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###
### Running command:
###
###   chmod a+r segmenter -R && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data segmenter
###
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* checking for file 'segmenter/DESCRIPTION' ... OK
* preparing 'segmenter':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'segmenter.Rmd' using rmarkdown

Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

    counts

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

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid
========================================
ComplexHeatmap version 2.11.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite:
Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
  genomic data. Bioinformatics 2016.

The new InteractiveComplexHeatmap package can directly export static 
complex heatmaps into an interactive Shiny app with zero effort. Have a try!

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================

Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
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")'.

Quitting from lines 540-558 (segmenter.Rmd) 
Error: processing vignette 'segmenter.Rmd' failed with diagnostics:
No method for subsetting an XMLInternalDocument with numeric
--- failed re-building 'segmenter.Rmd'

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

Error: Vignette re-building failed.
Execution halted