##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r MethylSeekR -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data MethylSeekR
###
##############################################################################
##############################################################################


* checking for file 'MethylSeekR/DESCRIPTION' ... OK
* preparing 'MethylSeekR':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'MethylSeekR.Rnw' using Sweave
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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: parallel
Loading required package: mhsmm
Loading required package: mvtnorm
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: BiocIO

Attaching package: 'BiocIO'

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

    FileForFormat

reading methylome data
Read 200000 records
reading SNP table
Read 11750 records
removing SNPs
11604 (6.2%) CpGs removed
determining alpha distribution for chromosome: chr22
training PMD-HMM on chromosome chr22
performing viterbi segmentation
creating GRanges object
determining alpha distribution for chromosome: chr22
Warning in getMethods(coerce, table = TRUE) :
  'getMethods' is deprecated.
Use 'getMethodsForDispatch(f, TRUE)' instead.
See help("Deprecated")
Warning in getMethods(coerce, table = TRUE) :
  'getMethods' is deprecated.
Use 'getMethodsForDispatch(f, TRUE)' instead.
See help("Deprecated")
Warning in getMethods(coerce, table = TRUE) :
  'getMethods' is deprecated.
Use 'getMethodsForDispatch(f, TRUE)' instead.
See help("Deprecated")

Error: processing vignette 'MethylSeekR.Rnw' failed with diagnostics:
 chunk 18 
Error in errorHandler(responseError) : Internal Server Error


--- failed re-building 'MethylSeekR.Rnw'

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

Error: Vignette re-building failed.
Execution halted