Error(s) in re-building vignettes:
--- re-building ‘plots_directed.Rmd’ using rmarkdown

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

--- finished re-building ‘plots_directed.Rmd’

Warning: elapsed-time limit of 30 minutes reached for sub-process
--- re-building ‘simulate_expression.Rmd’ using rmarkdown

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union


Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Warning in generate_expression(100, graph_structure, cor = 0.8, mean = 0,  :
  sigma matrix was not positive definite, nearest approximation used.
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "thincolsep" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "thincolsep" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "thincolsep" is not a graphical parameter
Warning in generate_expression(100, graph_structure, cor = 0.8, mean = 0,  :
  sigma matrix was not positive definite, nearest approximation used.
Warning in generate_expression(100, graph_structure, cor = 0.8, mean = 0,  :
  sigma matrix was not positive definite, nearest approximation used.
Warning in sd * t(sig) :
  longer object length is not a multiple of shorter object length
Warning in t(sd * t(sig)) * sd :
  longer object length is not a multiple of shorter object length
Warning in generate_expression(100, graph_structure, state, cor = 0.8, mean = 0,  :
  sigma matrix was not positive definite, nearest approximation used.
Warning in generate_expression(100, graph_diverging, cor = 0.8, mean = 0,  :
  sigma matrix was not positive definite, nearest approximation used.
Warning in sd * t(sig) :
  longer object length is not a multiple of shorter object length
Warning in t(sd * t(sig)) * sd :
  longer object length is not a multiple of shorter object length
Warning in generate_expression(100, graph_diverging, state, cor = 0.8, mean = 0,  :
  sigma matrix was not positive definite, nearest approximation used.
Warning in generate_expression(100, graph_converging, cor = 0.8, mean = 0,  :
  sigma matrix was not positive definite, nearest approximation used.
Warning in sd * t(sig) :
  longer object length is not a multiple of shorter object length
Warning in t(sd * t(sig)) * sd :
  longer object length is not a multiple of shorter object length
Warning in generate_expression(100, graph_converging, state, cor = 0.8,  :
  sigma matrix was not positive definite, nearest approximation used.
Warning in generate_expression(100, graph_reconnecting, cor = 0.8, mean = 0,  :
  sigma matrix was not positive definite, nearest approximation used.
Warning in eattrs[[name]][index] <- value :
  number of items to replace is not a multiple of replacement length
Warning in eattrs[[name]][index] <- value :
  number of items to replace is not a multiple of replacement length
Warning in sd * t(sig) :
  longer object length is not a multiple of shorter object length
Warning in t(sd * t(sig)) * sd :
  longer object length is not a multiple of shorter object length
Warning in generate_expression(100, graph_reconnecting, state, cor = 0.8,  :
  sigma matrix was not positive definite, nearest approximation used.
Warning in generate_expression(100, RAF_MAP_graph, cor = 0.8, mean = 0,  :
  sigma matrix was not positive definite, nearest approximation used.
Warning in generate_expression(100, Pi3K_graph, cor = 0.8, mean = 0, comm = FALSE,  :
  sigma matrix was not positive definite, nearest approximation used.

Execution halted
SUMMARY: processing the following file failed:
  ‘simulate_expression.Rmd’

Error: Vignette re-building failed.
Execution halted