Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ActiveDriverWGS)
  > 
  > test_check("ActiveDriverWGS")
  -- 1. Error: (unknown) (@test_ADWGS_test.R#3)  ---------------------------------
  package 'S4Vectors' could not be loaded
  Backtrace:
   1. base::library(GenomicRanges)
   2. base::.getRequiredPackages2(pkgInfo, quietly = quietly)
  
  -- 2. Error: (unknown) (@test_ActiveDriverWGS.R#3)  ----------------------------
  package 'S4Vectors' could not be loaded
  Backtrace:
   1. base::library(GenomicRanges)
   2. base::.getRequiredPackages2(pkgInfo, quietly = quietly)
  
  reversing 0 positions
  -- 3. Error: (unknown) (@test_format_muts.R#7)  --------------------------------
  .onLoad failed in loadNamespace() for 'S4Vectors', details:
    call: validObject(.Object)
    error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
  Backtrace:
    1. ActiveDriverWGS::format_muts(cll_mutations[1:10, ])
    2. ActiveDriverWGS:::.get_3n_context_of_mutations(mutations)
    3. GenomicRanges::GRanges
    4. base::getExportedValue(pkg, name)
    5. base::asNamespace(ns)
    6. base::getNamespace(ns)
    7. base::loadNamespace(name)
    9. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 4. Failure: mutations are formatted properly (@test_input_format.R#61)  -----
  `ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)` threw an error with unexpected message.
  Expected match: "Only the 22 autosomal and 2 sex chromosomes may be used at this time. Note that chr23 should be formatted as chrX and chr24 should be formatted as chrY"
  Actual message: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n  call: validObject(.Object)\n  error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
  Backtrace:
    1. testthat::expect_error(...)
    6. ActiveDriverWGS::ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)
    8. BSgenome::seqnames
    9. base::getExportedValue(pkg, name)
   10. base::asNamespace(ns)
   11. base::getNamespace(ns)
   12. base::loadNamespace(name)
   14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   15. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 5. Failure: mutations are formatted properly (@test_input_format.R#68)  -----
  `ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)` threw an error with unexpected message.
  Expected match: "Reference and alternate alleles must be A, T, C or G"
  Actual message: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n  call: validObject(.Object)\n  error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
  Backtrace:
    1. testthat::expect_error(...)
    6. ActiveDriverWGS::ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)
    8. BSgenome::seqnames
    9. base::getExportedValue(pkg, name)
   10. base::asNamespace(ns)
   11. base::getNamespace(ns)
   12. base::loadNamespace(name)
   14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   15. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 6. Failure: mutations are formatted properly (@test_input_format.R#74)  -----
  `ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)` threw an error with unexpected message.
  Expected match: "Reference and alternate alleles must be A, T, C or G"
  Actual message: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n  call: validObject(.Object)\n  error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
  Backtrace:
    1. testthat::expect_error(...)
    6. ActiveDriverWGS::ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)
    8. BSgenome::seqnames
    9. base::getExportedValue(pkg, name)
   10. base::asNamespace(ns)
   11. base::getNamespace(ns)
   12. base::loadNamespace(name)
   14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   15. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 7. Failure: mutations are formatted properly (@test_input_format.R#81)  -----
  `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 'S4Vectors', details:\n  call: validObject(.Object)\n  error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
  Backtrace:
    1. testthat::expect_error(...)
    6. ActiveDriverWGS::ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)
    8. BSgenome::seqnames
    9. base::getExportedValue(pkg, name)
   10. base::asNamespace(ns)
   11. base::getNamespace(ns)
   12. base::loadNamespace(name)
   14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   15. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 8. Failure: mutations are formatted properly (@test_input_format.R#87)  -----
  `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 'S4Vectors', details:\n  call: validObject(.Object)\n  error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
  Backtrace:
    1. testthat::expect_error(...)
    6. ActiveDriverWGS::ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)
    8. BSgenome::seqnames
    9. base::getExportedValue(pkg, name)
   10. base::asNamespace(ns)
   11. base::getNamespace(ns)
   12. base::loadNamespace(name)
   14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   15. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 9. Failure: mutations are formatted properly (@test_input_format.R#95)  -----
  `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 'S4Vectors', details:\n  call: validObject(.Object)\n  error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
  Backtrace:
    1. testthat::expect_error(...)
    6. ActiveDriverWGS::ActiveDriverWGS(elements = cancer_genes, mutations = this_mutations)
    8. BSgenome::seqnames
    9. base::getExportedValue(pkg, name)
   10. base::asNamespace(ns)
   11. base::getNamespace(ns)
   12. base::loadNamespace(name)
   14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   15. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 10. 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: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n  call: validObject(.Object)\n  error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
  Backtrace:
    1. testthat::expect_error(...)
    6. ActiveDriverWGS::ActiveDriverWGS(...)
    8. BSgenome::seqnames
    9. base::getExportedValue(pkg, name)
   10. base::asNamespace(ns)
   11. base::getNamespace(ns)
   12. base::loadNamespace(name)
   14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   15. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 11. 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: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n  call: validObject(.Object)\n  error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
  Backtrace:
    1. testthat::expect_error(...)
    6. ActiveDriverWGS::ActiveDriverWGS(...)
    8. BSgenome::seqnames
    9. base::getExportedValue(pkg, name)
   10. base::asNamespace(ns)
   11. base::getNamespace(ns)
   12. base::loadNamespace(name)
