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.
Quitting from lines 34-35 (PLNLDA.Rmd) 
Error: processing vignette 'PLNLDA.Rmd' failed with diagnostics:
package or namespace load failed for 'PLNmodels' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'rhdf5'
--- failed 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.
Quitting from lines 34-37 (PLNPCA.Rmd) 
Error: processing vignette 'PLNPCA.Rmd' failed with diagnostics:
package or namespace load failed for 'PLNmodels' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'rhdf5'
--- failed 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.
Quitting from lines 34-36 (PLNnetwork.Rmd) 
Error: processing vignette 'PLNnetwork.Rmd' failed with diagnostics:
package or namespace load failed for 'PLNmodels' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'rhdf5'
--- failed 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 files failed:
  ‘PLN.Rmd’ ‘PLNLDA.Rmd’ ‘PLNPCA.Rmd’ ‘PLNnetwork.Rmd’

Error: Vignette re-building failed.
Execution halted