Error(s) in re-building vignettes:
  ...
--- re-building ‘BD_shifts.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.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: phyloseq
Error: package or namespace load failed for 'phyloseq' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'ade4'
Quitting from lines 85-86 (BD_shifts.Rmd) 
Error: processing vignette 'BD_shifts.Rmd' failed with diagnostics:
unable to find required package 'phyloseq'
--- failed re-building ‘BD_shifts.Rmd’

--- re-building ‘HTSSIP_intro.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.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 94-97 (HTSSIP_intro.Rmd) 
Error: processing vignette 'HTSSIP_intro.Rmd' failed with diagnostics:
package or namespace load failed for 'phyloseq' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'ade4'
--- failed re-building ‘HTSSIP_intro.Rmd’

--- re-building ‘HTSSIP_sim.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.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 115-118 (HTSSIP_sim.Rmd) 
Error: processing vignette 'HTSSIP_sim.Rmd' failed with diagnostics:
there is no package called 'ade4'
--- failed re-building ‘HTSSIP_sim.Rmd’

--- re-building ‘MW_HR_SIP.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.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 49-50 (MW_HR_SIP.Rmd) 
Error: processing vignette 'MW_HR_SIP.Rmd' failed with diagnostics:
unable to find required package 'phyloseq'
--- failed re-building ‘MW_HR_SIP.Rmd’

--- re-building ‘beta_diversity_ordinations.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.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: phyloseq
Error: package or namespace load failed for 'phyloseq' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'ade4'
Quitting from lines 31-32 (beta_diversity_ordinations.Rmd) 
Error: processing vignette 'beta_diversity_ordinations.Rmd' failed with diagnostics:
unable to find required package 'phyloseq'
--- failed re-building ‘beta_diversity_ordinations.Rmd’

--- re-building ‘heavy_SIP.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.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 48-49 (heavy_SIP.Rmd) 
Error: processing vignette 'heavy_SIP.Rmd' failed with diagnostics:
unable to find required package 'phyloseq'
--- failed re-building ‘heavy_SIP.Rmd’

--- re-building ‘qSIP.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.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 48-50 (qSIP.Rmd) 
Error: processing vignette 'qSIP.Rmd' failed with diagnostics:
unable to find required package 'phyloseq'
--- failed re-building ‘qSIP.Rmd’

--- re-building ‘quant_incorp.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.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 46-48 (quant_incorp.Rmd) 
Error: processing vignette 'quant_incorp.Rmd' failed with diagnostics:
unable to find required package 'phyloseq'
--- failed re-building ‘quant_incorp.Rmd’

SUMMARY: processing the following files failed:
  ‘BD_shifts.Rmd’ ‘HTSSIP_intro.Rmd’ ‘HTSSIP_sim.Rmd’ ‘MW_HR_SIP.Rmd’
  ‘beta_diversity_ordinations.Rmd’ ‘heavy_SIP.Rmd’ ‘qSIP.Rmd’
  ‘quant_incorp.Rmd’

Error: Vignette re-building failed.
Execution halted