[R-SIG-Mac] segfault on R v. 3.4.1

[David Winsemius]

> On Sep 14, 2017, at 9:13 AM, James Plante <jimplante at me.com> wrote:
> 
> If I knew what a segfault was, I might be able to be more helpful. 
> Do any of you folks know what might’ve happened? I’ve d/l’d and installed the 3.4.1. Mac binary from CRAN three times, and each time I get the text below.

But ... did you also update your library packages?


> Any help will be appreciated; let me know if I can include anything else. A sysinfo() is out of the question, since my owly option is how I want to quit R. The only guess I have is that I don’t have enough memory installed. 

That's pretty unlikely.


> Main system info: 
> MacOS Sierra v. 10.12.8; 27” iMac, late 2013; 3.4GHz Core i%; 8GB 1600MHz DDR3
> Thanks in advance,
> Jim
> R version 3.4.1 (2017-06-30) -- "Single Candle"
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> Platform: x86_64-apple-darwin15.6.0 (64-bit)
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> *** caught segfault ***
> address 0x1310, 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,
> i[[2L]], from = package)
> .libPaths()), versionCheck = vI[[j]]),
> 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
> <- attachNamespace(ns, pos = pos, deps)}, error = function(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)
> msg), domain = NA)    else stop(msg, call. = FALSE, domain = NA)})
> 14: library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,
> warn.conflicts, quietly = quietly)
> 15: doTryCatch(return(expr), name, parentenv, handler)
> 16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> 17: tryCatchList(expr, classes, parentenv, handlers)
> 18: tryCatch(library(package, lib.loc = lib.loc, character.only = TRUE,     logical.return = TRUE,
> warn.conflicts = warn.conflicts, quietly = quietly),     error = function(e) e)
> 19: require(pkg, quietly = TRUE, warn.conflicts = FALSE, character.only = TRUE)
> 20: .First.sys()

The problem apparently starts with .First.sys(). The .First.sys() function is called after the function .First which may reside in one of the startup files. See:  ?Startup  ... in particular:

"Next, if a function .First is found on the search path, it is executed as .First(). Finally, function .First.sys() in the base package is run. This calls require to attach the default packages specified by options("defaultPackages"). If the methods package is included, this will have been attached earlier (by function .OptRequireMethods()) so that namespace initializations such as those from the user workspace will proceed correctly."

So you would need to examine your Renviron.site file and maybe .Rprofile files and see if one of them is attempting to load a package that has not been updated properly.

-- 
David.



> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> 2017-09-14 08:14:57.208 R[11081:2277811] IMKClient Stall detected, *please Report* your user scenario
> attaching a spindump (or sysdiagnose) that captures the problem - (imkxpc_attributesForCharacterIndex:reply:)
> block performed very slowly (1.16 secs).
> Selection:
> 	[[alternative HTML version deleted]]
> 
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David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   -Gehm's Corollary to Clarke's Third Law