Running ‘testthat.R’ [15s/23s]
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
  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
  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
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  0 remove hypermut, n= 0 ,  0 %
  hypermuted samples:   
  
  reversing 0 positions
  
   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_ADWGS_test.R:22:1): (code run outside of `test_that()`) ─────────
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ActiveDriverWGS::format_muts(...) test_ADWGS_test.R:22:0
    2.   └─ActiveDriverWGS:::.get_3n_context_of_mutations(mutations, this_genome)
    3.     ├─BSgenome::getSeq(this_genome, flank_ranges)
    4.     └─BSgenome::getSeq(this_genome, flank_ranges)
    5.       └─BSgenome:::.local(x, ...)
    6.         └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
    7.           ├─base::split(names, seqnames(names))
    8.           └─S4Vectors::split(names, seqnames(names))
    9.             ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   10.             └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   11.               └─S4Vectors:::.local(x, f, drop, ...)
   12.                 └─IRanges:::default_splitAsList(x, f, drop = drop)
   13.                   └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   14.                     └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_ActiveDriverWGS.R:22:1): (code run outside of `test_that()`) ────
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ActiveDriverWGS::format_muts(...) test_ActiveDriverWGS.R:22:0
    2.   └─ActiveDriverWGS:::.get_3n_context_of_mutations(mutations, this_genome)
    3.     ├─BSgenome::getSeq(this_genome, flank_ranges)
    4.     └─BSgenome::getSeq(this_genome, flank_ranges)
    5.       └─BSgenome:::.local(x, ...)
    6.         └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
    7.           ├─base::split(names, seqnames(names))
    8.           └─S4Vectors::split(names, seqnames(names))
    9.             ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   10.             └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   11.               └─S4Vectors:::.local(x, f, drop, ...)
   12.                 └─IRanges:::default_splitAsList(x, f, drop = drop)
   13.                   └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   14.                     └─S4Vectors:::isNotSorted(f_vals)
  ── Error (test_format_muts.R:8:1): (code run outside of `test_that()`) ─────────
  Error: 2 arguments passed to .Internal(is.unsorted) which requires 3
  Backtrace:
       █
    1. └─ActiveDriverWGS::format_muts(cll_mutations[1:10, ], this_genome = this_genome) test_format_muts.R:8:0
    2.   └─ActiveDriverWGS:::.get_3n_context_of_mutations(mutations, this_genome)
    3.     ├─BSgenome::getSeq(this_genome, flank_ranges)
    4.     └─BSgenome::getSeq(this_genome, flank_ranges)
    5.       └─BSgenome:::.local(x, ...)
    6.         └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
    7.           ├─base::split(names, seqnames(names))
    8.           └─S4Vectors::split(names, seqnames(names))
    9.             ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   10.             └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   11.               └─S4Vectors:::.local(x, f, drop, ...)
   12.                 └─IRanges:::default_splitAsList(x, f, drop = drop)
   13.                   └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   14.                     └─S4Vectors:::isNotSorted(f_vals)
  ── Failure (test_input_format.R:114:3): elements are formatted properly ────────
  `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: "2 arguments passed to .Internal(is.unsorted) which requires 3"
  Backtrace:
       █
    1. ├─testthat::expect_error(...) test_input_format.R:114:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat:::.capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─ActiveDriverWGS::ActiveDriverWGS(...)
    7.   └─ActiveDriverWGS::format_muts(...)
    8.     └─ActiveDriverWGS:::.get_3n_context_of_mutations(mutations, this_genome)
    9.       ├─BSgenome::getSeq(this_genome, flank_ranges)
   10.       └─BSgenome::getSeq(this_genome, flank_ranges)
   11.         └─BSgenome:::.local(x, ...)
   12.           └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   13.             ├─base::split(names, seqnames(names))
   14.             └─S4Vectors::split(names, seqnames(names))
   15.               ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.               └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                 └─S4Vectors:::.local(x, f, drop, ...)
   18.                   └─IRanges:::default_splitAsList(x, f, drop = drop)
   19.                     └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   20.                       └─S4Vectors:::isNotSorted(f_vals)
  ── Failure (test_input_format.R:119:3): elements are formatted properly ────────
  `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: "2 arguments passed to .Internal(is.unsorted) which requires 3"
  Backtrace:
       █
    1. ├─testthat::expect_error(...) test_input_format.R:119:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat:::.capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─ActiveDriverWGS::ActiveDriverWGS(...)
    7.   └─ActiveDriverWGS::format_muts(...)
    8.     └─ActiveDriverWGS:::.get_3n_context_of_mutations(mutations, this_genome)
    9.       ├─BSgenome::getSeq(this_genome, flank_ranges)
   10.       └─BSgenome::getSeq(this_genome, flank_ranges)
   11.         └─BSgenome:::.local(x, ...)
   12.           └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   13.             ├─base::split(names, seqnames(names))
   14.             └─S4Vectors::split(names, seqnames(names))
   15.               ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.               └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                 └─S4Vectors:::.local(x, f, drop, ...)
   18.                   └─IRanges:::default_splitAsList(x, f, drop = drop)
   19.                     └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   20.                       └─S4Vectors:::isNotSorted(f_vals)
  ── Failure (test_input_format.R:126:3): elements are formatted properly ────────
  `ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)` threw an error with unexpected message.
  Expected match: "elements may not contain missing values"
  Actual message: "2 arguments passed to .Internal(is.unsorted) which requires 3"
  Backtrace:
       █
    1. ├─testthat::expect_error(...) test_input_format.R:126:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat:::.capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─ActiveDriverWGS::ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)
    7.   └─ActiveDriverWGS::format_muts(...)
    8.     └─ActiveDriverWGS:::.get_3n_context_of_mutations(mutations, this_genome)
    9.       ├─BSgenome::getSeq(this_genome, flank_ranges)
   10.       └─BSgenome::getSeq(this_genome, flank_ranges)
   11.         └─BSgenome:::.local(x, ...)
   12.           └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   13.             ├─base::split(names, seqnames(names))
   14.             └─S4Vectors::split(names, seqnames(names))
   15.               ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.               └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                 └─S4Vectors:::.local(x, f, drop, ...)
   18.                   └─IRanges:::default_splitAsList(x, f, drop = drop)
   19.                     └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   20.                       └─S4Vectors:::isNotSorted(f_vals)
  ── Failure (test_input_format.R:132:3): elements are formatted properly ────────
  `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: "2 arguments passed to .Internal(is.unsorted) which requires 3"
  Backtrace:
       █
    1. ├─testthat::expect_error(...) test_input_format.R:132:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat:::.capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─ActiveDriverWGS::ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)
    7.   └─ActiveDriverWGS::format_muts(...)
    8.     └─ActiveDriverWGS:::.get_3n_context_of_mutations(mutations, this_genome)
    9.       ├─BSgenome::getSeq(this_genome, flank_ranges)
   10.       └─BSgenome::getSeq(this_genome, flank_ranges)
   11.         └─BSgenome:::.local(x, ...)
   12.           └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   13.             ├─base::split(names, seqnames(names))
   14.             └─S4Vectors::split(names, seqnames(names))
   15.               ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.               └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                 └─S4Vectors:::.local(x, f, drop, ...)
   18.                   └─IRanges:::default_splitAsList(x, f, drop = drop)
   19.                     └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   20.                       └─S4Vectors:::isNotSorted(f_vals)
  ── Failure (test_input_format.R:139:3): elements are formatted properly ────────
  `ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)` threw an error with unexpected message.
  Expected match: "start and end must be numeric"
  Actual message: "2 arguments passed to .Internal(is.unsorted) which requires 3"
  Backtrace:
       █
    1. ├─testthat::expect_error(...) test_input_format.R:139:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat:::.capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─ActiveDriverWGS::ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)
    7.   └─ActiveDriverWGS::format_muts(...)
    8.     └─ActiveDriverWGS:::.get_3n_context_of_mutations(mutations, this_genome)
    9.       ├─BSgenome::getSeq(this_genome, flank_ranges)
   10.       └─BSgenome::getSeq(this_genome, flank_ranges)
   11.         └─BSgenome:::.local(x, ...)
   12.           └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   13.             ├─base::split(names, seqnames(names))
   14.             └─S4Vectors::split(names, seqnames(names))
   15.               ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.               └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                 └─S4Vectors:::.local(x, f, drop, ...)
   18.                   └─IRanges:::default_splitAsList(x, f, drop = drop)
   19.                     └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   20.                       └─S4Vectors:::isNotSorted(f_vals)
  ── Failure (test_input_format.R:148:3): elements are formatted properly ────────
  `ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)` threw an error with unexpected message.
  Expected match: "Only autosomal and sex chromosomes may be used in element coordinates (24 for human, 21 for mouse). Note that chr23 and chr24 should be formatted as chrX and chrY, respectively"
  Actual message: "2 arguments passed to .Internal(is.unsorted) which requires 3"
  Backtrace:
       █
    1. ├─testthat::expect_error(...) test_input_format.R:148:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat:::.capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─ActiveDriverWGS::ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)
    7.   └─ActiveDriverWGS::format_muts(...)
    8.     └─ActiveDriverWGS:::.get_3n_context_of_mutations(mutations, this_genome)
    9.       ├─BSgenome::getSeq(this_genome, flank_ranges)
   10.       └─BSgenome::getSeq(this_genome, flank_ranges)
   11.         └─BSgenome:::.local(x, ...)
   12.           └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   13.             ├─base::split(names, seqnames(names))
   14.             └─S4Vectors::split(names, seqnames(names))
   15.               ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.               └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                 └─S4Vectors:::.local(x, f, drop, ...)
   18.                   └─IRanges:::default_splitAsList(x, f, drop = drop)
   19.                     └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   20.                       └─S4Vectors:::isNotSorted(f_vals)
  ── Failure (test_input_format.R:155:3): elements are formatted properly ────────
  `ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)` threw an error with unexpected message.
  Expected match: "element identifier must be a string"
  Actual message: "2 arguments passed to .Internal(is.unsorted) which requires 3"
  Backtrace:
       █
    1. ├─testthat::expect_error(...) test_input_format.R:155:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat:::.capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─ActiveDriverWGS::ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)
    7.   └─ActiveDriverWGS::format_muts(...)
    8.     └─ActiveDriverWGS:::.get_3n_context_of_mutations(mutations, this_genome)
    9.       ├─BSgenome::getSeq(this_genome, flank_ranges)
   10.       └─BSgenome::getSeq(this_genome, flank_ranges)
   11.         └─BSgenome:::.local(x, ...)
   12.           └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   13.             ├─base::split(names, seqnames(names))
   14.             └─S4Vectors::split(names, seqnames(names))
   15.               ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.               └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                 └─S4Vectors:::.local(x, f, drop, ...)
   18.                   └─IRanges:::default_splitAsList(x, f, drop = drop)
   19.                     └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   20.                       └─S4Vectors:::isNotSorted(f_vals)
  ── Failure (test_input_format.R:163:3): sites are formatted properly ───────────
  `ActiveDriverWGS(...)` threw an error with unexpected message.
  Expected match: "sites must be a data frame"
  Actual message: "2 arguments passed to .Internal(is.unsorted) which requires 3"
  Backtrace:
       █
    1. ├─testthat::expect_error(...) test_input_format.R:163:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat:::.capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─ActiveDriverWGS::ActiveDriverWGS(...)
    7.   └─ActiveDriverWGS::format_muts(...)
    8.     └─ActiveDriverWGS:::.get_3n_context_of_mutations(mutations, this_genome)
    9.       ├─BSgenome::getSeq(this_genome, flank_ranges)
   10.       └─BSgenome::getSeq(this_genome, flank_ranges)
   11.         └─BSgenome:::.local(x, ...)
   12.           └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   13.             ├─base::split(names, seqnames(names))
   14.             └─S4Vectors::split(names, seqnames(names))
   15.               ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.               └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                 └─S4Vectors:::.local(x, f, drop, ...)
   18.                   └─IRanges:::default_splitAsList(x, f, drop = drop)
   19.                     └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   20.                       └─S4Vectors:::isNotSorted(f_vals)
  ── Failure (test_input_format.R:169:3): sites are formatted properly ───────────
  `ActiveDriverWGS(...)` threw an error with unexpected message.
  Expected match: "sites must contain the following columns: chr, start, end & id"
  Actual message: "2 arguments passed to .Internal(is.unsorted) which requires 3"
  Backtrace:
       █
    1. ├─testthat::expect_error(...) test_input_format.R:169:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat:::.capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─ActiveDriverWGS::ActiveDriverWGS(...)
    7.   └─ActiveDriverWGS::format_muts(...)
    8.     └─ActiveDriverWGS:::.get_3n_context_of_mutations(mutations, this_genome)
    9.       ├─BSgenome::getSeq(this_genome, flank_ranges)
   10.       └─BSgenome::getSeq(this_genome, flank_ranges)
   11.         └─BSgenome:::.local(x, ...)
   12.           └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   13.             ├─base::split(names, seqnames(names))
   14.             └─S4Vectors::split(names, seqnames(names))
   15.               ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.               └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                 └─S4Vectors:::.local(x, f, drop, ...)
   18.                   └─IRanges:::default_splitAsList(x, f, drop = drop)
   19.                     └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   20.                       └─S4Vectors:::isNotSorted(f_vals)
  ── Failure (test_input_format.R:178:3): sites are formatted properly ───────────
  `ActiveDriverWGS(...)` threw an error with unexpected message.
  Expected match: "sites may not contain missing values"
  Actual message: "2 arguments passed to .Internal(is.unsorted) which requires 3"
  Backtrace:
       █
    1. ├─testthat::expect_error(...) test_input_format.R:178:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat:::.capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─ActiveDriverWGS::ActiveDriverWGS(...)
    7.   └─ActiveDriverWGS::format_muts(...)
    8.     └─ActiveDriverWGS:::.get_3n_context_of_mutations(mutations, this_genome)
    9.       ├─BSgenome::getSeq(this_genome, flank_ranges)
   10.       └─BSgenome::getSeq(this_genome, flank_ranges)
   11.         └─BSgenome:::.local(x, ...)
   12.           └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   13.             ├─base::split(names, seqnames(names))
   14.             └─S4Vectors::split(names, seqnames(names))
   15.               ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.               └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                 └─S4Vectors:::.local(x, f, drop, ...)
   18.                   └─IRanges:::default_splitAsList(x, f, drop = drop)
   19.                     └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   20.                       └─S4Vectors:::isNotSorted(f_vals)
  ── Failure (test_input_format.R:185:3): sites are formatted properly ───────────
  `ActiveDriverWGS(...)` threw an error with unexpected message.
  Expected match: "duplicated sites are present. please review your format"
  Actual message: "2 arguments passed to .Internal(is.unsorted) which requires 3"
  Backtrace:
       █
    1. ├─testthat::expect_error(...) test_input_format.R:185:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat:::.capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─ActiveDriverWGS::ActiveDriverWGS(...)
    7.   └─ActiveDriverWGS::format_muts(...)
    8.     └─ActiveDriverWGS:::.get_3n_context_of_mutations(mutations, this_genome)
    9.       ├─BSgenome::getSeq(this_genome, flank_ranges)
   10.       └─BSgenome::getSeq(this_genome, flank_ranges)
   11.         └─BSgenome:::.local(x, ...)
   12.           └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   13.             ├─base::split(names, seqnames(names))
   14.             └─S4Vectors::split(names, seqnames(names))
   15.               ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.               └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                 └─S4Vectors:::.local(x, f, drop, ...)
   18.                   └─IRanges:::default_splitAsList(x, f, drop = drop)
   19.                     └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   20.                       └─S4Vectors:::isNotSorted(f_vals)
  ── Failure (test_input_format.R:193:3): sites are formatted properly ───────────
  `ActiveDriverWGS(...)` threw an error with unexpected message.
