Running 'testthat.R' [46s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ActiveDriverWGS)
  > 
  > test_check("ActiveDriverWGS")
  -- 1. Error: (unknown) (@test_ADWGS_test.R#7)  ---------------------------------
  trying to get slot "className" from an object of a basic class ("character") with no slots
  Backtrace:
   1. GenomicRanges::GRanges(...)
   2. S4Vectors::DataFrame(..., check.names = FALSE)
   3. methods::is(listData[[1L]], getClass("Annotated"))
  
  -- 2. Error: (unknown) (@test_ActiveDriverWGS.R#7)  ----------------------------
  trying to get slot "className" from an object of a basic class ("character") with no slots
  Backtrace:
   1. GenomicRanges::GRanges(...)
   2. S4Vectors::DataFrame(..., check.names = FALSE)
   3. methods::is(listData[[1L]], getClass("Annotated"))
  
  reversing 0 positions
  Removing  0  invalid SNVs & indels
  
  reversing 0 positions
  Removing  0  invalid SNVs
  
  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 %
  hypermuted samples:   
  
  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
  Removing  0  invalid SNVs & indels
  
  -- 3. Failure: elements are formatted properly (@test_input_format.R#112)  -----
  `ActiveDriverWGS(elements = as.matrix(cancer_genes), mutations = cll_mutations)` threw an error with unexpected message.
  Expected match: "elements must be a data frame"
  Actual message: "trying to get slot \"className\" from an object of a basic class (\"character\") with no slots"
  Backtrace:
   1. testthat::expect_error(...)
   6. ActiveDriverWGS::ActiveDriverWGS(...)
   7. GenomicRanges::GRanges(...)
   8. S4Vectors::DataFrame(..., check.names = FALSE)
   9. methods::is(listData[[1L]], getClass("Annotated"))
  
  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
  Removing  0  invalid SNVs & indels
  
  -- 4. Failure: elements are formatted properly (@test_input_format.R#117)  -----
  `ActiveDriverWGS(elements = cancer_genes[, 1:3], mutations = cll_mutations)` threw an error with unexpected message.
  Expected match: "elements must contain the following columns: chr, start, end & id"
  Actual message: "trying to get slot \"className\" from an object of a basic class (\"character\") with no slots"
  Backtrace:
   1. testthat::expect_error(...)
   6. ActiveDriverWGS::ActiveDriverWGS(...)
   7. GenomicRanges::GRanges(...)
   8. S4Vectors::DataFrame(..., check.names = FALSE)
   9. methods::is(listData[[1L]], getClass("Annotated"))
  
  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
  Removing  0  invalid SNVs & indels
  
  -- 5. Failure: elements are formatted properly (@test_input_format.R#124)  -----
  `ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)` threw an error with unexpected message.
  Expected match: "elements may not contain missing values"
  Actual message: "trying to get slot \"className\" from an object of a basic class (\"character\") with no slots"
  Backtrace:
   1. testthat::expect_error(...)
   6. ActiveDriverWGS::ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)
   7. GenomicRanges::GRanges(...)
   8. S4Vectors::DataFrame(..., check.names = FALSE)
   9. methods::is(listData[[1L]], getClass("Annotated"))
  
  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
  Removing  0  invalid SNVs & indels
  
  -- 6. Failure: elements are formatted properly (@test_input_format.R#130)  -----
  `ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)` threw an error with unexpected message.
  Expected match: "duplicated elements are present. please review your format"
  Actual message: "trying to get slot \"className\" from an object of a basic class (\"character\") with no slots"
  Backtrace:
   1. testthat::expect_error(...)
   6. ActiveDriverWGS::ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)
   7. GenomicRanges::GRanges(...)
   8. S4Vectors::DataFrame(..., check.names = FALSE)
   9. methods::is(listData[[1L]], getClass("Annotated"))
  
  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
  Removing  0  invalid SNVs & indels
  
  -- 7. Failure: elements are formatted properly (@test_input_format.R#137)  -----
  `ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)` threw an error with unexpected message.
  Expected match: "start and end must be numeric"
  Actual message: "trying to get slot \"className\" from an object of a basic class (\"character\") with no slots"
  Backtrace:
   1. testthat::expect_error(...)
   6. ActiveDriverWGS::ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)
   7. GenomicRanges::GRanges(...)
   8. S4Vectors::DataFrame(..., check.names = FALSE)
   9. methods::is(listData[[1L]], getClass("Annotated"))
  
  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
  Removing  0  invalid SNVs & indels
  
  -- 8. Failure: elements are formatted properly (@test_input_format.R#144)  -----
  `ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)` threw an error with unexpected message.
  Expected match: "element identifier must be a string"
  Actual message: "trying to get slot \"className\" from an object of a basic class (\"character\") with no slots"
  Backtrace:
   1. testthat::expect_error(...)
   6. ActiveDriverWGS::ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)
   7. GenomicRanges::GRanges(...)
   8. S4Vectors::DataFrame(..., check.names = FALSE)
   9. methods::is(listData[[1L]], getClass("Annotated"))
  
  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
  Removing  0  invalid SNVs & indels
  
  -- 9. Failure: sites are formatted properly (@test_input_format.R#152)  --------
  `ActiveDriverWGS(...)` threw an error with unexpected message.
  Expected match: "sites must be a data frame"
  Actual message: "trying to get slot \"className\" from an object of a basic class (\"character\") with no slots"
  Backtrace:
   1. testthat::expect_error(...)
   6. ActiveDriverWGS::ActiveDriverWGS(...)
   7. GenomicRanges::GRanges(...)
   8. S4Vectors::DataFrame(..., check.names = FALSE)
   9. methods::is(listData[[1L]], getClass("Annotated"))
  
  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
  Removing  0  invalid SNVs & indels
  
  -- 10. Failure: sites are formatted properly (@test_input_format.R#158)  -------
  `ActiveDriverWGS(...)` threw an error with unexpected message.
  Expected match: "sites must contain the following columns: chr, start, end & id"
  Actual message: "trying to get slot \"className\" from an object of a basic class (\"character\") with no slots"
  Backtrace:
   1. testthat::expect_error(...)
   6. ActiveDriverWGS::ActiveDriverWGS(...)
   7. GenomicRanges::GRanges(...)
   8. S4Vectors::DataFrame(..., check.names = FALSE)
   9. methods::is(listData[[1L]], getClass("Annotated"))
  
  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
  Removing  0  invalid SNVs & indels
  
  -- 11. Failure: sites are formatted properly (@test_input_format.R#167)  -------
  `ActiveDriverWGS(...)` threw an error with unexpected message.
  Expected match: "sites may not contain missing values"
  Actual message: "trying to get slot \"className\" from an object of a basic class (\"character\") with no slots"
  Backtrace:
   1. testthat::expect_error(...)
   6. ActiveDriverWGS::ActiveDriverWGS(...)
   7. GenomicRanges::GRanges(...)
   8. S4Vectors::DataFrame(..., check.names = FALSE)
   9. methods::is(listData[[1L]], getClass("Annotated"))
  
  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
  Removing  0  invalid SNVs & indels
  
  -- 12. Failure: sites are formatted properly (@test_input_format.R#174)  -------
  `ActiveDriverWGS(...)` threw an error with unexpected message.
  Expected match: "duplicated sites are present. please review your format"
  Actual message: "trying to get slot \"className\" from an object of a basic class (\"character\") with no slots"
  Backtrace:
   1. testthat::expect_error(...)
   6. ActiveDriverWGS::ActiveDriverWGS(...)
   7. GenomicRanges::GRanges(...)
   8. S4Vectors::DataFrame(..., check.names = FALSE)
   9. methods::is(listData[[1L]], getClass("Annotated"))
  
  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
  Removing  0  invalid SNVs & indels
  
  -- 13. Failure: sites are formatted properly (@test_input_format.R#182)  -------
  `ActiveDriverWGS(...)` threw an error with unexpected message.
  Expected match: "start and end must be numeric"
  Actual message: "trying to get slot \"className\" from an object of a basic class (\"character\") with no slots"
  Backtrace:
   1. testthat::expect_error(...)
   6. ActiveDriverWGS::ActiveDriverWGS(...)
   7. GenomicRanges::GRanges(...)
   8. S4Vectors::DataFrame(..., check.names = FALSE)
   9. methods::is(listData[[1L]], getClass("Annotated"))
  
  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
  Removing  0  invalid SNVs & indels
  
  -- 14. Failure: sites are formatted properly (@test_input_format.R#190)  -------
  `ActiveDriverWGS(...)` threw an error with unexpected message.
  Expected match: "site identifier must be a string"
  Actual message: "trying to get slot \"className\" from an object of a basic class (\"character\") with no slots"
  Backtrace:
   1. testthat::expect_error(...)
   6. ActiveDriverWGS::ActiveDriverWGS(...)
   7. GenomicRanges::GRanges(...)
   8. S4Vectors::DataFrame(..., check.names = FALSE)
   9. methods::is(listData[[1L]], getClass("Annotated"))
  
  
   1189  Rows :: Processing row 100  200  300  400  500  600  700  800  900  1000  1100  
   Preparing Elements Complete 
   RM 0 lines
  
   5  Rows :: Processing row 
   5  Rows :: Processing row 
   5  Rows :: Processing row == testthat results  ===========================================================
  [ OK: 48 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 14 ]
  1. Error: (unknown) (@test_ADWGS_test.R#7) 
  2. Error: (unknown) (@test_ActiveDriverWGS.R#7) 
  3. Failure: elements are formatted properly (@test_input_format.R#112) 
  4. Failure: elements are formatted properly (@test_input_format.R#117) 
  5. Failure: elements are formatted properly (@test_input_format.R#124) 
  6. Failure: elements are formatted properly (@test_input_format.R#130) 
  7. Failure: elements are formatted properly (@test_input_format.R#137) 
  8. Failure: elements are formatted properly (@test_input_format.R#144) 
  9. Failure: sites are formatted properly (@test_input_format.R#152) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted