Error(s) in re-building vignettes:
--- re-building ‘my-vignette.Rmd’ using rmarkdown
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, 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
  % 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
  5 8141k    5  420k    0     0   344k      0  0:00:23  0:00:01  0:00:22  344k
 61 8141k   61 4985k    0     0  2300k      0  0:00:03  0:00:02  0:00:01 2299k
100 8141k  100 8141k    0     0  2963k      0  0:00:02  0:00:02 --:--:-- 2962k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  1 1373k    1 14220    0     0  31252      0  0:00:45 --:--:--  0:00:45 31184
100 1373k  100 1373k    0     0  1156k      0  0:00:01  0:00:01 --:--:-- 1156k
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                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 38 1233k   38  468k    0     0   434k      0  0:00:02  0:00:01  0:00:01  434k
100 1233k  100 1233k    0     0  1028k      0  0:00:01  0:00:01 --:--:-- 1027k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 14 3007k   14  435k    0     0   524k      0  0:00:05 --:--:--  0:00:05  529k
100 3007k  100 3007k    0     0  2214k      0  0:00:01  0:00:01 --:--:-- 2229k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  1 1870k    1 19776    0     0  49071      0  0:00:39 --:--:--  0:00:39 48950
100 1870k  100 1870k    0     0  1791k      0  0:00:01  0:00:01 --:--:-- 1791k
  % 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 3189k    0 14220    0     0  45286      0  0:01:12 --:--:--  0:01:12 45286
 93 3189k   93 2991k    0     0  2203k      0  0:00:01  0:00:01 --:--:-- 2203k
100 3189k  100 3189k    0     0  2335k      0  0:00:01  0:00:01 --:--:-- 2333k
  % 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   269  100   269    0     0    749      0 --:--:-- --:--:-- --:--:--   749
Loading regions
30 LD blocks intersect with DHS
16 LD blocks intersect with H3K27ac
5 LD blocks intersect with H3K27me3
9 LD blocks intersect with H3K36me3
10 LD blocks intersect with H3K4me1
6 LD blocks intersect with H3K4me3
Tallying MRVS 
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120
Execution halted