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 |
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