Error(s) in re-building vignettes:
  ...
--- re-building 'MSIseq.Rnw' using Sweave
Loading required package: IRanges
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
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: RWeka
Loading required package: rJava
Loading required package: R.utils
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.8.0 (2020-02-14 07:10:20 UTC) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.23.0 successfully loaded. See ?R.oo for help.

Attaching package: 'R.oo'

The following object is masked from 'package:R.methodsS3':

    throw

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

    clone

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

    trim

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

    getClasses, getMethods

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

    attach, detach, load, save

R.utils v2.9.2 successfully loaded. See ?R.utils for help.

Attaching package: 'R.utils'

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

    timestamp

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

    cat, commandArgs, getOption, inherits, isOpen, nullfile, parse,
    warnings

trying URL 'http://steverozen.net/data/Hg19repeats.rda'
Content type 'unknown' length 66808496 bytes (63.7 MB)
==================================================
downloaded 63.7 MB

trying URL 'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chr20.fa.gz'
Warning in download.file(url2, file) :
  URL 'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chr20.fa.gz': status was 'Failure when receiving data from the peer'

Error: processing vignette 'MSIseq.Rnw' failed with diagnostics:
 chunk 4 (label = download) 
Error in download.file(url2, file) : 
  cannot open URL 'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chr20.fa.gz'

--- failed re-building 'MSIseq.Rnw'

SUMMARY: processing the following file failed:
  'MSIseq.Rnw'

Error: Vignette re-building failed.
Execution halted