BioC 3.5: BUILD report for VariantFiltering on oaxaca

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data VariantFiltering
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* checking for file ‘VariantFiltering/DESCRIPTION’ ... OK
* preparing ‘VariantFiltering’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, 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: VariantAnnotation
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
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
matrixStats v0.51.0 (2016-10-08) successfully loaded. See ?matrixStats for help.

Attaching package: ‘matrixStats’

The following objects are masked from ‘package:Biobase’:

    anyMissing, rowMedians


Attaching package: ‘DelayedArray’

The following objects are masked from ‘package:matrixStats’:

    colMaxs, rowMaxs

The following object is masked from ‘package:base’:

    apply


Attaching package: ‘SummarizedExperiment’

The following object is masked from ‘package:matrixStats’:

    rowRanges

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

Attaching package: ‘Biostrings’

The following object is masked from ‘package:DelayedArray’:

    type


Attaching package: ‘VariantAnnotation’

The following object is masked from ‘package:base’:

    tabulate

Loading BSgenome annotation package BSgenome.Hsapiens.1000genomes.hs37d5
Loading OrgDb annotation package org.Hs.eg.db
Loading TxDb annotation package TxDb.Hsapiens.UCSC.hg19.knownGene
Loading SNPlocs annotation package SNPlocs.Hsapiens.dbSNP144.GRCh37
Loading annotation package MafDb.1Kgenomes.phase3.hs37d5
Loading annotation package MafDb.ExAC.r0.3.1.snvs.hs37d5
Loading annotation package PolyPhen.Hsapiens.dbSNP131
Loading annotation package SIFT.Hsapiens.dbSNP137
Loading annotation package phastCons100way.UCSC.hg19
Fetching annotation object humanGenesPhylostrata
Warning in `seqlevelsStyle<-`(`*tmp*`, value = c("NCBI", "Ensembl")) :
  more than one seqlevels style supplied, using the 1st one only
Assuming the genome build of the input variants is hs37d5.
Switching to the UCSC chromosome-name style from the transcript-centric annotation package.
Warning in .matchSeqinfo(variants, txdb, bsgenome) :
  Chromosome chrM has different lengths between the input VCF and the input TxDb pakage. This chromosome will be discarded from further analysis
Warning in .matchSeqinfo(variants, txdb, bsgenome) :
  Assumming hs37d5 and hg19 represent the same genome build.
Discarding scaffold sequences.
Annotating variant type (SNV, Insertion, Deletion, MNV, Delins)
Annotating dbSNP identifiers with SNPlocs.Hsapiens.dbSNP144.GRCh37
Warning in `seqlevelsStyle<-`(`*tmp*`, value = c("NCBI", "Ensembl")) :
  more than one seqlevels style supplied, using the 1st one only
Warning in .local(annObj, ...) :
  Assumming hg19 and GRCh37.p13 represent the same genome build between variants and the XtraSNPlocs package, respectively.

Error: processing vignette 'usingVariantFiltering.Rnw' failed with diagnostics:
 chunk 5 
Error in .local(x, seqname, ...) : unused argument (as.GRanges = TRUE)
Execution halted
BioC 3.5: BUILD report for VariantFiltering on oaxaca

Summary

Command output
