Error(s) in re-building vignettes:
--- re-building ‘strum-example.Rnw’ using Sweave
Loading required package: pedigree
Loading required package: Matrix
Loading required package: HaploSim
Loading required package: reshape

Attaching package: ‘reshape’

The following object is masked from ‘package:Matrix’:

    expand

Loading required package: Rgraphviz
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:Matrix’:

    which

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: grid
Error: processing vignette 'strum-example.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'strum-example.tex' failed.
LaTeX errors:
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.36 ...\textwidth]{./figures/fig_association.png}
                                                  
! Missing $ inserted.
<inserted text> 
                $
l.36 ...\textwidth]{./figures/fig_association.png}
                                                  
! Extra }, or forgotten $.
\Ginclude@graphics ...put@path \set@curr@file {#1}
                                                  \edef \uq@curr@file {\expa...
l.36 ...\textwidth]{./figures/fig_association.png}
                                                  
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.36 ...\textwidth]{./figures/fig_association.png}
                                                  
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.36 ...\textwidth]{./figures/fig_association.png}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.36 ...\textwidth]{./figures/fig_association.png}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.36 ...\textwidth]{./figures/fig_association.png}
                                                  
! LaTeX Error: File `./figures/fig_association.png' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.36 ...\textwidth]{./figures/fig_association.png}
                                                  
! Missing } inserted.
<inserted text> 
                }
l.36 ...\textwidth]{./figures/fig_association.png}
                                                  
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.229 ....45\textwidth]{./figures/fig_linkage.png}
                                                  
! Missing $ inserted.
<inserted text> 
                $
l.229 ....45\textwidth]{./figures/fig_linkage.png}
                                                  
! Extra }, or forgotten $.
\Ginclude@graphics ...put@path \set@curr@file {#1}
                                                  \edef \uq@curr@file {\expa...
l.229 ....45\textwidth]{./figures/fig_linkage.png}
                                                  
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.229 ....45\textwidth]{./figures/fig_linkage.png}
                                                  
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.229 ....45\textwidth]{./figures/fig_linkage.png}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.229 ....45\textwidth]{./figures/fig_linkage.png}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.229 ....45\textwidth]{./figures/fig_linkage.png}
                                                  
! LaTeX Error: File `./figures/fig_linkage.png' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.229 ....45\textwidth]{./figures/fig_linkage.png}
                                                  
! Missing } inserted.
<inserted text> 
                }
l.229 ....45\textwidth]{./figures/fig_linkage.png}
                                                  
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.399 ...=0.9\textwidth]{./figures/fig_model0.png}
                                                  
! Missing $ inserted.
<inserted text> 
                $
l.399 ...=0.9\textwidth]{./figures/fig_model0.png}
                                                  
! Extra }, or forgotten $.
\Ginclude@graphics ...put@path \set@curr@file {#1}
                                                  \edef \uq@curr@file {\expa...
l.399 ...=0.9\textwidth]{./figures/fig_model0.png}
                                                  
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.399 ...=0.9\textwidth]{./figures/fig_model0.png}
                                                  
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.399 ...=0.9\textwidth]{./figures/fig_model0.png}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.399 ...=0.9\textwidth]{./figures/fig_model0.png}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.399 ...=0.9\textwidth]{./figures/fig_model0.png}
                                                  
! LaTeX Error: File `./figures/fig_model0.png' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.399 ...=0.9\textwidth]{./figures/fig_model0.png}
                                                  
! Missing } inserted.
<inserted text> 
                }
l.399 ...=0.9\textwidth]{./figures/fig_model0.png}
                                                  
--- failed re-building ‘strum-example.Rnw’

--- re-building ‘strum-intro.Rnw’ using Sweave
Loading required package: pedigree
Loading required package: Matrix
Loading required package: HaploSim
Loading required package: reshape

Attaching package: ‘reshape’

The following object is masked from ‘package:Matrix’:

    expand

Loading required package: Rgraphviz
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:Matrix’:

    which

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: grid
Error: processing vignette 'strum-intro.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'strum-intro.tex' failed.
LaTeX errors:
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.82 ...eight=40mm]{./figures/fig_association.png}
                                                  
! Missing $ inserted.
<inserted text> 
                $
l.82 ...eight=40mm]{./figures/fig_association.png}
                                                  
! Extra }, or forgotten $.
\Ginclude@graphics ...put@path \set@curr@file {#1}
                                                  \edef \uq@curr@file {\expa...
l.82 ...eight=40mm]{./figures/fig_association.png}
                                                  
