Last updated on 2024-12-03 17:49:10 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.2 | 31.68 | 265.93 | 297.61 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.1.2 | 20.87 | 178.05 | 198.92 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.1.2 | 508.92 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.2 | 524.42 | ERROR | |||
| r-devel-windows-x86_64 | 1.1.2 | 36.00 | 298.00 | 334.00 | ERROR | |
| r-patched-linux-x86_64 | 1.1.2 | 32.52 | 267.70 | 300.22 | NOTE | |
| r-release-linux-x86_64 | 1.1.2 | 29.12 | 268.94 | 298.06 | NOTE | |
| r-release-macos-arm64 | 1.1.2 | 156.00 | NOTE | |||
| r-release-macos-x86_64 | 1.1.2 | 250.00 | NOTE | |||
| r-release-windows-x86_64 | 1.1.2 | 37.00 | 325.00 | 362.00 | NOTE | |
| r-oldrel-macos-arm64 | 1.1.2 | 176.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 1.1.2 | 317.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 1.1.2 | 43.00 | 453.00 | 496.00 | NOTE |
Version: 1.1.2
Check: package subdirectories
Result: NOTE
Problems with news in ‘NEWS.md’:
Cannot extract version info from the following section titles:
Misc
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 1.1.2
Check: Rd files
Result: NOTE
checkRd: (-1) abs_d_ppv_npv.Rd:27: Escaped LaTeX specials: \_ \_ \_
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 1.1.2
Check: examples
Result: ERROR
Running examples in ‘cutpointr-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: maximize_spline_metric
> ### Title: Optimize a metric function in binary classification after spline
> ### smoothing
> ### Aliases: maximize_spline_metric minimize_spline_metric
>
> ### ** Examples
>
> oc <- cutpointr(suicide, dsi, suicide, gender, method = maximize_spline_metric,
+ df = 5, metric = accuracy)
Assuming the positive class is yes
Assuming the positive class has higher x values
nknots: 10
Error in `purrr::pmap()`:
ℹ In index: 1.
Caused by error in `stats::smooth.spline()`:
! df.offset must be numeric and >= 0
Backtrace:
▆
1. ├─cutpointr::cutpointr(...)
2. ├─cutpointr:::cutpointr.default(...)
3. │ └─cutpointr:::cutpointr_internal(...)
4. │ └─purrr::pmap(...)
5. │ └─purrr:::pmap_("list", .l, .f, ..., .progress = .progress)
6. │ ├─purrr:::with_indexed_errors(...)
7. │ │ └─base::withCallingHandlers(...)
8. │ ├─purrr:::call_with_cleanup(...)
9. │ └─cutpointr (local) .f(.l[[1L]][[i]], .l[[2L]][[i]], ...)
10. │ └─cutpointr (local) method(...)
11. │ └─cutpointr:::optimize_metric(...)
12. │ └─stats::smooth.spline(...)
13. │ └─base::stop("df.offset must be numeric and >= 0")
14. └─base::.handleSimpleError(...)
15. └─purrr (local) h(simpleError(msg, call))
16. └─cli::cli_abort(...)
17. └─rlang::abort(...)
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.1.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [97s/118s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(cutpointr)
>
> test_check("cutpointr")
[ FAIL 3 | WARN 14 | SKIP 0 | PASS 444 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-cutpointr.R:910:5'): smoothing splines lead to plausible results ──
Error in `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)`: df.offset must be numeric and >= 0
Backtrace:
▆
1. ├─cutpointr::cutpointr(...) at test-cutpointr.R:910:5
2. └─cutpointr:::cutpointr.default(...)
3. └─cutpointr:::cutpointr_internal(...)
4. └─cutpointr (local) method(...)
5. └─cutpointr:::optimize_metric(...)
6. └─stats::smooth.spline(...)
── Error ('test-cutpointr.R:985:5'): this led to an error with get_rev_dups Rcpp function ──
Error in `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)`: df.offset must be numeric and >= 0
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-cutpointr.R:985:5
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. ├─cutpointr::cutpointr(...)
10. └─cutpointr:::cutpointr.default(...)
11. ├─base::suppressMessages(...)
12. │ └─base::withCallingHandlers(...)
13. └─cutpointr:::cutpointr_internal(...)
14. └─cutpointr (local) method(...)
