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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 ELMER
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* checking for file ‘ELMER/DESCRIPTION’ ... OK
* preparing ‘ELMER’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘analysis_data_input.Rmd’ using rmarkdown
--- finished re-building ‘analysis_data_input.Rmd’

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

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

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

--- re-building ‘analysis_motif_enrichment.Rmd’ using rmarkdown

Quitting from analysis_motif_enrichment.Rmd:67-85 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `fix.by()`:
! 'by' must specify a uniquely valid column
---
Backtrace:
    ▆
 1. └─ELMER::get.enriched.motif(...)
 2.   └─ELMER:::getHocomocoTable()
 3.     ├─base::merge(hocomoco, x, by = "Model")
 4.     ├─base::merge(hocomoco, x, by = "Model")
 5.     └─base::merge.data.frame(hocomoco, x, by = "Model")
 6.       └─base (local) fix.by(by.x, x)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'analysis_motif_enrichment.Rmd' failed with diagnostics:
'by' must specify a uniquely valid column
--- failed re-building ‘analysis_motif_enrichment.Rmd’

--- re-building ‘analysis_regulatory_tf.Rmd’ using rmarkdown

Quitting from analysis_regulatory_tf.Rmd:86-90 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `readChar()`:
! cannot open the connection
---
Backtrace:
    ▆
 1. └─base::load("result/getMotif.hypo.enriched.motifs.rda")
 2.   └─base::readChar(con, 5L, useBytes = TRUE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'analysis_regulatory_tf.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘analysis_regulatory_tf.Rmd’

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

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

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

--- re-building ‘plots_TF.Rmd’ using rmarkdown

Quitting from plots_TF.Rmd:40-48 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `readChar()`:
! cannot open the connection
---
Backtrace:
    ▆
 1. └─base::load("result/getTF.hypo.TFs.with.motif.pvalue.rda")
 2.   └─base::readChar(con, 5L, useBytes = TRUE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'plots_TF.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘plots_TF.Rmd’

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

--- re-building ‘plots_motif_enrichment.Rmd’ using rmarkdown

Quitting from plots_motif_enrichment.Rmd:35-40 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection
---
Backtrace:
    ▆
 1. └─ELMER::motif.enrichment.plot(...)
 2.   └─utils::read.csv(motif.enrichment, stringsAsFactors = FALSE)
 3.     └─utils::read.table(...)
 4.       └─base::file(file, "rt")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'plots_motif_enrichment.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘plots_motif_enrichment.Rmd’

--- re-building ‘plots_scatter.Rmd’ using rmarkdown

Quitting from plots_scatter.Rmd:68-77 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `readChar()`:
! cannot open the connection
---
Backtrace:
    ▆
 1. └─base::load("result/getMotif.hypo.enriched.motifs.rda")
 2.   └─base::readChar(con, 5L, useBytes = TRUE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'plots_scatter.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘plots_scatter.Rmd’

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

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

SUMMARY: processing the following files failed:
  ‘analysis_motif_enrichment.Rmd’ ‘analysis_regulatory_tf.Rmd’
  ‘plots_TF.Rmd’ ‘plots_motif_enrichment.Rmd’ ‘plots_scatter.Rmd’

Error: Vignette re-building failed.
Execution halted