Last updated on 2024-06-18 00:57:51 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-release-gcc/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$reset <- TRUE .msuccess("done") } } else { stop(e) }})
10: rxSolve.default(.args.object, events = .newEt, updateObject = TRUE)
11: rxSolve(.args.object, events = .newEt, updateObject = TRUE)
12: (function (...) { .newEt <- .et .newEt$clear.sampling() .newEt$add.sampling(...) invisible(rxSolve(.args.object, events = .newEt, updateObject = TRUE))})(c(0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10, 10.1, 10.2, 10.3, 10.4, 10.5, 10.6, 10.7, 10.8, 10.9, 11, 11.1, 11.2, 11.3, 11.4, 11.5, 11.6, 11.7, 11.8, 11.9, 12, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6, 12.7, 12.8, 12.9, 13, 13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8, 13.9, 14, 14.1, 14.2, 14.3, 14.4, 14.5, 14.6, 14.7, 14.8, 14.9, 15, 15.1, 15.2, 15.3, 15.4, 15.5, 15.6, 15.7, 15.8, 15.9, 16, 16.1, 16.2, 16.3, 16.4, 16.5, 16.6, 16.7, 16.8, 16.9, 17, 17.1, 17.2, 17.3, 17.4, 17.5, 17.6, 17.7, 17.8, 17.9, 18, 18.1, 18.2, 18.3, 18.4, 18.5, 18.6, 18.7, 18.8, 18.9, 19, 19.1, 19.2, 19.3, 19.4, 19.5, 19.6, 19.7, 19.8, 19.9, 20))
13: `$<-.rxSolve`(`*tmp*`, time, value = c(0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10, 10.1, 10.2, 10.3, 10.4, 10.5, 10.6, 10.7, 10.8, 10.9, 11, 11.1, 11.2, 11.3, 11.4, 11.5, 11.6, 11.7, 11.8, 11.9, 12, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6, 12.7, 12.8, 12.9, 13, 13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8, 13.9, 14, 14.1, 14.2, 14.3, 14.4, 14.5, 14.6, 14.7, 14.8, 14.9, 15, 15.1, 15.2, 15.3, 15.4, 15.5, 15.6, 15.7, 15.8, 15.9, 16, 16.1, 16.2, 16.3, 16.4, 16.5, 16.6, 16.7, 16.8, 16.9, 17, 17.1, 17.2, 17.3, 17.4, 17.5, 17.6, 17.7, 17.8, 17.9, 18, 18.1, 18.2, 18.3, 18.4, 18.5, 18.6, 18.7, 18.8, 18.9, 19, 19.1, 19.2, 19.3, 19.4, 19.5, 19.6, 19.7, 19.8, 19.9, 20))
14: `$<-`(`*tmp*`, time, value = c(0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10, 10.1, 10.2, 10.3, 10.4, 10.5, 10.6, 10.7, 10.8, 10.9, 11, 11.1, 11.2, 11.3, 11.4, 11.5, 11.6, 11.7, 11.8, 11.9, 12, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6, 12.7, 12.8, 12.9, 13, 13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8, 13.9, 14, 14.1, 14.2, 14.3, 14.4, 14.5, 14.6, 14.7, 14.8, 14.9, 15, 15.1, 15.2, 15.3, 15.4, 15.5, 15.6, 15.7, 15.8, 15.9, 16, 16.1, 16.2, 16.3, 16.4, 16.5, 16.6, 16.7, 16.8, 16.9, 17, 17.1, 17.2, 17.3, 17.4, 17.5, 17.6, 17.7, 17.8, 17.9, 18, 18.1, 18.2, 18.3, 18.4, 18.5, 18.6, 18.7, 18.8, 18.9, 19, 19.1, 19.2, 19.3, 19.4, 19.5, 19.6, 19.7, 19.8, 19.9, 20))
15: eval(expr, envir, enclos)
16: eval(expr, envir, enclos)
17: eval_with_user_handlers(expr, envir, enclos, user_handlers)
18: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
19: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)
20: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))
21: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)))
22: evaluate_call(expr, parsed$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)
23: evaluate::evaluate(...)
24: 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$render, options))
25: in_dir(input_dir(), expr)
26: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
27: eng_r(options)
28: block_exec(params)
29: call_block(x)
30: process_group(group)
31: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
32: 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(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
33: process_file(text, output)
34: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
35: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
36: vweave_rmarkdown(...)
37: engine$weave(file, quiet = quiet, encoding = enc)
38: doTryCatch(return(expr), name, parentenv, handler)
39: tryCatchOne(expr, names, parentenv, handlers[[1L]])
40: tryCatchList(expr, classes, parentenv, handlers)
41: tryCatch({ engine$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)))})
42: tools:::.buildOneVignette("a_priori_dosing.Rmd", "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/posologyr.Rcheck/vign_test/posologyr", TRUE, FALSE, "a_priori_dosing", "UTF-8", "/tmp/Rtmpu0zbez/file34f7ba4e7006e.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-release-gcc/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-release-gcc/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-release-gcc/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-release-gcc/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-release-linux-x86_64