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### Running command:
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###   chmod a+r ChIPpeakAnno -R && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data ChIPpeakAnno
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* checking for file 'ChIPpeakAnno/DESCRIPTION' ... OK
* preparing 'ChIPpeakAnno':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'ChIPpeakAnno.Rmd' using rmarkdown
duplicated or NA names found. Rename all the names by numbers.
If you are importing files downloaded from ensembl, 
          it will be better to import the files into a TxDb object,
          and then convert to GRanges by toGRanges. Here is the sample code:
          library(GenomicFeatures)
          txdb <- makeTxDbFromGFF('D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpS28Vum/Rinst31f83b8a6c0d/ChIPpeakAnno/extdata/GFF_peaks.gff')
          anno <- toGRanges(txdb, format='gene')
duplicated or NA names found. 
                Rename all the names by numbers.
Missing totalTest! totalTest is required for HyperG test. 
If totalTest is missing, pvalue will be calculated by estimating 
the total binding sites of encoding region of human.
totalTest = humanGenomeSize * (2%(codingDNA) + 
             1%(regulationRegion)) / ( 2 * averagePeakWidth )
          = 3.3e+9 * 0.03 / ( 2 * averagePeakWidth)
          = 5e+7 /averagePeakWidth
Warning in (function (seqlevels, genome, new_style)  :
  cannot switch some of GRCh37's seqlevels from NCBI to UCSC style
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
  403 genes were dropped because they have exons located on both strands
  of the same reference sequence or on more than one reference sequence,
  so cannot be represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a
  GRangesList object, or use suppressMessages() to suppress this message.
--- finished re-building 'ChIPpeakAnno.Rmd'

--- re-building 'FAQs.Rmd' using rmarkdown
--- finished re-building 'FAQs.Rmd'

--- re-building 'pipeline.Rmd' using rmarkdown
If you are importing files downloaded from ensembl, 
          it will be better to import the files into a TxDb object,
          and then convert to GRanges by toGRanges. Here is the sample code:
          library(GenomicFeatures)
          txdb <- makeTxDbFromGFF('D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpS28Vum/Rinst31f83b8a6c0d/ChIPpeakAnno/extdata/GFF_peaks.gff')
          anno <- toGRanges(txdb, format='gene')
duplicated or NA names found. 
                Rename all the names by numbers.
Missing totalTest! totalTest is required for HyperG test. 
If totalTest is missing, pvalue will be calculated by estimating 
the total binding sites of encoding region of human.
totalTest = humanGenomeSize * (2%(codingDNA) + 
             1%(regulationRegion)) / ( 2 * averagePeakWidth )
          = 3.3e+9 * 0.03 / ( 2 * averagePeakWidth)
          = 5e+7 /averagePeakWidth
  403 genes were dropped because they have exons located on both strands
  of the same reference sequence or on more than one reference sequence,
  so cannot be represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a
  GRangesList object, or use suppressMessages() to suppress this message.
Annotate peaks by annoPeaks, see ?annoPeaks for details.
maxgap will be ignored.
Quitting from lines 163-173 (pipeline.Rmd) 
Error: processing vignette 'pipeline.Rmd' failed with diagnostics:
unimplemented type 'list' in 'EncodeElement'

--- failed re-building 'pipeline.Rmd'

--- re-building 'quickStart.Rmd' using rmarkdown
  403 genes were dropped because they have exons located on both strands
  of the same reference sequence or on more than one reference sequence,
  so cannot be represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a
  GRangesList object, or use suppressMessages() to suppress this message.
Annotate peaks by annoPeaks, see ?annoPeaks for details.
maxgap will be ignored.
Annotate peaks by annoPeaks, see ?annoPeaks for details.
maxgap will be ignored.
--- finished re-building 'quickStart.Rmd'

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

Error: Vignette re-building failed.
In addition: Warning messages:
1: In formatStrand(strand) : All the characters for strand, 
            other than '1', '-1', '+', '-' and '*', 
            will be converted into '*'.
2: In formatStrand(strand) : All the characters for strand, 
            other than '1', '-1', '+', '-' and '*', 
            will be converted into '*'.
3: In formatStrand(strand) : All the characters for strand, 
            other than '1', '-1', '+', '-' and '*', 
            will be converted into '*'.
4: In (function (seqlevels, genome, new_style)  :
  cannot switch some of GRCh37's seqlevels from NCBI to UCSC style
Execution halted