1.23.11 GenomicAlignments_1.1.11 [4] Rsamtools_1.17.16 GenomicRanges_1.17.16 GenomeInfoDb_1.1.5 [7] BiocParallel_0.7.1 Biostrings_2.33.9 XVector_0.5.6 [10] IRanges_1.99.15 S4Vectors_0.0.6 BiocGenerics_0.11.2 [13] BiocInstaller_1.15.5 loaded via a namespace (and not attached): [1] BatchJobs_1.2 BBmisc_1.6 Biobase_2.25.0 [4] bitops_1.0-6 brew_1.0-6 codetools_0.2-8 [7] DBI_0.2-7 digest_0.6.4 fail_1.2 [10] foreach_1.4.2 grid_3.1.0 hwriter_1.3 [13] iterators_1.0.7 lattice_0.20-29 latticeExtra_0.6-26 [16] plyr_1.8.1 RColorBrewer_1.0-5 Rcpp_0.11.1 [19] RSQLite_0.11.4 sendmailR_1.1-2 stats4_3.1.0 [22] stringr_0.6.2 tools_3.1.0 zlibbioc_1.11.1 > Thanks, > Rebecca > > -- output of sessionInfo(): > >> library(SimRAD) > Loading required package: Biostrings > Loading required package: BiocGenerics > Loading required package: parallel > > Attaching package: ???BiocGenerics??? > > The following objects are masked from ???package:parallel???: > > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, > parSapplyLB > > The following object is masked from ???package:stats???: > > xtabs > > The following objects are masked from ???package:base???: > > anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, > mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, > union, unique, unlist > > Loading required package: IRanges > Loading required package: XVector > Loading required package: ShortRead > Loading required package: BiocParallel > > *** caught segfault *** > address 0x18, cause 'memory not mapped' > > Traceback: > 1: dyn.load(file, DLLpath = DLLpath, ...) > 2: library.dynam(lib, package, package.lib) > 3: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) > 4: asNamespace(ns) > 5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) > 6: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) > 7: asNamespace(ns) > 8: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) > 9: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) > 10: asNamespace(ns) > 11: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) > 12: loadNamespace(package, c(which.lib.loc, lib.loc)) > 13: doTryCatch(return(expr), name, parentenv, handler) > 14: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > 15: tryCatchList(expr, classes, parentenv, handlers) > 16: 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))}) > 17: try({ ns <- loadNamespace(package, c(which.lib.loc, lib.loc)) env <- attachNamespace(ns, pos = pos, deps)}) > 18: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) > 19: .getRequiredPackages2(pkgInfo, quietly = quietly) > 20: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) > 21: .getRequiredPackages2(pkgInfo, quietly = quietly) > 22: library(SimRAD) > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
ADD COMMENTlink written 4.1 years ago by Martin Morgan ♦♦ 21k
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