• using R Under development (unstable) (2024-11-15 r87338)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (GCC) 14.2.0     GNU Fortran (GCC) 14.2.0
• running under: Fedora Linux 36 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘cutpointr/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘cutpointr’ version ‘1.1.2’
• package encoding: UTF-8
• 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 ‘cutpointr’ can be installed ... [61s/47s] OK See the install log for details.
• used C++ compiler: ‘g++-14 (GCC) 14.2.0’
• checking package directory ... 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 ... NOTE Problems with news in ‘NEWS.md’:   Cannot extract version info from the following section titles:     Misc
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... 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 ... [24s/29s] OK
• checking Rd files ... NOTE checkRd: (-1) abs_d_ppv_npv.Rd:27: Escaped LaTeX specials: \_ \_ \_
• 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 ... OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking line endings in C/C++/Fortran sources/headers ... 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 ... [28s/32s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [85s/103s] ERROR   Running ‘testthat.R’ [85s/102s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(cutpointr)   >   > test_check("cutpointr")       *** caught segfault ***   address 0x1, cause 'memory not mapped'      Traceback:    1: stats::smooth.spline(x = roccurve$x.sorted[finite_roc], y = roccurve$m[finite_roc], w = args[["w"]], spar = args[["spar"]], cv = FALSE, nknots = nknots, df.offset = args[["df_offset"]], penalty = args[["penalty"]], control.spar = args[["control_spar"]], tol = 1e-100)    2: optimize_metric(data = data, x = x, class = class, metric_func = metric_func, pos_class = pos_class, neg_class = neg_class, minmax = "max", direction = direction, metric_name = metric_name, w = w, df = df, spar = spar, nknots = nknots, df_offset = df_offset, penalty = penalty, control_spar = control_spar, spline = TRUE, tol_metric = tol_metric, use_midpoints = use_midpoints, ...)    3: method(data = dat$data[[1]], x = predictor, class = outcome, metric_func = metric, direction = direction, pos_class = pos_class, neg_class = neg_class, tol_metric = tol_metric, boot_stratify = boot_stratify, use_midpoints = use_midpoints, ...)    4: cutpointr_internal(x, class, subgroup, method, metric, pos_class, neg_class, direction, boot_runs, boot_stratify, use_midpoints, break_ties, na.rm, allowParallel, predictor, outcome, mod_name, subgroup_var, tol_metric, ...)    5: cutpointr.default(suicide, dsi, suicide, method = maximize_spline_metric, nknots = 5, spar = 0.3)    6: cutpointr(suicide, dsi, suicide, method = maximize_spline_metric, nknots = 5, spar = 0.3)    7: eval(code, test_env)    8: eval(code, test_env)    9: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)   10: doTryCatch(return(expr), name, parentenv, handler)   11: tryCatchOne(expr, names, parentenv, handlers[[1L]])   12: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])   13: doTryCatch(return(expr), name, parentenv, handler)   14: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])   15: tryCatchList(expr, classes, parentenv, handlers)   16: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })   17: test_code(desc, code, env = parent.frame(), default_reporter = local_interactive_reporter())   18: test_that("smoothing splines lead to plausible results", { cp <- cutpointr(suicide, dsi, suicide, method = maximize_spline_metric, nknots = 5, spar = 0.3) expect_equal(cp$optimal_cutpoint, 3) test_plot.cutpointr(cp) test_ggplot_functions(cp) expect_silent(summary(cp)) cp <- cutpointr(suicide, dsi, suicide, gender, method = maximize_spline_metric, nknots = 5, spar = 0.3) expect_equal(cp$optimal_cutpoint, c(3, 3)) test_plot.cutpointr(cp) test_ggplot_functions(cp) expect_silent(summary(cp)) cp <- cutpointr(suicide, dsi, suicide, method = minimize_spline_metric, nknots = 5, spar = 0.3, df = 5, metric = abs_d_sens_spec) expect_equal(cp$optimal_cutpoint, 3) test_plot.cutpointr(cp) test_ggplot_functions(cp) expect_silent(summary(cp))})   19: eval(code, test_env)   20: eval(code, test_env)   21: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)   22: doTryCatch(return(expr), name, parentenv, handler)   23: tryCatchOne(expr, names, parentenv, handlers[[1L]])   24: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])   25: doTryCatch(return(expr), name, parentenv, handler)   26: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])   27: tryCatchList(expr, classes, parentenv, handlers)   28: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })   29: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())   30: source_file(path, env = env(env), desc = desc, error_call = error_call)   31: FUN(X[[i]], ...)   32: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)   33: doTryCatch(return(expr), name, parentenv, handler)   34: tryCatchOne(expr, names, parentenv, handlers[[1L]])   35: tryCatchList(expr, classes, parentenv, handlers)   36: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})   37: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call))   38: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, error_call = error_call)   39: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel)   40: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")   41: test_check("cutpointr")   An irrecoverable exception occurred. R is aborting now ...
