Billie,
I'm not having issues loading WGCNA on my iMac. macOS Sierra 10.12.4 (16E195).
Entire session below:
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> library(WGCNA)
Loading required package: dynamicTreeCut
Loading required package: fastcluster
Attaching package: ‘fastcluster’
The following object is masked from ‘package:stats’:
hclust
==========================================================================
*
* Package WGCNA 1.51 loaded.
*
* Important note: It appears that your system supports multi-threading,
* but it is not enabled within WGCNA in R.
* To allow multi-threading within WGCNA with all available cores, use
*
* allowWGCNAThreads()
*
* within R. Use disableWGCNAThreads() to disable threading if necessary.
* Alternatively, set the following environment variable on your system:
*
* ALLOW_WGCNA_THREADS=<number_of_processors>
*
* for example
*
* ALLOW_WGCNA_THREADS=8
*
* To set the environment variable in linux bash shell, type
*
* export ALLOW_WGCNA_THREADS=8
*
* before running R. Other operating systems or shells will
* have a similar command to achieve the same aim.
*
==========================================================================
Attaching package: ‘WGCNA’
The following object is masked from ‘package:stats’:
cor
> devtools::session_info()
Session info
----------------------------------------------------------------------
setting value
version R version 3.3.3 (2017-03-06)
system x86_64, darwin13.4.0
ui AQUA
language (EN)
collate en_US.UTF-8
tz America/Los_Angeles
date 2017-04-11
Packages
--------------------------------------------------------------------------
package * version date source
acepack 1.3-3.3 2014-11-24 CRAN (R 3.3.0)
AnnotationDbi 1.34.2 2016-05-16 Bioconductor
Biobase 2.32.0 2016-05-04 Bioconductor
BiocGenerics 0.18.0 2016-05-04 Bioconductor
cluster 2.0.5 2016-10-08 CRAN (R 3.3.3)
codetools 0.2-15 2016-10-05 CRAN (R 3.3.3)
colorspace 1.3-2 2016-12-14 cran (@1.3-2)
data.table 1.9.7 2016-05-10 Github (Rdatatable/data.table@be96b6f)
DBI 0.6-1 2017-04-01 cran (@0.6-1)
devtools 1.12.0.9000 2017-03-24 Github (hadley/devtools@d8ab190)
digest 0.6.12 2017-01-27 cran (@0.6.12)
doParallel 1.0.10 2015-10-14 CRAN (R 3.3.0)
dynamicTreeCut * 1.63-1 2016-03-11 CRAN (R 3.3.0)
fastcluster * 1.1.20 2016-03-31 CRAN (R 3.3.0)
foreach 1.4.3 2015-10-13 CRAN (R 3.3.0)
foreign 0.8-67 2016-09-13 CRAN (R 3.3.3)
Formula 1.2-1 2015-04-07 CRAN (R 3.3.0)
ggplot2 2.2.1.9000 2017-04-10 Github (tidyverse/ggplot2@f4398b6)
GO.db 3.3.0 2016-05-19 Bioconductor
gridExtra 2.2.1 2016-02-29 CRAN (R 3.3.0)
gtable 0.2.0 2016-02-26 CRAN (R 3.3.0)
Hmisc 3.17-4 2016-05-02 CRAN (R 3.3.0)
impute 1.46.0 2016-05-04 Bioconductor
IRanges 2.6.0 2016-05-04 Bioconductor
iterators 1.0.8 2015-10-13 CRAN (R 3.3.0)
lattice 0.20-34 2016-09-06 CRAN (R 3.3.3)
latticeExtra 0.6-28 2016-02-09 CRAN (R 3.3.0)
lazyeval 0.2.0 2016-06-12 CRAN (R 3.3.0)
Matrix 1.2-8 2017-01-20 CRAN (R 3.3.3)
matrixStats 0.50.2 2016-04-24 CRAN (R 3.3.0)
memoise 1.0.0 2016-01-29 CRAN (R 3.3.0)
munsell 0.4.3 2016-02-13 CRAN (R 3.3.0)
nnet 7.3-12 2016-02-02 CRAN (R 3.3.3)
pkgbuild 0.0.0.9000 2017-03-24 Github (r-pkgs/pkgbuild@5ed87aa)
pkgload 0.0.0.9000 2017-03-24 Github (r-pkgs/pkgload@3a96cf2)
plyr 1.8.4 2016-06-08 CRAN (R 3.3.0)
preprocessCore 1.34.0 2016-05-04 Bioconductor
RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.3.0)
Rcpp 0.12.10 2017-03-19 cran (@0.12.10)
rpart 4.1-10 2015-06-29 CRAN (R 3.3.3)
RSQLite 1.0.0 2014-10-25 CRAN (R 3.3.0)
S4Vectors 0.10.0 2016-05-04 Bioconductor
scales 0.4.1 2016-11-09 CRAN (R 3.3.2)
survival 2.40-1 2016-10-30 CRAN (R 3.3.3)
tibble 1.3.0 2017-04-01 cran (@1.3.0)
WGCNA * 1.51 2016-03-15 CRAN (R 3.3.0)
withr 1.0.2 2016-06-20 CRAN (R 3.3.0)
On Tue, Apr 11, 2017 at 11:43 AM, Billie Gould <bgo...@msu.edu> wrote:
> Hello fellow Macs,
> I’m hoping to ask your help. I’m an R user with MacOSX Sierra (v10.12.3) and
> I am encountering R (v3.3.3) crash problems loading a specific package for
> genetic analysis: WGCNA
> (https://cran.r-project.org/web/packages/WGCNA/index.html
> <https://cran.r-project.org/web/packages/WGCNA/index.html>). I’ve contacted
> the authors of the package and they suggested someone here might know
> something.
> 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 on OSX
> Sierra?
> Any suggestions would be much appreciated.
>
> Thanks very much,
>
> Billie
>
>
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>
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