• using R version 4.5.0 beta (2025-03-29 r88069)
  • using platform: aarch64-apple-darwin20
  • R was compiled by     Apple clang version 14.0.0 (clang-1400.0.29.202)     GNU Fortran (GCC) 14.2.0
  • running under: macOS Ventura 13.4
  • using session charset: UTF-8
  • checking for file ‘NicheBarcoding/DESCRIPTION’ ... OK
  • this is package ‘NicheBarcoding’ version ‘1.0’
  • package encoding: UTF-8
  • checking package namespace information ... OK
  • checking package dependencies ... OK
  • checking if this is a source package ... OK
  • checking if there is a namespace ... OK
  • checking for executable files ... OK
  • checking for hidden files and directories ... OK
  • checking for portable file names ... OK
  • checking for sufficient/correct file permissions ... OK
  • checking whether package ‘NicheBarcoding’ can be installed ... [2s/3s] OK See the install log for details.
  • checking installed package size ... OK
  • checking package directory ... OK
  • checking ‘build’ directory ... OK
  • checking DESCRIPTION meta-information ... OK
  • checking top-level files ... OK
  • checking for left-over files ... OK
  • checking index information ... OK
  • checking package subdirectories ... OK
  • checking code files for non-ASCII characters ... OK
  • checking R files for syntax errors ... OK
  • checking whether the package can be loaded ... [0s/0s] OK
  • checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
  • checking whether the package can be unloaded cleanly ... [0s/0s] OK
  • checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
  • checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
  • checking loading without being on the library search path ... [0s/0s] OK
  • checking dependencies in R code ... OK
  • checking S3 generic/method consistency ... OK
  • checking replacement functions ... OK
  • checking foreign function calls ... OK
  • checking R code for possible problems ... [2s/2s] OK
  • checking Rd files ... [0s/0s] OK
  • checking Rd metadata ... OK
  • checking Rd cross-references ... OK
  • checking for missing documentation entries ... OK
  • checking for code/documentation mismatches ... OK
  • checking Rd \usage sections ... OK
  • checking Rd contents ... OK
  • checking for unstated dependencies in examples ... OK
  • checking contents of ‘data’ directory ... OK
  • checking data for non-ASCII characters ... [3s/4s] OK
  • checking LazyData ... OK
  • checking data for ASCII and uncompressed saves ... OK
  • checking installed files from ‘inst/doc’ ... OK
  • checking files in ‘vignettes’ ... OK
  • checking examples ... [10s/11s] OK
  • checking for unstated dependencies in ‘tests’ ... OK
  • checking tests ... [24s/26s] 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 ...
  • checking for unstated dependencies in vignettes ... OK
  • checking package vignettes ... OK
  • checking re-building of vignette outputs ... [9s/16s] OK
  • checking PDF version of manual ... [4s/5s] OK
  • DONE Status: 1 ERROR
  • using check arguments '--no-clean-on-error '