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

   /// adegenet 2.1.3 is loaded ////////////

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


This is poppr version 2.8.6. To get started, type package?poppr
OMP parallel support: available
Loading required package: ape

Attaching package: 'phangorn'

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

    AICc

pandoc-citeproc: Error in $: Incompatible API versions: encoded with [1,20] but attempted to decode with [1,17,5,4].
CallStack (from HasCallStack):
  error, called at ./Text/Pandoc/JSON.hs:111:48 in pandoc-types-1.17.5.4-5tHZ3B61A58JaKOMxwGQR4:Text.Pandoc.JSON
Error running filter /usr/bin/pandoc-citeproc:
Filter returned error status 1
Error: processing vignette 'mlg.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- 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
pandoc-citeproc: Error in $: Incompatible API versions: encoded with [1,20] but attempted to decode with [1,17,5,4].
CallStack (from HasCallStack):
  error, called at ./Text/Pandoc/JSON.hs:111:48 in pandoc-types-1.17.5.4-5tHZ3B61A58JaKOMxwGQR4:Text.Pandoc.JSON
Error running filter /usr/bin/pandoc-citeproc:
Filter returned error status 1
Error: processing vignette 'poppr_manual.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed re-building 'poppr_manual.Rmd'

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

   /// adegenet 2.1.3 is loaded ////////////

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


This is poppr version 2.8.6. To get started, type package?poppr
OMP parallel support: available
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