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@guest-user-4897
Last seen 9.6 years ago
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)
--
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