Running 'testthat.R' [23s]
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 [ FAIL 30 | WARN 0 | SKIP 0 | PASS 31 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_ADWGS_test.R:4:1'): (code run outside of `test_that()`) ────────
  Error: package 'rtracklayer' could not be loaded
  Backtrace:
      ▆
   1. └─base::library(BSgenome.Hsapiens.UCSC.hg19) at test_ADWGS_test.R:4:0
   2.   └─base::.getRequiredPackages2(...)
   3.     └─base::library(...)
   4.       └─base::.getRequiredPackages2(...)
  ── Error ('test_ActiveDriverWGS.R:21:1'): (code run outside of `test_that()`) ──
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. └─base::loadNamespace(x) at test_ActiveDriverWGS.R:21:0
    2.   ├─base::namespaceImport(...)
    3.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    4.     ├─base::namespaceImport(...)
    5.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    6.       ├─base::namespaceImportClasses(...)
    7.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
    8.       │ │ └─base::asNamespace(ns)
    9.       │ └─base::asNamespace(ns)
   10.       └─base::loadNamespace(...)
   11.         ├─base::namespaceImport(...)
   12.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   13.           ├─base::namespaceImport(...)
   14.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   15.             └─base::namespaceImportFrom(...)
   16.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test_format_muts.R:7:1'): (code run outside of `test_that()`) ───────
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. └─base::loadNamespace(x) at test_format_muts.R:7:0
    2.   ├─base::namespaceImport(...)
    3.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    4.     ├─base::namespaceImport(...)
    5.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    6.       ├─base::namespaceImportClasses(...)
    7.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
    8.       │ │ └─base::asNamespace(ns)
    9.       │ └─base::asNamespace(ns)
   10.       └─base::loadNamespace(...)
   11.         ├─base::namespaceImport(...)
   12.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   13.           ├─base::namespaceImport(...)
   14.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   15.             └─base::namespaceImportFrom(...)
   16.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── 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: "objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_input_format.R:26:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .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::namespaceImport(...)
    9.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10.     ├─base::namespaceImport(...)
   11.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12.       ├─base::namespaceImportClasses(...)
   13.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   14.       │ │ └─base::asNamespace(ns)
   15.       │ └─base::asNamespace(ns)
   16.       └─base::loadNamespace(...)
   17.         ├─base::namespaceImport(...)
   18.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   19.           ├─base::namespaceImport(...)
   20.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   21.             └─base::namespaceImportFrom(...)
   22.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── 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: "objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_input_format.R:33:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .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::namespaceImport(...)
    9.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10.     ├─base::namespaceImport(...)
   11.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12.       ├─base::namespaceImportClasses(...)
   13.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   14.       │ │ └─base::asNamespace(ns)
   15.       │ └─base::asNamespace(ns)
   16.       └─base::loadNamespace(...)
   17.         ├─base::namespaceImport(...)
   18.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   19.           ├─base::namespaceImport(...)
   20.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   21.             └─base::namespaceImportFrom(...)
   22.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── 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: "objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_input_format.R:39:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .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::namespaceImport(...)
    9.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10.     ├─base::namespaceImport(...)
   11.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12.       ├─base::namespaceImportClasses(...)
   13.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   14.       │ │ └─base::asNamespace(ns)
   15.       │ └─base::asNamespace(ns)
   16.       └─base::loadNamespace(...)
   17.         ├─base::namespaceImport(...)
   18.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   19.           ├─base::namespaceImport(...)
   20.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   21.             └─base::namespaceImportFrom(...)
   22.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── 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: "objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_input_format.R:46:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .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::namespaceImport(...)
    9.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10.     ├─base::namespaceImport(...)
   11.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12.       ├─base::namespaceImportClasses(...)
   13.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   14.       │ │ └─base::asNamespace(ns)
   15.       │ └─base::asNamespace(ns)
   16.       └─base::loadNamespace(...)
   17.         ├─base::namespaceImport(...)
   18.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   19.           ├─base::namespaceImport(...)
   20.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   21.             └─base::namespaceImportFrom(...)
   22.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── 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: "objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_input_format.R:53:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .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::namespaceImport(...)
    9.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10.     ├─base::namespaceImport(...)
   11.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12.       ├─base::namespaceImportClasses(...)
   13.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   14.       │ │ └─base::asNamespace(ns)
   15.       │ └─base::asNamespace(ns)
   16.       └─base::loadNamespace(...)
   17.         ├─base::namespaceImport(...)
   18.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   19.           ├─base::namespaceImport(...)
   20.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   21.             └─base::namespaceImportFrom(...)
   22.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── 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: "objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_input_format.R:63:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .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::namespaceImport(...)
    9.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10.     ├─base::namespaceImport(...)
   11.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12.       ├─base::namespaceImportClasses(...)
   13.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   14.       │ │ └─base::asNamespace(ns)
   15.       │ └─base::asNamespace(ns)
   16.       └─base::loadNamespace(...)
   17.         ├─base::namespaceImport(...)
   18.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   19.           ├─base::namespaceImport(...)
   20.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   21.             └─base::namespaceImportFrom(...)
   22.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── 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: "objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_input_format.R:70:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .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::namespaceImport(...)
    9.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10.     ├─base::namespaceImport(...)
   11.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12.       ├─base::namespaceImportClasses(...)
   13.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   14.       │ │ └─base::asNamespace(ns)
   15.       │ └─base::asNamespace(ns)
   16.       └─base::loadNamespace(...)
   17.         ├─base::namespaceImport(...)
   18.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   19.           ├─base::namespaceImport(...)
   20.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   21.             └─base::namespaceImportFrom(...)
   22.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── 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: "objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_input_format.R:76:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .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::namespaceImport(...)
    9.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10.     ├─base::namespaceImport(...)
   11.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12.       ├─base::namespaceImportClasses(...)
   13.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   14.       │ │ └─base::asNamespace(ns)
   15.       │ └─base::asNamespace(ns)
   16.       └─base::loadNamespace(...)
   17.         ├─base::namespaceImport(...)
   18.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   19.           ├─base::namespaceImport(...)
   20.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   21.             └─base::namespaceImportFrom(...)
   22.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── 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: "objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_input_format.R:83:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .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::namespaceImport(...)
    9.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10.     ├─base::namespaceImport(...)
   11.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12.       ├─base::namespaceImportClasses(...)
   13.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   14.       │ │ └─base::asNamespace(ns)
   15.       │ └─base::asNamespace(ns)
   16.       └─base::loadNamespace(...)
   17.         ├─base::namespaceImport(...)
   18.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   19.           ├─base::namespaceImport(...)
   20.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   21.             └─base::namespaceImportFrom(...)
   22.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── 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: "objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_input_format.R:89:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .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::namespaceImport(...)
    9.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10.     ├─base::namespaceImport(...)
   11.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12.       ├─base::namespaceImportClasses(...)
   13.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   14.       │ │ └─base::asNamespace(ns)
   15.       │ └─base::asNamespace(ns)
   16.       └─base::loadNamespace(...)
   17.         ├─base::namespaceImport(...)
   18.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   19.           ├─base::namespaceImport(...)
   20.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   21.             └─base::namespaceImportFrom(...)
   22.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── 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: "objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_input_format.R:97:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .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::namespaceImport(...)
    9.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10.     ├─base::namespaceImport(...)
   11.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12.       ├─base::namespaceImportClasses(...)
   13.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   14.       │ │ └─base::asNamespace(ns)
   15.       │ └─base::asNamespace(ns)
   16.       └─base::loadNamespace(...)
   17.         ├─base::namespaceImport(...)
   18.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   19.           ├─base::namespaceImport(...)
   20.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   21.             └─base::namespaceImportFrom(...)
   22.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── 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: "objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_input_format.R:105:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .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::namespaceImport(...)
    9.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10.     ├─base::namespaceImport(...)
   11.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12.       ├─base::namespaceImportClasses(...)
   13.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   14.       │ │ └─base::asNamespace(ns)
   15.       │ └─base::asNamespace(ns)
   16.       └─base::loadNamespace(...)
   17.         ├─base::namespaceImport(...)
   18.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   19.           ├─base::namespaceImport(...)