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.82 ...eight=40mm]{./figures/fig_association.png}
                                                  
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.82 ...eight=40mm]{./figures/fig_association.png}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.82 ...eight=40mm]{./figures/fig_association.png}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.82 ...eight=40mm]{./figures/fig_association.png}
                                                  
! LaTeX Error: File `./figures/fig_association.png' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.82 ...eight=40mm]{./figures/fig_association.png}
                                                  
! Missing } inserted.
<inserted text> 
                }
l.82 ...eight=40mm]{./figures/fig_association.png}
                                                  
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.108 ..., height=40mm]{./figures/fig_linkage.png}
                                                  
! Missing $ inserted.
<inserted text> 
                $
l.108 ..., height=40mm]{./figures/fig_linkage.png}
                                                  
! Extra }, or forgotten $.
\Ginclude@graphics ...put@path \set@curr@file {#1}
                                                  \edef \uq@curr@file {\expa...
l.108 ..., height=40mm]{./figures/fig_linkage.png}
                                                  
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.108 ..., height=40mm]{./figures/fig_linkage.png}
                                                  
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.108 ..., height=40mm]{./figures/fig_linkage.png}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.108 ..., height=40mm]{./figures/fig_linkage.png}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.108 ..., height=40mm]{./figures/fig_linkage.png}
                                                  
! LaTeX Error: File `./figures/fig_linkage.png' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.108 ..., height=40mm]{./figures/fig_linkage.png}
                                                  
! Missing } inserted.
<inserted text> 
                }
l.108 ..., height=40mm]{./figures/fig_linkage.png}
                                                  
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.131 ...m, height=40mm]{./figures/fig_model0.png}
                                                  
! Missing $ inserted.
<inserted text> 
                $
l.131 ...m, height=40mm]{./figures/fig_model0.png}
                                                  
! Extra }, or forgotten $.
\Ginclude@graphics ...put@path \set@curr@file {#1}
                                                  \edef \uq@curr@file {\expa...
l.131 ...m, height=40mm]{./figures/fig_model0.png}
                                                  
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.131 ...m, height=40mm]{./figures/fig_model0.png}
                                                  
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.131 ...m, height=40mm]{./figures/fig_model0.png}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.131 ...m, height=40mm]{./figures/fig_model0.png}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.131 ...m, height=40mm]{./figures/fig_model0.png}
                                                  
! LaTeX Error: File `./figures/fig_model0.png' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.131 ...m, height=40mm]{./figures/fig_model0.png}
                                                  
! Missing } inserted.
<inserted text> 
                }
l.131 ...m, height=40mm]{./figures/fig_model0.png}
                                                  
! Undefined control sequence.
\Ginclude@graphics ...\Ginput@path \set@curr@file 
                                                  {#1}\edef \uq@curr@file {\...
l.158 ...h, height=50mm]{./figures/fig_model1.png}
                                                  
! Missing $ inserted.
<inserted text> 
                $
l.158 ...h, height=50mm]{./figures/fig_model1.png}
                                                  
! Extra }, or forgotten $.
\Ginclude@graphics ...put@path \set@curr@file {#1}
                                                  \edef \uq@curr@file {\expa...
l.158 ...h, height=50mm]{./figures/fig_model1.png}
                                                  
! Undefined control sequence.
\Ginclude@graphics ...e \expandafter {\@curr@file 
                                                  }}\expandafter \filename@p...
l.158 ...h, height=50mm]{./figures/fig_model1.png}
                                                  
! Undefined control sequence.
<recently read> \unquote@name 
                              
l.158 ...h, height=50mm]{./figures/fig_model1.png}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.158 ...h, height=50mm]{./figures/fig_model1.png}
                                                  
! Undefined control sequence.
<recently read> \quote@name 
                            
l.158 ...h, height=50mm]{./figures/fig_model1.png}
                                                  
! LaTeX Error: File `./figures/fig_model1.png' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.158 ...h, height=50mm]{./figures/fig_model1.png}
                                                  
! Missing } inserted.
<inserted text> 
                }
l.158 ...h, height=50mm]{./figures/fig_model1.png}
     
--- failed re-building ‘strum-intro.Rnw’

SUMMARY: processing the following files failed:
  ‘strum-example.Rnw’ ‘strum-intro.Rnw’

Error: Vignette re-building failed.
Execution halted