Error(s) in re-building vignettes:
  ...
--- re-building ‘Import_data.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.
1 samples were dropped from the abundance matrix for lack of associated covariates.
--- finished re-building ‘Import_data.Rmd’

--- re-building ‘PLN.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.
corrplot 0.84 loaded

Attaching package: 'dplyr'

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

    combine

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

    filter, lag

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

    intersect, setdiff, setequal, union

Warning: Transformation introduced infinite values in continuous x-axis
Quitting from lines 186-190 (PLN.Rmd) 
Error: processing vignette 'PLN.Rmd' failed with diagnostics:
unused argument (options = options)
--- failed re-building ‘PLN.Rmd’

--- re-building ‘PLNLDA.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.
Warning in kable_markdown(x = c("3302930", "3307296", "3348069", "3394105",  :
  The table should have a header (column names)
Warning in kable_markdown(x = c("Che", "Hyc", "Hym", "Hys", "Psy", "Aga",  :
  The table should have a header (column names)
Warning: glm.fit: algorithm did not converge
Warning: glm.fit: fitted rates numerically 0 occurred
--- finished re-building ‘PLNLDA.Rmd’

--- re-building ‘PLNPCA.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.
corrplot 0.84 loaded
Warning in kable_markdown(x = c("Che", "Hyc", "Hym", "Hys", "Psy", "Aga",  :
  The table should have a header (column names)
Warning in kable_markdown(x = c("-1.606816", "3.835259", "7.562147", "6.244162",  :
  The table should have a header (column names)
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Removed 584 rows containing missing values (geom_point).
--- finished re-building ‘PLNPCA.Rmd’

--- re-building ‘PLNnetwork.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.
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Removed 588 rows containing missing values (geom_point).
--- finished re-building ‘PLNnetwork.Rmd’

--- re-building ‘Trichoptera.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 ‘Trichoptera.Rmd’

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

Error: Vignette re-building failed.
Execution halted