################################################################################################################################################################## Running command:###### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 ELMER###############################################################################################################################################################* 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 rmarkdownQuitting 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 rmarkdownQuitting 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 rmarkdownQuitting 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 rmarkdownQuitting 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 rmarkdownQuitting 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