I'm getting two different error messages when attempting to load packages using the 'require' or 'library' functions in R 3.4.1. Since the problem has started, I've only been able to load one package (ggplot2), while others (including any phylogenetics-oriented package, e.g. ape) cause the following error:
*** caught segfault ***
address 0x0, cause 'memory not mapped'
Traceback:
1: getDLLRegisteredRoutines.DLLInfo(dll, addNames = FALSE)
2: assignNativeRoutines(dlls[[lib]], lib, env, nsInfo$nativeRoutines[[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(package, lib.loc)
7: doTryCatch(return(expr), name, parentenv, handler)
8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: tryCatchList(expr, classes, parentenv, handlers)
10: 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)})
11: library(ape)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
[EDIT: The following error was resolved, see first comment below] When I try to load the package rJava, I get the following error. Other packages that give similar errors:
library(rJava)
Error: package or namespace load failed for ‘rJava’:
.onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Users/dummyname/R_libs/rJava/libs/rJava.so':
dlopen(/Users/dummyname/R_libs/rJava/libs/rJava.so, 6): Library not loaded: @rpath/libjvm.dylib
Referenced from: /Users/dummyname/R_libs/rJava/libs/rJava.so
Reason: image not found
I've tried uninstalling all packages, as suggested here: caught segfault error in R I also re-installed R. The same error appears after reinstalling packages. Session info is below the error message. Suggestions?
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.4.1
