Running ‘testthat.R’ [75s/111s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > # library(ActiveDriverWGS)
  > 
  > test_check("ActiveDriverWGS")
  Loading required package: ActiveDriverWGS
  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
  Removing  0  invalid SNVs & indels
  
  .0 remove hypermut, n= 0 ,  0 %
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  reversing 0 positions
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  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
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  Number of Elements with 0 Mutations:  0 
  Tests to do:  11 
  ......reversing 0 positions
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  reversing 0 positions
  Removing  0  invalid SNVs & indels
  
  28 remove hypermut, n= 58256 ,  100 %
  hypermuted samples:  001-0002-03TD 003-0005-09TD 012-02-1TD 125 128 137 141 151 178 192 26 277 282 294 306 308 318 342 343 367 393 467 473 477 519 523 564 CLL4-ARTICLE 
  
  0 remove hypermut, n= 0 ,  0 %
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  reversing 0 positions
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  hypermuted samples:   
  
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  0 remove hypermut, n= 0 ,  0 %
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  0 remove hypermut, n= 0 ,  0 %
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  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
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  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
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  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
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  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
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  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
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  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
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  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
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  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
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  0 remove hypermut, n= 0 ,  0 %
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   1189  Rows :: Processing row 100  200  300  400  500  600  700  800  900  1000  1100  
   Preparing Elements Complete 
   RM 0 lines
  
   Preparing Elements Complete 
   RM 0 lines
  
   5  Rows :: Processing row 
   5  Rows :: Processing row 
   5  Rows :: Processing row ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_ActiveDriverWGS.R:38:1): (code run outside of `test_that()`) ────
  Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'splitAsList': error in evaluating the argument 'x' in selecting a method for function 'end': invalid class "GRanges" object: 
      'seqlevels(seqinfo(x))' and 'levels(seqnames(x))' are not identical
  Backtrace:
       █
    1. ├─ActiveDriverWGS::ActiveDriverWGS(...) test_ActiveDriverWGS.R:38:0
    2. │ ├─base::do.call(...)
    3. │ └─parallel::mclapply(...)
    4. │   └─base::lapply(X = X, FUN = FUN, ...)
    5. │     └─ActiveDriverWGS:::FUN(X[[i]], ...)
    6. │       └─ActiveDriverWGS::ADWGS_test(...)
    7. │         ├─GenomicRanges::intersect(gr_sites, gr_elements)
    8. │         └─GenomicRanges::intersect(gr_sites, gr_elements)
    9. │           └─GenomicRanges:::.local(x, y, ...)
   10. │             ├─GenomicRanges:::.maxEndPerGRangesSequence(c(x, y))
   11. │             │ ├─S4Vectors::splitAsList(end(x), seqnames(x))
   12. │             │ └─stats::end(x)
   13. │             ├─methods:::c(x, y)
   14. │             └─S4Vectors:::c(x, y)
   15. │               └─S4Vectors:::.local(x, ...)
   16. │                 ├─S4Vectors::bindROWS(x, list(...), ignore.mcols = ignore.mcols)
   17. │                 └─GenomicRanges::bindROWS(x, list(...), ignore.mcols = ignore.mcols)
   18. │                   ├─methods::callNextMethod()
   19. │                   └─S4Vectors:::.nextMethod(x = x, objects = objects, ignore.mcols = ignore.mcols)
   20. │                     └─methods::validObject(ans)
   21. │                       └─base::stop(msg, ": ", errors, domain = NA)
   22. ├─base::.handleSimpleError(...)
   23. │ └─base:::h(simpleError(msg, call))
   24. └─base::.handleSimpleError(...)
   25.   └─base:::h(simpleError(msg, call))
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 83 ]
  Error: Test failures
  Execution halted