CRAN Package Check Results for Package posologyr

Last updated on 2024-05-17 08:54:17 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.2.4 8.74 1281.23 1289.97 OK
r-devel-linux-x86_64-debian-gcc 1.2.4 5.98 588.21 594.19 OK
r-devel-linux-x86_64-fedora-clang 1.2.4 3103.53 OK
r-devel-linux-x86_64-fedora-gcc 1.2.4 1888.20 OK
r-devel-windows-x86_64 1.2.4 8.00 522.00 530.00 OK
r-patched-linux-x86_64 1.2.4 7.73 1571.20 1578.93 OK
r-release-linux-x86_64 1.2.4 9.11 1604.05 1613.16 ERROR
r-release-macos-arm64 1.2.4 233.00 OK
r-release-macos-x86_64 1.2.4 604.00 OK
r-release-windows-x86_64 1.2.4 9.00 548.00 557.00 OK
r-oldrel-macos-arm64 1.2.4 302.00 OK
r-oldrel-macos-x86_64 1.2.4 533.00 OK
r-oldrel-windows-x86_64 1.2.4 11.00 642.00 653.00 OK

Check Details

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 0x271006109, 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-release-gcc/Work/PKGS/posologyr.Rcheck/vign_test/posologyr", TRUE, FALSE, "a_priori_dosing", "UTF-8", "/tmp/RtmpJMwxpq/file2d6c422484de05.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