Last updated on 2026-09-30 01:55:41 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.4.1 | 0.34 | 5.13 | 5.47 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.4.1 | 44.74 | 348.72 | 393.46 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.4.1 | 36.00 | 271.22 | 307.22 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.4.1 | 53.00 | 318.72 | 371.72 | OK | |
| r-devel-windows-x86_64 | 0.4.1 | 65.00 | 533.00 | 598.00 | OK | |
| r-patched-linux-x86_64 | 0.4.1 | 58.48 | 423.38 | 481.86 | OK | |
| r-release-linux-x86_64 | 0.4.1 | 59.17 | 426.17 | 485.34 | OK | |
| r-release-macos-arm64 | 0.4.1 | 13.00 | 99.00 | 112.00 | OK | |
| r-release-macos-x86_64 | 0.4.1 | 41.00 | 400.00 | 441.00 | OK | |
| r-release-windows-x86_64 | 0.4.1 | 57.00 | 502.00 | 559.00 | OK | |
| r-oldrel-macos-arm64 | 0.4.1 | 12.00 | 109.00 | 121.00 | OK | |
| r-oldrel-macos-x86_64 | 0.4.1 | 41.00 | 410.00 | 451.00 | OK | |
| r-oldrel-windows-x86_64 | 0.4.1 | 80.00 | 584.00 | 664.00 | OK |
Version: 0.4.1
Check: package dependencies
Result: ERROR
Packages required but not available: 'nlmixr2est', 'rxode2'
Package suggested but not available for checking: 'nlmixr2'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.4.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘admixr2.Rmd’ using rmarkdown
*** 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$..inner, ifelse(.getRxPredLlikOption(), "inner llik model", "inner model"), parallel = cores)
5: .rxFinalizeInner(.s, .sumProd, .optExpression, .cores)
6: rxUiGet.foceiEnv(x, ...)
7: rxUiGet.focei(x, ...)
8: rxUiGet.foceiModel(.obj)
9: rxUiGet(.obj)
10: `$.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 = "/data/localhost/ripley/R/packages/tests-clang/admixr2.Rcheck/vign_test/admixr2", skip = TRUE, ser_elibs = "/tmp/RtmptUvWnS/file3f97771d5b2500.rds")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-clang