15. └─cutpointr:::optimize_metric(...)
16. └─stats::smooth.spline(...)
── Error ('test-cutpointr.R:1202:5'): predict behaves as expected ──────────────
Error in `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)`: df.offset must be numeric and >= 0
Backtrace:
▆
1. ├─cutpointr::cutpointr(...) at test-cutpointr.R:1202:5
2. └─cutpointr:::cutpointr.default(...)
3. └─cutpointr:::cutpointr_internal(...)
4. └─cutpointr (local) method(...)
5. └─cutpointr:::optimize_metric(...)
6. └─stats::smooth.spline(...)
[ FAIL 3 | WARN 14 | SKIP 0 | PASS 444 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.1.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘cutpointr.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/cutpointr.Rcheck/vign_test/cutpointr/vignettes/cutpointr_files/figure-html/unnamed-chunk-18-1.png
576x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 73441 bytes
Input file size = 73615 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 61523
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 = 61523
Output IDAT size = 61523 bytes (11918 bytes decrease)
Output file size = 61601 bytes (12014 bytes = 16.32% decrease)
--- finished re-building ‘cutpointr.Rmd’
--- re-building ‘cutpointr_benchmarks.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 = 62068 bytes
Input file size = 62230 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 50502
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 = 50502
Output IDAT size = 50502 bytes (11566 bytes decrease)
Output file size = 50580 bytes (11650 bytes = 18.72% decrease)
--- finished re-building ‘cutpointr_benchmarks.Rmd’
--- re-building ‘cutpointr_bootstrapping.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 = 21548
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 = 21548
Output IDAT size = 21548 bytes (2131 bytes decrease)
Output file size = 21626 bytes (2935 bytes = 11.95% decrease)
--- finished re-building ‘cutpointr_bootstrapping.Rmd’
--- re-building ‘cutpointr_estimation.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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)
Quitting from lines 135-139 [unnamed-chunk-8] (cutpointr_estimation.Rmd)
Error: processing vignette 'cutpointr_estimation.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `stats::smooth.spline()`:
! df.offset must be numeric and >= 0
--- failed re-building ‘cutpointr_estimation.Rmd’
--- re-building ‘cutpointr_plotting.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 = 20799 bytes
Input file size = 20901 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18762
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 = 18762
Output IDAT size = 18762 bytes (2037 bytes decrease)
Output file size = 18840 bytes (2061 bytes = 9.86% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 = 19980 bytes
Input file size = 20082 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17529
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 = 17529
Output IDAT size = 17529 bytes (2451 bytes decrease)
Output file size = 17607 bytes (2475 bytes = 12.32% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 = 19061 bytes
Input file size = 19163 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15240
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 = 15240
Output IDAT size = 15240 bytes (3821 bytes decrease)
Output file size = 15318 bytes (3845 bytes = 20.06% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 = 17919 bytes
Input file size = 18021 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14673
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 = 14673
Output IDAT size = 14673 bytes (3246 bytes decrease)
Output file size = 14751 bytes (3270 bytes = 18.15% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 = 8422 bytes
Input file size = 9292 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7586
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 = 7586
Output IDAT size = 7586 bytes (836 bytes decrease)
Output file size = 7664 bytes (1628 bytes = 17.52% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.1.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [62s/78s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(cutpointr)
>
> test_check("cutpointr")
[ FAIL 3 | WARN 14 | SKIP 0 | PASS 444 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-cutpointr.R:910:5'): smoothing splines lead to plausible results ──
Error in `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)`: df.offset must be numeric and >= 0
Backtrace:
▆
1. ├─cutpointr::cutpointr(...) at test-cutpointr.R:910:5
2. └─cutpointr:::cutpointr.default(...)
3. └─cutpointr:::cutpointr_internal(...)
4. └─cutpointr (local) method(...)
5. └─cutpointr:::optimize_metric(...)
6. └─stats::smooth.spline(...)
── Error ('test-cutpointr.R:985:5'): this led to an error with get_rev_dups Rcpp function ──
Error in `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)`: df.offset must be numeric and >= 0
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-cutpointr.R:985:5
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. ├─cutpointr::cutpointr(...)
10. └─cutpointr:::cutpointr.default(...)
11. ├─base::suppressMessages(...)
