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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data phyloseq
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* checking for file ‘phyloseq/DESCRIPTION’ ... OK
* preparing ‘phyloseq’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘phyloseq-FAQ.Rmd’ using rmarkdown
--- finished re-building ‘phyloseq-FAQ.Rmd’

--- re-building ‘phyloseq-analysis.Rmd’ using rmarkdown
Warning: Transformation introduced infinite values in discrete y-axis
Warning: Transformation introduced infinite values in discrete y-axis
Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
Warning: stat_contour(): Zero contours were generated
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Warning: stat_contour(): Zero contours were generated
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Warning: stat_contour(): Zero contours were generated
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Warning: stat_contour(): Zero contours were generated
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
--- finished re-building ‘phyloseq-analysis.Rmd’

--- re-building ‘phyloseq-basics.Rmd’ using rmarkdown
Quitting from lines 487-495 (phyloseq-basics.Rmd) 
Error: processing vignette 'phyloseq-basics.Rmd' failed with diagnostics:
there is no package called 'genefilter'
--- failed re-building ‘phyloseq-basics.Rmd’

--- re-building ‘phyloseq-mixture-models.Rmd’ using rmarkdown
Warning in microbio_me_qiime(filepath) : NAs introduced by coercion
Quitting from lines 101-102 (phyloseq-mixture-models.Rmd) 
Error: processing vignette 'phyloseq-mixture-models.Rmd' failed with diagnostics:
there is no package called 'DESeq2'
--- failed re-building ‘phyloseq-mixture-models.Rmd’

SUMMARY: processing the following files failed:
  ‘phyloseq-basics.Rmd’ ‘phyloseq-mixture-models.Rmd’

Error: Vignette re-building failed.
Execution halted