Package: VariantAnnotation

Version: 1.29.25

Command: chmod a+r VariantAnnotation -R && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data VariantAnnotation

StartedAt: 2019-04-08 21:33:23 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 21:34:52 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 89.6 seconds

RetCode: 1

Status:  ERROR

PackageFile: None

PackageFileSize: NA

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### Running command:
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###   chmod a+r VariantAnnotation -R && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data VariantAnnotation
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* checking for file 'VariantAnnotation/DESCRIPTION' ... OK
* preparing 'VariantAnnotation':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'VariantAnnotation.Rnw' using Sweave
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, colMeans, colSums,
    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, rowMeans, rowSums, rownames, sapply, setdiff, sort,
    table, tapply, union, unique, unsplit, which, which.max,
    which.min

Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum

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

Attaching package: 'Biostrings'

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

    type

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

    strsplit


Attaching package: 'VariantAnnotation'

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

    tabulate


Error: processing vignette 'VariantAnnotation.Rnw' failed with diagnostics:
 chunk 3 (label = readVcf) 
Error in validObject(.Object) : 
  invalid class "VCFHeader" object: 1: 'info(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description
invalid class "VCFHeader" object: 2: 'geno(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description

--- failed re-building 'VariantAnnotation.Rnw'

--- re-building 'filterVcf.Rnw' using Sweave
starting prefilter
prefiltering 3791 records
prefiltered to C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpCWbfew\file2a98267b5aa5
prefilter compressing and indexing 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpCWbfew\file2a98267b5aa5'
starting filter

Error: processing vignette 'filterVcf.Rnw' failed with diagnostics:
 chunk 5 (label = createFilteredFile) 
Error in validObject(.Object) : 
  invalid class "VCFHeader" object: 'info(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description

--- failed re-building 'filterVcf.Rnw'

SUMMARY: processing the following files failed:
  'VariantAnnotation.Rnw' 'filterVcf.Rnw'

Error: Vignette re-building failed.
Execution halted