Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [44s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(iRfcb)
  > 
  > test_check("iRfcb")
  Starting 2 test processes.
  > test-ifcb_create_manifest.R: v MANIFEST.txt has been created at '/home/hornik/tmp/scratch/Rtmp93rQxY/mock_dir/test_data/MANIFEST.txt'
  > test-ifcb_create_manifest.R: v MANIFEST.txt has been created at '/home/hornik/tmp/scratch/Rtmp93rQxY/mock_dir/test_data/MANIFEST.txt'
  > test-ifcb_create_manifest.R: v MANIFEST.txt has been created at '/home/hornik/tmp/scratch/Rtmp93rQxY/mock_dir/test_data/MANIFEST.txt'
  > test-ifcb_download_whoi_plankton.R: v Download and extraction complete.
  > test-ifcb_extract_biovolumes.R: Reading feature files...
  > test-ifcb_list_dashboard_bins.R: Fetching bin list from <https://example.invalid/api/list_bins?dataset=mvco>
  > test-ifcb_read_hdr_data.R: v Processing completed.
  > test-ifcb_read_hdr_data.R: Found 1 '.hdr' file.
  Saving _problems/test-ifcb_save_classification-7.R
  Saving _problems/test-ifcb_save_classification-35.R
  > test-ifcb_zip_matlab.R: Listing all files...
  > test-ifcb_zip_matlab.R: Copying manual files...
  > test-ifcb_zip_matlab.R: Copying feature files...
  > test-ifcb_zip_matlab.R: Copying data files...
  > test-ifcb_zip_matlab.R: Copying class2use file...
  > test-ifcb_zip_matlab.R: Creating README file...
  > test-ifcb_zip_matlab.R: Creating MANIFEST.txt...
  > test-ifcb_zip_matlab.R: Creating zip archive...
  > test-ifcb_zip_matlab.R: v Zip archive created: '/home/hornik/tmp/scratch/Rtmp93rQxY/ifcb_zip_matlab/output/test_output.zip'
  > test-ifcb_zip_matlab.R: The zip file is already smaller than the specified max size (500 MB).
  > test-ifcb_zip_pngs.R: Creating README file...
  > test-ifcb_zip_pngs.R: Creating MANIFEST.txt...
  > test-ifcb_zip_pngs.R: Creating zip archive...
  > test-ifcb_zip_pngs.R: v Zip archive created: '/home/hornik/tmp/scratch/Rtmp93rQxY/ifcb_zip_pngs/test_output.zip'
  > test-ifcb_zip_pngs.R: Creating README file...
  > test-ifcb_zip_pngs.R: Creating MANIFEST.txt...
  > test-ifcb_zip_pngs.R: Creating zip archive...
  > test-ifcb_zip_pngs.R: v Zip archive created: '/home/hornik/tmp/scratch/Rtmp93rQxY/ifcb_zip_pngs/test_output.zip'
  > test-ifcb_zip_pngs.R: '/home/hornik/tmp/scratch/Rtmp93rQxY/ifcb_zip_pngs/test_output.zip' is larger than 1e-07 MB. Splitting the zip file into smaller parts...
  > test-ifcb_zip_pngs.R: v Created 1 smaller zip file:
  > test-ifcb_zip_pngs.R: '/home/hornik/tmp/scratch/Rtmp93rQxY/ifcb_zip_pngs/test_output_part_1.zip'
  > test-ifcb_zip_pngs.R: Creating README file...
  > test-ifcb_zip_pngs.R: Creating MANIFEST.txt...
  > test-ifcb_zip_pngs.R: Creating zip archive...
  > test-ifcb_zip_pngs.R: v Zip archive created: '/home/hornik/tmp/scratch/Rtmp93rQxY/ifcb_zip_pngs/test_output.zip'
  [ FAIL 2 | WARN 0 | SKIP 81 | PASS 316 ]
  
  ══ Skipped tests (81) ══════════════════════════════════════════════════════════
  • On CRAN (41): 'test-get_latest_github_release.R:2:3',
    'test-get_latest_github_release.R:18:3', 'test-ifcb_classify_models.R:4:3',
    'test-ifcb_classify_sample.R:110:3', 'test-ifcb_classify_images.R:9:3',
    'test-ifcb_classify_images.R:126:3', 'test-ifcb_classify_images.R:161:3',
    'test-ifcb_download_dashboard_data.R:4:3',
    'test-ifcb_download_dashboard_metadata.R:3:3',
    'test-ifcb_download_test_data.R:3:3',
    'test-ifcb_extract_annotated_images.R:2:3',
    'test-ifcb_extract_annotated_images.R:61:3',
    'test-ifcb_extract_biovolumes.R:18:3',
    'test-ifcb_extract_biovolumes.R:112:3',
    'test-ifcb_extract_biovolumes.R:130:3',
    'test-ifcb_extract_biovolumes.R:165:3',
    'test-ifcb_extract_biovolumes.R:202:3',
    'test-ifcb_extract_classified_images.R:2:3',
    'test-ifcb_extract_classified_images.R:67:3',
    'test-ifcb_extract_classified_images.R:103:3',
    'test-ifcb_extract_classified_images.R:138:3',
    'test-ifcb_extract_classified_images.R:172:3',
    'test-ifcb_extract_classified_images.R:211:3',
