Error(s) in re-building vignettes:
--- re-building ‘methodComparison.Rnw’ using Sweave
Loading required package: sm
Package 'sm', version 2.2-5.6: type help(sm) for summary information
Loading required package: zoo

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric

Error: processing vignette 'methodComparison.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'methodComparison.tex' failed.
LaTeX errors:
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.86 \includegraphics{methodComparison-plotSimmed}
                                                  
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.86 \includegraphics{methodComparison-plotSimmed}
                                                  
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.86 \includegraphics{methodComparison-plotSimmed}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.86 \includegraphics{methodComparison-plotSimmed}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.86 \includegraphics{methodComparison-plotSimmed}
                                                  
! LaTeX Error: File `methodComparison-plotSimmed' 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.113 ...egraphics{methodComparison-plotSimmedBox}
                                                  
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.113 ...egraphics{methodComparison-plotSimmedBox}
                                                  
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.113 ...egraphics{methodComparison-plotSimmedBox}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.113 ...egraphics{methodComparison-plotSimmedBox}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.113 ...egraphics{methodComparison-plotSimmedBox}
                                                  
! LaTeX Error: File `methodComparison-plotSimmedBox' 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.155 ...king_dir/RtmpNH4m4t/file3f7425ba8fa6.png}
                                                  
! Missing $ inserted.
<inserted text> 
                $
l.155 ...king_dir/RtmpNH4m4t/file3f7425ba8fa6.png}
                                                  
! Extra }, or forgotten $.
\Ginclude@graphics ...put@path \set@curr@file {#1}
                                                  \edef \uq@curr@file {\expa...
l.155 ...king_dir/RtmpNH4m4t/file3f7425ba8fa6.png}
                                                  
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.155 ...king_dir/RtmpNH4m4t/file3f7425ba8fa6.png}
                                                  
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.155 ...king_dir/RtmpNH4m4t/file3f7425ba8fa6.png}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.155 ...king_dir/RtmpNH4m4t/file3f7425ba8fa6.png}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.155 ...king_dir/RtmpNH4m4t/file3f7425ba8fa6.png}
                                                  
! LaTeX Error: File `/tmp/RtmpIBsHM2/working_dir/RtmpNH4m4t/file3f7425ba8fa6.pn
g' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! Missing $ inserted.
<inserted text> 
                $
l.155 ...king_dir/RtmpNH4m4t/file3f7425ba8fa6.png}
                                                  
! Missing } inserted.
<inserted text> 
                }
l.155 ...king_dir/RtmpNH4m4t/file3f7425ba8fa6.png}
                                                  
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.203 ...egraphics{methodComparison-showVpOrchard}
                                                  
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.203 ...egraphics{methodComparison-showVpOrchard}
                                                  
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.203 ...egraphics{methodComparison-showVpOrchard}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.203 ...egraphics{methodComparison-showVpOrchard}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.203 ...egraphics{methodComparison-showVpOrchard}
                                                  
! LaTeX Error: File `methodComparison-showVpOrchard' 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.239 ...degraphics{methodComparison-showVpSinger}
                                                  
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.239 ...degraphics{methodComparison-showVpSinger}
                                                  
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.239 ...degraphics{methodComparison-showVpSinger}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.239 ...degraphics{methodComparison-showVpSinger}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.239 ...degraphics{methodComparison-showVpSinger}
                                                  
! LaTeX Error: File `methodComparison-showVpSinger' 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.273 ...ludegraphics{methodComparison-showBeaver}
                                                  
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.273 ...ludegraphics{methodComparison-showBeaver}
                                                  
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.273 ...ludegraphics{methodComparison-showBeaver}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.273 ...ludegraphics{methodComparison-showBeave
--- failed re-building ‘methodComparison.Rnw’

--- re-building ‘usageExamples.Rnw’ using Sweave
Loading required package: ggplot2
Error: processing vignette 'usageExamples.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'usageExamples.tex' failed.
LaTeX errors:
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.43 \includegraphics{usageExamples-showVpPlot}
                                               
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.43 \includegraphics{usageExamples-showVpPlot}
                                               
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.43 \includegraphics{usageExamples-showVpPlot}
                                               
! Undefined control sequence.
<recently read> \quote@name 
                            
l.43 \includegraphics{usageExamples-showVpPlot}
                                               
! Undefined control sequence.
<recently read> \quote@name 
                            
l.43 \includegraphics{usageExamples-showVpPlot}
                                               
! LaTeX Error: File `usageExamples-showVpPlot' 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.56 \includegraphics{usageExamples-showVpOpts}
                                               
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.56 \includegraphics{usageExamples-showVpOpts}
                                               
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.56 \includegraphics{usageExamples-showVpOpts}
                                               
! Undefined control sequence.
<recently read> \quote@name 
                            
l.56 \includegraphics{usageExamples-showVpOpts}
                                               
! Undefined control sequence.
<recently read> \quote@name 
                            
l.56 \includegraphics{usageExamples-showVpOpts}
                                               
! LaTeX Error: File `usageExamples-showVpOpts' 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.68 \includegraphics{usageExamples-showVpFactors}
                                                  
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.68 \includegraphics{usageExamples-showVpFactors}
                                                  
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.68 \includegraphics{usageExamples-showVpFactors}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.68 \includegraphics{usageExamples-showVpFactors}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.68 \includegraphics{usageExamples-showVpFactors}
                                                  
! LaTeX Error: File `usageExamples-showVpFactors' 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.135 ...udegraphics{usageExamples-showDistAdjust}
                                                  
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.135 ...udegraphics{usageExamples-showDistAdjust}
                                                  
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.135 ...udegraphics{usageExamples-showDistAdjust}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.135 ...udegraphics{usageExamples-showDistAdjust}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.135 ...udegraphics{usageExamples-showDistAdjust}
                                                  
! LaTeX Error: File `usageExamples-showDistAdjust' 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.155 \includegraphics{usageExamples-showVarwidth}
                                                  
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.155 \includegraphics{usageExamples-showVarwidth}
                                                  
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.155 \includegraphics{usageExamples-showVarwidth}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.155 \includegraphics{usageExamples-showVarwidth}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.155 \includegraphics{usageExamples-showVarwidth}
                                                  
! LaTeX Error: File `usageExamples-showVarwidth' 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.172 \includegraphics{usageExamples-showBeaver}
                                                
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.172 \includegraphics{usageExamples-showBeaver}
                                                
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.172 \includegraphics{usageExamples-showBeaver}
                                                
! Undefined control sequence.
<recently read> \quote@name 
                            
l.172 \includegraphics{usageExamples-showBeaver}
                                                
! Undefined control sequence.
<recently read> \quote@name 
                            
l.172 \includegraphics{usageExamples-showBeaver}
                                                
! LaTeX Error: File `usageExamples-showBeaver' 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.194 \includegraphics{usageExamples-showGene}
                                              
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                               
--- failed re-building ‘usageExamples.Rnw’

SUMMARY: processing the following files failed:
  ‘methodComparison.Rnw’ ‘usageExamples.Rnw’

Error: Vignette re-building failed.
Execution halted