   14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   15. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 12. 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: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n  call: validObject(.Object)\n  error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
  Backtrace:
    1. testthat::expect_error(...)
    6. ActiveDriverWGS::ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)
    8. BSgenome::seqnames
    9. base::getExportedValue(pkg, name)
   10. base::asNamespace(ns)
   11. base::getNamespace(ns)
   12. base::loadNamespace(name)
   14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   15. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 13. 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: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n  call: validObject(.Object)\n  error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
  Backtrace:
    1. testthat::expect_error(...)
    6. ActiveDriverWGS::ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)
    8. BSgenome::seqnames
    9. base::getExportedValue(pkg, name)
   10. base::asNamespace(ns)
   11. base::getNamespace(ns)
   12. base::loadNamespace(name)
   14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   15. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 14. 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: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n  call: validObject(.Object)\n  error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
  Backtrace:
    1. testthat::expect_error(...)
    6. ActiveDriverWGS::ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)
    8. BSgenome::seqnames
    9. base::getExportedValue(pkg, name)
   10. base::asNamespace(ns)
   11. base::getNamespace(ns)
   12. base::loadNamespace(name)
   14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   15. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 15. 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: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n  call: validObject(.Object)\n  error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
  Backtrace:
    1. testthat::expect_error(...)
    6. ActiveDriverWGS::ActiveDriverWGS(elements = this_elements, mutations = cll_mutations)
    8. BSgenome::seqnames
    9. base::getExportedValue(pkg, name)
   10. base::asNamespace(ns)
   11. base::getNamespace(ns)
   12. base::loadNamespace(name)
   14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   15. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 16. 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: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n  call: validObject(.Object)\n  error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
  Backtrace:
    1. testthat::expect_error(...)
    6. ActiveDriverWGS::ActiveDriverWGS(...)
    8. BSgenome::seqnames
    9. base::getExportedValue(pkg, name)
   10. base::asNamespace(ns)
   11. base::getNamespace(ns)
   12. base::loadNamespace(name)
   14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   15. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 17. 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: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n  call: validObject(.Object)\n  error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
  Backtrace:
    1. testthat::expect_error(...)
    6. ActiveDriverWGS::ActiveDriverWGS(...)
    8. BSgenome::seqnames
    9. base::getExportedValue(pkg, name)
   10. base::asNamespace(ns)
   11. base::getNamespace(ns)
   12. base::loadNamespace(name)
   14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   15. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 18. 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: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n  call: validObject(.Object)\n  error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
  Backtrace:
    1. testthat::expect_error(...)
    6. ActiveDriverWGS::ActiveDriverWGS(...)
    8. BSgenome::seqnames
    9. base::getExportedValue(pkg, name)
   10. base::asNamespace(ns)
   11. base::getNamespace(ns)
   12. base::loadNamespace(name)
   14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   15. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 19. 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: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n  call: validObject(.Object)\n  error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
  Backtrace:
    1. testthat::expect_error(...)
    6. ActiveDriverWGS::ActiveDriverWGS(...)
    8. BSgenome::seqnames
    9. base::getExportedValue(pkg, name)
   10. base::asNamespace(ns)
   11. base::getNamespace(ns)
   12. base::loadNamespace(name)
   14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   15. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 20. 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: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n  call: validObject(.Object)\n  error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
  Backtrace:
    1. testthat::expect_error(...)
    6. ActiveDriverWGS::ActiveDriverWGS(...)
    8. BSgenome::seqnames
    9. base::getExportedValue(pkg, name)
   10. base::asNamespace(ns)
   11. base::getNamespace(ns)
   12. base::loadNamespace(name)
   14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   15. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 21. 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: ".onLoad failed in loadNamespace() for 'S4Vectors', details:\n  call: validObject(.Object)\n  error: invalid class \"LLint\" object: superclass \"integer_OR_LLint\" not defined in the environment of the object's class"
  Backtrace:
    1. testthat::expect_error(...)
    6. ActiveDriverWGS::ActiveDriverWGS(...)
    8. BSgenome::seqnames
    9. base::getExportedValue(pkg, name)
   10. base::asNamespace(ns)
   11. base::getNamespace(ns)
   12. base::loadNamespace(name)
   14. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   15. base:::runHook(".onLoad", env, package.lib, package)
  
  
   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: 27 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 21 ]
  1. Error: (unknown) (@test_ADWGS_test.R#3) 
  2. Error: (unknown) (@test_ActiveDriverWGS.R#3) 
  3. Error: (unknown) (@test_format_muts.R#7) 
  4. Failure: mutations are formatted properly (@test_input_format.R#61) 
  5. Failure: mutations are formatted properly (@test_input_format.R#68) 
  6. Failure: mutations are formatted properly (@test_input_format.R#74) 
  7. Failure: mutations are formatted properly (@test_input_format.R#81) 
  8. Failure: mutations are formatted properly (@test_input_format.R#87) 
  9. Failure: mutations are formatted properly (@test_input_format.R#95) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted