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Last updated on 2026-04-17 11:54:36 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| NicheBarcoding | 2 | 4 | 8 |
Current CRAN status: ERROR: 2, NOTE: 4, OK: 8
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.
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