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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data 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

Quitting from lines 64-85 [unnamed-chunk-3] (analysis_data_input.Rmd)
Error: processing vignette 'analysis_data_input.Rmd' failed with diagnostics:
'getURL()' failed:
  URL: https://api.gdc.cancer.gov/cases/?pretty=true&expand=samples,project,diagnoses,diagnoses.treatments,annotations,family_histories,demographic,exposures&size=2&filters=%7B%22op%22:%22or%22,%22content%22:[%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.submitter_id%22,%22value%22:["TCGA-43-3394-11A","TCGA-56-8305-01A%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22submitter_sample_ids%22,%22value%22:["TCGA-43-3394-11A","TCGA-56-8305-01A%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22submitter_aliquot_ids%22,%22value%22:["TCGA-43-3394-11A","TCGA-56-8305-01A%22]%7D%7D]%7D
  error: Recv failure: Connection reset by peer
--- failed re-building ‘analysis_data_input.Rmd’

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

Quitting from lines 69-83 [unnamed-chunk-2] (analysis_diff_meth.Rmd)
Error: processing vignette 'analysis_diff_meth.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'get': cannot open the connection
--- failed re-building ‘analysis_diff_meth.Rmd’

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

Quitting from lines 109-138 [unnamed-chunk-2] (analysis_get_pair.Rmd)
Error: processing vignette 'analysis_get_pair.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'get': cannot open the connection
--- failed 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 lines 68-85 [unnamed-chunk-2] (analysis_motif_enrichment.Rmd)
Error: processing vignette 'analysis_motif_enrichment.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'get': cannot open the connection
--- failed re-building ‘analysis_motif_enrichment.Rmd’

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

Quitting from lines 87-90 [unnamed-chunk-2] (analysis_regulatory_tf.Rmd)
Error: processing vignette 'analysis_regulatory_tf.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'get': 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

Quitting from lines 133-190 [unnamed-chunk-4] (input.Rmd)
Error: processing vignette 'input.Rmd' failed with diagnostics:
'getURL()' failed:
  URL: https://api.gdc.cancer.gov/cases/?pretty=true&expand=samples,project,diagnoses,diagnoses.treatments,annotations,family_histories,demographic,exposures&size=2&filters=%7B%22op%22:%22or%22,%22content%22:[%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.submitter_id%22,%22value%22:["TCGA-43-3394-11A","TCGA-56-8305-01A%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22submitter_sample_ids%22,%22value%22:["TCGA-43-3394-11A","TCGA-56-8305-01A%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22submitter_aliquot_ids%22,%22value%22:["TCGA-43-3394-11A","TCGA-56-8305-01A%22]%7D%7D]%7D
  error: Recv failure: Connection reset by peer
--- failed re-building ‘input.Rmd’

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

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

Quitting from lines 41-48 [unnamed-chunk-2] (plots_TF.Rmd)
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

Quitting from lines 33-35 [unnamed-chunk-2] (plots_heatmap.Rmd)
Error: processing vignette 'plots_heatmap.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'get': cannot open the connection
--- failed re-building ‘plots_heatmap.Rmd’

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

Quitting from lines 36-40 [unnamed-chunk-2] (plots_motif_enrichment.Rmd)
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 lines 33-35 [unnamed-chunk-2] (plots_scatter.Rmd)
Error: processing vignette 'plots_scatter.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'get': cannot open the connection
--- failed re-building ‘plots_scatter.Rmd’

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

Quitting from lines 32-35 [unnamed-chunk-2] (plots_schematic.Rmd)
Error: processing vignette 'plots_schematic.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'get': cannot open the connection
--- failed re-building ‘plots_schematic.Rmd’

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

SUMMARY: processing the following files failed:
  ‘analysis_data_input.Rmd’ ‘analysis_diff_meth.Rmd’
  ‘analysis_get_pair.Rmd’ ‘analysis_motif_enrichment.Rmd’
  ‘analysis_regulatory_tf.Rmd’ ‘input.Rmd’ ‘plots_TF.Rmd’
  ‘plots_heatmap.Rmd’ ‘plots_motif_enrichment.Rmd’ ‘plots_scatter.Rmd’
  ‘plots_schematic.Rmd’

Error: Vignette re-building failed.
Execution halted