Error(s) in re-building vignettes:
--- re-building ‘examples.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/PopED.Rcheck/vign_test/PopED/vignettes/examples_files/figure-html/simulate_multi-response_model-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 15867 bytes
Input file size = 16737 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 14286
  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 = 14286

Output IDAT size = 14286 bytes (1581 bytes decrease)
Output file size = 14364 bytes (2373 bytes = 14.18% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-devel/PopED.Rcheck/vign_test/PopED/vignettes/examples_files/figure-html/simulate_ODE_model-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 24718 bytes
Input file size = 25612 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 22151
  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 = 18259
  zc = 9  zm = 8  zs = 1  f = 5		IDAT size = 18173
  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 = 5		IDAT size = 18173

Output IDAT size = 18173 bytes (6545 bytes decrease)
Output file size = 18251 bytes (7361 bytes = 28.74% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-devel/PopED.Rcheck/vign_test/PopED/vignettes/examples_files/figure-html/simulate_different_dose_regimen-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 66345 bytes
Input file size = 66519 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 55123
  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 = 55123

Output IDAT size = 55123 bytes (11222 bytes decrease)
Output file size = 55201 bytes (11318 bytes = 17.01% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-devel/PopED.Rcheck/vign_test/PopED/vignettes/examples_files/figure-html/unnamed-chunk-24-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 9787 bytes
Input file size = 10657 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 7998
  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 = 7998

Output IDAT size = 7998 bytes (1789 bytes decrease)
Output file size = 8076 bytes (2581 bytes = 24.22% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-devel/PopED.Rcheck/vign_test/PopED/vignettes/examples_files/figure-html/simulate_IOV_with_IIV-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 45473 bytes
Input file size = 45611 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 = 41110
  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 = 41110

Output IDAT size = 41110 bytes (4363 bytes decrease)
Output file size = 41188 bytes (4423 bytes = 9.70% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-devel/PopED.Rcheck/vign_test/PopED/vignettes/examples_files/figure-html/simulate_with_cov_matrix-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 14139 bytes
Input file size = 15009 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 12194
  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 = 12194

Output IDAT size = 12194 bytes (1945 bytes decrease)
Output file size = 12272 bytes (2737 bytes = 18.24% decrease)


Quitting from lines 971-988 [unnamed-chunk-46] (examples.Rmd)
Error: processing vignette 'examples.Rmd' failed with diagnostics:
incorrect number of dimensions
--- failed re-building ‘examples.Rmd’

--- re-building ‘intro-poped.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/PopED.Rcheck/vign_test/PopED/vignettes/intro-poped_files/figure-html/simulate_without_BSV-1.png
576x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 42543 bytes
Input file size = 42681 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 36728
  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 = 36728

Output IDAT size = 36728 bytes (5815 bytes decrease)
Output file size = 36806 bytes (5875 bytes = 13.76% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-devel/PopED.Rcheck/vign_test/PopED/vignettes/intro-poped_files/figure-html/simulate_with_BSV-1.png
576x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 17206 bytes
Input file size = 18088 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 15887
  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 = 15393
  zc = 9  zm = 8  zs = 1  f = 5		IDAT size = 15294
  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 = 5		IDAT size = 15294

Output IDAT size = 15294 bytes (1912 bytes decrease)
Output file size = 15372 bytes (2716 bytes = 15.02% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-devel/PopED.Rcheck/vign_test/PopED/vignettes/intro-poped_files/figure-html/simulate_optimal_design-1.png
576x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 42239 bytes
Input file size = 42377 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 36095
  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 = 36095

Output IDAT size = 36095 bytes (6144 bytes decrease)
Output file size = 36173 bytes (6204 bytes = 14.64% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-devel/PopED.Rcheck/vign_test/PopED/vignettes/intro-poped_files/figure-html/simulate_efficiency_windows-1.png
576x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 137872 bytes
Input file size = 138142 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 121576
  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 = 120826
  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 = 120826

Output IDAT size = 120826 bytes (17046 bytes decrease)
Output file size = 120904 bytes (17238 bytes = 12.48% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-devel/PopED.Rcheck/vign_test/PopED/vignettes/intro-poped_files/figure-html/simulate_discrete_optimization-1.png
576x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 42507 bytes
Input file size = 42645 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 36718
  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 = 36718

Output IDAT size = 36718 bytes (5789 bytes decrease)
Output file size = 36796 bytes (5849 bytes = 13.72% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-devel/PopED.Rcheck/vign_test/PopED/vignettes/intro-poped_files/figure-html/unnamed-chunk-16-1.png
576x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 22122 bytes
Input file size = 22224 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 17836
  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 = 17836

Output IDAT size = 17836 bytes (4286 bytes decrease)
Output file size = 17914 bytes (4310 bytes = 19.39% decrease)

--- finished re-building ‘intro-poped.Rmd’

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

Error: Vignette re-building failed.
Execution halted