Error(s) in re-building vignettes:
  ...
--- re-building ‘Import_data.Rmd’ using rmarkdown
1 samples were dropped from the abundance matrix for lack of associated covariates.
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 'Import_data.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed re-building ‘Import_data.Rmd’

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

`summarise()` regrouping output by 'x' (override with `.groups` argument)
Warning: Transformation introduced infinite values in continuous x-axis
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 'PLN.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed re-building ‘PLN.Rmd’

--- re-building ‘PLNLDA.Rmd’ using rmarkdown
Warning: glm.fit: algorithm did not converge
Warning: glm.fit: fitted rates numerically 0 occurred
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 'PLNLDA.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed re-building ‘PLNLDA.Rmd’

--- re-building ‘PLNPCA.Rmd’ using rmarkdown
corrplot 0.84 loaded
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Removed 583 rows containing missing values (geom_point).
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 'PLNPCA.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed re-building ‘PLNPCA.Rmd’

--- re-building ‘PLNnetwork.Rmd’ using rmarkdown
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Removed 588 rows containing missing values (geom_point).
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 'PLNnetwork.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed re-building ‘PLNnetwork.Rmd’

--- re-building ‘Trichoptera.Rmd’ using rmarkdown
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 'Trichoptera.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed re-building ‘Trichoptera.Rmd’

SUMMARY: processing the following files failed:
  ‘Import_data.Rmd’ ‘PLN.Rmd’ ‘PLNLDA.Rmd’ ‘PLNPCA.Rmd’
  ‘PLNnetwork.Rmd’ ‘Trichoptera.Rmd’

Error: Vignette re-building failed.
Execution halted