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

--- re-building ‘B_Reading_data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Read 6 items
Read 1494 items
Read 0 items
Read 864 items
Read 1433376 items
Read 0 items
Read 6 items
Read 1494 items
Read 0 items
Read 864 items
Read 1433376 items
Read 0 items
--- finished re-building ‘B_Reading_data.Rmd’

--- re-building ‘C_Running_Haplin.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Read 6 items
Read 1494 items
Read 0 items
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Read 8 items
Read 9112 items
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Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  no font could be found for family "Arial"
Read 864 items
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Quitting from lines 150-151 (C_Running_Haplin.Rmd) 
Error: processing vignette 'C_Running_Haplin.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘C_Running_Haplin.Rmd’

--- re-building ‘D_Running_Haplin_on_cluster.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘D_Running_Haplin_on_cluster.Rmd’

--- re-building ‘E_hapRelEff.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘E_hapRelEff.Rmd’

SUMMARY: processing the following file failed:
  ‘C_Running_Haplin.Rmd’

Error: Vignette re-building failed.
Execution halted