Error(s) in re-building vignettes:
--- re-building ‘CI_fix.Rmd’ using rmarkdown
--- finished re-building ‘CI_fix.Rmd’

--- re-building ‘FAQ_and_limitations.Rmd’ using rmarkdown
--- finished re-building ‘FAQ_and_limitations.Rmd’

--- re-building ‘New_rmcorr_paper_analyses_figures.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/rmcorr.Rcheck/vign_test/rmcorr/vignettes/New_rmcorr_paper_analyses_figures_files/figure-html/unnamed-chunk-3-1.png
768x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 40261 bytes
Input file size = 40387 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 31777
  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 = 31777

Output IDAT size = 31777 bytes (8484 bytes decrease)
Output file size = 31855 bytes (8532 bytes = 21.13% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-clang/rmcorr.Rcheck/vign_test/rmcorr/vignettes/New_rmcorr_paper_analyses_figures_files/figure-html/unnamed-chunk-4-1.png
768x768 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 43872 bytes
Input file size = 44010 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 32123
  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 = 32123

Output IDAT size = 32123 bytes (11749 bytes decrease)
Output file size = 32201 bytes (11809 bytes = 26.83% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-clang/rmcorr.Rcheck/vign_test/rmcorr/vignettes/New_rmcorr_paper_analyses_figures_files/figure-html/unnamed-chunk-5-1.png
1152x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 24262 bytes
Input file size = 24364 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 21811
  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		IDAT size = 21515
  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 = 5		IDAT size = 21515

Output IDAT size = 21515 bytes (2747 bytes decrease)
Output file size = 21593 bytes (2771 bytes = 11.37% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-clang/rmcorr.Rcheck/vign_test/rmcorr/vignettes/New_rmcorr_paper_analyses_figures_files/figure-html/unnamed-chunk-6-1.png
576x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 50894 bytes
Input file size = 51044 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0
  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		IDAT size = 47267
  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 = 5		IDAT size = 47267

Output IDAT size = 47267 bytes (3627 bytes decrease)
Output file size = 47345 bytes (3699 bytes = 7.25% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-clang/rmcorr.Rcheck/vign_test/rmcorr/vignettes/New_rmcorr_paper_analyses_figures_files/figure-html/unnamed-chunk-7-1.png
864x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 72200 bytes
Input file size = 72374 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 56271
  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 = 56271

Output IDAT size = 56271 bytes (15929 bytes decrease)
Output file size = 56349 bytes (16025 bytes = 22.14% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-clang/rmcorr.Rcheck/vign_test/rmcorr/vignettes/New_rmcorr_paper_analyses_figures_files/figure-html/unnamed-chunk-8-1.png
864x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 32545 bytes
Input file size = 32659 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 24935
  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 = 24935

Output IDAT size = 24935 bytes (7610 bytes decrease)
Output file size = 25013 bytes (7646 bytes = 23.41% decrease)


Quitting from lines 647-701 [unnamed-chunk-9] (New_rmcorr_paper_analyses_figures.Rmd)
Error: processing vignette 'New_rmcorr_paper_analyses_figures.Rmd' failed with diagnostics:
Profiling over both the residual variance and
fixed effects is not numerically consistent with
profiling over the fixed effects only (relative difference: 1);
consider adjusting devmatchtol
--- failed re-building ‘New_rmcorr_paper_analyses_figures.Rmd’

--- re-building ‘compcor.Rmd’ using rmarkdown
--- finished re-building ‘compcor.Rmd’

--- re-building ‘estimates_w_NaN.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/rmcorr.Rcheck/vign_test/rmcorr/vignettes/estimates_w_NaN_files/figure-html/unnamed-chunk-3-1.png
288x288 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 4840 bytes
Input file size = 5695 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 4266
  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 = 4266

