Package: customProDB

Version: 1.23.1

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

StartedAt: 2019-04-08 21:59:36 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 22:02:03 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 147.1 seconds

RetCode: 1

Status:  ERROR

PackageFile: None

PackageFileSize: NA

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


* checking for file 'customProDB/DESCRIPTION' ... OK
* preparing 'customProDB':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'customProDB.Rnw' using Sweave
Loading required package: GenomicRanges
Loading required package: stats4
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: S4Vectors

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: GenomeInfoDb
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")'.

Loading required package: biomaRt
Build TranscriptDB object (txdb.sqlite) ... 
Download the refGene table ... OK
Download the hgFixed.refLink table ... OK
Extract the 'transcripts' data frame ... OK
Extract the 'splicings' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
 done
Prepare gene/transcript/protein id mapping information (ids.RData) ...  done
Prepare exon annotation information (exon_anno.RData) ...  done
Prepare protein sequence (proseq.RData) ...  done
Prepare protein coding sequence (procodingseq.RData)...  done

[W::bcf_hdr_check_sanity] PL should be declared as Number=G
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
Error: processing vignette 'customProDB.Rnw' failed with diagnostics:
 chunk 8 (label = inpvcf) 
Error : scanVcf: 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
  path: C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpWsKcxM\Rinst1d7c720f4a5f\customProDB\extdata\vcfs\test1.vcf

--- failed re-building 'customProDB.Rnw'

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

Error: Vignette re-building failed.
Execution halted