Error(s) in re-building vignettes:
  ...
--- re-building ‘doby.rmd’ using knitr
** Processing: figure/unnamed-chunk-27-1.png
504x504 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 32155 bytes
Input file size = 32269 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 25263
  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 = 25263

Output IDAT size = 25263 bytes (6892 bytes decrease)
Output file size = 25341 bytes (6928 bytes = 21.47% decrease)

** Processing: figure/unnamed-chunk-28-1.png
504x504 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 24608 bytes
Input file size = 24722 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 19536
  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 = 19536

Output IDAT size = 19536 bytes (5072 bytes decrease)
Output file size = 19614 bytes (5108 bytes = 20.66% decrease)

** Processing: figure/unnamed-chunk-29-1.png
504x504 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 18315 bytes
Input file size = 18417 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 14654
  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 = 14654

Output IDAT size = 14654 bytes (3661 bytes decrease)
Output file size = 14732 bytes (3685 bytes = 20.01% decrease)

** Processing: figure/unnamed-chunk-31-1.png
504x504 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 18551 bytes
Input file size = 19433 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 16965
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 16961
  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 = 13764
  zc = 9  zm = 8  zs = 1  f = 5		IDAT size = 13760
  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 = 13760

Output IDAT size = 13760 bytes (4791 bytes decrease)
Output file size = 13838 bytes (5595 bytes = 28.79% decrease)

** Processing: figure/unnamed-chunk-33-1.png
504x504 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 26183 bytes
Input file size = 26297 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 = 24104
  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 = 24104

Output IDAT size = 24104 bytes (2079 bytes decrease)
Output file size = 24182 bytes (2115 bytes = 8.04% decrease)

** Processing: figure/unnamed-chunk-37-1.png
504x504 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8484 bytes
Input file size = 9354 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 7340
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 7335
  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 = 7335

Output IDAT size = 7335 bytes (1149 bytes decrease)
Output file size = 7413 bytes (1941 bytes = 20.75% decrease)

** Processing: figure/unnamed-chunk-38-1.png
504x504 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 46287 bytes
Input file size = 46425 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 43654
  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 = 43207
  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 = 43207

Output IDAT size = 43207 bytes (3080 bytes decrease)
Output file size = 43285 bytes (3140 bytes = 6.76% decrease)

--- finished re-building ‘doby.rmd’

--- re-building ‘linest_lsmeans.rnw’ using knitr

Quitting from lines 513-516 [unnamed-chunk-26] (linest_lsmeans.rnw)
Error: processing vignette 'linest_lsmeans.rnw' failed with diagnostics:
there is no package called ‘lme4’
--- failed re-building ‘linest_lsmeans.rnw’

--- re-building ‘section_fun.rmd’ using knitr
--- finished re-building ‘section_fun.rmd’

SUMMARY: processing the following file failed:
  ‘linest_lsmeans.rnw’

Error: Vignette re-building failed.
Execution halted