Output IDAT size = 4266 bytes (574 bytes decrease)
Output file size = 4344 bytes (1351 bytes = 23.72% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-clang/rmcorr.Rcheck/vign_test/rmcorr/vignettes/estimates_w_NaN_files/figure-html/unnamed-chunk-3-2.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 6479 bytes
Input file size = 6557 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 4863
  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 = 4863

Output IDAT size = 4863 bytes (1616 bytes decrease)
Output file size = 4941 bytes (1616 bytes = 24.65% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-clang/rmcorr.Rcheck/vign_test/rmcorr/vignettes/estimates_w_NaN_files/figure-html/unnamed-chunk-4-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 13408 bytes
Input file size = 13498 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 10162
  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 = 10162

Output IDAT size = 10162 bytes (3246 bytes decrease)
Output file size = 10240 bytes (3258 bytes = 24.14% decrease)

--- finished re-building ‘estimates_w_NaN.Rmd’

--- re-building ‘model_diag.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/rmcorr.Rcheck/vign_test/rmcorr/vignettes/model_diag_files/figure-html/unnamed-chunk-3-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 49346 bytes
Input file size = 49496 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 31391
  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 = 31391

Output IDAT size = 31391 bytes (17955 bytes decrease)
Output file size = 31469 bytes (18027 bytes = 36.42% decrease)

--- finished re-building ‘model_diag.Rmd’

--- re-building ‘overfitting.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/rmcorr.Rcheck/vign_test/rmcorr/vignettes/overfitting_files/figure-html/unnamed-chunk-4-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 29440 bytes
Input file size = 29554 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 20809
  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 = 20809

Output IDAT size = 20809 bytes (8631 bytes decrease)
Output file size = 20887 bytes (8667 bytes = 29.33% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-clang/rmcorr.Rcheck/vign_test/rmcorr/vignettes/overfitting_files/figure-html/unnamed-chunk-5-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 35625 bytes
Input file size = 35751 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 26855
  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 = 26855

Output IDAT size = 26855 bytes (8770 bytes decrease)
Output file size = 26933 bytes (8818 bytes = 24.67% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-clang/rmcorr.Rcheck/vign_test/rmcorr/vignettes/overfitting_files/figure-html/unnamed-chunk-6-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 15905 bytes
Input file size = 15995 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 11135
  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 = 11135

Output IDAT size = 11135 bytes (4770 bytes decrease)
Output file size = 11213 bytes (4782 bytes = 29.90% decrease)

--- finished re-building ‘overfitting.Rmd’

--- re-building ‘repro_bootstrapping.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/rmcorr.Rcheck/vign_test/rmcorr/vignettes/repro_bootstrapping_files/figure-html/unnamed-chunk-3-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 13369 bytes
Input file size = 13459 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 9945
  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 = 9945

Output IDAT size = 9945 bytes (3424 bytes decrease)
Output file size = 10023 bytes (3436 bytes = 25.53% decrease)

--- finished re-building ‘repro_bootstrapping.Rmd’

--- re-building ‘rmcorr_mat.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/rmcorr.Rcheck/vign_test/rmcorr/vignettes/rmcorr_mat_files/figure-html/unnamed-chunk-3-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 30648 bytes
Input file size = 30762 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 24895
  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 = 24895

Output IDAT size = 24895 bytes (5753 bytes decrease)
Output file size = 24973 bytes (5789 bytes = 18.82% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-clang/rmcorr.Rcheck/vign_test/rmcorr/vignettes/rmcorr_mat_files/figure-html/unnamed-chunk-4-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 20913 bytes
Input file size = 21015 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 17457
  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 = 17457

Output IDAT size = 17457 bytes (3456 bytes decrease)
Output file size = 17535 bytes (3480 bytes = 16.56% decrease)

--- finished re-building ‘rmcorr_mat.Rmd’

SUMMARY: processing the following file failed:
  ‘New_rmcorr_paper_analyses_figures.Rmd’

Error: Vignette re-building failed.
Execution halted