Error(s) in re-building vignettes:
--- re-building 'MUFASA_Workflow_Example.Rmd' using rmarkdown
Warning: The closing backticks on line 169 ("```") in MUFASA_Workflow_Example.Rmd do not match the opening backticks "````" on line 167. You are recommended to fix either the opening or closing delimiter of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote).
Warning: The closing backticks on line 178 ("```") in MUFASA_Workflow_Example.Rmd do not match the opening backticks "````" on line 176. You are recommended to fix either the opening or closing delimiter of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote).
--- finished re-building 'MUFASA_Workflow_Example.Rmd'

--- re-building 'Parallel_Execution_for_Confidence_Intervals.Rmd' using rmarkdown
--- finished re-building 'Parallel_Execution_for_Confidence_Intervals.Rmd'

--- re-building 'QFASA_Workflow_Example.Rmd' using rmarkdown
--- finished re-building 'QFASA_Workflow_Example.Rmd'

--- re-building 'SMUFASA_Workflow_Example.Rmd' using rmarkdown
Warning: The closing backticks on line 116 ("```") in SMUFASA_Workflow_Example.Rmd do not match the opening backticks "````" on line 114. You are recommended to fix either the opening or closing delimiter of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote).
Warning: The closing backticks on line 125 ("```") in SMUFASA_Workflow_Example.Rmd do not match the opening backticks "````" on line 123. You are recommended to fix either the opening or closing delimiter of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote).
Warning: The closing backticks on line 133 ("```") in SMUFASA_Workflow_Example.Rmd do not match the opening backticks "````" on line 131. You are recommended to fix either the opening or closing delimiter of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote).

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

Welcome to compositions, a package for compositional data analysis.
Find an intro with "? compositions"


Attaching package: 'compositions'

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

    anova, cor, cov, dist, var

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

    %*%, norm, scale, scale.default

--- finished re-building 'SMUFASA_Workflow_Example.Rmd'