• using R Under development (unstable) (2026-10-06 r90643)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 23.1.2     flang version 23.1.2
• running under: Fedora Linux 44 (Server Edition)
• using session charset: UTF-8 * current time: 2026-10-07 11:53:43 UTC
• using option ‘--no-stop-on-test-error’
• checking for file ‘babelmixr2/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘babelmixr2’ version ‘0.1.11’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... INFO Package suggested but not available for checking: 'lixoftConnectors'
• 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 ‘babelmixr2’ can be installed ... [49s/39s] OK See the install log for details.
• used C compiler: ‘clang version 23.1.2’
• used C++ compiler: ‘clang version 23.1.2’
• checking installed package size ... OK
• checking package 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 ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking whether startup messages can be suppressed ... OK
• checking use of S3 registration ... 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 ... [27s/30s] NOTE Found calls to structure() using deprecated special names:   babelmixr2/R/monolixNlmixr2est.R (.Label: 1) '.Label' should be changed to 'levels'.
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... 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 line endings in shell scripts ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking compilation flags in Makevars ... OK
• checking for GNU extensions in Makefiles ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking examples ... [6s/15s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [8s/22s] ERROR   Running ‘spelling.R’   Running ‘testthat.R’ [8s/21s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(babelmixr2)   >   > test_check("babelmixr2")       *** caught segfault ***   address 0x4, cause 'memory not mapped'   tracked pnodes      Traceback:    1: .rxOptExprC(.norm)    2: rxOptExpr(.txt, msg = msg, chunkLines = 0L)    3: .rxOptExprChunked(x, msg = msg, chunkLines = .chunkLines, parallel = parallel)    4: rxode2::rxOptExpr(.s$..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 ...
• checking PDF version of manual ... [6s/14s] OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR, 1 NOTE