Package: ensemblVEP

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ensemblVEP

StartedAt: 2013-05-01 01:11:07 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 01:11:57 -0700 (Wed, 01 May 2013)

EllapsedTime: 50.5 seconds

RetCode: 1

Status:  ERROR

PackageFile: None

PackageFileSize: NA

* checking for file 'ensemblVEP/DESCRIPTION' ... OK
* preparing 'ensemblVEP':
* checking DESCRIPTION meta-information ... OK
* installing the package to re-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 object is masked from 'package:stats':

    xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, as.data.frame,
    cbind, colnames, duplicated, eval, get, intersect, lapply, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rep.int, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unlist

Loading required package: GenomicRanges
Loading required package: IRanges
Loading required package: VariantAnnotation
Loading required package: Rsamtools
Loading required package: Biostrings
Unknown option: database
ERROR: Failed to parse command-line flags

Error: processing vignette 'ensemblVEP.Rnw' failed with diagnostics:
 chunk 4 (label = rtn_GRanges) 
Error in .io_check_exists(path(con)) : file(s) do not exist:
  '/tmp/RtmpiUGa8y/file12b6fa99083f'
Execution halted