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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data rnaseqGene
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* checking for file ‘rnaseqGene/DESCRIPTION’ ... OK
* preparing ‘rnaseqGene’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘rnaseqGene.Rmd’ using rmarkdown

Attaching package: 'rmarkdown'

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

    html_document, md_document, pdf_document

Loading required package: SummarizedExperiment
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, 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, 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
Loading required package: GenomeInfoDb
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


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

trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz'
Content type 'unknown' length 39387922 bytes (37.6 MB)
============================================
Warning in download.file(resource(con), destfile) :
  downloaded length 34837506 != reported length 39387922
Warning in download.file(resource(con), destfile) :
  URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz': Timeout of 60 seconds was reached
Quitting from lines 348-350 (rnaseqGene.Rmd) 
Error: processing vignette 'rnaseqGene.Rmd' failed with diagnostics:
cannot open URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz'
--- failed re-building ‘rnaseqGene.Rmd’

SUMMARY: processing the following file failed:
  ‘rnaseqGene.Rmd’

Error: Vignette re-building failed.
Execution halted