  Expected match: "start and end must be numeric"
  Actual message: "2 arguments passed to .Internal(is.unsorted) which requires 3"
  Backtrace:
       █
    1. ├─testthat::expect_error(...) test_input_format.R:193:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat:::.capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─ActiveDriverWGS::ActiveDriverWGS(...)
    7.   └─ActiveDriverWGS::format_muts(...)
    8.     └─ActiveDriverWGS:::.get_3n_context_of_mutations(mutations, this_genome)
    9.       ├─BSgenome::getSeq(this_genome, flank_ranges)
   10.       └─BSgenome::getSeq(this_genome, flank_ranges)
   11.         └─BSgenome:::.local(x, ...)
   12.           └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   13.             ├─base::split(names, seqnames(names))
   14.             └─S4Vectors::split(names, seqnames(names))
   15.               ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.               └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                 └─S4Vectors:::.local(x, f, drop, ...)
   18.                   └─IRanges:::default_splitAsList(x, f, drop = drop)
   19.                     └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   20.                       └─S4Vectors:::isNotSorted(f_vals)
  ── Failure (test_input_format.R:201:3): sites are formatted properly ───────────
  `ActiveDriverWGS(...)` threw an error with unexpected message.
  Expected match: "site identifier must be a string"
  Actual message: "2 arguments passed to .Internal(is.unsorted) which requires 3"
  Backtrace:
       █
    1. ├─testthat::expect_error(...) test_input_format.R:201:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat:::.capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─ActiveDriverWGS::ActiveDriverWGS(...)
    7.   └─ActiveDriverWGS::format_muts(...)
    8.     └─ActiveDriverWGS:::.get_3n_context_of_mutations(mutations, this_genome)
    9.       ├─BSgenome::getSeq(this_genome, flank_ranges)
   10.       └─BSgenome::getSeq(this_genome, flank_ranges)
   11.         └─BSgenome:::.local(x, ...)
   12.           └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   13.             ├─base::split(names, seqnames(names))
   14.             └─S4Vectors::split(names, seqnames(names))
   15.               ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.               └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                 └─S4Vectors:::.local(x, f, drop, ...)
   18.                   └─IRanges:::default_splitAsList(x, f, drop = drop)
   19.                     └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   20.                       └─S4Vectors:::isNotSorted(f_vals)
  ── Failure (test_input_format.R:211:3): sites are formatted properly ───────────
  `ActiveDriverWGS(...)` threw an error with unexpected message.
  Expected match: "Only autosomal and sex chromosomes may be used in site coordinates (24 for human, 21 for mouse). Note that chr23 and chr24 should be formatted as chrX and chrY, respectively"
  Actual message: "2 arguments passed to .Internal(is.unsorted) which requires 3"
  Backtrace:
       █
    1. ├─testthat::expect_error(...) test_input_format.R:211:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat:::.capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─ActiveDriverWGS::ActiveDriverWGS(...)
    7.   └─ActiveDriverWGS::format_muts(...)
    8.     └─ActiveDriverWGS:::.get_3n_context_of_mutations(mutations, this_genome)
    9.       ├─BSgenome::getSeq(this_genome, flank_ranges)
   10.       └─BSgenome::getSeq(this_genome, flank_ranges)
   11.         └─BSgenome:::.local(x, ...)
   12.           └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   13.             ├─base::split(names, seqnames(names))
   14.             └─S4Vectors::split(names, seqnames(names))
   15.               ├─S4Vectors::splitAsList(x, f, drop = drop, ...)
   16.               └─S4Vectors::splitAsList(x, f, drop = drop, ...)
   17.                 └─S4Vectors:::.local(x, f, drop, ...)
   18.                   └─IRanges:::default_splitAsList(x, f, drop = drop)
   19.                     └─IRanges:::.splitAsList_by_Rle(x, f, drop)
   20.                       └─S4Vectors:::isNotSorted(f_vals)
  
  [ FAIL 17 | WARN 0 | SKIP 0 | PASS 44 ]
  Error: Test failures
  Execution halted