12. │ └─base::withCallingHandlers(...)
13. └─cutpointr:::cutpointr_internal(...)
14. └─cutpointr (local) method(...)
15. └─cutpointr:::optimize_metric(...)
16. └─stats::smooth.spline(...)
── Error ('test-cutpointr.R:1202:5'): predict behaves as expected ──────────────
Error in `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)`: df.offset must be numeric and >= 0
Backtrace:
▆
1. ├─cutpointr::cutpointr(...) at test-cutpointr.R:1202:5
2. └─cutpointr:::cutpointr.default(...)
3. └─cutpointr:::cutpointr_internal(...)
4. └─cutpointr (local) method(...)
5. └─cutpointr:::optimize_metric(...)
6. └─stats::smooth.spline(...)
[ FAIL 3 | WARN 14 | SKIP 0 | PASS 444 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘cutpointr.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cutpointr.Rcheck/vign_test/cutpointr/vignettes/cutpointr_files/figure-html/unnamed-chunk-18-1.png
576x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 73441 bytes
Input file size = 73615 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 61523
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 = 61523
Output IDAT size = 61523 bytes (11918 bytes decrease)
Output file size = 61601 bytes (12014 bytes = 16.32% decrease)
--- finished re-building ‘cutpointr.Rmd’
--- re-building ‘cutpointr_benchmarks.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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 = 62068 bytes
Input file size = 62230 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 50502
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 = 50502
Output IDAT size = 50502 bytes (11566 bytes decrease)
Output file size = 50580 bytes (11650 bytes = 18.72% decrease)
--- finished re-building ‘cutpointr_benchmarks.Rmd’
--- re-building ‘cutpointr_bootstrapping.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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 = 21548
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 = 21548
Output IDAT size = 21548 bytes (2131 bytes decrease)
Output file size = 21626 bytes (2935 bytes = 11.95% decrease)
--- finished re-building ‘cutpointr_bootstrapping.Rmd’
--- re-building ‘cutpointr_estimation.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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)
Quitting from lines 135-139 [unnamed-chunk-8] (cutpointr_estimation.Rmd)
Error: processing vignette 'cutpointr_estimation.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `stats::smooth.spline()`:
! df.offset must be numeric and >= 0
--- failed re-building ‘cutpointr_estimation.Rmd’
--- re-building ‘cutpointr_plotting.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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 = 20799 bytes
Input file size = 20901 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18762
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 = 18762
Output IDAT size = 18762 bytes (2037 bytes decrease)
Output file size = 18840 bytes (2061 bytes = 9.86% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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 = 19980 bytes
Input file size = 20082 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17529
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 = 17529
Output IDAT size = 17529 bytes (2451 bytes decrease)
Output file size = 17607 bytes (2475 bytes = 12.32% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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 = 19061 bytes
Input file size = 19163 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15240
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 = 15240
Output IDAT size = 15240 bytes (3821 bytes decrease)
Output file size = 15318 bytes (3845 bytes = 20.06% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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 = 17919 bytes
Input file size = 18021 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14673
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 = 14673
Output IDAT size = 14673 bytes (3246 bytes decrease)
Output file size = 14751 bytes (3270 bytes = 18.15% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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 = 8422 bytes
Input file size = 9292 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7586
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 = 7586
Output IDAT size = 7586 bytes (836 bytes decrease)
Output file size = 7664 bytes (1628 bytes = 17.52% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.2
Check: examples
Result: ERROR
Running examples in ‘cutpointr-Ex.R’ failed
The error most likely occurred in:
> ### Name: maximize_spline_metric
> ### Title: Optimize a metric function in binary classification after spline
> ### smoothing
> ### Aliases: maximize_spline_metric minimize_spline_metric
>
> ### ** Examples
>
> oc <- cutpointr(suicide, dsi, suicide, gender, method = maximize_spline_metric,
+ df = 5, metric = accuracy)
Assuming the positive class is yes
Assuming the positive class has higher x values
nknots: 10
Error in `purrr::pmap()`:
ℹ In index: 1.
Caused by error in `stats::smooth.spline()`:
! df.offset must be numeric and >= 0
Backtrace:
▆
1. ├─cutpointr::cutpointr(...)
2. ├─cutpointr:::cutpointr.default(...)
3. │ └─cutpointr:::cutpointr_internal(...)
