CRAN Package Check Results for Package NicheBarcoding

Last updated on 2025-02-08 19:49:26 CET.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	1.0	5.38	325.75	331.13	OK
r-devel-linux-x86_64-debian-gcc	1.0	3.72	215.81	219.53	OK
r-devel-linux-x86_64-fedora-clang	1.0			582.97	NOTE
r-devel-linux-x86_64-fedora-gcc	1.0			535.03	NOTE
r-devel-windows-x86_64	1.0	7.00	279.00	286.00	OK
r-patched-linux-x86_64	1.0	4.93	302.37	307.30	OK
r-release-linux-x86_64	1.0	4.93	305.63	310.56	OK
r-release-macos-arm64	1.0			81.00	ERROR
r-release-macos-x86_64	1.0			223.00	OK
r-release-windows-x86_64	1.0	7.00	281.00	288.00	OK
r-oldrel-macos-arm64	1.0			158.00	OK
r-oldrel-macos-x86_64	1.0			276.00	OK
r-oldrel-windows-x86_64	1.0	7.00	352.00	359.00	OK

Check Details

Version: 1.0
Check: dependencies in R code
Result: NOTE Namespace in Imports field not imported from: ‘rJava’ All declared Imports should be used. Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [25s/27s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(NicheBarcoding) > > test_check("NicheBarcoding") Loading required namespace: rJava *** caught illegal operation *** address 0x1139eef78, cause 'illegal trap' Traceback: 1: rJava::.jcall(mxe, "S", "fit", c("autorun", "-e", afn, "-o", dirout, "-s", pfn, args)) 2: .local(x, p, ...) 3: dismo::maxent(Data[, -1], Data[, 1], args = "outputformat=logistic") 4: dismo::maxent(Data[, -1], Data[, 1], args = "outputformat=logistic") 5: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning")) 6: suppressWarnings(dismo::maxent(Data[, -1], Data[, 1], args = "outputformat=logistic")) 7: niche.Model.Build(prese = NULL, absen = NULL, prese.env = prese.env, absen.env = NULL, model = "MAXENT", bak.vir = bak.vir, en.vir = en.vir) 8: NBSI(ref.seq, que.seq, ref.add = NULL, independence = TRUE, model = "MAXENT", variables = "ALL", en.vir = en.vir, bak.vir = bak.vir) 9: eval(code, test_env) 10: eval(code, test_env) 11: 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) 12: doTryCatch(return(expr), name, parentenv, handler) 13: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) 15: doTryCatch(return(expr), name, parentenv, handler) 16: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]]) 17: tryCatchList(expr, classes, parentenv, handlers) 18: 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) { }) 19: test_code(desc, code, env = parent.frame(), reporter = reporter) 20: test_that("tests of different parameter combinations", { data(en.vir) data(bak.vir) library(ape) data(LappetMoths) ref.seq <- LappetMoths$ref.seq que.seq <- LappetMoths$que.seq NBSI.out <- NBSI(ref.seq, que.seq, ref.add = NULL, independence = TRUE, model = "MAXENT", variables = "ALL", en.vir = en.vir, bak.vir = bak.vir) expect_equal(ncol(NBSI.out), 7) NBSI.out <- NBSI(ref.seq, que.seq, ref.add = NULL, independence = TRUE, model = "MAXENT", variables = "SELECT", en.vir = en.vir, bak.vir = bak.vir) expect_equal(ncol(NBSI.out), 7) ref.add <- LappetMoths$ref.add NBSI.out <- NBSI(ref.seq, que.seq, ref.add = ref.add, independence = TRUE, model = "MAXENT", variables = "ALL", en.vir = en.vir, bak.vir = bak.vir) expect_equal(ncol(NBSI.out), 7) NBSI.out <- NBSI(ref.seq, que.seq, ref.add = ref.add, independence = TRUE, model = "MAXENT", variables = "SELECT", en.vir = en.vir, bak.vir = bak.vir) expect_equal(ncol(NBSI.out), 7)}) 21: eval(code, test_env) 22: eval(code, test_env) 23: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error) 24: doTryCatch(return(expr), name, parentenv, handler) 25: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 26: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) 27: doTryCatch(return(expr), name, parentenv, handler) 28: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]]) 29: tryCatchList(expr, classes, parentenv, handlers) 30: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { }) 31: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new()) 32: source_file(path, env = env(env), desc = desc, error_call = error_call) 33: FUN(X[[i]], ...) 34: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call) 35: doTryCatch(return(expr), name, parentenv, handler) 36: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 37: tryCatchList(expr, classes, parentenv, handlers) 38: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL}) 39: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)) 40: test_files_serial(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, desc = desc, load_package = load_package, error_call = error_call) 41: 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, load_package = load_package, parallel = parallel) 42: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed") 43: test_check("NicheBarcoding") An irrecoverable exception occurred. R is aborting now ... Flavor: r-release-macos-arm64