Last updated on 2026-09-30 01:55:41 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.11 | 0.36 | 4.42 | 4.78 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.1.11 | 48.35 | 225.92 | 274.27 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 0.1.11 | 50.00 | 93.57 | 143.57 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.1.11 | 59.00 | 218.96 | 277.96 | NOTE | |
| r-devel-windows-x86_64 | 0.1.11 | 89.00 | 496.00 | 585.00 | NOTE | |
| r-patched-linux-x86_64 | 0.1.11 | 61.34 | 317.28 | 378.62 | OK | |
| r-release-linux-x86_64 | 0.1.11 | 66.43 | 306.26 | 372.69 | OK | |
| r-release-macos-arm64 | 0.1.11 | 13.00 | 76.00 | 89.00 | OK | |
| r-release-macos-x86_64 | 0.1.11 | 38.00 | 331.00 | 369.00 | OK | |
| r-release-windows-x86_64 | 0.1.11 | 90.00 | 408.00 | 498.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.11 | 12.00 | 105.00 | 117.00 | OK | |
| r-oldrel-macos-x86_64 | 0.1.11 | 42.00 | 393.00 | 435.00 | OK | |
| r-oldrel-windows-x86_64 | 0.1.11 | 103.00 | 497.00 | 600.00 | OK |
Version: 0.1.11
Check: package dependencies
Result: ERROR
Packages required but not available:
'nlmixr2extra', 'nlmixr2plot', 'nlmixr2est', 'nonmem2rx',
'monolix2rx', 'rxode2'
Package suggested but not available for checking: 'lixoftConnectors'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.1.11
Check: R code for possible problems
Result: NOTE
Found calls to structure() using deprecated special names:
babelmixr2/R/monolixNlmixr2est.R (.Label: 1)
'.Label' should be changed to 'levels'.
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64
Version: 0.1.11
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(babelmixr2)
>
> test_check("babelmixr2")
tracked pnodes
*** caught segfault ***
address 0x4, cause 'memory not mapped'
Traceback:
1: .rxOptExprC(.norm)
2: rxOptExpr(.txt, msg = msg, chunkLines = 0L)
3: .rxOptExprChunked(x, msg = msg, chunkLines = .chunkLines, parallel = parallel)
4: rxode2::rxOptExpr(.s$..pred, ifelse(.getRxPredLlikOption(), "Llik EBE model", "EBE model"), parallel = cores)
5: .rxFinalizePred(.s, .sumProd, .optExpression, .optExprCores(x[[1]]))
6: rxUiGet.getEBEEnv(x, ...)
7: rxUiGet.ebe(.obj)
8: rxUiGet(.obj)
9: `$.rxUi`(.ui, "ebe")
10: .ui$ebe
11: .monolixFinalizeEnv(.ret, .ui)
12: .monolixFamilyFit(env, ...)
13: nlmixr2est::.uiFinalizeMu2(.monolixFamilyFit(env, ...), .model)
14: nlmixr2Est.monolix(env, ...)
15: nlmixr2Est(env, ...)
16: withCallingHandlers(expr, warning = function(w) { assign("ws", unique(c(w$message, ws)), this.env)}, error = function(e) { assign("es", unique(c(e$message, es)), this.env)})
17: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
18: suppressWarnings(withCallingHandlers(expr, warning = function(w) { assign("ws", unique(c(w$message, ws)), this.env)}, error = function(e) { assign("es", unique(c(e$message, es)), this.env)}))
19: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: tryCatchList(expr, classes, parentenv, handlers)
22: tryCatch(suppressWarnings(withCallingHandlers(expr, warning = function(w) { assign("ws", unique(c(w$message, ws)), this.env)}, error = function(e) { assign("es", unique(c(e$message, es)), this.env)})), error = function(e) { assign("errored", TRUE, this.env) NULL})
23: .collectWarn(nlmixr2Est(env, ...), lst = TRUE, collectErr = TRUE)
24: nlmixr2Est0(.env)
25: nlmixr2.function(...)
26: nlmixr2est::nlmixr(...)
27: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage"))
28: suppressMessages(nlmixr2est::nlmixr(...))
29: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
30: suppressWarnings(suppressMessages(nlmixr2est::nlmixr(...)))
31: .nlmixr(pk.turnover.emax3, nlmixr2data::warfarin, "monolix", control = monolixControl(modelName = "pk.turnover.emax3"))
32: force(code)
33: withr::with_dir(tmp, code)
34: withr::with_tempdir({ unzip(.path) f <- .nlmixr(pk.turnover.emax3, nlmixr2data::warfarin, "monolix", control = monolixControl(modelName = "pk.turnover.emax3")) expect_true(inherits(f, "nlmixr2FitData"))})
35: eval(code, test_env)
36: eval(code, test_env)
37: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
38: doTryCatch(return(expr), name, parentenv, handler)
39: tryCatchOne(expr, names, parentenv, handlers[[1L]])
40: tryCatchList(expr, classes, parentenv, handlers)
41: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
42: doWithOneRestart(return(expr), restart)
43: withOneRestart(expr, restarts[[1L]])
44: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
45: test_code(code, parent.frame())
46: test_that("test monolix reading for 2019, 2020, and 2021", { if (file.exists(test_path("pk.turnover.emax3-2019.zip"))) { .path <- normalizePath(test_path("pk.turnover.emax3-2019.zip")) withr::with_tempdir({ unzip(.path) f <- .nlmixr(pk.turnover.emax3, nlmixr2data::warfarin, "monolix", control = monolixControl(modelName = "pk.turnover.emax3")) expect_true(inherits(f, "nlmixr2FitData")) }) } if (file.exists("pk.turnover.emax3-2020.zip")) { .path <- normalizePath(test_path("pk.turnover.emax3-2020.zip")) withr::with_tempdir({ unzip(.path) f <- .nlmixr(pk.turnover.emax3, nlmixr2data::warfarin, "monolix", control = monolixControl(modelName = "pk.turnover.emax3")) expect_true(inherits(f, "nlmixr2FitData")) }) } if (file.exists("pk.turnover.emax3-2021.zip")) { .path <- normalizePath(test_path("pk.turnover.emax3-2021.zip")) withr::with_tempdir({ unzip(.path) f <- .nlmixr(pk.turnover.emax3, nlmixr2data::warfarin, "monolix", control = monolixControl(modelName = "pk.turnover.emax3")) expect_true(inherits(f, "nlmixr2FitData")) }) }})
47: eval(code, test_env)
48: eval(code, test_env)
49: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
50: doTryCatch(return(expr), name, parentenv, handler)
51: tryCatchOne(expr, names, parentenv, handlers[[1L]])
52: tryCatchList(expr, classes, parentenv, handlers)
53: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
54: doWithOneRestart(return(expr), restart)
55: withOneRestart(expr, restarts[[1L]])
56: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
57: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
58: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
59: FUN(X[[i]], ...)
60: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
61: doTryCatch(return(expr), name, parentenv, handler)
62: tryCatchOne(expr, names, parentenv, handlers[[1L]])
63: tryCatchList(expr, classes, parentenv, handlers)
64: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
65: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
66: 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, shuffle = shuffle, error_call = error_call)
67: 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, shuffle = shuffle)
68: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
69: test_check("babelmixr2")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-clang