Error(s) in re-building vignettes:
  ...
--- re-building ‘run_example_pathways.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘run_example_pathways.Rmd’

--- re-building ‘plots_directed.Rmd’ using knitr

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’

--- re-building ‘plots_viral_quantitate.Rmd’ using knitr

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Output at: demo.gif
--- finished re-building ‘plots_viral_quantitate.Rmd’

--- re-building ‘test_graph_convergent.Rmd’ using knitr

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

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

--- re-building ‘test_graph_divergent.Rmd’ using knitr

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

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

Profiling Timer Expired
--- re-building ‘test_graph_network.Rmd’ using knitr

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

Profiling Timer Expired
--- re-building ‘test_graph_network_inhibiting.Rmd’ using knitr

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

--- re-building ‘test_graph_reconvergent.Rmd’ using knitr

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

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

SUMMARY: processing the following files failed:
  ‘test_graph_network.Rmd’ ‘test_graph_network_inhibiting.Rmd’

Error: Vignette re-building failed.
Execution halted