Error(s) in re-building vignettes:
  ...
--- re-building ‘different_thinners.Rmd’ using rmarkdown
--- finished re-building ‘different_thinners.Rmd’

--- re-building ‘simulate_rnaseq.Rmd’ using rmarkdown
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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    clusterExport, clusterMap, parApply, parCapply, parLapply,
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    IQR, mad, sd, var, xtabs

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    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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Attaching package: 'limma'

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Loading required package: mgcv
Loading required package: nlme

Attaching package: 'nlme'

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This is mgcv 1.8-31. For overview type 'help("mgcv-package")'.
Loading required package: genefilter

Attaching package: 'genefilter'

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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
Quitting from lines 124-128 (simulate_rnaseq.Rmd) 
Error: processing vignette 'simulate_rnaseq.Rmd' failed with diagnostics:
trying to get slot "className" from an object of a basic class ("character") with no slots
--- failed re-building ‘simulate_rnaseq.Rmd’

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

Error: Vignette re-building failed.
Execution halted