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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ensemblVEP
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* checking for file ‘ensemblVEP/DESCRIPTION’ ... OK
* preparing ‘ensemblVEP’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘ensemblVEP.Rnw’ using Sweave
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

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, aperm, append,
    as.data.frame, basename, cbind, 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, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

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

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: VariantAnnotation
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

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")'.


Attaching package: ‘Biobase’

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

    rowMedians

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

    anyMissing, rowMedians

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

Attaching package: ‘Biostrings’

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

    strsplit


Attaching package: ‘VariantAnnotation’

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

    tabulate

Warning in system2(.getVepPath(), stdout = TRUE, stderr = TRUE) :
  running command ''/usr/local/ensembl-vep/vep' 2>&1' had status 2

Attaching package: ‘ensemblVEP’

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

    cache

Can't locate Bio/EnsEMBL/Registry.pm in @INC (you may need to install the Bio::EnsEMBL::Registry module) (@INC contains: /usr/local/ensembl-vep/modules /usr/local/ensembl-vep /Library/Perl/5.30/darwin-thread-multi-2level /Library/Perl/5.30 /Network/Library/Perl/5.30/darwin-thread-multi-2level /Network/Library/Perl/5.30 /Library/Perl/Updates/5.30.3/darwin-thread-multi-2level /Library/Perl/Updates/5.30.3 /System/Library/Perl/5.30/darwin-thread-multi-2level /System/Library/Perl/5.30 /System/Library/Perl/Extras/5.30/darwin-thread-multi-2level /System/Library/Perl/Extras/5.30) at /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm line 58.
BEGIN failed--compilation aborted at /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm line 58.
Compilation failed in require at /System/Library/Perl/5.30/base.pm line 137.
	...propagated at /System/Library/Perl/5.30/base.pm line 159.
BEGIN failed--compilation aborted at /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm line 56.
Compilation failed in require at /System/Library/Perl/5.30/base.pm line 137.
	...propagated at /System/Library/Perl/5.30/base.pm line 159.
BEGIN failed--compilation aborted at /usr/local/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm line 71.
Compilation failed in require at /usr/local/ensembl-vep/vep line 20.
BEGIN failed--compilation aborted at /usr/local/ensembl-vep/vep line 20.

Error: processing vignette 'ensemblVEP.Rnw' failed with diagnostics:
 chunk 5 (label = rtn_GRanges) 
Error in .io_check_exists(path(con)) : file(s) do not exist:
  '/tmp/Rtmp1PaRrw/file63d1130c4943'

--- failed re-building ‘ensemblVEP.Rnw’

SUMMARY: processing the following file failed:
  ‘ensemblVEP.Rnw’

Error: Vignette re-building failed.
Execution halted