• using R Under development (unstable) (2026-09-30 r90605)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 23.1.2 (1)     Debian flang version 23.1.2 (1)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-10-01 21:15:49 UTC
• checking for file ‘admixr2/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘admixr2’ version ‘0.4.1’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [3s/4s] OK
• 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 ‘admixr2’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘Debian clang version 23.1.2 (1)’
• checking C++ specification ... INFO   specified C++17
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [3s/4s] OK
• checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
• checking whether the package can be unloaded cleanly ... [3s/4s] OK
• checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
• checking whether the namespace can be unloaded cleanly ... [3s/4s] OK
• checking loading without being on the library search path ... [3s/5s] OK
• checking whether startup messages can be suppressed ... [3s/4s] 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 ... [65s/83s] OK
• checking Rd files ... [1s/1s] 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 contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... [0s/1s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... 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 $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [3s/5s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [133s/87s] OK   Running ‘testthat.R’ [133s/86s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [127s/68s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘admixr2.Rmd’ using rmarkdown  *** caught segfault *** address (nil), cause 'memory not mapped' Traceback:  1: .rxOptExprC(.norm)  2: rxOptExpr(.txt, msg = msg, chunkLines = 0L)  3: .rxOptExprChunked(x, msg = msg, chunkLines = .chunkLines, parallel = parallel)  4: rxode2::rxOptExpr(.s$..inner, ifelse(.getRxPredLlikOption(), "inner llik model", "inner model"), parallel = cores)  5: .rxFinalizeInner(.s, .sumProd, .optExpression, .cores)  6: rxUiGet.foceiEnv(x, ...)  7: rxUiGet.focei(x, ...)  8: rxUiGet.foceiModel(.obj)  9: rxUiGet(.obj) 10: `$.rxUi`(.ui, "foceiModel") 11: .ui$foceiModel 12: doTryCatch(return(expr), name, parentenv, handler) 13: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14: tryCatchList(expr, classes, parentenv, handlers) 15: tryCatch(.ui$foceiModel, error = function(e) NULL) 16: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage")) 17: suppressMessages(tryCatch(.ui$foceiModel, error = function(e) NULL)) 18: .admFinaliseFit(.ret, .ui, .ctl, est = "admc", objective = opt$objective, ov = ov, studies = studies, cov = .cov, cov_nms = .cov_nms, multi_out = multi_out, extra_field = "admExtra", handle_ctl = nmObjHandleControlObject.admControl, t_opt = t_opt, t_cov = t_cov, t_elapsed = t_elapsed) 19: nlmixr2Est.admc(env, ...) 20: nlmixr2Est(env, ...) 21: withCallingHandlers(expr, warning = function(w) { assign("ws", unique(c(w$message, ws)), this.env)}, error = function(e) { assign("es", unique(c(e$message, es)), this.env)}) 22: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning")) 23: suppressWarnings(withCallingHandlers(expr, warning = function(w) { assign("ws", unique(c(w$message, ws)), this.env)}, error = function(e) { assign("es", unique(c(e$message, es)), this.env)})) 24: doTryCatch(return(expr), name, parentenv, handler) 25: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 26: tryCatchList(expr, classes, parentenv, handlers) 27: tryCatch(suppressWarnings(withCallingHandlers(expr, warning = function(w) { assign("ws", unique(c(w$message, ws)), this.env)}, error = function(e) { assign("es", unique(c(e$message, es)), this.env)})), error = function(e) { assign("errored", TRUE, this.env) NULL}) 28: .collectWarn(nlmixr2Est(env, ...), lst = TRUE, collectErr = TRUE) 29: nlmixr2Est0(.env) 30: nlmixr2.function(pk_model, admData(), est = "admc", control = admControl(studies = list(examplomycin = study), n_sim = 5000L, cov_n_sim = 10000L, maxeval = 300L, seed = 1L)) 31: nlmixr2(pk_model, admData(), est = "admc", control = admControl(studies = list(examplomycin = study), n_sim = 5000L, cov_n_sim = 10000L, maxeval = 300L, seed = 1L)) 32: eval(expr, envir) 33: eval(expr, envir) 34: withVisible(eval(expr, envir)) 35: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)}) 36: eval(call) 37: eval(call) 38: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers) 39: doWithOneRestart(return(expr), restart) 40: withOneRestart(expr, restarts[[1L]]) 41: withRestartList(expr, restarts[-nr]) 42: doWithOneRestart(return(expr), restart) 43: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 44: withRestartList(expr, restarts) 45: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) 46: evaluate::evaluate(...) 47: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)) 48: in_dir(input_dir(), expr) 49: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))) 50: eng_r(options) 51: block_exec(params) 52: call_block(x) 53: process_group(group) 54: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }) 55: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())) 56: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 57: process_file(text, output) 58: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 59: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 60: vweave_rmarkdown(...) 61: engine$weave(file, quiet = quiet, encoding = enc) 62: doTryCatch(return(expr), name, parentenv, handler) 63: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 64: tryCatchList(expr, classes, parentenv, handlers) 65: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)), domain = NA)}) 66: tools::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/admixr2.Rcheck/vign_test/admixr2", skip = TRUE, ser_elibs = "/home/hornik/tmp/scratch/RtmpBEfM43/file18b57e1ccf7a32.rds") An irrecoverable exception occurred. R is aborting now ... Segmentation fault
• checking PDF version of manual ... [6s/9s] OK
• checking HTML version of manual ... [2s/4s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR