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


Analyze database: 100.0% (1000.0)                    
  Index database: 100.0% (1000.0)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
 Search database: 10.4% (104.0)                    
 Search database: 74.4% (744.0)                    
 Search database: 100.0% (1000.0)                    
      Write hits: 100.0% (3324.0)                    
Quitting from lines 706-713 [unnamed-chunk-34] (User_manual.Rmd)
Error: processing vignette 'User_manual.Rmd' failed with diagnostics:
BiocParallel errors
  1 remote errors, element index: 1
  1 unevaluated and other errors
  first remote error:
Error in XStringSet.stringDist(x = BStringSet(x), method = method, ignoreCase = ignoreCase, : 'substitutionMatrix' must be a numeric matrix

--- failed re-building ‘User_manual.Rmd’

SUMMARY: processing the following file failed:
  ‘User_manual.Rmd’

Error: Vignette re-building failed.
Execution halted