Error(s) in re-building vignettes:
  ...
--- re-building ‘LDheatmap.Rnw’ using Sweave
Loading required package: grid
Error: processing vignette 'LDheatmap.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'LDheatmap.tex' failed.
LaTeX errors:
! Argument of \@tempa has an extra }.
<inserted text> 
                \par 
l.57 \begin{document}
                     
! Paragraph ended before \@tempa was complete.
<to be read again> 
                   \par 
l.57 \begin{document}
                     
! Extra }, or forgotten \endgroup.
<recently read> }
                 
l.57 \begin{document}
                     
! Argument of \@tempa has an extra }.
<inserted text> 
                \par 
l.177 ..., angle=0, scale=0.9]{LDheatmap-Original}
                                                  
! Paragraph ended before \@tempa was complete.
<to be read again> 
                   \par 
l.177 ..., angle=0, scale=0.9]{LDheatmap-Original}
                                                  
! Extra }, or forgotten \endgroup.
<recently read> }
                 
l.177 ..., angle=0, scale=0.9]{LDheatmap-Original}
                                                  
! Extra }, or forgotten \endgroup.
\Gin@erotate ...angle {#1}\setbox \z@ \hbox {{#2}}
                                                  \Grot@x \z@ \Grot@y \z@ \G...
l.177 ..., angle=0, scale=0.9]{LDheatmap-Original}
                                                  
! Extra }, or forgotten \endgroup.
\Gscale@box ...scale@y {#2}\setbox \z@ \hbox {{#3}
                                                  }\setbox \tw@ \hbox {\Gsca...
l.177 ..., angle=0, scale=0.9]{LDheatmap-Original}
                                                  
! Extra }, or forgotten \endgroup.
\Gscale@box ...cale@y {#2}\setbox \z@ \hbox {{#3}}
                                                  \setbox \tw@ \hbox {\Gscal...
l.177 ..., angle=0, scale=0.9]{LDheatmap-Original}
                                                  
! Extra }, or forgotten \endgroup.
\mbox  #1->\leavevmode \hbox {#1}
                                 
l.177 ..., angle=0, scale=0.9]{LDheatmap-Original}
                                                  
! Missing \endgroup inserted.
<inserted text> 
                \endgroup 
l.179 ...EUSNP} produced by \code{LDheatmap()}.  }
                                                  
! Missing } inserted.
<inserted text> 
                }
l.179 ...EUSNP} produced by \code{LDheatmap()}.  }
                                                  
! Missing } inserted.
<inserted text> 
                }
l.179 ...EUSNP} produced by \code{LDheatmap()}.  }
                                                  
! Missing } inserted.
<inserted text> 
                }
l.179 ...EUSNP} produced by \code{LDheatmap()}.  }
                                                  
! Missing } inserted.
<inserted text> 
                }
l.179 ...EUSNP} produced by \code{LDheatmap()}.  }
                                                  
! Missing } inserted.
<inserted text> 
                }
l.179 ...EUSNP} produced by \code{LDheatmap()}.  }
                                                  
! Argument of \@tempa has an extra }.
<inserted text> 
                \par 
l.229 ...ht=4.5in, angle=0, scale=0.85]{gTree.pdf}
                                                  
! Paragraph ended before \@tempa was complete.
<to be read again> 
                   \par 
l.229 ...ht=4.5in, angle=0, scale=0.85]{gTree.pdf}
                                                  
! Extra }, or forgotten \endgroup.
<recently read> }
                 
l.229 ...ht=4.5in, angle=0, scale=0.85]{gTree.pdf}
                                                  
! Extra }, or forgotten \endgroup.
\Gin@erotate ...angle {#1}\setbox \z@ \hbox {{#2}}
                                                  \Grot@x \z@ \Grot@y \z@ \G...
l.229 ...ht=4.5in, angle=0, scale=0.85]{gTree.pdf}
                                                  
! Extra }, or forgotten \endgroup.
\Gscale@box ...scale@y {#2}\setbox \z@ \hbox {{#3}
                                                  }\setbox \tw@ \hbox {\Gsca...
l.229 ...ht=4.5in, angle=0, scale=0.85]{gTree.pdf}
                                                  
! Extra }, or forgotten \endgroup.
\Gscale@box ...cale@y {#2}\setbox \z@ \hbox {{#3}}
                                                  \setbox \tw@ \hbox {\Gscal...
l.229 ...ht=4.5in, angle=0, scale=0.85]{gTree.pdf}
                                                  
! Extra }, or forgotten \endgroup.
\mbox  #1->\leavevmode \hbox {#1}
                                 
l.229 ...ht=4.5in, angle=0, scale=0.85]{gTree.pdf}
                                                  
! Missing \endgroup inserted.
<inserted text> 
                \endgroup 
l.233 }
       
