Last updated on 2024-05-04 13:49:35 CEST.
| Package | ERROR | OK |
|---|---|---|
| posologyr | 1 | 12 |
Current CRAN status: ERROR: 1, OK: 12
Version: 1.2.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘a_posteriori_dosing.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/posologyr.Rcheck/vign_test/posologyr/vignettes/a_posteriori_dosing_files/figure-html/map_plot_tdm-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 11831 bytes
Input file size = 11921 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10243
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10243
Output IDAT size = 10243 bytes (1588 bytes decrease)
Output file size = 10321 bytes (1600 bytes = 13.42% decrease)
--- finished re-building ‘a_posteriori_dosing.Rmd’
--- re-building ‘a_priori_dosing.Rmd’ using rmarkdown
*** caught segfault ***
address (nil), cause 'memory not mapped'
Traceback:
1: rxSolveSEXP(object, .ctl, .nms, .xtra, params, events, inits, setupOnlyS = .setupOnly)
2: withCallingHandlers(expr, warning = function(w) { assign(".ws", unique(c(w$message, .ws)), .thisEnv)})
3: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
4: suppressWarnings(withCallingHandlers(expr, warning = function(w) { assign(".ws", unique(c(w$message, .ws)), .thisEnv)}))
5: .collectWarnings(rxSolveSEXP(object, .ctl, .nms, .xtra, params, events, inits, setupOnlyS = .setupOnly), lst = TRUE)
6: doTryCatch(return(expr), name, parentenv, handler)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: tryCatchList(expr, classes, parentenv, handlers)
9: tryCatch({ .envReset$ret <- .collectWarnings(rxSolveSEXP(object, .ctl, .nms, .xtra, params, events, inits, setupOnlyS = .setupOnly), lst = TRUE)}, error = function(e) { if (regexpr("not provided by package", e$message) != -1) { if (.envReset$cacheReset) { .malert("unsuccessful cache reset; try manual reset with 'rxClean()'") stop(e) } else { gc() .minfo("try resetting cache") rxode2::rxClean() .envReset$cacheReset <- TRUE .envReset$reset <- TRUE .msuccess("done") } } else if (regexpr("maximal number of DLLs reached", e$message) != -1) { if (.envReset$unload) { .malert("Could not unload rxode2 models, try restarting R") stop(e) } else { gc() .minfo("try resetting cache and unloading all rxode2 models") try(rxode2::rxUnloadAll()) rxode2::rxClean() .envReset$unload <- TRUE .envReset$reset <- TRUE .msuccess("done") } } else { stop(e) }})
10: rxSolve.default(.args.object, events = .newEt, updateObject = TRUE)
11: rxSolve(.args.object, events = .newEt, updateObject = TRUE)
12: simu_patA$model$add.dosing(dose = prior_dose$dose, rate = prior_dose$dose/0.5)
13: eval(expr, envir, enclos)
14: eval(expr, envir, enclos)
15: eval_with_user_handlers(expr, envir, enclos, user_handlers)
16: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
17: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)
18: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))
19: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)))
20: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, log_echo = log_echo, log_warning = log_warning, output_handler = output_handler, include_timing = include_timing)
21: evaluate::evaluate(...)
22: 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$render, options))
23: in_dir(input_dir(), expr)
24: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
25: eng_r(options)
26: block_exec(params)
27: call_block(x)
28: process_group(group)
29: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
30: withCallingHandlers(expr, error = function(e) { loc = if (is.function(fun)) trimws(fun(label)) else "" if (loc != "") loc = sprintf(" at lines %s", loc) message(one_string(handler(e, loc)))})
31: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(e, loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
32: process_file(text, output)
33: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
34: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
35: vweave_rmarkdown(...)
36: engine$weave(file, quiet = quiet, encoding = enc)
37: doTryCatch(return(expr), name, parentenv, handler)
38: tryCatchOne(expr, names, parentenv, handlers[[1L]])
39: tryCatchList(expr, classes, parentenv, handlers)
40: tryCatch({ engine$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) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
41: tools:::.buildOneVignette("a_priori_dosing.Rmd", "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/posologyr.Rcheck/vign_test/posologyr", TRUE, FALSE, "a_priori_dosing", "UTF-8", "/tmp/RtmpXEQLHO/file99cfc2addf631.rds")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
--- re-building ‘auc_based_dosing.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/posologyr.Rcheck/vign_test/posologyr/vignettes/auc_based_dosing_files/figure-html/unnamed-chunk-2-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 13037 bytes
Input file size = 13127 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11407
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11407
Output IDAT size = 11407 bytes (1630 bytes decrease)
Output file size = 11485 bytes (1642 bytes = 12.51% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/posologyr.Rcheck/vign_test/posologyr/vignettes/auc_based_dosing_files/figure-html/map_plot_tdm-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 16685 bytes
Input file size = 16787 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13685
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13685
Output IDAT size = 13685 bytes (3000 bytes decrease)
Output file size = 13763 bytes (3024 bytes = 18.01% decrease)
--- finished re-building ‘auc_based_dosing.Rmd’
--- re-building ‘multiple_endpoints.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/posologyr.Rcheck/vign_test/posologyr/vignettes/multiple_endpoints_files/figure-html/unnamed-chunk-5-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 12527 bytes
Input file size = 12617 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10620
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10620
Output IDAT size = 10620 bytes (1907 bytes decrease)
Output file size = 10698 bytes (1919 bytes = 15.21% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/posologyr.Rcheck/vign_test/posologyr/vignettes/multiple_endpoints_files/figure-html/unnamed-chunk-6-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 11957 bytes
Input file size = 12047 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9769
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9769
Output IDAT size = 9769 bytes (2188 bytes decrease)
Output file size = 9847 bytes (2200 bytes = 18.26% decrease)
--- finished re-building ‘multiple_endpoints.Rmd’
--- re-building ‘patient_data_input.Rmd’ using rmarkdown
--- finished re-building ‘patient_data_input.Rmd’
--- re-building ‘posologyr_user_defined_models.Rmd’ using rmarkdown
--- finished re-building ‘posologyr_user_defined_models.Rmd’
SUMMARY: processing the following file failed:
‘a_priori_dosing.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang