Error(s) in re-building vignettes:
--- re-building ‘decision-vegan.Rnw’ using Sweave
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-6
Error: processing vignette 'decision-vegan.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'decision-vegan.tex' failed.
LaTeX errors:
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.237 \includegraphics{decision-vegan-004}
                                          
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.237 \includegraphics{decision-vegan-004}
                                          
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.237 \includegraphics{decision-vegan-004}
                                          
! Undefined control sequence.
<recently read> \quote@name 
                            
l.237 \includegraphics{decision-vegan-004}
                                          
! Undefined control sequence.
<recently read> \quote@name 
                            
l.237 \includegraphics{decision-vegan-004}
                                          
! LaTeX Error: File `decision-vegan-004' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.551 \includegraphics{decision-vegan-007}
                                          
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.551 \includegraphics{decision-vegan-007}
                                          
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.551 \includegraphics{decision-vegan-007}
                                          
! Undefined control sequence.
<recently read> \quote@name 
                            
l.551 \includegraphics{decision-vegan-007}
                                          
! Undefined control sequence.
<recently read> \quote@name 
                            
l.551 \includegraphics{decision-vegan-007}
                                          
! LaTeX Error: File `decision-vegan-007' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.566 \includegraphics{decision-vegan-009}
                                          
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.566 \includegraphics{decision-vegan-009}
                                          
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.566 \includegraphics{decision-vegan-009}
                                          
! Undefined control sequence.
<recently read> \quote@name 
                            
l.566 \includegraphics{decision-vegan-009}
                                          
! Undefined control sequence.
<recently read> \quote@name 
                            
l.566 \includegraphics{decision-vegan-009}
                                          
! LaTeX Error: File `decision-vegan-009' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.580 \includegraphics{decision-vegan-011}
                                          
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.580 \includegraphics{decision-vegan-011}
                                          
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.580 \includegraphics{decision-vegan-011}
                                          
! Undefined control sequence.
<recently read> \quote@name 
                            
l.580 \includegraphics{decision-vegan-011}
                                          
! Undefined control sequence.
<recently read> \quote@name 
                            
l.580 \includegraphics{decision-vegan-011}
                                          
! LaTeX Error: File `decision-vegan-011' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.595 \includegraphics{decision-vegan-013}
                                          
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.595 \includegraphics{decision-vegan-013}
                                          
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.595 \includegraphics{decision-vegan-013}
                                          
! Undefined control sequence.
<recently read> \quote@name 
                            
l.595 \includegraphics{decision-vegan-013}
                                          
! Undefined control sequence.
<recently read> \quote@name 
                            
l.595 \includegraphics{decision-vegan-013}
                                          
! LaTeX Error: File `decision-vegan-013' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.664 \includegraphics{decision-vegan-015}
                                          
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.664 \includegraphics{decision-vegan-015}
                                          
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.664 \includegraphics{decision-vegan-015}
                                          
! Undefined control sequence.
<recently read> \quote@name 
                            
l.664 \includegraphics{decision-vegan-015}
                                          
! Undefined control sequence.
<recently read> \quote@name 
                            
l.664 \includegraphics{decision-vegan-015}
                                          
! LaTeX Error: File `decision-vegan-015' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.708 \includegraphics{decision-vegan-018}
                                          
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.708 \includegraphics{decision-vegan-018}
                                          
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.708 \includegraphics{decision-vegan-018}
                                          
! Undefined control sequence.
<recently read> \quote@name 
                            
l.708 \includegraphics{decision-vegan-018}
        
--- failed re-building ‘decision-vegan.Rnw’

--- re-building ‘diversity-vegan.Rnw’ using Sweave
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-6
forced matching of 'tree' labels and 'comm' names
Warning in cor(x > 0) : the standard deviation is zero
Warning in cor(x > 0) : the standard deviation is zero
Warning in betadisper(z, Management) :
  some squared distances are negative and changed to zero
Error: processing vignette 'diversity-vegan.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'diversity-vegan.tex' failed.
LaTeX errors:
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.123 \includegraphics{diversity-vegan-006}
                                           
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.123 \includegraphics{diversity-vegan-006}
                                           
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.123 \includegraphics{diversity-vegan-006}
                                           