   20.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   21.             └─base::namespaceImportFrom(...)
   22.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── 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: "objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_input_format.R:114:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .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::namespaceImport(...)
    9.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10.     ├─base::namespaceImport(...)
   11.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12.       ├─base::namespaceImportClasses(...)
   13.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   14.       │ │ └─base::asNamespace(ns)
   15.       │ └─base::asNamespace(ns)
   16.       └─base::loadNamespace(...)
   17.         ├─base::namespaceImport(...)
   18.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   19.           ├─base::namespaceImport(...)
   20.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   21.             └─base::namespaceImportFrom(...)
   22.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── 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: "objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_input_format.R:119:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .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::namespaceImport(...)
    9.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10.     ├─base::namespaceImport(...)
   11.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12.       ├─base::namespaceImportClasses(...)
   13.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   14.       │ │ └─base::asNamespace(ns)
   15.       │ └─base::asNamespace(ns)
   16.       └─base::loadNamespace(...)
   17.         ├─base::namespaceImport(...)
   18.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   19.           ├─base::namespaceImport(...)
   20.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   21.             └─base::namespaceImportFrom(...)
   22.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── 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: "objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_input_format.R:126:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .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::namespaceImport(...)
    9.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10.     ├─base::namespaceImport(...)
   11.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12.       ├─base::namespaceImportClasses(...)
   13.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   14.       │ │ └─base::asNamespace(ns)
   15.       │ └─base::asNamespace(ns)
   16.       └─base::loadNamespace(...)
   17.         ├─base::namespaceImport(...)
   18.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   19.           ├─base::namespaceImport(...)
   20.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   21.             └─base::namespaceImportFrom(...)
   22.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── 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: "objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_input_format.R:132:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .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::namespaceImport(...)
    9.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10.     ├─base::namespaceImport(...)
   11.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12.       ├─base::namespaceImportClasses(...)
   13.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   14.       │ │ └─base::asNamespace(ns)
   15.       │ └─base::asNamespace(ns)
   16.       └─base::loadNamespace(...)
   17.         ├─base::namespaceImport(...)
   18.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   19.           ├─base::namespaceImport(...)
   20.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   21.             └─base::namespaceImportFrom(...)
   22.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── 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: "objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_input_format.R:139:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .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::namespaceImport(...)
    9.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10.     ├─base::namespaceImport(...)
   11.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12.       ├─base::namespaceImportClasses(...)
   13.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   14.       │ │ └─base::asNamespace(ns)
   15.       │ └─base::asNamespace(ns)
   16.       └─base::loadNamespace(...)
   17.         ├─base::namespaceImport(...)
   18.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   19.           ├─base::namespaceImport(...)
   20.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   21.             └─base::namespaceImportFrom(...)
   22.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── 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: "objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_input_format.R:148:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .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::namespaceImport(...)
    9.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10.     ├─base::namespaceImport(...)
   11.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12.       ├─base::namespaceImportClasses(...)
   13.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   14.       │ │ └─base::asNamespace(ns)
   15.       │ └─base::asNamespace(ns)
   16.       └─base::loadNamespace(...)
   17.         ├─base::namespaceImport(...)
   18.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   19.           ├─base::namespaceImport(...)
   20.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   21.             └─base::namespaceImportFrom(...)
   22.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── 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: "objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_input_format.R:155:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .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::namespaceImport(...)
    9.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10.     ├─base::namespaceImport(...)
   11.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12.       ├─base::namespaceImportClasses(...)
   13.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   14.       │ │ └─base::asNamespace(ns)
   15.       │ └─base::asNamespace(ns)
   16.       └─base::loadNamespace(...)
   17.         ├─base::namespaceImport(...)
   18.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   19.           ├─base::namespaceImport(...)
   20.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   21.             └─base::namespaceImportFrom(...)
   22.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── 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: "objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_input_format.R:163:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .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::namespaceImport(...)
    9.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10.     ├─base::namespaceImport(...)
   11.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12.       ├─base::namespaceImportClasses(...)
   13.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   14.       │ │ └─base::asNamespace(ns)
   15.       │ └─base::asNamespace(ns)
   16.       └─base::loadNamespace(...)
