Error(s) in re-building vignettes:
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-1'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    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.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-3'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-4'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-5'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  9339  100  9339    0     0  25172      0 --:--:-- --:--:-- --:--:-- 25104
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  9339  100  9339    0     0  77825      0 --:--:-- --:--:-- --:--:-- 78478
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  9339  100  9339    0     0  76549      0 --:--:-- --:--:-- --:--:-- 76549
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  9339  100  9339    0     0  78478      0 --:--:-- --:--:-- --:--:-- 78478
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  9339  100  9339    0     0  75314      0 --:--:-- --:--:-- --:--:-- 75314
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 67  9339   67  6276    0     0  51442      0 --:--:-- --:--:-- --:--:-- 51024
100  9339  100  9339    0     0  76549      0 --:--:-- --:--:-- --:--:-- 75926
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  9339  100  9339    0     0  54296      0 --:--:-- --:--:-- --:--:-- 54296
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-6'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in file(file, "rt") :
  'raw = FALSE' but '/tmp/RtmpFZ2E7K/working_dir/Rtmps2vLFx/VSE_samples/' is not a regular file
Warning in file(file, "rt") :
  cannot open file '/tmp/RtmpFZ2E7K/working_dir/Rtmps2vLFx/VSE_samples/': it is a directory
Quitting from lines 136-146 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘my-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘my-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted