Running ‘testthat.R’ [62s/96s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(GenomeAdmixR) # nolint
  > 
  > test_check("GenomeAdmixR")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • empty test (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-LD.R:19:3): calculate_average_LD ────────────────────────────────
  <Rcpp::not_compatible/C++Error/error/condition>
  Error in `simulation_data_to_genomeadmixr_data_cpp(pop_for_cpp, markers)`: Not compatible with requested type: [type=list; target=double].
  Backtrace:
      █
   1. └─GenomeAdmixR::calculate_ld(pop1, markers = markers) test-LD.R:19:2
   2.   └─GenomeAdmixR:::simulation_data_to_genomeadmixr_data_cpp(...)
  ── Error (test-LD.R:61:3): calculate_LD_matrix ─────────────────────────────────
  <Rcpp::not_compatible/C++Error/error/condition>
  Error in `simulation_data_to_genomeadmixr_data_cpp(pop_for_cpp, markers)`: Not compatible with requested type: [type=list; target=double].
  Backtrace:
      █
   1. └─GenomeAdmixR::calculate_ld(pop1, sampled_individuals, markers = 10) test-LD.R:61:2
   2.   └─GenomeAdmixR:::simulation_data_to_genomeadmixr_data_cpp(...)
  ── Error (test-allele_frequencies.R:69:3): calculate_allele_frequencies ────────
  <Rcpp::not_compatible/C++Error/error/condition>
  Error in `calculate_allele_spectrum_cpp(pop_for_cpp, locations, progress_bar)`: Not compatible with requested type: [type=list; target=double].
  Backtrace:
      █
   1. └─GenomeAdmixR::calculate_allele_frequencies(sourcepop$population) test-allele_frequencies.R:69:2
   2.   └─GenomeAdmixR:::calculate_allele_spectrum_cpp(...)
  ── Error (test-combined_input_data.R:83:3): input data simulation ──────────────
  <Rcpp::not_compatible/C++Error/error/condition>
  Error in `simulation_data_to_genomeadmixr_data_cpp(pop_for_cpp, output$markers)`: Not compatible with requested type: [type=list; target=double].
  Backtrace:
      █
   1. └─GenomeAdmixR::simulation_data_to_genomeadmixr_data(...) test-combined_input_data.R:83:2
   2.   └─GenomeAdmixR:::simulation_data_to_genomeadmixr_data_cpp(...)
  ── Error (test-general_usage.R:34:3): general usage ────────────────────────────
  <Rcpp::not_compatible/C++Error/error/condition>
  Error in `simulation_data_to_genomeadmixr_data_cpp(pop_for_cpp, output$markers)`: Not compatible with requested type: [type=list; target=double].
  Backtrace:
       █
    1. ├─testthat::expect_message(...) test-general_usage.R:34:2
    2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)
    3. │   ├─testthat:::.capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─GenomeAdmixR::simulate_admixture(...)
    7.   └─GenomeAdmixR:::simulate_sequence(...)
    8.     └─GenomeAdmixR:::verify_genomeadmixr_data(input_data, markers)
    9.       └─GenomeAdmixR:::verify_genomeadmixr_data(input_data[[i]], markers)
   10.         └─GenomeAdmixR::simulation_data_to_genomeadmixr_data(...)
   11.           └─GenomeAdmixR:::simulation_data_to_genomeadmixr_data_cpp(...)
  ── Error (test-general_usage.R:117:3): isofemale usage ─────────────────────────
  <Rcpp::not_compatible/C++Error/error/condition>
  Error in `simulation_data_to_genomeadmixr_data_cpp(pop_for_cpp, output$markers)`: Not compatible with requested type: [type=list; target=double].
  Backtrace:
       █
    1. ├─testthat::expect_message(...) test-general_usage.R:117:2
    2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)
    3. │   ├─testthat:::.capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─GenomeAdmixR::create_iso_female(...)
    7.   └─GenomeAdmixR::iso_female_sequence(...)
    8.     └─GenomeAdmixR:::verify_genomeadmixr_data(input_data)
    9.       └─GenomeAdmixR::simulation_data_to_genomeadmixr_data(...)
   10.         └─GenomeAdmixR:::simulation_data_to_genomeadmixr_data_cpp(...)
  ── Error (test-plink.R:26:3): plink data ───────────────────────────────────────
  <Rcpp::not_compatible/C++Error/error/condition>
  Error in `simulation_data_to_plink_cpp(pop_for_cpp, marker_locations)`: Not compatible with requested type: [type=list; target=double].
  Backtrace:
      █
   1. └─GenomeAdmixR::write_as_plink(...) test-plink.R:26:2
   2.   └─GenomeAdmixR:::simulation_data_to_plink_cpp(pop_for_cpp, marker_locations)
  ── Error (test-simulate_admixture_data.R:39:3): simulate_admixture_data ────────
  <Rcpp::not_compatible/C++Error/error/condition>
  Error in `calculate_allele_spectrum_cpp(pop_for_cpp, locations, progress_bar)`: Not compatible with requested type: [type=list; target=double].
  Backtrace:
       █
    1. ├─testthat::expect_silent(...) test-simulate_admixture_data.R:39:2
    2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. │   ├─testthat:::.capture(...)
    4. │   │ ├─withr::with_output_sink(...)
    5. │   │ │ └─base::force(code)
    6. │   │ ├─base::withCallingHandlers(...)
    7. │   │ └─base::withVisible(code)
    8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. └─GenomeAdmixR::calculate_allele_frequencies(...)
   10.   └─GenomeAdmixR:::calculate_allele_spectrum_cpp(...)
  ── Error (test-simulate_admixture_until.R:6:3): simulate_admixture_until ───────
  <Rcpp::not_compatible/C++Error/error/condition>
  Error in `simulate_migration_cpp(input_population_1, input_population_2, 
      select_matrix, pop_size, init_freq_matrix, total_runtime, 
      morgan, verbose, track_frequency, markers, track_junctions, 
      multiplicative_selection, migration_rate, num_threads)`: Not compatible with requested type: [type=list; target=double].
  Backtrace:
      █
   1. └─GenomeAdmixR::simulate_admixture(...) test-simulate_admixture_until.R:6:2
   2.   └─GenomeAdmixR::simulate_ancestry_migration(...)
   3.     └─GenomeAdmixR:::simulate_ancestry_until(...)
   4.       └─GenomeAdmixR::simulate_ancestry_migration(...)
   5.         └─GenomeAdmixR:::simulate_migration_cpp(...)
  ── Error (test-simulate_migration.R:19:3): simulate_migration ──────────────────
  <Rcpp::not_compatible/C++Error/error/condition>
  Error in `simulate_migration_cpp(input_population_1, input_population_2, 
      select_matrix, pop_size, init_freq_matrix, total_runtime, 
      morgan, verbose, track_frequency, markers, track_junctions, 
      multiplicative_selection, migration_rate, num_threads)`: Not compatible with requested type: [type=list; target=double].
  Backtrace:
       █
    1. ├─testthat::expect_silent(...) test-simulate_migration.R:19:2
    2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. │   ├─testthat:::.capture(...)
    4. │   │ ├─withr::with_output_sink(...)
    5. │   │ │ └─base::force(code)
    6. │   │ ├─base::withCallingHandlers(...)
    7. │   │ └─base::withVisible(code)
    8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. └─GenomeAdmixR::simulate_admixture(...)
   10.   └─GenomeAdmixR::simulate_ancestry_migration(...)
   11.     └─GenomeAdmixR:::simulate_migration_cpp(...)
  
  [ FAIL 10 | WARN 0 | SKIP 1 | PASS 202 ]
  Error: Test failures
  Execution halted