! Undefined control sequence.
<recently read> \quote@name 
                            
l.123 \includegraphics{diversity-vegan-006}
                                           
! Undefined control sequence.
<recently read> \quote@name 
                            
l.123 \includegraphics{diversity-vegan-006}
                                           
! LaTeX Error: File `diversity-vegan-006' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.290 \includegraphics{diversity-vegan-014}
                                           
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.290 \includegraphics{diversity-vegan-014}
                                           
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.290 \includegraphics{diversity-vegan-014}
                                           
! Undefined control sequence.
<recently read> \quote@name 
                            
l.290 \includegraphics{diversity-vegan-014}
                                           
! Undefined control sequence.
<recently read> \quote@name 
                            
l.290 \includegraphics{diversity-vegan-014}
                                           
! LaTeX Error: File `diversity-vegan-014' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.354 \includegraphics{diversity-vegan-017}
                                           
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.354 \includegraphics{diversity-vegan-017}
                                           
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.354 \includegraphics{diversity-vegan-017}
                                           
! Undefined control sequence.
<recently read> \quote@name 
                            
l.354 \includegraphics{diversity-vegan-017}
                                           
! Undefined control sequence.
<recently read> \quote@name 
                            
l.354 \includegraphics{diversity-vegan-017}
                                           
! LaTeX Error: File `diversity-vegan-017' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.455 \includegraphics{diversity-vegan-020}
                                           
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.455 \includegraphics{diversity-vegan-020}
                                           
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.455 \includegraphics{diversity-vegan-020}
                                           
! Undefined control sequence.
<recently read> \quote@name 
                            
l.455 \includegraphics{diversity-vegan-020}
                                           
! Undefined control sequence.
<recently read> \quote@name 
                            
l.455 \includegraphics{diversity-vegan-020}
                                           
! LaTeX Error: File `diversity-vegan-020' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.526 \includegraphics{diversity-vegan-022}
                                           
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.526 \includegraphics{diversity-vegan-022}
                                           
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.526 \includegraphics{diversity-vegan-022}
                                           
! Undefined control sequence.
<recently read> \quote@name 
                            
l.526 \includegraphics{diversity-vegan-022}
                                           
! Undefined control sequence.
<recently read> \quote@name 
                            
l.526 \includegraphics{diversity-vegan-022}
                                           
! LaTeX Error: File `diversity-vegan-022' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.687 \includegraphics{diversity-vegan-028}
                                           
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.687 \includegraphics{diversity-vegan-028}
                                           
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.687 \includegraphics{diversity-vegan-028}
                                           
! Undefined control sequence.
<recently read> \quote@name 
                            
l.687 \includegraphics{diversity-vegan-028}
                                           
! Undefined control sequence.
<recently read> \quote@name 
                            
l.687 \includegraphics{diversity-vegan-028}
                                           
! LaTeX Error: File `diversity-vegan-028' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.958 \includegraphics{diversity-vegan-035}
                                           
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.958 \includegraphics{diversity-vegan-035}
                                           
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.958 \includegraphics{diversity-vegan-035}
                                           
! Undefined control sequence.
<recently read> \quote@name 
       
--- failed re-building ‘diversity-vegan.Rnw’

--- re-building ‘intro-vegan.Rnw’ using Sweave
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-6
Error: processing vignette 'intro-vegan.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'intro-vegan.tex' failed.
LaTeX errors:
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.195 \includegraphics{intro-vegan-006}
                                       
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.195 \includegraphics{intro-vegan-006}
                                       
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.195 \includegraphics{intro-vegan-006}
                                       
! Undefined control sequence.
<recently read> \quote@name 
                            
l.195 \includegraphics{intro-vegan-006}
                                       
! Undefined control sequence.
<recently read> \quote@name 
                            
l.195 \includegraphics{intro-vegan-006}
                                       
! LaTeX Error: File `intro-vegan-006' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.217 \includegraphics{intro-vegan-008}
                                       
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.217 \includegraphics{intro-vegan-008}
                                       
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.217 \includegraphics{intro-vegan-008}
                                       
! Undefined control sequence.
<recently read> \quote@name 
                            
l.217 \includegraphics{intro-vegan-008}
                                       
! Undefined control sequence.
<recently read> \quote@name 
                            
l.217 \includegraphics{intro-vegan-008}
                                       
! LaTeX Error: File `intro-vegan-008' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.298 \includegraphics{intro-vegan-011}
                                       