    'test-ifcb_extract_pngs.R:2:3', 'test-ifcb_get_runtime.R:59:3',
    'test-ifcb_is_diatom.R:3:3', 'test-ifcb_is_diatom.R:22:3',
    'test-ifcb_is_diatom.R:50:3', 'test-ifcb_is_near_land.R:3:3',
    'test-ifcb_is_near_land.R:25:3', 'test-ifcb_is_near_land.R:46:3',
    'test-ifcb_list_dashboard_bins.R:12:3', 'test-ifcb_match_taxa_names.R:3:3',
    'test-ifcb_match_taxa_names.R:22:3', 'test-ifcb_py_install.R:3:3',
    'test-ifcb_py_install.R:35:3', 'test-ifcb_save_classification.R:292:3',
    'test-ifcb_save_classification.R:426:3',
    'test-ifcb_summarize_biovolumes.R:13:3',
    'test-ifcb_summarize_biovolumes.R:65:3', 'test-ifcb_which_basin.R:37:3'
  • Python not available for testing (CRAN) (4):
    'test-ifcb_extract_features.R:3:3', 'test-ifcb_extract_features.R:50:3',
    'test-ifcb_extract_features.R:112:3', 'test-ifcb_extract_features.R:134:3'
  • scipy not available for testing (CRAN) (27):
    'test-ifcb_adjust_classes.R:3:3', 'test-ifcb_annotate_batch.R:4:3',
    'test-ifcb_annotate_batch.R:66:3', 'test-ifcb_annotate_samples.R:3:3',
    'test-ifcb_annotate_samples.R:50:3', 'test-ifcb_annotate_samples.R:108:3',
    'test-ifcb_correct_annotation.R:3:3', 'test-ifcb_correct_annotation.R:67:3',
    'test-ifcb_correct_annotation.R:122:3',
    'test-ifcb_correct_annotation.R:181:3', 'test-ifcb_create_class2use.R:3:3',
    'test-ifcb_create_empty_manual_file.R:3:3',
    'test-ifcb_create_empty_manual_file.R:20:3',
    'test-ifcb_create_manual_file.R:5:3', 'test-ifcb_create_manual_file.R:27:3',
    'test-ifcb_get_mat_names.R:28:3', 'test-ifcb_merge_manual.R:3:3',
    'test-ifcb_merge_manual.R:68:3', 'test-ifcb_prepare_whoi_plankton.R:3:3',
    'test-ifcb_prepare_whoi_plankton.R:124:3', 'test-ifcb_psd.R:3:3',
    'test-ifcb_replace_mat_values.R:3:3', 'test-ifcb_replace_mat_values.R:46:3',
    'test-ifcb_replace_mat_values.R:59:3', 'test-ifcb_replace_mat_values.R:82:3',
    'test-ifcb_replace_mat_values.R:108:3', 'test-ifcb_read_summary.R:40:3'
  • {hdf5r} is not installed (9): 'test-ifcb_save_classification.R:41:3',
    'test-ifcb_save_classification.R:205:3', 'test-read_class_file.R:46:3',
    'test-read_class_file.R:66:3', 'test-read_class_file.R:80:3',
    'test-read_class_file.R:136:3', 'test-read_class_file.R:151:3',
    'test-read_class_file.R:162:3', 'test-read_class_file.R:173:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-ifcb_save_classification.R:4:3'): ifcb_save_classification errors when roi_file does not exist ──
  Error in `ifcb_save_classification("nonexistent.roi", output_folder = tempdir())`: Package hdf5r is required for `format = "h5"`.
  i Install it with `install.packages("hdf5r")`
  Backtrace:
      ▆
   1. ├─testthat::expect_error(...) at test-ifcb_save_classification.R:4:3
   2. │ └─testthat:::expect_condition_matching_(...)
   3. │   └─testthat:::quasi_capture(...)
   4. │     ├─testthat (local) .capture(...)
   5. │     │ └─base::withCallingHandlers(...)
   6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   7. └─iRfcb::ifcb_save_classification("nonexistent.roi", output_folder = tempdir())
   8.   └─cli::cli_abort(...)
   9.     └─rlang::abort(...)
  ── Error ('test-ifcb_save_classification.R:32:3'): ifcb_save_classification errors when no PNGs are extracted ──
  Error in `ifcb_save_classification(fake_roi, output_folder = tempdir(), verbose = FALSE)`: Package hdf5r is required for `format = "h5"`.
  i Install it with `install.packages("hdf5r")`
  Backtrace:
      ▆
   1. ├─testthat::expect_error(...) at test-ifcb_save_classification.R:32:3
   2. │ └─testthat:::expect_condition_matching_(...)
   3. │   └─testthat:::quasi_capture(...)
   4. │     ├─testthat (local) .capture(...)
   5. │     │ └─base::withCallingHandlers(...)
   6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   7. └─iRfcb::ifcb_save_classification(fake_roi, output_folder = tempdir(), verbose = FALSE)
   8.   └─cli::cli_abort(...)
   9.     └─rlang::abort(...)
  
  [ FAIL 2 | WARN 0 | SKIP 81 | PASS 316 ]
  Error:
  ! Test failures.
  Execution halted