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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data IHWpaper
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* checking for file ‘IHWpaper/DESCRIPTION’ ... OK
* preparing ‘IHWpaper’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘BH-explanation.Rmd’ using rmarkdown
--- finished re-building ‘BH-explanation.Rmd’

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

--- re-building ‘explaining_tdr.Rmd’ using rmarkdown
Quitting from lines 28-57 (explaining_tdr.Rmd) 
Error: processing vignette 'explaining_tdr.Rmd' failed with diagnostics:
attempt to use zero-length variable name
--- failed re-building ‘explaining_tdr.Rmd’

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

--- re-building ‘hqtl_IHW_BY.Rmd’ using rmarkdown
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:gridExtra':

    combine

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.max, which.min

Registered S3 method overwritten by 'GGally':
  method from   
  +.gg   ggplot2
Need specific help about ggbio? try mailing 
 the maintainer or visit http://tengfei.github.com/ggbio/

Attaching package: 'ggbio'

The following objects are masked from 'package:ggplot2':

    geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity,
    xlim


Attaching package: 'scales'

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

    rescale

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

    alpha

--- finished re-building ‘hqtl_IHW_BY.Rmd’

--- re-building ‘real_data_examples.Rmd’ using rmarkdown
Quitting from lines 300-308 (real_data_examples.Rmd) 
Error: processing vignette 'real_data_examples.Rmd' failed with diagnostics:
attempt to use zero-length variable name
--- failed re-building ‘real_data_examples.Rmd’

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

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

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

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

--- re-building ‘weights_vs_filtering.Rmd’ using rmarkdown
Using only 1 fold! Only use this if you want to learn the weights, but NEVER for testing!
--- finished re-building ‘weights_vs_filtering.Rmd’

SUMMARY: processing the following files failed:
  ‘explaining_tdr.Rmd’ ‘real_data_examples.Rmd’

Error: Vignette re-building failed.
Execution halted