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [163s/348s] ERROR Error(s) in re-building vignettes: --- re-building ‘cutpointr.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/cutpointr.Rcheck/vign_test/cutpointr/vignettes/cutpointr_files/figure-html/unnamed-chunk-4-1.png 576x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 13405 bytes Input file size = 14275 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11964   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 = 11964 Output IDAT size = 11964 bytes (1441 bytes decrease) Output file size = 12042 bytes (2233 bytes = 15.64% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/cutpointr.Rcheck/vign_test/cutpointr/vignettes/cutpointr_files/figure-html/unnamed-chunk-6-1.png 576x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 11924 bytes Input file size = 12794 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9803   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 = 9803 Output IDAT size = 9803 bytes (2121 bytes decrease) Output file size = 9881 bytes (2913 bytes = 22.77% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/cutpointr.Rcheck/vign_test/cutpointr/vignettes/cutpointr_files/figure-html/unnamed-chunk-10-1.png 576x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 23494 bytes Input file size = 24376 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21295   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 = 21295 Output IDAT size = 21295 bytes (2199 bytes decrease) Output file size = 21373 bytes (3003 bytes = 12.32% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/cutpointr.Rcheck/vign_test/cutpointr/vignettes/cutpointr_files/figure-html/unnamed-chunk-16-1.png 576x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 8950 bytes Input file size = 9820 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8292   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 = 8292 Output IDAT size = 8292 bytes (658 bytes decrease) Output file size = 8370 bytes (1450 bytes = 14.77% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/cutpointr.Rcheck/vign_test/cutpointr/vignettes/cutpointr_files/figure-html/unnamed-chunk-18-1.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 73442 bytes Input file size = 73616 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 61521   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 = 61521 Output IDAT size = 61521 bytes (11921 bytes decrease) Output file size = 61599 bytes (12017 bytes = 16.32% decrease) --- finished re-building ‘cutpointr.Rmd’ --- re-building ‘cutpointr_benchmarks.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/cutpointr.Rcheck/vign_test/cutpointr/vignettes/cutpointr_benchmarks_files/figure-html/unnamed-chunk-8-1.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 62069 bytes Input file size = 62231 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 50500   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 = 50500 Output IDAT size = 50500 bytes (11569 bytes decrease) Output file size = 50578 bytes (11653 bytes = 18.73% decrease) --- finished re-building ‘cutpointr_benchmarks.Rmd’ --- re-building ‘cutpointr_bootstrapping.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/cutpointr.Rcheck/vign_test/cutpointr/vignettes/cutpointr_bootstrapping_files/figure-html/unnamed-chunk-8-1.png 576x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 23679 bytes Input file size = 24561 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21545   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 = 21545 Output IDAT size = 21545 bytes (2134 bytes decrease) Output file size = 21623 bytes (2938 bytes = 11.96% decrease) --- finished re-building ‘cutpointr_bootstrapping.Rmd’ --- re-building ‘cutpointr_estimation.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/cutpointr.Rcheck/vign_test/cutpointr/vignettes/cutpointr_estimation_files/figure-html/unnamed-chunk-4-1.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 30112 bytes Input file size = 30226 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26131   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 = 26131 Output IDAT size = 26131 bytes (3981 bytes decrease) Output file size = 26209 bytes (4017 bytes = 13.29% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/cutpointr.Rcheck/vign_test/cutpointr/vignettes/cutpointr_estimation_files/figure-html/unnamed-chunk-6-1.png 576x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 37904 bytes Input file size = 38030 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 31621   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 = 31621 Output IDAT size = 31621 bytes (6283 bytes decrease) Output file size = 31699 bytes (6331 bytes = 16.65% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/cutpointr.Rcheck/vign_test/cutpointr/vignettes/cutpointr_estimation_files/figure-html/unnamed-chunk-7-1.png 576x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 14342 bytes Input file size = 15212 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12653   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 = 12653 Output IDAT size = 12653 bytes (1689 bytes decrease) Output file size = 12731 bytes (2481 bytes = 16.31% decrease)  *** caught segfault *** address 0x1, cause 'memory not mapped' Traceback:  1: stats::smooth.spline(x = roccurve$x.sorted[finite_roc], y = roccurve$m[finite_roc], w = args[["w"]], spar = args[["spar"]], cv = FALSE, nknots = nknots, df.offset = args[["df_offset"]], penalty = args[["penalty"]], control.spar = args[["control_spar"]], tol = 1e-100)  2: optimize_metric(data = data, x = x, class = class, metric_func = metric_func, pos_class = pos_class, neg_class = neg_class, minmax = "min", direction = direction, metric_name = metric_name, w = w, df = df, spar = spar, nknots = nknots, df_offset = df_offset, penalty = penalty, control_spar = control_spar, spline = TRUE, tol_metric = tol_metric, use_midpoints = use_midpoints, ...)  3: method(data = d, x = predictor, class = outcome, metric_func = metric, direction = direction, pos_class = pos_class, neg_class = neg_class, tol_metric = tol_metric, use_midpoints = use_midpoints, boot_stratify = boot_stratify, ...)  4: .f(.l[[1L]][[i]], .l[[2L]][[i]], ...)  5: .Primitive(".Call")(list(name = "pmap_impl", address = <pointer: 0x2b730a0>, dll = list(name = "purrr", path = "/data/gannet/ripley/R/test-dev/purrr/libs/purrr.so", dynamicLookup = FALSE, handle = <pointer: 0x7f9f390>, info = <pointer: 0x4b898e0>, forceSymbols = FALSE), numParameters = 8L), <environment>, "list", FALSE, 2L, NULL, 1L, NULL, 2L)  6: call_with_cleanup(pmap_impl, environment(), .type, .progress, n, names, i, call_names, call_n)  7: withCallingHandlers(expr, error = function(cnd) { if (i == 0L) { } else { message <- c(i = "In index: {i}.") if (!is.null(names) && !is.na(names[[i]]) && names[[i]] != "") { name <- names[[i]] message <- c(message, i = "With name: {name}.") } else { name <- NULL } cli::cli_abort(message, location = i, name = name, parent = cnd, call = error_call, class = "purrr_error_indexed") }})  8: with_indexed_errors(i = i, names = names, error_call = .purrr_error_call, call_with_cleanup(pmap_impl, environment(), .type, .progress, n, names, i, call_names, call_n))  9: pmap_("list", .l, .f, ..., .progress = .progress) 10: purrr::pmap(list(dat$subgroup, dat$data), function(g, d) { if (nrow(d) <= 1) stop(paste("Subgroup", g, "has <= 1 observations")) optcut <- tibble::tibble(subgroup = g) method_result <- method(data = d, x = predictor, class = outcome, metric_func = metric, direction = direction, pos_class = pos_class, neg_class = neg_class, tol_metric = tol_metric, use_midpoints = use_midpoints, boot_stratify = boot_stratify, ...) method_result <- check_method_cols(method_result) optcut <- dplyr::bind_cols(optcut, method_result) if (length(optcut[["optimal_cutpoint"]][[1]]) > 1) { message("Multiple optimal cutpoints found, applying break_ties.") } optcut <- apply_break_ties(optcut, break_ties) if (!(has_column(optcut, "roc_curve"))) { roc_curve <- roc(data = d, x = !!predictor, class = !!outcome, pos_class = pos_class, neg_class = neg_class, direction = direction) roc_curve <- tibble::tibble(roc_curve = list(roc_curve)) optcut <- dplyr::bind_cols(tibble::as_tibble(roc_curve), tibble::as_tibble(optcut)) } else { check_roc_curve(optcut) } if (ncol(optcut) <= 3) { opt_ind <- get_opt_ind(optcut$roc_curve[[1]], oc = unlist(optcut$optimal_cutpoint), direction = direction) m <- metric(tp = optcut$roc_curve[[1]]$tp[opt_ind], fp = optcut$roc_curve[[1]]$fp[opt_ind], tn = optcut$roc_curve[[1]]$tn[opt_ind], fn = optcut$roc_curve[[1]]$fn[opt_ind], .roc_curve = optcut$roc_curve[[1]], ...) m <- check_metric_name(m) colnames(m) <- make.names(colnames(m)) optcut <- dplyr::bind_cols(optcut, tibble::as_tibble(m)) } optcut <- check_colnames(optcut) opt_ind <- get_opt_ind(optcut$roc_curve[[1]], oc = unlist(optcut$optimal_cutpoint), direction = direction) m <- metric(tp = optcut$roc_curve[[1]]$tp[opt_ind], fp = optcut$roc_curve[[1]]$fp[opt_ind], tn = optcut$roc_curve[[1]]$tn[opt_ind], fn = optcut$roc_curve[[1]]$fn[opt_ind], .roc_curve = optcut$roc_curve[[1]], ...) optcut <- add_list(optcut, as.numeric(m), optcut$metric_name) sesp <- sesp_from_oc(optcut$roc_curve[[1]], oc = optcut$optimal_cutpoint, direction = direction) optcut <- add_list(optcut, sesp[, "sensitivity"], "sensitivity") optcut <- add_list(optcut, sesp[, "specificity"], "specificity") acc <- accuracy_from_oc(optcut$roc_curve[[1]], oc = optcut$optimal_cutpoint[[1]], direction = direction)[, "accuracy"] optcut <- add_list(optcut, acc, "acc") return(optcut)}) 11: cutpointr_internal(x, class, subgroup, method, metric, pos_class, neg_class, direction, boot_runs, boot_stratify, use_midpoints, break_ties, na.rm, allowParallel, predictor, outcome, mod_name, subgroup_var, tol_metric, ...) 