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antoinefelden
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10
@antoinefelden-16088
Last seen 6.2 years ago
Hi,
I keep running in the following error when trying to load WGCNA with library("WGCNA"), and I couldn't extract any good lead from the logs. I already tried to reinstall the package, but got the same error. Any lead? Cheers.
*** caught segfault ***
address (nil), 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(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
7: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
8: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
9: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
10: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
11: asNamespace(ns)
12: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
13: loadNamespace(package, lib.loc)
14: doTryCatch(return(expr), name, parentenv, handler)
15: tryCatchOne(expr, names, parentenv, handlers[[1L]])
16: tryCatchList(expr, classes, parentenv, handlers)
17: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps)}, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA)})
18: library("WGCNA", lib.loc = "/srv/global/scratch/feldenan/ZZ_misc_tests/install_test_WGCNA")
An irrecoverable exception occurred. R is aborting now ...
/var/opt/sge/default/spool/scifachpc-c04n04/job_scripts/753709: line 695: 64854 Segmentation fault (core dumped) Rscript ./WGCNA_test.R
And here are my session infos:
R version 3.4.3 (2017-11-30) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS release 6.9 (Final) Matrix products: default BLAS: /usr/lib64/R/lib/libRblas.so LAPACK: /usr/lib64/R/lib/libRlapack.so 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] stats4 parallel methods stats graphics grDevices utils [8] datasets base other attached packages: [1] edgeR_3.10.2 limma_3.24.5 preprocessCore_1.40.0 [4] GO.db_3.5.0 pkgconfig_2.0.1 impute_1.52.0 [7] AnnotationDbi_1.40.0 IRanges_2.12.0 S4Vectors_0.16.0 [10] Biobase_2.38.0 BiocGenerics_0.24.0 Rcpp_0.12.18 [13] BiocInstaller_1.28.0 loaded via a namespace (and not attached): [1] digest_0.6.9 DBI_0.8 RSQLite_2.1.0 blob_1.1.1 bit64_0.9-7 [6] bit_1.1-12 compiler_3.4.3 memoise_1.1.0 R version 3.4.3 (2017-11-30) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS release 6.9 (Final) Matrix products: default BLAS: /usr/lib64/R/lib/libRblas.so LAPACK: /usr/lib64/R/lib/libRlapack.so 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] stats4 parallel methods stats graphics grDevices utils [8] datasets base other attached packages: [1] edgeR_3.10.2 limma_3.24.5 preprocessCore_1.40.0 [4] GO.db_3.5.0 pkgconfig_2.0.1 impute_1.52.0 [7] AnnotationDbi_1.40.0 IRanges_2.12.0 S4Vectors_0.16.0 [10] Biobase_2.38.0 BiocGenerics_0.24.0 Rcpp_0.12.18 [13] BiocInstaller_1.28.0 loaded via a namespace (and not attached): [1] digest_0.6.9 DBI_0.8 RSQLite_2.1.0 blob_1.1.1 bit64_0.9-7 [6] bit_1.1-12 compiler_3.4.3 memoise_1.1.0
One possibility is that it is not WGCNA at all, but a stale dependency. You could try
trace(loadNamespace, tracer=quote(print(package)), exit=quote(print(paste("leaving", package))), print=FALSE ) library(WGCNA)it'll print the package names as each is loaded; the output is a bit confusing as one descends through package dependencies repeatedly; mine ends with
If yours were to end, immediately before the segfault, with some package other than "utils", then you'd look for the last package that had been entered and not yet left.
I would recommend to use the latest R version (and the latest WGCNA version). This seems to be from a problem in the C++ code of WGCNA
I suggest posting this issue on the R-users list (https://www.r-project.org/mail.html). As Luis suggested, try installing the latest version of R since the maintainers of R may not be willing to look into an older version. I personally don't see this bug, but I also don't use CentOS.
Personally, I would try to investigate whether R was compiled using the same compiler version as WGCNA - one possible cause of such segfaults could be incompatible compiler or library versions used for compilation of R and WGCNA. Presumably this would resolve by compiling and installing fresh R.
Peter