Error(s) in re-building vignettes:
--- re-building ‘gsea.Rmd’ using rmarkdown
Error: processing vignette 'gsea.Rmd' failed with diagnostics:
The closing fence on line 87 ("````") in gsea.Rmd does not match the opening fence "```" on line 85. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info.
--- failed re-building ‘gsea.Rmd’

--- re-building ‘interpreting.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-2-1.png
1344x960 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8741 bytes
Input file size = 9611 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 7175
  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 = 7175

Output IDAT size = 7175 bytes (1566 bytes decrease)
Output file size = 7253 bytes (2358 bytes = 24.53% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-devel/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-5-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 65958 bytes
Input file size = 66132 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 53106
  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 = 53106

Output IDAT size = 53106 bytes (12852 bytes decrease)
Output file size = 53184 bytes (12948 bytes = 19.58% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-devel/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-6-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 64263 bytes
Input file size = 64425 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 52689
  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 = 52689

Output IDAT size = 52689 bytes (11574 bytes decrease)
Output file size = 52767 bytes (11658 bytes = 18.10% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-devel/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-7-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 73537 bytes
Input file size = 73711 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 61615
  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 = 61615

Output IDAT size = 61615 bytes (11922 bytes decrease)
Output file size = 61693 bytes (12018 bytes = 16.30% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-devel/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-8-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 74765 bytes
Input file size = 74951 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 63428
  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 = 63428

Output IDAT size = 63428 bytes (11337 bytes decrease)
Output file size = 63506 bytes (11445 bytes = 15.27% decrease)

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

--- re-building ‘permpvals.Rmd’ using rmarkdown
Error: processing vignette 'permpvals.Rmd' failed with diagnostics:
The closing fence on line 69 ("````") in permpvals.Rmd does not match the opening fence "```" on line 67. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info.
--- failed re-building ‘permpvals.Rmd’

--- re-building ‘simulation.Rmd’ using rmarkdown
Error: processing vignette 'simulation.Rmd' failed with diagnostics:
The closing fence on line 93 ("````") in simulation.Rmd does not match the opening fence "```" on line 91. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info.
--- failed re-building ‘simulation.Rmd’

SUMMARY: processing the following files failed:
  ‘gsea.Rmd’ ‘permpvals.Rmd’ ‘simulation.Rmd’

Error: Vignette re-building failed.
Execution halted