12: cutpointr.default(suicide, dsi, suicide, gender, method = minimize_spline_metric, spar = 0.4, metric = misclassification_cost, cost_fp = 1, cost_fn = 10) 13: cutpointr(suicide, dsi, suicide, gender, method = minimize_spline_metric, spar = 0.4, metric = misclassification_cost, cost_fp = 1, cost_fn = 10) 14: eval(expr, envir) 15: eval(expr, envir) 16: withVisible(eval(expr, envir)) 17: withCallingHandlers(code, message = function (cnd) { watcher$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$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = invokeRestart("eval_error", cnd))}) 18: eval(call) 19: eval(call) 20: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers) 21: doWithOneRestart(return(expr), restart) 22: withOneRestart(expr, restarts[[1L]]) 23: withRestartList(expr, restarts[-nr]) 24: doWithOneRestart(return(expr), restart) 25: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 26: withRestartList(expr, restarts[-nr]) 27: doWithOneRestart(return(expr), restart) 28: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 29: withRestartList(expr, restarts) 30: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE, eval_error = function(cnd) { signalCondition(cnd) stop(cnd) }) 31: evaluate::evaluate(...) 32: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)) 33: in_dir(input_dir(), expr) 34: 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$render, options))) 35: eng_r(options) 36: block_exec(params) 37: call_block(x) 38: process_group(group) 39: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)) 40: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 41: process_file(text, output) 42: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 43: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 44: vweave_rmarkdown(...) 45: engine$weave(file, quiet = quiet, encoding = enc) 46: doTryCatch(return(expr), name, parentenv, handler) 47: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 48: tryCatchList(expr, classes, parentenv, handlers) 49: 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)))}) 50: tools:::.buildOneVignette("cutpointr_estimation.Rmd", "/data/gannet/ripley/R/packages/tests-devel/cutpointr.Rcheck/vign_test/cutpointr", TRUE, FALSE, "cutpointr_estimation", "UTF-8", "/tmp/RtmpxJ8fve/working_dir/Rtmp3bqaNN/file3ab37c3e074f77.rds") An irrecoverable exception occurred. R is aborting now ... --- re-building ‘cutpointr_plotting.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/cutpointr.Rcheck/vign_test/cutpointr/vignettes/cutpointr_plotting_files/figure-html/unnamed-chunk-2-1.png 384x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 20797 bytes Input file size = 20899 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18771   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 = 18771 Output IDAT size = 18771 bytes (2026 bytes decrease) Output file size = 18849 bytes (2050 bytes = 9.81% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/cutpointr.Rcheck/vign_test/cutpointr/vignettes/cutpointr_plotting_files/figure-html/unnamed-chunk-2-2.png 384x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 25202 bytes Input file size = 25316 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20506   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 = 20506 Output IDAT size = 20506 bytes (4696 bytes decrease) Output file size = 20584 bytes (4732 bytes = 18.69% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/cutpointr.Rcheck/vign_test/cutpointr/vignettes/cutpointr_plotting_files/figure-html/unnamed-chunk-2-3.png 384x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 19983 bytes Input file size = 20085 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17530   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 = 17530 Output IDAT size = 17530 bytes (2453 bytes decrease) Output file size = 17608 bytes (2477 bytes = 12.33% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/cutpointr.Rcheck/vign_test/cutpointr/vignettes/cutpointr_plotting_files/figure-html/unnamed-chunk-2-4.png 384x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 19058 bytes Input file size = 19160 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15236   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 = 15236 Output IDAT size = 15236 bytes (3822 bytes decrease) Output file size = 15314 bytes (3846 bytes = 20.07% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/cutpointr.Rcheck/vign_test/cutpointr/vignettes/cutpointr_plotting_files/figure-html/unnamed-chunk-2-5.png 384x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 29786 bytes Input file size = 29900 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22864   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 = 22864 Output IDAT size = 22864 bytes (6922 bytes decrease) Output file size = 22942 bytes (6958 bytes = 23.27% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/cutpointr.Rcheck/vign_test/cutpointr/vignettes/cutpointr_plotting_files/figure-html/unnamed-chunk-2-6.png 384x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 17918 bytes Input file size = 18020 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14671   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 = 14671 Output IDAT size = 14671 bytes (3247 bytes decrease) Output file size = 14749 bytes (3271 bytes = 18.15% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/cutpointr.Rcheck/vign_test/cutpointr/vignettes/cutpointr_plotting_files/figure-html/unnamed-chunk-3-1.png 384x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 20518 bytes Input file size = 20620 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16158   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 = 16158 Output IDAT size = 16158 bytes (4360 bytes decrease) Output file size = 16236 bytes (4384 bytes = 21.26% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/cutpointr.Rcheck/vign_test/cutpointr/vignettes/cutpointr_plotting_files/figure-html/unnamed-chunk-4-1.png 384x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 8423 bytes Input file size = 9293 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7585   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 = 7585 Output IDAT size = 7585 bytes (838 bytes decrease) Output file size = 7663 bytes (1630 bytes = 17.54% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/cutpointr.Rcheck/vign_test/cutpointr/vignettes/cutpointr_plotting_files/figure-html/unnamed-chunk-4-2.png 384x288 pixels, 8 bits/pixel, 254 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 5602 bytes Input file size = 6454 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4728   zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 4724   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 = 1 f = 0 IDAT size = 4724 Output IDAT size = 4724 bytes (878 bytes decrease) Output file size = 4802 bytes (1652 bytes = 25.60% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/cutpointr.Rcheck/vign_test/cutpointr/vignettes/cutpointr_plotting_files/figure-html/unnamed-chunk-4-3.png 384x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 6813 bytes Input file size = 7671 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6179   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 = 6179 Output IDAT size = 6179 bytes (634 bytes decrease) Output file size = 6257 bytes (1414 bytes = 18.43% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/cutpointr.Rcheck/vign_test/cutpointr/vignettes/cutpointr_plotting_files/figure-html/unnamed-chunk-5-1.png 384x288 pixels, 8 bits/pixel, 249 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 4497 bytes Input file size = 5334 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3864   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 = 3864 Output IDAT size = 3864 bytes (633 bytes decrease) Output file size = 3942 bytes (1392 bytes = 26.10% decrease) --- finished re-building ‘cutpointr_plotting.Rmd’ --- re-building ‘cutpointr_roc.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/cutpointr.Rcheck/vign_test/cutpointr/vignettes/cutpointr_roc_files/figure-html/unnamed-chunk-2-1.png 384x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 6302 bytes Input file size = 7160 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5358   zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 5356   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 = 1 f = 0 IDAT size = 5356 Output IDAT size = 5356 bytes (946 bytes decrease) Output file size = 5434 bytes (1726 bytes = 24.11% decrease) --- finished re-building ‘cutpointr_roc.Rmd’ --- re-building ‘cutpointr_user_functions.Rmd’ using rmarkdown --- finished re-building ‘cutpointr_user_functions.Rmd’ SUMMARY: processing the following file failed:   ‘cutpointr_estimation.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [12s/18s] OK
• checking HTML version of manual ... [6s/11s] OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 2 ERRORs, 2 NOTEs