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### Running command:
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###   /home/biocbuild/R/R/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: 6.4% (64.0)                    
 Search database: 48.8% (488.0)                    
 Search database: 100.0% (1000.0)                    
      Write hits: 100.0% (3286.0)                    
Quitting from lines 706-713 [unnamed-chunk-34] (User_manual.Rmd)
Error: processing vignette 'User_manual.Rmd' failed with diagnostics:
'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