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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 glmSparseNet
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* checking for file ‘glmSparseNet/DESCRIPTION’ ... OK
* preparing ‘glmSparseNet’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘example_brca_logistic.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: MultiAssayExperiment
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:dplyr':

    combine, intersect, setdiff, union

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 objects are masked from 'package:dplyr':

    first, rename

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    collapse, desc, slice

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

The following object is masked from 'package:dplyr':

    count


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

Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Loading required package: glmnet
Loaded glmnet 4.0-2
Quitting from lines 55-57 (example_brca_logistic.Rmd) 
Error: processing vignette 'example_brca_logistic.Rmd' failed with diagnostics:
failed to load resource
  name: EH596
  title: BRCA_RNASeq2GeneNorm-20160128
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
--- failed re-building ‘example_brca_logistic.Rmd’

--- re-building ‘example_brca_protein-protein-interactions_survival.Rmd’ using rmarkdown
Loading required package: grid
Quitting from lines 137-139 (example_brca_protein-protein-interactions_survival.Rmd) 
Error: processing vignette 'example_brca_protein-protein-interactions_survival.Rmd' failed with diagnostics:
failed to load resource
  name: EH596
  title: BRCA_RNASeq2GeneNorm-20160128
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
--- failed re-building ‘example_brca_protein-protein-interactions_survival.Rmd’

--- re-building ‘example_brca_survival.Rmd’ using rmarkdown
Quitting from lines 55-57 (example_brca_survival.Rmd) 
Error: processing vignette 'example_brca_survival.Rmd' failed with diagnostics:
failed to load resource
  name: EH596
  title: BRCA_RNASeq2GeneNorm-20160128
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
--- failed re-building ‘example_brca_survival.Rmd’

--- re-building ‘example_prad_survival.Rmd’ using rmarkdown
--- finished re-building ‘example_prad_survival.Rmd’

--- re-building ‘example_skcm_survival.Rmd’ using rmarkdown
Quitting from lines 55-57 (example_skcm_survival.Rmd) 
Error: processing vignette 'example_skcm_survival.Rmd' failed with diagnostics:
failed to load resource
  name: EH1035
  title: SKCM_RNASeq2GeneNorm-20160128
  reason: 1 resources failed to download
--- failed re-building ‘example_skcm_survival.Rmd’

SUMMARY: processing the following files failed:
  ‘example_brca_logistic.Rmd’
  ‘example_brca_protein-protein-interactions_survival.Rmd’
  ‘example_brca_survival.Rmd’ ‘example_skcm_survival.Rmd’

Error: Vignette re-building failed.
Execution halted