##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r OGRE -R && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data OGRE
###
##############################################################################
##############################################################################


* checking for file 'OGRE/DESCRIPTION' ... OK
* preparing 'OGRE':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'OGRE.Rmd' using rmarkdown
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Warning: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'OGRE'
Warning: replacing previous import 'S4Vectors::second' by 'data.table::second' when loading 'OGRE'
Warning: replacing previous import 'S4Vectors::first' by 'data.table::first' when loading 'OGRE'
Quitting from lines 126-127 (OGRE.Rmd) 
Error: processing vignette 'OGRE.Rmd' failed with diagnostics:
No method for subsetting an XMLInternalDocument with numeric
--- failed re-building 'OGRE.Rmd'

SUMMARY: processing the following file failed:
  'OGRE.Rmd'

Error: Vignette re-building failed.
Execution halted