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--- re-building ‘different_thinners.Rmd’ using rmarkdown
Quitting from lines 176-182 (different_thinners.Rmd) 
Error: processing vignette 'different_thinners.Rmd' failed with diagnostics:

Package optmatch must be installed to use`permute_method = "optmatch"`
You can install it with

install.packages("optmatch")

Note that optmatch uses a strange non-standard license:
https://cran.r-project.org/package=optmatch/LICENSE

--- failed re-building ‘different_thinners.Rmd’

--- re-building ‘simulate_rnaseq.Rmd’ using rmarkdown
Warning: The closing backticks on line 80 ("````") in simulate_rnaseq.Rmd do not match the opening backticks "```" on line 78. 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).
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Welcome to Bioconductor

    Vignettes contain introductory material; view with
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Loading required package: BiocParallel
renaming the first element in assays to 'counts'
  the design formula contains one or more numeric variables with integer values,
  specifying a model with increasing fold change for higher values.
  did you mean for this to be a factor? if so, first convert
  this variable to a factor using the factor() function
--- finished re-building ‘simulate_rnaseq.Rmd’

SUMMARY: processing the following file failed:
  ‘different_thinners.Rmd’

Error: Vignette re-building failed.
Execution halted