CRAN Package Check Results for Package PCMBaseCpp

Last updated on 2020-01-09 07:48:08 CET.

Check Details

Version: 0.1.7
Check: installed package size
Result: NOTE
     installed size is 31.4Mb
     sub-directories of 1Mb or more:
     libs 30.2Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.1.7
Check: tests
Result: ERROR
     Running ‘testthat.R’ [173s/200s]
    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 0.039 0.0020
     2: 2 MGPM (A-F) 100 4 11 -4.293882e+03 -4.293882e+03 0.362 0.0062
     3: 2 MGPM (A-F) 1000 11 11 -1.699739e+05 -1.699739e+05 4.993 0.0422
     4: 2 MGPM (A-F) 10000 11 11 -1.210177e+06 -1.210177e+06 49.750 0.4037
     5: 2 BM (B) 10 2 11 -4.451277e+03 -4.451277e+03 0.049 0.0008
     6: 2 BM (B) 100 4 11 -8.426814e+03 -8.426814e+03 0.338 0.0034
     7: 2 BM (B) 1000 11 11 -1.829699e+04 -1.829699e+04 4.186 0.0344
     8: 2 BM (B) 10000 11 11 -6.574333e+05 -6.574333e+05 34.015 0.3096
     9: 2 OU (E) 10 2 11 -1.126026e+04 -1.126026e+04 0.061 0.0031
     10: 2 OU (E) 100 4 11 -8.485692e+05 -8.485692e+05 0.468 0.0068
     11: 2 OU (E) 1000 11 11 -1.234342e+06 -1.234342e+06 5.184 0.0561
     12: 2 OU (E) 10000 11 11 -1.057830e+07 -1.057830e+07 52.953 0.3576
    
     *** caught segfault ***
     address 0x7f1e4ee5d2c8, cause 'invalid permissions'
    
     Traceback:
     1: .External(list(name = "CppMethod__invoke_notvoid", address = <pointer: 0x2423d60>, dll = list(name = "Rcpp", path = "/data/gannet/ripley/R/test-clang/Rcpp/libs/Rcpp.so", dynamicLookup = TRUE, handle = <pointer: 0x22bf6e0>, info = <pointer: 0x1e1c8e0>), numParameters = -1L), <pointer: 0xae09c90>, <pointer: 0x9a2c000>, .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 ...
Flavor: r-devel-linux-x86_64-fedora-clang