Last updated on 2025-05-15 09:53:13 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| NicheBarcoding | 2 | 4 | 7 |
Current CRAN status: ERROR: 2, NOTE: 4, OK: 7
Version: 1.0
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Cai-qing YANG <yangcq_ivy@163.com>’
Package CITATION file contains call(s) to old-style personList() or
as.personList(). Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry(). Please
use bibentry() instead.
The BugReports field in DESCRIPTION has
https://github.com/Yangcq-Ivy/NicheBarcoding
which should likely be
https://github.com/Yangcq-Ivy/NicheBarcoding/issues
instead.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
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’ [24s/26s]
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 0x10a12ef78, 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
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-oldrel-macos-arm64
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.