CRAN Package Check Results for Package GenomeAdmixR

Last updated on 2021-12-03 11:51:49 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.1.1 98.85 276.76 375.61 OK
r-devel-linux-x86_64-debian-gcc 2.1.1 76.95 129.48 206.43 ERROR
r-devel-linux-x86_64-fedora-clang 2.1.1 271.41 ERROR
r-devel-linux-x86_64-fedora-gcc 2.1.1 346.59 ERROR
r-devel-windows-x86_64-new-UL 2.1.1 152.00 383.00 535.00 OK
r-devel-windows-x86_64-new-TK 2.1.1 OK
r-devel-windows-x86_64-old 2.1.1 135.00 265.00 400.00 OK
r-patched-linux-x86_64 2.1.1 91.10 307.14 398.24 OK
r-patched-solaris-x86 2.1.1 302.30 OK
r-release-linux-x86_64 2.1.1 89.68 296.51 386.19 OK
r-release-macos-arm64 2.1.1 NOTE
r-release-macos-x86_64 2.1.1 NOTE
r-release-windows-ix86+x86_64 2.1.1 258.00 481.00 739.00 NOTE
r-oldrel-macos-x86_64 2.1.1 NOTE
r-oldrel-windows-ix86+x86_64 2.1.1 62.00 8.00 70.00 ERROR

Check Details

Version: 2.1.1
Check: examples
Result: ERROR
    Running examples in ‘GenomeAdmixR-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: calculate_allele_frequencies
    > ### Title: Calculate allele frequencies
    > ### Aliases: calculate_allele_frequencies
    >
    > ### ** Examples
    >
    > number_founders = 20
    > wildpop = simulate_admixture(
    + module = ancestry_module(number_of_founders = 20, morgan = 1),
    + pop_size = 1000,
    + total_runtime = 10,
    + num_threads = 1)
    >
    > freq_output <- calculate_allele_frequencies(wildpop,
    + progress_bar = TRUE)
    Error in calculate_allele_spectrum_cpp(pop_for_cpp, locations, progress_bar) :
     Not compatible with requested type: [type=list; target=double].
    Calls: calculate_allele_frequencies -> calculate_allele_spectrum_cpp
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 2.1.1
Check: tests
Result: ERROR
     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
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 2.1.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘Demonstrate_isofemales.Rmd’ using rmarkdown
    Quitting from lines 56-64 (Demonstrate_isofemales.Rmd)
    Error: processing vignette ‘Demonstrate_isofemales.Rmd’ failed with diagnostics:
    Not compatible with requested type: [type=list; target=double].
    --- failed re-building ‘Demonstrate_isofemales.Rmd’
    
    --- re-building ‘Empirical_data.Rmd’ using rmarkdown
    Quitting from lines 147-159 (Empirical_data.Rmd)
    Error: processing vignette ‘Empirical_data.Rmd’ failed with diagnostics:
    Not compatible with requested type: [type=list; target=double].
    --- failed re-building ‘Empirical_data.Rmd’
    
    --- re-building ‘Joyplots.Rmd’ using rmarkdown
    --- finished re-building ‘Joyplots.Rmd’
    
    --- re-building ‘Visualization.Rmd’ using rmarkdown
    Quitting from lines 48-49 (Visualization.Rmd)
    Error: processing vignette ‘Visualization.Rmd’ failed with diagnostics:
    Not compatible with requested type: [type=list; target=double].
    --- failed re-building ‘Visualization.Rmd’
    
    --- re-building ‘Walkthrough.Rmd’ using rmarkdown
    Quitting from lines 183-198 (Walkthrough.Rmd)
    Error: processing vignette ‘Walkthrough.Rmd’ failed with diagnostics:
    Not compatible with requested type: [type=list; target=double].
    --- failed re-building ‘Walkthrough.Rmd’
    
    SUMMARY: processing the following files failed:
     ‘Demonstrate_isofemales.Rmd’ ‘Empirical_data.Rmd’ ‘Visualization.Rmd’
     ‘Walkthrough.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 2.1.1
Check: installed package size
Result: NOTE
     installed size is 6.4Mb
     sub-directories of 1Mb or more:
     doc 2.1Mb
     libs 3.7Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64

Version: 2.1.1
Check: examples
Result: ERROR
    Running examples in ‘GenomeAdmixR-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: calculate_allele_frequencies
    > ### Title: Calculate allele frequencies
    > ### Aliases: calculate_allele_frequencies
    >
    > ### ** Examples
    >
    > number_founders = 20
    > wildpop = simulate_admixture(
    + module = ancestry_module(number_of_founders = 20, morgan = 1),
    + pop_size = 1000,
    + total_runtime = 10,
    + num_threads = 1)
    >
    > freq_output <- calculate_allele_frequencies(wildpop,
    + progress_bar = TRUE)
    Error in calculate_allele_spectrum_cpp(pop_for_cpp, locations, progress_bar) :
     Not compatible with requested type: [type=list; target=double].
    Calls: calculate_allele_frequencies -> calculate_allele_spectrum_cpp
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 2.1.1
Check: tests
Result: ERROR
     Running ‘testthat.R’ [55s/55s]
    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
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 2.1.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘Demonstrate_isofemales.Rmd’ using rmarkdown
    Quitting from lines 56-64 (Demonstrate_isofemales.Rmd)
    Error: processing vignette 'Demonstrate_isofemales.Rmd' failed with diagnostics:
    Not compatible with requested type: [type=list; target=double].
    --- failed re-building ‘Demonstrate_isofemales.Rmd’
    
    --- re-building ‘Empirical_data.Rmd’ using rmarkdown
    Quitting from lines 147-159 (Empirical_data.Rmd)
    Error: processing vignette 'Empirical_data.Rmd' failed with diagnostics:
    Not compatible with requested type: [type=list; target=double].
    --- failed re-building ‘Empirical_data.Rmd’
    
    --- re-building ‘Joyplots.Rmd’ using rmarkdown
    --- finished re-building ‘Joyplots.Rmd’
    
    --- re-building ‘Visualization.Rmd’ using rmarkdown
    Quitting from lines 48-49 (Visualization.Rmd)
    Error: processing vignette 'Visualization.Rmd' failed with diagnostics:
    Not compatible with requested type: [type=list; target=double].
    --- failed re-building ‘Visualization.Rmd’
    
    --- re-building ‘Walkthrough.Rmd’ using rmarkdown
    Quitting from lines 183-198 (Walkthrough.Rmd)
    Error: processing vignette 'Walkthrough.Rmd' failed with diagnostics:
    Not compatible with requested type: [type=list; target=double].
    --- failed re-building ‘Walkthrough.Rmd’
    
    SUMMARY: processing the following files failed:
     ‘Demonstrate_isofemales.Rmd’ ‘Empirical_data.Rmd’ ‘Visualization.Rmd’
     ‘Walkthrough.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 2.1.1
Check: tests
Result: ERROR
     Running ‘testthat.R’ [96s/114s]
    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
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 2.1.1
Check: whether package can be installed
Result: ERROR
    Installation failed.
Flavor: r-oldrel-windows-ix86+x86_64