Error(s) in re-building vignettes:
--- re-building ‘mlg.Rmd’ using rmarkdown
Loading required package: adegenet
Loading required package: ade4

   /// adegenet 2.1.2 is loaded ////////////

   > overview: '?adegenet'
   > tutorials/doc/questions: 'adegenetWeb()' 
   > bug reports/feature requests: adegenetIssues()


This is poppr version 2.8.5. To get started, type package?poppr
OMP parallel support: unavailable
Loading required package: ape

Attaching package: 'phangorn'

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

    AICc

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'mlg.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘mlg.Rmd’

--- re-building ‘poppr_manual.Rmd’ using rmarkdown

Found 617 missing values.

2 loci contained missing values greater than 5%

Removing 2 loci: fca8, fca45

Found 617 missing values.

38 genotypes contained missing values greater than 5%

Removing 38 genotypes: N215, N216, N188, N189, N190, N191, N192, N298, N299,
N300, N301, N302, N303, N304, N310, N195, N197, N198, N199, N200, N201, N206,
N182, N184, N186, N282, N283, N288, N291, N292, N293, N294, N295, N296, N297,
N281, N289, N290
Warning in plot.window(...) : "border" is not a graphical parameter
Warning in plot.window(...) : "fill" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "border" is not a graphical parameter
Warning in plot.xy(xy, type, ...) : "fill" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
  "border" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
  "fill" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
  "border" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
  "fill" is not a graphical parameter
Warning in box(...) : "border" is not a graphical parameter
Warning in box(...) : "fill" is not a graphical parameter
Warning in title(...) : "border" is not a graphical parameter
Warning in title(...) : "fill" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  "border" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  "fill" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  "border" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  "fill" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  "border" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  "fill" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  "border" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  "fill" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  "border" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  "fill" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "border" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "fill" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "border" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "fill" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "border" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "fill" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "border" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "fill" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "border" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "fill" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "border" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "fill" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "border" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "fill" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "border" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "fill" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "border" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "fill" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "border" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "fill" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "border" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "fill" is not a graphical parameter
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin
  Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
  Expected in: /usr/lib/libSystem.B.dylib

Error: processing vignette 'poppr_manual.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘poppr_manual.Rmd’

--- re-building ‘algo.Rnw’ using knitr
Loading required package: adegenet
Loading required package: ade4

   /// adegenet 2.1.2 is loaded ////////////

   > overview: '?adegenet'
   > tutorials/doc/questions: 'adegenetWeb()' 
   > bug reports/feature requests: adegenetIssues()


This is poppr version 2.8.5. To get started, type package?poppr
OMP parallel support: unavailable
Warning in infinite_vals_replacement(D, warning) :
  Infinite values detected.
--- finished re-building ‘algo.Rnw’

SUMMARY: processing the following files failed:
  ‘mlg.Rmd’ ‘poppr_manual.Rmd’

Error: Vignette re-building failed.
Execution halted