[BioC] BiocParallel fatal error

[Martin Morgan]

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and making sure that no packages are out-of-date or too new for your installation.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)
>
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