CRAN Package Check Results for Package treenomial

Last updated on 2022-09-25 12:56:11 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1.4 104.70 44.51 149.21 OK
r-devel-linux-x86_64-debian-gcc 1.1.4 86.36 33.21 119.57 ERROR
r-devel-linux-x86_64-fedora-clang 1.1.4 259.27 OK
r-devel-linux-x86_64-fedora-gcc 1.1.4 207.78 OK
r-devel-windows-x86_64 1.1.4 83.00 97.00 180.00 OK
r-patched-linux-x86_64 1.1.4 89.77 44.25 134.02 OK
r-release-linux-x86_64 1.1.4 86.51 42.88 129.39 OK
r-release-macos-arm64 1.1.4 54.00 NOTE
r-release-macos-x86_64 1.1.4 72.00 NOTE
r-release-windows-x86_64 1.1.4 187.00 95.00 282.00 OK
r-oldrel-macos-arm64 1.1.4 61.00 NOTE
r-oldrel-macos-x86_64 1.1.4 81.00 NOTE
r-oldrel-windows-ix86+x86_64 1.1.4 234.00 105.00 339.00 OK

Check Details

Version: 1.1.4
Check: tests
Result: ERROR
     Running ‘testthat.R’ [2s/5s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(treenomial)
     >
     > test_check("treenomial")
    
     *** caught segfault ***
     address 0x55dd5393b130, cause 'memory not mapped'
    
     Traceback:
     1: coeffMatList(wedgeSeq, y = 0, type = type, tipLabA = uniqueTipLabFirst[[1]], tipLabB = uniqueTipLabFirst[[2]], nThreads = numThreads)
     2: treeToPoly(differentSizeTrees, type = "tipLabel", numThreads = 0)
     3: eval(code, test_env)
     4: eval(code, test_env)
     5: 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)
     6: doTryCatch(return(expr), name, parentenv, handler)
     7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     8: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     9: doTryCatch(return(expr), name, parentenv, handler)
     10: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     11: tryCatchList(expr, classes, parentenv, handlers)
     12: 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) { })
     13: test_code(desc, code, env = parent.frame(), reporter = reporter)
     14: test_that("test different size trees with binary trait labels", { largerTree <- rtree(30) largerTree$tip.label <- sample(c("t1", "t2"), size = 30, replace = TRUE) smallerTree <- rtree(2) coeffs <- treeToPoly(c(largerTree, smallerTree), type = "tipLabel", numThreads = 0) coeffs <- alignPoly(coeffs) firstDims <- dim(coeffs[[1]]) res <- lapply(coeffs, function(i) dim(i) == firstDims) expect_condition(all(res)) largerTrees <- rmtree(10, 10) largerTrees <- lapply(largerTrees, function(i) { i$tip.label <- sample(c("t1", "t2"), size = 10, replace = TRUE) return(i) }) differentSizeTrees <- c(largerTrees, list(rtree(2))) coeffs <- treeToPoly(differentSizeTrees, type = "tipLabel", numThreads = 0) coeffs <- alignPoly(coeffs) firstDims <- dim(coeffs[[1]]) res <- lapply(coeffs, function(i) dim(i) == firstDims) expect_condition(all(res)) largerTrees <- rmtree(10, 10) largerTrees <- lapply(largerTrees, function(i) { i$tip.label <- sample(c("t1", "t2"), size = 10, replace = TRUE) return(i) }) smallerTrees <- rmtree(50, 5) smallerTrees <- lapply(smallerTrees, function(i) { i$tip.label <- sample(c("t1", "t2"), size = 5, replace = TRUE) return(i) }) differentSizeTrees <- c(largerTrees, smallerTrees) coeffs <- treeToPoly(differentSizeTrees, type = "tipLabel", numThreads = 0) coeffs <- alignPoly(coeffs) firstDims <- dim(coeffs[[1]]) res <- lapply(coeffs, function(i) dim(i) == firstDims) expect_condition(all(res)) })
     15: eval(code, test_env)
     16: eval(code, test_env)
     17: 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)
     18: doTryCatch(return(expr), name, parentenv, handler)
     19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     20: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     21: doTryCatch(return(expr), name, parentenv, handler)
     22: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     23: tryCatchList(expr, classes, parentenv, handlers)
     24: 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) { })
     25: test_code(NULL, exprs, env)
     26: source_file(path, child_env(env), wrap = wrap)
     27: FUN(X[[i]], ...)
     28: lapply(test_paths, test_one_file, env = env, wrap = wrap)
     29: doTryCatch(return(expr), name, parentenv, handler)
     30: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     31: tryCatchList(expr, classes, parentenv, handlers)
     32: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
     33: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, wrap = wrap))
     34: test_files(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package)
     35: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package, parallel = parallel)
     36: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
     37: test_check("treenomial")
     An irrecoverable exception occurred. R is aborting now ...
     Segmentation fault
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.1.4
Check: installed package size
Result: NOTE
     installed size is 11.2Mb
     sub-directories of 1Mb or more:
     libs 11.0Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64