CRAN Package Check Results for Package metaumbrella

Last updated on 2024-10-31 17:49:36 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.11 18.01 683.47 701.48 OK
r-devel-linux-x86_64-debian-gcc 1.0.11 12.34 407.71 420.05 OK
r-devel-linux-x86_64-fedora-clang 1.0.11 1091.78 ERROR
r-devel-linux-x86_64-fedora-gcc 1.0.11 ERROR
r-devel-windows-x86_64 1.0.11 19.00 643.00 662.00 OK
r-patched-linux-x86_64 1.0.11 17.18 629.57 646.75 OK
r-release-linux-x86_64 1.0.11 18.25 636.11 654.36 OK
r-release-macos-arm64 1.0.11 299.00 OK
r-release-macos-x86_64 1.0.11 479.00 OK
r-release-windows-x86_64 1.0.11 18.00 663.00 681.00 OK
r-oldrel-macos-arm64 1.0.11 260.00 OK
r-oldrel-macos-x86_64 1.0.11 456.00 OK
r-oldrel-windows-x86_64 1.0.11 26.00 895.00 921.00 OK

Check Details

Version: 1.0.11
Check: tests
Result: ERROR Running ‘spelling.R’ Running ‘testthat.R’ [10m/11m] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(metaumbrella) > > test_check("metaumbrella") Analyzing factor: A Analyzing factor: A Analyzing factor: Pharmacological Analyzing factor: Pharmacological Analyzing factor: Pharmacological Analyzing factor: Physically_active Analyzing factor: Physically_active Analyzing factor: Physically_active The pre/post correlation was calculated using values indicated in studies: Ray (2014) / Livingston (2010) / Israel (2014) / Sosa (2018) / Haulman (2015) / Esquibel (2007) / Ledoux (1982) / Bell (1989) / Canchola (2008) / Gonzalez (2003) / Boucneau (2000) Analyzing factor: gestational_diabetes Analyzing factor: gestational_diabetes Analyzing factor: ASD Analyzing factor: ASD Analyzing factor: ASD Analyzing factor: SSRI Analyzing factor: SSRI Analyzing factor: Smoking Analyzing factor: Smoking Analyzing factor: Smoking Analyzing factor: Smoking Analyzing factor: Gestational_hypertension Analyzing factor: Gestational_hypertension Analyzing factor: Pharmacological Analyzing factor: Pharmacological Analyzing factor: Surgical Analyzing factor: ADHD Analyzing factor: ASD Analyzing factor: dyslexia Analyzing factor: ID Analyzing factor: Yoga Analyzing factor: Aerobic training Analyzing factor: Resistance training Analyzing factor: Mindfulness Analyzing factor: ID Analyzing factor: Smoking Analyzing factor: SSRI Analyzing factor: Yoga Analyzing factor: Pharmacological Analyzing factor: ADHD Analyzing factor: Pharmacological Analyzing factor: ADHD Analyzing factor: A Analyzing factor: Pharmacological Analyzing factor: Pharmacological Analyzing factor: Weisel 2020 In factor 'Weisel 2020': - study: 'Enock (2014)' contains multiple outcomes - study: 'Pham (2016)' contains multiple outcomes In factor 'Weisel 2020' some studies have multiple outcomes but they are not associated with any within-study correlation (which can be indicated in the 'r' column of the dataset). A value of r = 0.5 is assumed. [ FAIL 2 | WARN 7 | SKIP 59 | PASS 614 ] ══ Skipped tests (59) ══════════════════════════════════════════════════════════ • On CRAN (59): 'test-esb_test.R:10:5', 'test-esb_test.R:77:5', 'test-esb_test.R:138:5', 'test-esb_test.R:181:5', 'test-esb_test.R:234:5', 'test-esb_test.R:247:5', 'test-esb_test.R:299:5', 'test-esb_test.R:354:5', 'test-estimate_n_from_es.R:10:3', 'test-estimate_n_from_es.R:47:3', 'test-estimate_n_from_es.R:94:3', 'test-estimate_n_from_es.R:135:3', 'test-format_dataset.R:12:3', 'test-format_dataset.R:30:3', 'test-format_dataset.R:53:3', 'test-format_dataset.R:75:3', 'test-format_dataset.R:101:3', 'test-format_dataset.R:142:3', 'test-format_dataset.R:176:3', 'test-format_dataset.R:214:3', 'test-format_dataset.R:254:3', 'test-format_dataset.R:305:3', 'test-functions_multilevel.R:5:3', 'test-functions_multilevel.R:51:3', 'test-functions_multilevel.R:86:3', 'test-functions_multilevel.R:119:3', 'test-functions_multilevel.R:164:3', 'test-umbrella.R:8:3', 'test-umbrella.R:15:3', 'test-umbrella.R:47:3', 'test-umbrella.R:61:3', 'test-umbrella.R:82:3', 'test-umbrella.R:96:3', 'test-umbrella.R:124:3', 'test-umbrella.R:153:3', 'test-umbrella.R:172:3', 'test-umbrella.R:191:3', 'test-umbrella.R:415:3', 'test-umbrella.R:428:3', 'test-umbrella.R:446:3', 'test-umbrella.R:461:3', 'test-umbrella.R:477:3', 'test-umbrella.R:491:3', 'test-umbrella.R:510:3', 'test-umbrella.R:529:3', 'test-umbrella.R:547:3', 'test-umbrella.R:572:3', 'test-umbrella.R:589:3', 'test-umbrella.R:604:3', 'test-umbrella.R:624:3', 'test-umbrella.R:641:3', 'test-umbrella.R:658:3', 'test-umbrella.R:675:3', 'test-umbrella.R:692:3', 'test-umbrella.R:709:3', 