   17.         ├─base::namespaceImport(...)
   18.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   19.           ├─base::namespaceImport(...)
   20.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   21.             └─base::namespaceImportFrom(...)
   22.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── 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: "objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_input_format.R:169:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .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::namespaceImport(...)
    9.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10.     ├─base::namespaceImport(...)
   11.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12.       ├─base::namespaceImportClasses(...)
   13.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   14.       │ │ └─base::asNamespace(ns)
   15.       │ └─base::asNamespace(ns)
   16.       └─base::loadNamespace(...)
   17.         ├─base::namespaceImport(...)
   18.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   19.           ├─base::namespaceImport(...)
   20.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   21.             └─base::namespaceImportFrom(...)
   22.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── 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: "objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_input_format.R:178:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .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::namespaceImport(...)
    9.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10.     ├─base::namespaceImport(...)
   11.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12.       ├─base::namespaceImportClasses(...)
   13.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   14.       │ │ └─base::asNamespace(ns)
   15.       │ └─base::asNamespace(ns)
   16.       └─base::loadNamespace(...)
   17.         ├─base::namespaceImport(...)
   18.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   19.           ├─base::namespaceImport(...)
   20.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   21.             └─base::namespaceImportFrom(...)
   22.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── 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: "objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_input_format.R:185:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .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::namespaceImport(...)
    9.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10.     ├─base::namespaceImport(...)
   11.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12.       ├─base::namespaceImportClasses(...)
   13.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   14.       │ │ └─base::asNamespace(ns)
   15.       │ └─base::asNamespace(ns)
   16.       └─base::loadNamespace(...)
   17.         ├─base::namespaceImport(...)
   18.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   19.           ├─base::namespaceImport(...)
   20.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   21.             └─base::namespaceImportFrom(...)
   22.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── 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: "objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_input_format.R:193:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .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::namespaceImport(...)
    9.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10.     ├─base::namespaceImport(...)
   11.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12.       ├─base::namespaceImportClasses(...)
   13.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   14.       │ │ └─base::asNamespace(ns)
   15.       │ └─base::asNamespace(ns)
   16.       └─base::loadNamespace(...)
   17.         ├─base::namespaceImport(...)
   18.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   19.           ├─base::namespaceImport(...)
   20.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   21.             └─base::namespaceImportFrom(...)
   22.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── 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: "objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_input_format.R:201:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .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::namespaceImport(...)
    9.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10.     ├─base::namespaceImport(...)
   11.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12.       ├─base::namespaceImportClasses(...)
   13.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   14.       │ │ └─base::asNamespace(ns)
   15.       │ └─base::asNamespace(ns)
   16.       └─base::loadNamespace(...)
   17.         ├─base::namespaceImport(...)
   18.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   19.           ├─base::namespaceImport(...)
   20.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   21.             └─base::namespaceImportFrom(...)
   22.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── 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: "objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_input_format.R:211:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .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::namespaceImport(...)
    9.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10.     ├─base::namespaceImport(...)
   11.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12.       ├─base::namespaceImportClasses(...)
   13.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   14.       │ │ └─base::asNamespace(ns)
   15.       │ └─base::asNamespace(ns)
   16.       └─base::loadNamespace(...)
   17.         ├─base::namespaceImport(...)
   18.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   19.           ├─base::namespaceImport(...)
   20.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   21.             └─base::namespaceImportFrom(...)
   22.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── 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: "objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test_input_format.R:246:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .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::namespaceImport(...)
    9.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10.     ├─base::namespaceImport(...)
   11.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12.       ├─base::namespaceImportClasses(...)
   13.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   14.       │ │ └─base::asNamespace(ns)
   15.       │ └─base::asNamespace(ns)
   16.       └─base::loadNamespace(...)
   17.         ├─base::namespaceImport(...)
   18.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   19.           ├─base::namespaceImport(...)
   20.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   21.             └─base::namespaceImportFrom(...)
   22.               └─base::importIntoEnv(impenv, impnames, ns, impvars)
  
  [ FAIL 30 | WARN 0 | SKIP 0 | PASS 31 ]
  Error: Test failures
  Execution halted