! Missing } inserted.
<inserted text> 
                }
l.233 }
       
! Missing } inserted.
<inserted text> 
                }
l.233 }
       
! Missing } inserted.
<inserted text> 
                }
l.233 }
       
! Missing } inserted.
<inserted text> 
                }
l.233 }
       
! Missing } inserted.
<inserted text> 
                }
l.233 }
       
! Argument of \@tempa has an extra }.
<inserted text> 
                \par 
l.287 ...gle=0, scale=0.9]{LDheatmap-Modified.pdf}
                                                  
! Paragraph ended before \@tempa was complete.
<to be read again> 
                   \par 
l.287 ...gle=0, scale=0.9]{LDheatmap-Modified.pdf}
                                                  
! Extra }, or forgotten \endgroup.
<recently read> }
                 
l.287 ...gle=0, scale=0.9]{LDheatmap-Modified.pdf}
                                                  
! Extra }, or forgotten \endgroup.
\Gin@erotate ...angle {#1}\setbox \z@ \hbox {{#2}}
                                                  \Grot@x \z@ \Grot@y \z@ \G...
l.287 ...gle=0, scale=0.9]{LDheatmap-Modified.pdf}
                                                  
! Extra }, or forgotten \endgroup.
\Gscale@box ...scale@y {#2}\setbox \z@ \hbox {{#3}
                                                  }\setbox \tw@ \hbox {\Gsca...
l.287 ...gle=0, scale=0.9]{LDheatmap-Modified.pdf}
                                                  
! Extra }, or forgotten \endgroup.
\Gscale@box ...cale@y {#2}\setbox \z@ \hbox {{#3}}
                                                  \setbox \tw@ \hbox {\Gscal...
l.287 ...gle=0, scale=0.9]{LDheatmap-Modified.pdf}
                                                  
! Extra }, or forgotten \endgroup.
\mbox  #1->\leavevmode \hbox {#1}
                                 
l.287 ...gle=0, scale=0.9]{LDheatmap-Modified.pdf}
                                                  
! Missing \endgroup inserted.
<inserted text> 
                \endgroup 
l.288 ... \code{"Color Key"} (color-scale title).}
                                                  
! Missing } inserted.
<inserted text> 
                }
l.288 ... \code{"Color Key"} (color-scale title).}
                                                  
! Missing } inserted.
<inserted text> 
                }
l.288 ... \code{"Color Key"} (color-scale title).}
                                                  
! Missing } inserted.
<inserted text> 
                }
l.288 ... \code{"Color Key"} (color-scale title).}
                                                  
! Missing } inserted.
<inserted text> 
                }
l.288 ... \code{"Color Key"} (color-scale title).}
                                                  
! Missing } inserted.
<inserted text> 
                }
l.288 ... \code{"Color Key"} (color-scale title).}
                                                  
! Argument of \@tempa has an extra }.
<inserted text> 
                \par 
l.364 scale=0.9]{LDheatmap-multiple.pdf}
                                        
! Paragraph ended before \@tempa was complete.
<to be read again> 
                   \par 
l.364 scale=0.9]{LDheatmap-multiple.pdf}
                                        
! Extra }, or forgotten \endgroup.
<recently read> }
                 
l.364 scale=0.9]{LDheatmap-multiple.pdf}
                                        
! Extra }, or forgotten \endgroup.
\Gin@erotate ...angle {#1}\setbox \z@ \hbox {{#2}}
                                                  \Grot@x \z@ \Grot@y \z@ \G...
l.364 scale=0.9]{LDheatmap-multiple.pdf}
   
--- failed re-building ‘LDheatmap.Rnw’

--- re-building ‘addTracks.Rnw’ using Sweave
Loading required package: survival
Loading required package: Matrix
Loading required package: ggplot2
Error: processing vignette 'addTracks.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'addTracks.tex' failed.
LaTeX errors:
! Paragraph ended before \@tempa was complete.
<to be read again> 
                   \par 
l.89 
     
! LaTeX Error: Not in outer par mode.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Paragraph ended before \@tempa was complete.
<to be read again> 
                   \par 
l.119 
      
! LaTeX Error: Not in outer par mode.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Paragraph ended before \@tempa was complete.
<to be read again> 
                   \par 
l.142 
      
! LaTeX Error: Not in outer par mode.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Paragraph ended before \@tempa was complete.
<to be read again> 
                   \par 
l.176 
      
! Paragraph ended before \@tempa was complete.
<to be read again> 
                   \par 
l.219 
      
! Paragraph ended before \@tempa was complete.
<to be read again> 
                   \par 
l.295 
      
! LaTeX Error: \begin{center} on input line 288 ended by \end{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! You can't use `\end' in internal vertical mode.
\enddocument ... \endgroup \deadcycles \z@ \@@end 
                                                  
l.388 \end{document}
                    
! LaTeX Error: \begin{center} on input line 288 ended by \end{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Emergency stop.
<*> \nonstopmode \input ./addTracks.tex
                                       
*** (job aborted, no legal \end found)

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘addTracks.Rnw’

SUMMARY: processing the following files failed:
  ‘LDheatmap.Rnw’ ‘addTracks.Rnw’

Error: Vignette re-building failed.
Execution halted