Update: I haven't run a memory checker, but what I did do is test binaries compiled on the working OSX machine and they worked fine. So it's a compiler problem most likely. Working hypothesis: this is some flavor of the XCode 4.2 compiler problem I've seen mentioned in a few other emails to this list, and some obscure difference between the two machines makes it pop up on one and not the other. I've got a reasonable workaround and am on a deadline so I'm unlikely to investigate this further :). Mike.
On Feb 8, 2012, at 9:28 AM, Dirk Eddelbuettel wrote:
On 7 February 2012 at 15:47, Michael Shvartsman wrote:
| Hi everyone -
|
| I'm running the same R/Rcpp codebase on about 8 machines, 4 of them OSX and 4 Ubuntu. Rcpp passes unit tests and my non-unittest code runs fine on 7 of the 8 and gives sensible results, so I'm reasonably sure it's correct. However, test.NumericMatrix.cumsum gives me a segfault on the 8th machine, as does my own code (which does some indexing into, multiplying and summing of NumericVector's and NumericMatrix's). I am guessing / thinking that these might be related, which is why I am mentioning both.
| The machine is a dual-hexacore Mac Pro box with OSX lion, Xcode 4.2, R 2.14.1. One of the functioning machines has slightly older hardware but the same version of OSX, same version of Xcode, and same version of R. I'm a bit at a loss. Unittest error reproduced below. My code just gives a 'memory not mapped' segfault. Any ideas of where else to look? Thanks,
No good idea here. You seem to checked the obvious culprits. Maybe run a
memory checker on that machine?
Dirk
|
| Mike Shvartsman.
|
| ========== The unitTest segfault ===========
| Executing test function test.NumericMatrix.cumsum ...
| *** caught segfault ***
| address 0x0, cause 'unknown'
|
| Traceback:
| 1: .Primitive(".Call")(<pointer: 0x104c03f80>, x)
| 2: funx(x)
| 3: all.equal(target, current, tolerance = tolerance, ...)
| 4: checkEquals(funx(x), t(apply(x, 1, cumsum)), msg = "cumsum")
| 5: func()
| 6: system.time(func())
| 7: doTryCatch(return(expr), name, parentenv, handler)
| 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
| 9: tryCatchList(expr, classes, parentenv, handlers)
| 10: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste(prefix, "\n ", sep = "") } else prefix <- "Error : " msg <- paste(prefix, conditionMessage(e), "\n", sep = "") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
| 11: try(system.time(func()))
| 12: .executeTestCase(funcName, envir = sandbox, setUpFunc = .setUp, tearDownFunc = .tearDown)
| 13: .sourceTestFile(testFile, testSuite$testFuncRegexp)
| 14: runTestSuite(testSuite)
| aborting ...
| Segmentation fault: 11
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