4. │ └─purrr::pmap(...)
5. │ └─purrr:::pmap_("list", .l, .f, ..., .progress = .progress)
6. │ ├─purrr:::with_indexed_errors(...)
7. │ │ └─base::withCallingHandlers(...)
8. │ ├─purrr:::call_with_cleanup(...)
9. │ └─cutpointr (local) .f(.l[[1L]][[i]], .l[[2L]][[i]], ...)
10. │ └─cutpointr (local) method(...)
11. │ └─cutpointr:::optimize_metric(...)
12. │ └─stats::smooth.spline(...)
13. │ └─base::stop("df.offset must be numeric and >= 0")
14. └─base::.handleSimpleError(...)
15. └─purrr (local) h(simpleError(msg, call))
16. └─cli::cli_abort(...)
17. └─rlang::abort(...)
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64
Version: 1.1.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [157s/282s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(cutpointr)
>
> test_check("cutpointr")
[ FAIL 3 | WARN 14 | SKIP 0 | PASS 444 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-cutpointr.R:910:5'): smoothing splines lead to plausible results ──
Error in `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)`: df.offset must be numeric and >= 0
Backtrace:
▆
1. ├─cutpointr::cutpointr(...) at test-cutpointr.R:910:5
2. └─cutpointr:::cutpointr.default(...)
3. └─cutpointr:::cutpointr_internal(...)
4. └─cutpointr (local) method(...)
5. └─cutpointr:::optimize_metric(...)
6. └─stats::smooth.spline(...)
── Error ('test-cutpointr.R:985:5'): this led to an error with get_rev_dups Rcpp function ──
Error in `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)`: df.offset must be numeric and >= 0
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-cutpointr.R:985:5
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. ├─cutpointr::cutpointr(...)
10. └─cutpointr:::cutpointr.default(...)
11. ├─base::suppressMessages(...)
12. │ └─base::withCallingHandlers(...)
13. └─cutpointr:::cutpointr_internal(...)
14. └─cutpointr (local) method(...)
15. └─cutpointr:::optimize_metric(...)
16. └─stats::smooth.spline(...)
── Error ('test-cutpointr.R:1202:5'): predict behaves as expected ──────────────
Error in `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)`: df.offset must be numeric and >= 0
Backtrace:
▆
1. ├─cutpointr::cutpointr(...) at test-cutpointr.R:1202:5
2. └─cutpointr:::cutpointr.default(...)
3. └─cutpointr:::cutpointr_internal(...)
4. └─cutpointr (local) method(...)
5. └─cutpointr:::optimize_metric(...)
6. └─stats::smooth.spline(...)
[ FAIL 3 | WARN 14 | SKIP 0 | PASS 444 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.1.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘cutpointr.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/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-clang/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-clang/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-clang/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-clang/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-clang/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-clang/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-clang/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-clang/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-clang/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)
Quitting from lines 135-139 [unnamed-chunk-8] (cutpointr_estimation.Rmd)
Error: processing vignette 'cutpointr_estimation.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `stats::smooth.spline()`:
! df.offset must be numeric and >= 0
--- failed re-building ‘cutpointr_estimation.Rmd’
--- re-building ‘cutpointr_plotting.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/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-clang/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-clang/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-clang/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-clang/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-clang/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-clang/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-clang/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-clang/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-clang/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-clang/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-clang/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
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.1.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [164s/518s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(cutpointr)
>
> test_check("cutpointr")
[ FAIL 3 | WARN 14 | SKIP 0 | PASS 444 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-cutpointr.R:910:5'): smoothing splines lead to plausible results ──
Error in `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)`: df.offset must be numeric and >= 0
Backtrace:
▆
1. ├─cutpointr::cutpointr(...) at test-cutpointr.R:910:5
2. └─cutpointr:::cutpointr.default(...)
3. └─cutpointr:::cutpointr_internal(...)
4. └─cutpointr (local) method(...)
5. └─cutpointr:::optimize_metric(...)
6. └─stats::smooth.spline(...)
── Error ('test-cutpointr.R:985:5'): this led to an error with get_rev_dups Rcpp function ──
Error in `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)`: df.offset must be numeric and >= 0
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-cutpointr.R:985:5
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. ├─cutpointr::cutpointr(...)