'test-umbrella.R:726:3', 'test-umbrella.R:746:3', 'test-umbrella.R:791:3', 'test-umbrella.R:836:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-functions_meta.R:411:3'): meta_gen correctly estimates the prediction interval size from R ── as.numeric(as.character(umb$pi_lo)) (`actual`) not equal to as.numeric(as.character(meta$lower.predict)) (`expected`). `actual`: -0.566 `expected`: -0.563 ── Failure ('test-functions_meta.R:412:3'): meta_gen correctly estimates the prediction interval size from R ── as.numeric(as.character(umb$pi_up)) (`actual`) not equal to as.numeric(as.character(meta$upper.predict)) (`expected`). `actual`: 0.881 `expected`: 0.878 [ FAIL 2 | WARN 7 | SKIP 59 | PASS 614 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.0.11
Check: tests
Result: ERROR Running ‘spelling.R’ Running ‘testthat.R’ [11m/27m] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(metaumbrella) > > test_check("metaumbrella") Analyzing factor: A Analyzing factor: A Analyzing factor: Pharmacological Analyzing factor: Pharmacological Analyzing factor: Pharmacological Analyzing factor: Physically_active Analyzing factor: Physically_active Analyzing factor: Physically_active The pre/post correlation was calculated using values indicated in studies: Ray (2014) / Livingston (2010) / Israel (2014) / Sosa (2018) / Haulman (2015) / Esquibel (2007) / Ledoux (1982) / Bell (1989) / Canchola (2008) / Gonzalez (2003) / Boucneau (2000) Analyzing factor: gestational_diabetes Analyzing factor: gestational_diabetes Analyzing factor: ASD Analyzing factor: ASD Analyzing factor: ASD Analyzing factor: SSRI Analyzing factor: SSRI Analyzing factor: Smoking Analyzing factor: Smoking Analyzing factor: Smoking Analyzing factor: Smoking Analyzing factor: Gestational_hypertension Analyzing factor: Gestational_hypertension Analyzing factor: Pharmacological Analyzing factor: Pharmacological Analyzing factor: Surgical Analyzing factor: ADHD Analyzing factor: ASD Analyzing factor: dyslexia Analyzing factor: ID Analyzing factor: Yoga Analyzing factor: Aerobic training Analyzing factor: Resistance training Analyzing factor: Mindfulness Analyzing factor: ID Analyzing factor: Smoking Analyzing factor: SSRI Analyzing factor: Yoga Analyzing factor: Pharmacological Analyzing factor: ADHD Analyzing factor: Pharmacological Analyzing factor: ADHD Analyzing factor: A Analyzing factor: Pharmacological Analyzing factor: Pharmacological Analyzing factor: Weisel 2020 In factor 'Weisel 2020': - study: 'Enock (2014)' contains multiple outcomes - study: 'Pham (2016)' contains multiple outcomes In factor 'Weisel 2020' some studies have multiple outcomes but they are not associated with any within-study correlation (which can be indicated in the 'r' column of the dataset). A value of r = 0.5 is assumed. [ FAIL 2 | WARN 7 | SKIP 59 | PASS 614 ] ══ Skipped tests (59) ══════════════════════════════════════════════════════════ • On CRAN (59): 'test-esb_test.R:10:5', 'test-esb_test.R:77:5', 'test-esb_test.R:138:5', 'test-esb_test.R:181:5', 'test-esb_test.R:234:5', 'test-esb_test.R:247:5', 'test-esb_test.R:299:5', 'test-esb_test.R:354:5', 'test-estimate_n_from_es.R:10:3', 'test-estimate_n_from_es.R:47:3', 'test-estimate_n_from_es.R:94:3', 'test-estimate_n_from_es.R:135:3', 'test-format_dataset.R:12:3', 'test-format_dataset.R:30:3', 'test-format_dataset.R:53:3', 'test-format_dataset.R:75:3', 'test-format_dataset.R:101:3', 'test-format_dataset.R:142:3', 'test-format_dataset.R:176:3', 'test-format_dataset.R:214:3', 'test-format_dataset.R:254:3', 'test-format_dataset.R:305:3', 'test-functions_multilevel.R:5:3', 'test-functions_multilevel.R:51:3', 'test-functions_multilevel.R:86:3', 'test-functions_multilevel.R:119:3', 'test-functions_multilevel.R:164:3', 'test-umbrella.R:8:3', 'test-umbrella.R:15:3', 'test-umbrella.R:47:3', 'test-umbrella.R:61:3', 'test-umbrella.R:82:3', 'test-umbrella.R:96:3', 'test-umbrella.R:124:3', 'test-umbrella.R:153:3', 'test-umbrella.R:172:3', 'test-umbrella.R:191:3', 'test-umbrella.R:415:3', 'test-umbrella.R:428:3', 'test-umbrella.R:446:3', 'test-umbrella.R:461:3', 'test-umbrella.R:477:3', 'test-umbrella.R:491:3', 'test-umbrella.R:510:3', 'test-umbrella.R:529:3', 'test-umbrella.R:547:3', 'test-umbrella.R:572:3', 'test-umbrella.R:589:3', 'test-umbrella.R:604:3', 'test-umbrella.R:624:3', 'test-umbrella.R:641:3', 'test-umbrella.R:658:3', 'test-umbrella.R:675:3', 'test-umbrella.R:692:3', 'test-umbrella.R:709:3', 'test-umbrella.R:726:3', 'test-umbrella.R:746:3', 