Running 'testthat.R' [17s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > # library(ActiveDriverWGS)
  > 
  > test_check("ActiveDriverWGS")
  Loading required package: ActiveDriverWGS
  
   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:21:1): (code run outside of `test_that()`) ---------
  Error: .onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")
  Backtrace:
      x
   1. \-base::loadNamespace(x) test_ADWGS_test.R:21:0
   2.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- Error (test_ActiveDriverWGS.R:21:1): (code run outside of `test_that()`) ----
  Error: .onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")
  Backtrace:
      x
   1. \-base::loadNamespace(x) test_ActiveDriverWGS.R:21:0
   2.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- Error (test_format_muts.R:7:1): (code run outside of `test_that()`) ---------
  Error: .onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:
    call: validObject(.Object)
    error: invalid class "TwoBitFile" object: undefined class for slot "resource" ("characterORconnection")
  Backtrace:
      x
   1. \-base::loadNamespace(x) test_format_muts.R:7:0
   2.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- Failure (test_input_format.R:26:3): mutations are formatted properly --------
  `ActiveDriverWGS(elements = cancer_genes, mutations = as.matrix(cll_mutations))` threw an error with unexpected message.
  Expected match: "mutations must be a data frame"
  Actual message: ".onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:\n  call: validObject(.Object)\n  error: invalid class \"TwoBitFile\" object: undefined class for slot \"resource\" (\"characterORconnection\")"
  Backtrace:
      x
   1. +-testthat::expect_error(...) test_input_format.R:26:2
   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 = cancer_genes, mutations = as.matrix(cll_mutations))
   7. \-base::loadNamespace(x)
   8.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- Failure (test_input_format.R:33:3): mutations are formatted properly --------
  `ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)` threw an error with unexpected message.
  Expected match: "mutations must contain the following columns: chr, pos1, pos2, ref, alt & patient"
  Actual message: ".onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:\n  call: validObject(.Object)\n  error: invalid class \"TwoBitFile\" object: undefined class for slot \"resource\" (\"characterORconnection\")"
  Backtrace:
      x
   1. +-testthat::expect_error(...) test_input_format.R:33:2
   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 = cancer_genes, mutations = this_mutations)
   7. \-base::loadNamespace(x)
   8.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- Failure (test_input_format.R:39:3): mutations are formatted properly --------
  `ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)` threw an error with unexpected message.
  Expected match: "mutations must contain the following columns: chr, pos1, pos2, ref, alt & patient"
  Actual message: ".onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:\n  call: validObject(.Object)\n  error: invalid class \"TwoBitFile\" object: undefined class for slot \"resource\" (\"characterORconnection\")"
  Backtrace:
      x
   1. +-testthat::expect_error(...) test_input_format.R:39:2
   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 = cancer_genes, mutations = this_mutations)
   7. \-base::loadNamespace(x)
   8.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- Failure (test_input_format.R:46:3): mutations are formatted properly --------
  `ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)` threw an error with unexpected message.
  Expected match: "mutations may not contain missing values"
  Actual message: ".onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:\n  call: validObject(.Object)\n  error: invalid class \"TwoBitFile\" object: undefined class for slot \"resource\" (\"characterORconnection\")"
  Backtrace:
      x
   1. +-testthat::expect_error(...) test_input_format.R:46:2
   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 = cancer_genes, mutations = this_mutations)
   7. \-base::loadNamespace(x)
   8.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- Failure (test_input_format.R:53:3): mutations are formatted properly --------
  `ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)` threw an error with unexpected message.
  Expected match: "duplicated mutations are present. please review your format"
  Actual message: ".onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:\n  call: validObject(.Object)\n  error: invalid class \"TwoBitFile\" object: undefined class for slot \"resource\" (\"characterORconnection\")"
  Backtrace:
      x
   1. +-testthat::expect_error(...) test_input_format.R:53:2
   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 = cancer_genes, mutations = this_mutations)
   7. \-base::loadNamespace(x)
   8.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- Failure (test_input_format.R:63:3): mutations are formatted properly --------
  `ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)` threw an error with unexpected message.
  Expected match: "Only autosomal and sex chromosomes may be used in mutation data (24 for human, 21 for mouse). Note that chr23 and chr24 should be formatted as chrX and chrY, respectively"
  Actual message: ".onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:\n  call: validObject(.Object)\n  error: invalid class \"TwoBitFile\" object: undefined class for slot \"resource\" (\"characterORconnection\")"
  Backtrace:
      x
   1. +-testthat::expect_error(...) test_input_format.R:63:2
   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 = cancer_genes, mutations = this_mutations)
   7. \-base::loadNamespace(x)
   8.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- Failure (test_input_format.R:70:3): mutations are formatted properly --------
  `ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)` threw an error with unexpected message.
  Expected match: "Reference and alternate alleles must be A, T, C, G or -"
  Actual message: ".onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:\n  call: validObject(.Object)\n  error: invalid class \"TwoBitFile\" object: undefined class for slot \"resource\" (\"characterORconnection\")"
  Backtrace:
      x
   1. +-testthat::expect_error(...) test_input_format.R:70:2
   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 = cancer_genes, mutations = this_mutations)
   7. \-base::loadNamespace(x)
   8.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- Failure (test_input_format.R:76:3): mutations are formatted properly --------
  `ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)` threw an error with unexpected message.
  Expected match: "Reference and alternate alleles must be A, T, C, G or -"
  Actual message: ".onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:\n  call: validObject(.Object)\n  error: invalid class \"TwoBitFile\" object: undefined class for slot \"resource\" (\"characterORconnection\")"
  Backtrace:
      x
   1. +-testthat::expect_error(...) test_input_format.R:76:2
   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 = cancer_genes, mutations = this_mutations)
   7. \-base::loadNamespace(x)
   8.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- Failure (test_input_format.R:83:3): mutations are formatted properly --------
  `ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)` threw an error with unexpected message.
  Expected match: "pos1 and pos2 must be numeric"
  Actual message: ".onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:\n  call: validObject(.Object)\n  error: invalid class \"TwoBitFile\" object: undefined class for slot \"resource\" (\"characterORconnection\")"
  Backtrace:
      x
   1. +-testthat::expect_error(...) test_input_format.R:83:2
   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 = cancer_genes, mutations = this_mutations)
   7. \-base::loadNamespace(x)
   8.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- Failure (test_input_format.R:89:3): mutations are formatted properly --------
  `ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)` threw an error with unexpected message.
  Expected match: "pos1 and pos2 must be numeric"
  Actual message: ".onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:\n  call: validObject(.Object)\n  error: invalid class \"TwoBitFile\" object: undefined class for slot \"resource\" (\"characterORconnection\")"
  Backtrace:
      x
   1. +-testthat::expect_error(...) test_input_format.R:89:2
   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 = cancer_genes, mutations = this_mutations)
   7. \-base::loadNamespace(x)
   8.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- Failure (test_input_format.R:97:3): mutations are formatted properly --------
  `ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)` threw an error with unexpected message.
  Expected match: "patient identifier must be a string"
  Actual message: ".onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:\n  call: validObject(.Object)\n  error: invalid class \"TwoBitFile\" object: undefined class for slot \"resource\" (\"characterORconnection\")"
  Backtrace:
      x
   1. +-testthat::expect_error(...) test_input_format.R:97:2
   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 = cancer_genes, mutations = this_mutations)
   7. \-base::loadNamespace(x)
   8.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- Failure (test_input_format.R:105:3): mutations are formatted properly -------
  `ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)` threw an error with unexpected message.
  Expected match: "chr, ref and alt must be character"
  Actual message: ".onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:\n  call: validObject(.Object)\n  error: invalid class \"TwoBitFile\" object: undefined class for slot \"resource\" (\"characterORconnection\")"
  Backtrace:
      x
   1. +-testthat::expect_error(...) test_input_format.R:105:2
   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 = cancer_genes, mutations = this_mutations)
   7. \-base::loadNamespace(x)
   8.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- 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: ".onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:\n  call: validObject(.Object)\n  error: invalid class \"TwoBitFile\" object: undefined class for slot \"resource\" (\"characterORconnection\")"
  Backtrace:
      x
   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. \-base::loadNamespace(x)
   8.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- 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: ".onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:\n  call: validObject(.Object)\n  error: invalid class \"TwoBitFile\" object: undefined class for slot \"resource\" (\"characterORconnection\")"
  Backtrace:
      x
   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. \-base::loadNamespace(x)
   8.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- 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: ".onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:\n  call: validObject(.Object)\n  error: invalid class \"TwoBitFile\" object: undefined class for slot \"resource\" (\"characterORconnection\")"
  Backtrace:
      x
   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. \-base::loadNamespace(x)
   8.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- 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: ".onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:\n  call: validObject(.Object)\n  error: invalid class \"TwoBitFile\" object: undefined class for slot \"resource\" (\"characterORconnection\")"
  Backtrace:
      x
   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. \-base::loadNamespace(x)
   8.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- 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: ".onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:\n  call: validObject(.Object)\n  error: invalid class \"TwoBitFile\" object: undefined class for slot \"resource\" (\"characterORconnection\")"
  Backtrace:
      x
   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. \-base::loadNamespace(x)
   8.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- 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: ".onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:\n  call: validObject(.Object)\n  error: invalid class \"TwoBitFile\" object: undefined class for slot \"resource\" (\"characterORconnection\")"
  Backtrace:
      x
   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. \-base::loadNamespace(x)
   8.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- 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: ".onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:\n  call: validObject(.Object)\n  error: invalid class \"TwoBitFile\" object: undefined class for slot \"resource\" (\"characterORconnection\")"
  Backtrace:
      x
   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. \-base::loadNamespace(x)
   8.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- 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: ".onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:\n  call: validObject(.Object)\n  error: invalid class \"TwoBitFile\" object: undefined class for slot \"resource\" (\"characterORconnection\")"
  Backtrace:
      x
   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. \-base::loadNamespace(x)
   8.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- 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: ".onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:\n  call: validObject(.Object)\n  error: invalid class \"TwoBitFile\" object: undefined class for slot \"resource\" (\"characterORconnection\")"
  Backtrace:
      x
   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. \-base::loadNamespace(x)
   8.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- 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: ".onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:\n  call: validObject(.Object)\n  error: invalid class \"TwoBitFile\" object: undefined class for slot \"resource\" (\"characterORconnection\")"
  Backtrace:
      x
   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. \-base::loadNamespace(x)
   8.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- 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: ".onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:\n  call: validObject(.Object)\n  error: invalid class \"TwoBitFile\" object: undefined class for slot \"resource\" (\"characterORconnection\")"
  Backtrace:
      x
   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. \-base::loadNamespace(x)
   8.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- 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: ".onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:\n  call: validObject(.Object)\n  error: invalid class \"TwoBitFile\" object: undefined class for slot \"resource\" (\"characterORconnection\")"
  Backtrace:
      x
   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. \-base::loadNamespace(x)
   8.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- 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: ".onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:\n  call: validObject(.Object)\n  error: invalid class \"TwoBitFile\" object: undefined class for slot \"resource\" (\"characterORconnection\")"
  Backtrace:
      x
   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. \-base::loadNamespace(x)
   8.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- 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: ".onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:\n  call: validObject(.Object)\n  error: invalid class \"TwoBitFile\" object: undefined class for slot \"resource\" (\"characterORconnection\")"
  Backtrace:
      x
   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. \-base::loadNamespace(x)
   8.   \-base:::runHook(".onLoad", env, package.lib, package)
  -- Failure (test_input_format.R:246:3): recover.dir is appropriate -------------
  `ActiveDriverWGS(...)` threw an error with unexpected message.
  Expected match: "recovery.dir must be a string"
  Actual message: ".onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:\n  call: validObject(.Object)\n  error: invalid class \"TwoBitFile\" object: undefined class for slot \"resource\" (\"characterORconnection\")"
  Backtrace:
      x
   1. +-testthat::expect_error(...) test_input_format.R:246:2
   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. \-base::loadNamespace(x)
   8.   \-base:::runHook(".onLoad", env, package.lib, package)
  
  [ FAIL 30 | WARN 1 | SKIP 0 | PASS 31 ]
  Error: Test failures
  Execution halted