10. └─cutpointr:::cutpointr.default(...)
11. ├─base::suppressMessages(...)
12. │ └─base::withCallingHandlers(...)
13. └─cutpointr:::cutpointr_internal(...)
14. └─cutpointr (local) method(...)
15. └─cutpointr:::optimize_metric(...)
16. └─stats::smooth.spline(...)
── Error ('test-cutpointr.R:1202:5'): predict behaves as expected ──────────────
Error in `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)`: df.offset must be numeric and >= 0
Backtrace:
▆
1. ├─cutpointr::cutpointr(...) at test-cutpointr.R:1202:5
2. └─cutpointr:::cutpointr.default(...)
3. └─cutpointr:::cutpointr_internal(...)
4. └─cutpointr (local) method(...)
5. └─cutpointr:::optimize_metric(...)
6. └─stats::smooth.spline(...)
[ FAIL 3 | WARN 14 | SKIP 0 | PASS 444 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.1.2
Check: re-building of vignette outputs
Result: 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)
Quitting from lines 135-139 [unnamed-chunk-8] (cutpointr_estimation.Rmd)
Error: processing vignette 'cutpointr_estimation.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `stats::smooth.spline()`:
! df.offset must be numeric and >= 0
--- failed re-building ‘cutpointr_estimation.Rmd’
--- 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
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.1.2
Check: tests
Result: ERROR
Running 'testthat.R' [73s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(cutpointr)
>
> test_check("cutpointr")
[ FAIL 3 | WARN 14 | SKIP 0 | PASS 444 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-cutpointr.R:910:5'): smoothing splines lead to plausible results ──
Error in `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)`: df.offset must be numeric and >= 0
Backtrace:
▆
1. ├─cutpointr::cutpointr(...) at test-cutpointr.R:910:5
2. └─cutpointr:::cutpointr.default(...)
3. └─cutpointr:::cutpointr_internal(...)
4. └─cutpointr (local) method(...)
5. └─cutpointr:::optimize_metric(...)
6. └─stats::smooth.spline(...)
── Error ('test-cutpointr.R:985:5'): this led to an error with get_rev_dups Rcpp function ──
Error in `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)`: df.offset must be numeric and >= 0
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-cutpointr.R:985:5
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. ├─cutpointr::cutpointr(...)
10. └─cutpointr:::cutpointr.default(...)
11. ├─base::suppressMessages(...)
12. │ └─base::withCallingHandlers(...)
13. └─cutpointr:::cutpointr_internal(...)
14. └─cutpointr (local) method(...)
15. └─cutpointr:::optimize_metric(...)
16. └─stats::smooth.spline(...)
── Error ('test-cutpointr.R:1202:5'): predict behaves as expected ──────────────
Error in `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)`: df.offset must be numeric and >= 0
Backtrace:
▆
1. ├─cutpointr::cutpointr(...) at test-cutpointr.R:1202:5
2. └─cutpointr:::cutpointr.default(...)
3. └─cutpointr:::cutpointr_internal(...)
4. └─cutpointr (local) method(...)
5. └─cutpointr:::optimize_metric(...)
6. └─stats::smooth.spline(...)
[ FAIL 3 | WARN 14 | SKIP 0 | PASS 444 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64
Version: 1.1.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'cutpointr.Rmd' using rmarkdown
--- finished re-building 'cutpointr.Rmd'
--- re-building 'cutpointr_benchmarks.Rmd' using rmarkdown
--- finished re-building 'cutpointr_benchmarks.Rmd'
--- re-building 'cutpointr_bootstrapping.Rmd' using rmarkdown
--- finished re-building 'cutpointr_bootstrapping.Rmd'
--- re-building 'cutpointr_estimation.Rmd' using rmarkdown
Quitting from lines 135-139 [unnamed-chunk-8] (cutpointr_estimation.Rmd)
Error: processing vignette 'cutpointr_estimation.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `stats::smooth.spline()`:
! df.offset must be numeric and >= 0
--- failed re-building 'cutpointr_estimation.Rmd'
--- re-building 'cutpointr_plotting.Rmd' using rmarkdown
--- finished re-building 'cutpointr_plotting.Rmd'
--- re-building 'cutpointr_roc.Rmd' using rmarkdown
--- 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
Flavor: r-devel-windows-x86_64