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


* checking for file 'methylPipe/DESCRIPTION' ... OK
* preparing 'methylPipe':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'methylPipe.rnw' using knitr
Loading required package: GenomicRanges
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

Loading required package: S4Vectors

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: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins,
    colOrderStats, colProds, colQuantiles, colRanges, colRanks,
    colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs,
    colVars, colWeightedMads, colWeightedMeans,
    colWeightedMedians, colWeightedSds, colWeightedVars,
    rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse,
    rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums,
    rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs,
    rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs,
    rowVars, rowWeightedMads, rowWeightedMeans,
    rowWeightedMedians, rowWeightedSds, rowWeightedVars

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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: BSgenome
Loading required package: rtracklayer

Extracting methylation information from input SAM files and creating output files for each sample...

Creating temporary BAM files from input SAM files...

Creating uncovered regions objects for each sample from BAM files...

Removing all temporary BAM files...

Methylation info and Uncovered regions output files created for each sample in output_folder...

Processing done Successfully...

Warning in in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,  :
  You changed the working directory to D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpA1siDH (probably via setwd()). It will be restored to D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpANr1xY/Rbuild40d8352526f7/methylPipe/vignettes. See the Note section in ?knitr::knit
S4 Object of class BSdata

TABIX indexed file for this BSdata:
D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpANr1xY/Rinst40d84daf2e68/methylPipe/extdata/H1_chr20_CG_10k_tabix_out.txt.gz

The first lines of the uncovered regions of this BSdata:
Associated organism genome:
Homo sapiens

Chromosomes available:
The first lines of the data:
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Quitting from lines 240-245 (methylPipe.rnw) 
Error: processing vignette 'methylPipe.rnw' failed with diagnostics:
No method for subsetting an XMLInternalDocument with numeric
--- failed re-building 'methylPipe.rnw'

SUMMARY: processing the following file failed:
  'methylPipe.rnw'

Error: Vignette re-building failed.
Execution halted