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Question: WGCNA crashes R on OSX
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gravatar for bag59
14 months ago by
bag590
bag590 wrote:

I’m an R user with MacOSX Sierra (v10.12.3) and I am encountering R (v3.3.3) crash problems loading a specific Bioconductor package: WGCNA. I'm hoping someone here might have encountered/fixed the same issue somehow . . .
Basically the package installs fine, but loading the library causes immediate crash with the following error output:
> library("WGCNA")
Loading required package: dynamicTreeCut
Loading required package: fastcluster

Attaching package: ‘fastcluster’

The following object is masked from ‘package:stats’:

   hclust


*** caught segfault ***
address 0x18, cause 'memory not mapped'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
6: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
7: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
8: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
9: loadNamespace(package, lib.loc)
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: 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))})
14: try({    attr(package, "LibPath") <- which.lib.loc    ns <-
loadNamespace(package, lib.loc)    env <- attachNamespace(ns, pos = pos,
deps)})
15: library("WGCNA”)

Is anyone here perhaps familiar with this issue or something similar? Might this be an actual issue with the installation of hclust (above)?
Any suggestions would be much appreciated.

Thanks very much,

Billie

ADD COMMENTlink written 14 months ago by bag590

Neither WGCNA nor fastcluster (not hclust - that's a function within fastcluster) are Bioconductor packages...  so this may not be the right forum.

ADD REPLYlink written 14 months ago by Peter Langfelder1.5k

Where is a good forum/place to ask about WGCNA? I have seen many questions and answers here on support.bioconductor.

ADD REPLYlink written 14 months ago by Lluís R330

My guess is that it is not WGCNA that is segfaulting, but one of it's dependencies. You could try to 'bisect' this by loading each of the WGCNA dependencies in turn, and then loading each of the dependencies of the dependency that crashes, etc.

> packageDescription("WGCNA")[c("Depends", "Imports")]
$Depends
[1] "R (>= 3.0), dynamicTreeCut (>= 1.62), fastcluster"

$Imports
[1] "stats, grDevices, utils, matrixStats (>= 0.8.1), Hmisc,\nimpute, splines, foreach, doParallel, preprocessCore, survival,\nparallel, GO.db, AnnotationDbi"

Also, BiocInstaller::biocValid() might indicate paackages (CRAN or Bioconductor) that are not consistent with current releases.

ADD REPLYlink written 14 months ago by Martin Morgan ♦♦ 21k
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