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

[Duncan Murdoch]

On 14/09/2017 12:13 PM, James Plante wrote:
> If I knew what a segfault was, I might be able to be more helpful.

In your case, it means that some part of the code is trying to refer to 
a nonexistent memory address.  This is certainly a bug somewhere or other.

 From the traceback you posted, this appears to happen when R is trying 
to load the compiled library of some package.  I don't see information 
on what package that is.

If it is a contributed package, the bug likely lies there.  You might be 
able to see this by going into the console and running

R --vanilla

which will load R with reduced startup code -- an old workspace won't be 
loaded, etc.  If that works, then you can gradually add back the things 
you usually use (see ?Startup for the startup process) until you find 
what triggers the problem.

If that fails, then the problem is likely with R, or some basic part of 
your system.  Four years old doesn't seem old, but it's long enough for 
hardware problems to develop.

Duncan Murdoch

> 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.
> 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.
> 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"
> Copyright (C) 2017 The R Foundation for Statistical Computing
> 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()
> 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:
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> 
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