'test-umbrella.R:791:3', 'test-umbrella.R:836:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-functions_meta.R:411:3'): meta_gen correctly estimates the prediction interval size from R ── as.numeric(as.character(umb$pi_lo)) (`actual`) not equal to as.numeric(as.character(meta$lower.predict)) (`expected`). `actual`: -0.566 `expected`: -0.563 ── Failure ('test-functions_meta.R:412:3'): meta_gen correctly estimates the prediction interval size from R ── as.numeric(as.character(umb$pi_up)) (`actual`) not equal to as.numeric(as.character(meta$upper.predict)) (`expected`). `actual`: 0.881 `expected`: 0.878 [ FAIL 2 | WARN 7 | SKIP 59 | PASS 614 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.0.11
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘calculations-details.Rmd’ using rmarkdown --- finished re-building ‘calculations-details.Rmd’ --- re-building ‘conduct-umbrella.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/metaumbrella.Rcheck/vign_test/metaumbrella/vignettes/conduct-umbrella_files/figure-html/unnamed-chunk-14-1.png 768x691 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 14913 bytes Input file size = 15783 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13714 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 13678 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 = 13678 Output IDAT size = 13678 bytes (1235 bytes decrease) Output file size = 13756 bytes (2027 bytes = 12.84% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/metaumbrella.Rcheck/vign_test/metaumbrella/vignettes/conduct-umbrella_files/figure-html/unnamed-chunk-22-1.png 768x672 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 11117 bytes Input file size = 11987 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10140 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 10108 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 = 10108 Output IDAT size = 10108 bytes (1009 bytes decrease) Output file size = 10186 bytes (1801 bytes = 15.02% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/metaumbrella.Rcheck/vign_test/metaumbrella/vignettes/conduct-umbrella_files/figure-html/unnamed-chunk-33-1.png 768x691 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 13822 bytes Input file size = 14692 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12677 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 12585 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 = 12585 Output IDAT size = 12585 bytes (1237 bytes decrease) Output file size = 12663 bytes (2029 bytes = 13.81% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/metaumbrella.Rcheck/vign_test/metaumbrella/vignettes/conduct-umbrella_files/figure-html/unnamed-chunk-45-1.png 768x691 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 21356 bytes Input file size = 22238 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19848 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 19681 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 = 19681 Output IDAT size = 19681 bytes (1675 bytes decrease) Output file size = 19759 bytes (2479 bytes = 11.15% decrease) --- finished re-building ‘conduct-umbrella.Rmd’ --- re-building ‘format-dataset.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/metaumbrella.Rcheck/vign_test/metaumbrella/vignettes/format-dataset_files/figure-html/unnamed-chunk-23-1.png 672x672 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 16062 bytes Input file size = 16932 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14732 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 14681 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 = 14681 Output IDAT size = 14681 bytes (1381 bytes decrease) Output file size = 14759 bytes (2173 bytes = 12.83% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/metaumbrella.Rcheck/vign_test/metaumbrella/vignettes/format-dataset_files/figure-html/unnamed-chunk-28-1.png 672x672 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 16122 bytes Input file size = 16992 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14754 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 14713 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 = 14713 Output IDAT size = 14713 bytes (1409 bytes decrease) Output file size = 14791 bytes (2201 bytes = 12.95% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/metaumbrella.Rcheck/vign_test/metaumbrella/vignettes/format-dataset_files/figure-html/unnamed-chunk-31-1.png 672x672 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 16075 bytes Input file size = 16945 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14701 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 14654 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 = 14654 Output IDAT size = 14654 bytes (1421 bytes decrease) Output file size = 14732 bytes (2213 bytes = 13.06% decrease) --- finished re-building ‘format-dataset.Rmd’ --- re-building ‘generate-forest.Rmd’ using rmarkdown *** caught segfault *** address 0x5b70, cause 'memory not mapped' Traceback: 1: grid.newpage() 2: forest.meta(res, digits = digits, layout = layout, type.study = type.study, common = FALSE, random = FALSE, overall = FALSE, subgroup = ifelse(is.null(subgroup), FALSE, TRUE), subgroup.name = subgroup.name, smlab = smlab, xlab = xlab, leftcols = leftcols, leftlabs = leftlabs, rightcols = rightcols, rightlabs = rightlabs, hetstat = FALSE, col.study = col.study, col.square = col.square, col.square.lines = col.square.lines, fontsize = fontsize, spacing = spacing, squaresize = squaresize, backtransf = ifelse(measure == "eOR", TRUE, FALSE), ...) 3: forest(res, digits = digits, layout = layout, type.study = type.study, common = FALSE, random = FALSE, overall = FALSE, subgroup = ifelse(is.null(subgroup), FALSE, TRUE), subgroup.name = subgroup.name, smlab = smlab, xlab = xlab, leftcols = leftcols, leftlabs = leftlabs, rightcols = rightcols, rightlabs = rightlabs, hetstat = FALSE, col.study = col.study, col.square = col.square, col.square.lines = col.square.lines, fontsize = fontsize, spacing = spacing, squaresize = squaresize, backtransf = ifelse(measure == "eOR", TRUE, FALSE), ...) 4: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning")) 5: suppressWarnings(forest(res, digits = digits, layout = layout, type.study = type.study, common = FALSE, random = FALSE, overall = FALSE, subgroup = ifelse(is.null(subgroup), FALSE, TRUE), subgroup.name = subgroup.name, smlab = smlab, xlab = xlab, leftcols = leftcols, leftlabs = leftlabs, rightcols = rightcols, rightlabs = rightlabs, hetstat = FALSE, col.study = col.study, col.square = col.square, col.square.lines = col.square.lines, fontsize = fontsize, spacing = spacing, squaresize = squaresize, backtransf = ifelse(measure == "eOR", TRUE, FALSE), ...)) 6: forest.umbrella(umb) 7: forest(umb) 8: force(x) 9: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage")) 10: suppressMessages(invisible(force(x))) 11: metaumbrella:::.quiet(forest(umb)) 12: eval(expr, envir) 13: eval(expr, envir) 14: withVisible(eval(expr, envir)) 15: 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))}) 16: eval(call) 17: eval(call) 18: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers) 19: doWithOneRestart(return(expr), restart) 20: withOneRestart(expr, restarts[[1L]]) 21: withRestartList(expr, restarts[-nr]) 22: doWithOneRestart(return(expr), restart) 23: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 24: withRestartList(expr, restarts[-nr]) 25: doWithOneRestart(return(expr), restart) 26: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 27: withRestartList(expr, restarts) 28: withRestarts(with_handlers({ for (expr in tle$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) }) 29: evaluate::evaluate(...) 30: 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$render, options)) 31: in_dir(input_dir(), expr) 32: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))) 33: eng_r(options) 34: block_exec(params) 35: call_block(x) 36: process_group(group) 37: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)) 38: 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) 39: process_file(text, output) 40: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 41: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 42: vweave_rmarkdown(...) 43: engine$weave(file, quiet = quiet, encoding = enc) 44: doTryCatch(return(expr), name, parentenv, handler) 45: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 46: tryCatchList(expr, classes, parentenv, handlers) 47: tryCatch({ engine$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)))}) 48: tools:::.buildOneVignette("generate-forest.Rmd", "/data/gannet/ripley/R/packages/tests-devel/metaumbrella.Rcheck/vign_test/metaumbrella", TRUE, FALSE, "generate-forest", "UTF-8", "/tmp/Rtmpv6iuh2/working_dir/RtmpL2UJHt/file2f1df447198016.rds") An irrecoverable exception occurred. R is aborting now ... SUMMARY: processing the following file failed: ‘generate-forest.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc