Running ‘testthat.R’ [175s/224s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(PCMBase)
  > 
  > test_check("PCMBaseCpp")
  Loading required package: PCMBaseCpp
  Loading required package: Rcpp
  Performing benchmark for k:  2 ; optionSet:  serial / 1D-multiv. ...
      k  modelType     N  R mode        logLik     logLikCpp  timeR timeCpp
   1: 2 MGPM (A-F)    10  2   11 -7.415912e+02 -7.415912e+02  0.042  0.0021
   2: 2 MGPM (A-F)   100  4   11 -4.293882e+03 -4.293882e+03  0.485  0.0130
   3: 2 MGPM (A-F)  1000 11   11 -1.699739e+05 -1.699739e+05  4.638  0.0443
   4: 2 MGPM (A-F) 10000 11   11 -1.210177e+06 -1.210177e+06 58.351  0.4371
   5: 2     BM (B)    10  2   11 -4.451277e+03 -4.451277e+03  0.032  0.0010
   6: 2     BM (B)   100  4   11 -8.426814e+03 -8.426814e+03  0.293  0.0053
   7: 2     BM (B)  1000 11   11 -1.829699e+04 -1.829699e+04  3.740  0.0302
   8: 2     BM (B) 10000 11   11 -6.574333e+05 -6.574333e+05 38.989  0.2952
   9: 2     OU (E)    10  2   11 -1.126026e+04 -1.126026e+04  0.057  0.0018
  10: 2     OU (E)   100  4   11 -8.485692e+05 -8.485692e+05  0.572  0.0066
  11: 2     OU (E)  1000 11   11 -1.234342e+06 -1.234342e+06  5.206  0.0672
  12: 2     OU (E) 10000 11   11 -1.057830e+07 -1.057830e+07 61.982  0.4485
  
   *** caught segfault ***
  address 0x7f95b45bb2c8, cause 'invalid permissions'
  
  Traceback:
   1: .External(list(name = "CppMethod__invoke_notvoid", address = <pointer: 0x3894700>,     dll = list(name = "Rcpp", path = "/data/gannet/ripley/R/test-clang/Rcpp/libs/Rcpp.so",         dynamicLookup = TRUE, handle = <pointer: 0x11d6d20>,         info = <pointer: 0xe668e0>), numParameters = -1L), <pointer: 0x7c905a0>,     <pointer: 0xa0bc880>, .pointer, ...)
   2: metaI$TraverseTree(par, mode = getOption("PCMBase.Lmr.mode",     as.integer(11)))
   3: PCMLmr.PCMInfoCpp(X = X, tree = tree, model = model, SE = SE,     metaI = metaI, verbose = verbose, root.only = TRUE)
   4: PCMLmr(X = X, tree = tree, model = model, SE = SE, metaI = metaI,     verbose = verbose, root.only = TRUE)
   5: doTryCatch(return(expr), name, parentenv, handler)
   6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
   7: tryCatchList(expr, classes, parentenv, handlers)
   8: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call)[1L]        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
   9: try(PCMLmr(X = X, tree = tree, model = model, SE = SE, metaI = metaI,     verbose = verbose, root.only = TRUE), silent = TRUE)
  10: PCMLik.GaussianPCM(mTraits, phyltree, modelBM, metaI = metaICpp)
  11: PCMLik(mTraits, phyltree, modelBM, metaI = metaICpp)
  12: eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  13: withCallingHandlers(code, warning = function(condition) {    out$push(condition)    maybe_restart("muffleWarning")})
  14: .capture(act$val <- eval_bare(quo_get_expr(.quo), quo_get_env(.quo)),     ...)
  15: quasi_capture(enquo(object), label, capture_warnings)
  16: expect_warning(loglik_PCMBaseCpp <- PCMLik(mTraits, phyltree,     modelBM, metaI = metaICpp))
  17: eval(code, test_env)
  18: eval(code, test_env)
  19: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
  20: doTryCatch(return(expr), name, parentenv, handler)
  21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  23: doTryCatch(return(expr), name, parentenv, handler)
  24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
  25: tryCatchList(expr, classes, parentenv, handlers)
  26: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
  27: test_code(desc, code, env = parent.frame())
  28: test_that("Singular V matrix raises a warning (PCMBase.Errors.As.Warnings=TRUE):",     {        options(PCMBase.Errors.As.Warnings = TRUE)        expect_warning(loglik_PCMBase <- PCMLik(mTraits, phyltree,             modelBM, metaI = metaI))        expect_warning(loglik_PCMBaseCpp <- PCMLik(mTraits, phyltree,             modelBM, metaI = metaICpp))        expect_true(is.na(loglik_PCMBase) && is.na(loglik_PCMBaseCpp))    })
  29: eval(code, test_env)
  30: eval(code, test_env)
  31: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
  32: doTryCatch(return(expr), name, parentenv, handler)
  33: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  34: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  35: doTryCatch(return(expr), name, parentenv, handler)
  36: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
  37: tryCatchList(expr, classes, parentenv, handlers)
  38: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
  39: test_code(NULL, exprs, env)
  40: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
  41: force(code)
  42: doWithOneRestart(return(expr), restart)
  43: withOneRestart(expr, restarts[[1L]])
  44: withRestarts(testthat_abort_reporter = function() NULL, force(code))
  45: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,     {        reporter$start_file(basename(path))        lister$start_file(basename(path))        source_file(path, new.env(parent = env), chdir = TRUE,             wrap = wrap)        reporter$.end_context()        reporter$end_file()    })
  46: FUN(X[[i]], ...)
  47: lapply(paths, test_file, env = env, reporter = current_reporter,     start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
  48: force(code)
  49: doWithOneRestart(return(expr), restart)
  50: withOneRestart(expr, restarts[[1L]])
  51: withRestarts(testthat_abort_reporter = function() NULL, force(code))
  52: with_reporter(reporter = current_reporter, results <- lapply(paths,     test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,     load_helpers = FALSE, wrap = wrap))
  53: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  54: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,     ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     wrap = wrap)
  55: test_package_dir(package = package, test_path = test_path, filter = filter,     reporter = reporter, ..., stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  56: test_check("PCMBaseCpp")
  An irrecoverable exception occurred. R is aborting now ...