Error(s) in re-building vignettes:
--- re-building ‘A-summarise_clinical_tables_records.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/A-summarise_clinical_tables_records_files/figure-html/unnamed-chunk-9-1.png
1344x960 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 56502 bytes
Input file size = 57432 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 50304
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 50136
  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 = 50136

Output IDAT size = 50136 bytes (6366 bytes decrease)
Output file size = 50214 bytes (7218 bytes = 12.57% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-devel/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/A-summarise_clinical_tables_records_files/figure-html/unnamed-chunk-10-1.png
1344x960 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 82012 bytes
Input file size = 82990 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 73229
  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 = 68729
  zc = 9  zm = 8  zs = 1  f = 5		IDAT size = 67516
  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 = 67516

Output IDAT size = 67516 bytes (14496 bytes decrease)
Output file size = 67594 bytes (15396 bytes = 18.55% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-devel/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/A-summarise_clinical_tables_records_files/figure-html/unnamed-chunk-11-1.png
1344x960 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 69353 bytes
Input file size = 70307 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 61240
  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		IDAT size = 61134
  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 = 61134

Output IDAT size = 61134 bytes (8219 bytes decrease)
Output file size = 61212 bytes (9095 bytes = 12.94% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-devel/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/A-summarise_clinical_tables_records_files/figure-html/unnamed-chunk-13-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 269390 bytes
Input file size = 269852 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 219451
  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 = 219451

Output IDAT size = 219451 bytes (49939 bytes decrease)
Output file size = 219529 bytes (50323 bytes = 18.65% decrease)

--- finished re-building ‘A-summarise_clinical_tables_records.Rmd’

--- re-building ‘B-summarise_concept_set_counts.Rmd’ using rmarkdown

Quitting from lines 17-26 [unnamed-chunk-1] (B-summarise_concept_set_counts.Rmd)
Error: processing vignette 'B-summarise_concept_set_counts.Rmd' failed with diagnostics:
could not find function "eunomia_is_available"
--- failed re-building ‘B-summarise_concept_set_counts.Rmd’

--- re-building ‘C-summarise_observation_period.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-7-1.png
1344x960 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 15443 bytes
Input file size = 16310 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 11852
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 11816
  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 = 10566
  zc = 9  zm = 8  zs = 1  f = 5		IDAT size = 10475
  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 = 10475

Output IDAT size = 10475 bytes (4968 bytes decrease)
Output file size = 10553 bytes (5757 bytes = 35.30% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-devel/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-8-1.png
1344x960 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 18157 bytes
Input file size = 19039 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 14339
  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 = 11642
  zc = 9  zm = 8  zs = 1  f = 5		IDAT size = 11536
  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 = 11536

Output IDAT size = 11536 bytes (6621 bytes decrease)
Output file size = 11614 bytes (7425 bytes = 39.00% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-devel/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-8-2.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 39648 bytes
Input file size = 39774 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 = 34672
  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 = 34672

Output IDAT size = 34672 bytes (4976 bytes decrease)
Output file size = 34750 bytes (5024 bytes = 12.63% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-devel/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-13-1.png
1344x960 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 41772 bytes
Input file size = 42690 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 36493
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 35955
  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 = 35955

Output IDAT size = 35955 bytes (5817 bytes decrease)
Output file size = 36033 bytes (6657 bytes = 15.59% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-devel/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-14-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 185866 bytes
Input file size = 186208 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 144562
  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 = 144562

Output IDAT size = 144562 bytes (41304 bytes decrease)
Output file size = 144640 bytes (41568 bytes = 22.32% decrease)

--- finished re-building ‘C-summarise_observation_period.Rmd’

SUMMARY: processing the following file failed:
  ‘B-summarise_concept_set_counts.Rmd’

Error: Vignette re-building failed.
Execution halted