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.298 \includegraphics{intro-vegan-011}
                                       
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.298 \includegraphics{intro-vegan-011}
                                       
! Undefined control sequence.
<recently read> \quote@name 
                            
l.298 \includegraphics{intro-vegan-011}
                                       
! Undefined control sequence.
<recently read> \quote@name 
                            
l.298 \includegraphics{intro-vegan-011}
                                       
! LaTeX Error: File `intro-vegan-011' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.390 \includegraphics{intro-vegan-015}
                                       
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.390 \includegraphics{intro-vegan-015}
                                       
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.390 \includegraphics{intro-vegan-015}
                                       
! Undefined control sequence.
<recently read> \quote@name 
                            
l.390 \includegraphics{intro-vegan-015}
                                       
! Undefined control sequence.
<recently read> \quote@name 
                            
l.390 \includegraphics{intro-vegan-015}
                                       
! LaTeX Error: File `intro-vegan-015' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.441 \includegraphics{intro-vegan-018}
                                       
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.441 \includegraphics{intro-vegan-018}
                                       
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.441 \includegraphics{intro-vegan-018}
                                       
! Undefined control sequence.
<recently read> \quote@name 
                            
l.441 \includegraphics{intro-vegan-018}
                                       
! Undefined control sequence.
<recently read> \quote@name 
                            
l.441 \includegraphics{intro-vegan-018}
                                       
! LaTeX Error: File `intro-vegan-018' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
--- failed re-building ‘intro-vegan.Rnw’

--- re-building ‘partitioning.Rnw’ using Sweave
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-6
Error: processing vignette 'partitioning.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'partitioning.tex' failed.
LaTeX errors:
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.32 \includegraphics{partitioning-002}
                                       
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.32 \includegraphics{partitioning-002}
                                       
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.32 \includegraphics{partitioning-002}
                                       
! Undefined control sequence.
<recently read> \quote@name 
                            
l.32 \includegraphics{partitioning-002}
                                       
! Undefined control sequence.
<recently read> \quote@name 
                            
l.32 \includegraphics{partitioning-002}
                                       
! LaTeX Error: File `partitioning-002' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.42 \includegraphics{partitioning-003}
                                       
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.42 \includegraphics{partitioning-003}
                                       
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.42 \includegraphics{partitioning-003}
                                       
! Undefined control sequence.
<recently read> \quote@name 
                            
l.42 \includegraphics{partitioning-003}
                                       
! Undefined control sequence.
<recently read> \quote@name 
                            
l.42 \includegraphics{partitioning-003}
                                       
! LaTeX Error: File `partitioning-003' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.53 \includegraphics{partitioning-004}
                                       
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.53 \includegraphics{partitioning-004}
                                       
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.53 \includegraphics{partitioning-004}
                                       
! Undefined control sequence.
<recently read> \quote@name 
                            
l.53 \includegraphics{partitioning-004}
                                       
! Undefined control sequence.
<recently read> \quote@name 
                            
l.53 \includegraphics{partitioning-004}
                                       
! LaTeX Error: File `partitioning-004' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.65 ...epdf[fitpaper=true,pages=-]{varpart23.pdf}
                                                  
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.65 ...epdf[fitpaper=true,pages=-]{varpart23.pdf}
                                                  
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.65 ...epdf[fitpaper=true,pages=-]{varpart23.pdf}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.65 ...epdf[fitpaper=true,pages=-]{varpart23.pdf}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.65 ...epdf[fitpaper=true,pages=-]{varpart23.pdf}
                                                  
! LaTeX Error: File `varpart23.pdf' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
\AM@getpagecount ...ource {\AM@currentdocname@fix 
                                                  }\edef \AM@pagecount {\the...
l.65 ...epdf[fitpaper=true,pages=-]{varpart23.pdf}
                                                  
!pdfTeX error: pdflatex (file /usr/local/texlive/2019/texmf-dist/tex/latex/tool
s/.tex): unknown type of image
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘partitioning.Rnw’

--- re-building ‘FAQ-vegan.Rmd’ using knitr
--- finished re-building ‘FAQ-vegan.Rmd’

SUMMARY: processing the following files failed:
  ‘decision-vegan.Rnw’ ‘diversity-vegan.Rnw’ ‘intro-vegan.Rnw’
  ‘partitioning.Rnw’

Error: Vignette re-building failed.
Execution halted