macOS fresh install of R - devtools are giving segfault error - - r

Question

I've done a fresh reinstall of R 3.6 on a macOS Mojava v 10.14.6
I've install clang 7 here from the provided installer /usr/local/clang7
I have xcode
But there's something wrong with the install that I can seem to figure out
.libPaths()
[1] "/Users/annaleigh/Library/R/3.6/library"
[2] "/Library/Frameworks/R.framework/Versions/3.6/Resources/library"
> install.packages("devtools")
Installing package into ‘/Users/annaleigh/Library/R/3.6/library’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.6/devtools_2.2.1.tgz'
Content type 'application/x-gzip' length 339075 bytes (331 KB)
==================================================
downloaded 331 KB
The downloaded binary packages are in
/var/folders/xr/lmkkh0p10t948k1n104z1jsh0000gn/T//Rtmpf54J79/downloaded_packages
> library(devtools)
\Loading required package: usethis
*** caught segfault ***
address 0x2c2e0, cause 'memory not mapped'
However the usethis library seem to load fine
> library(usethis)
> library(devtools)
*** caught segfault ***
address 0x2c2e0, 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(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({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)}, 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)})
14: library(devtools)

Answer 1

Answer found here:
https://github.com/r-lib/devtools/issues/1292
"Finally looked at .libPath() and realized that both instances of R were looking at the user library before the system library. So if the packages were linked to different system libraries from the compiled versions (OS X Sierra and El Capitan in my case) this could create the seg fault.
Removing libraries in the user library ~/user/Library/R/version# fixed the issue (with installing to different locations)"