R Under development (unstable) (2025-03-05 r87885 ucrt) -- "Unsuffered Consequences" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # 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") Skipping virtual environment setup on CRAN. Missing Python packages: scipy, matplotlib, pandas -- Column specification -------------------------------------------------------- cols( sample = col_character(), time = col_time(format = ""), ifcb_number = col_character() ) -- Column specification -------------------------------------------------------- cols( sample = col_character(), time = col_time(format = ""), ifcb_number = col_character() ) MANIFEST.txt has been created at D:\temp\2025_03_05_16_50_17_24433\RtmpAbFTDf/mock_dir/test_data/MANIFEST.txt MANIFEST.txt has been created at D:\temp\2025_03_05_16_50_17_24433\RtmpAbFTDf/mock_dir/test_data/MANIFEST.txt MANIFEST.txt has been created at D:\temp\2025_03_05_16_50_17_24433\RtmpAbFTDf/mock_dir/test_data/MANIFEST.txt Reading feature files... | | | 0% | |======================================================================| 100% Retrieving WoRMS records... INFO: The following classes are considered NOT diatoms for carbon calculations: Mesodinium_rubrum Reading feature files... Reading feature files... | | | 0% | |======================================================================| 100% Retrieving WoRMS records... INFO: The following classes are considered NOT diatoms for carbon calculations: Mesodinium_rubrum Reading feature files... | | | 0% | |======================================================================| 100% Retrieving WoRMS records... INFO: The following classes are considered NOT diatoms for carbon calculations: Mesodinium_rubrum Writing 2 ROIs from D20220522T003051_IFCB134.roi to D:\temp\2025_03_05_16_50_17_24433\RtmpAbFTDf/ifcb_extract_classified_images/output_images/Mesodinium_rubrum Writing 2 ROIs from D20220522T003051_IFCB134.roi to D:\temp\2025_03_05_16_50_17_24433\RtmpAbFTDf/ifcb_extract_classified_images/output_images/Mesodinium_rubrum Writing 2 ROIs from D20220522T003051_IFCB134.roi to D:\temp\2025_03_05_16_50_17_24433\RtmpAbFTDf/ifcb_extract_classified_images/output_images/Mesodinium_rubrum Writing 2 ROIs from D20220522T003051_IFCB134.roi to D:\temp\2025_03_05_16_50_17_24433\RtmpAbFTDf/ifcb_extract_classified_images/output_images/Mesodinium_rubrum Writing 1 ROIs from D20220522T003051_IFCB134.roi to D:\temp\2025_03_05_16_50_17_24433\RtmpAbFTDf/ifcb_extract_pngs/output/D20220522T003051_IFCB134 PNG file already exists: D:\temp\2025_03_05_16_50_17_24433\RtmpAbFTDf/ifcb_extract_pngs/output/D20220522T003051_IFCB134/D20220522T003051_IFCB134_00002.png | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% Reading feature files... | | | 0% | |======================================================================| 100% Retrieving WoRMS records... INFO: The following classes are considered NOT diatoms for carbon calculations: Mesodinium_rubrum Reading layer `baltic_sea_buffered' from data source `D:\temp\2025_03_05_16_50_17_24433\RtmpAbFTDf\ifcb_which_basin\baltic_sea_buffered.shp' using driver `ESRI Shapefile' Simple feature collection with 1 feature and 1 field Geometry type: MULTIPOLYGON Dimension: XY Bounding box: xmin: 11.71566 ymin: 53.81987 xmax: 30.524 ymax: 65.99361 Geodetic CRS: WGS 84 Writing layer `baltic_sea_buffered_4324' to data source `D:\temp\2025_03_05_16_50_17_24433\RtmpAbFTDf/ifcb_which_basin/baltic_sea_buffered_4324.shp' using driver `ESRI Shapefile' Writing 1 features with 1 fields and geometry type Multi Polygon. Listing all files... Copying manual files... [==================================================] 100% Copying feature files... [==================================================] 100% Copying data files... [==================================================] 100% Copying class2use file... Creating README file... Creating MANIFEST.txt... Creating zip archive... Zip archive created successfully: D:/temp/2025_03_05_16_50_17_24433/RtmpAbFTDf/ifcb_zip_matlab/test_output.zip [==================================================] 100% Creating README file... Creating MANIFEST.txt... Creating zip archive... Zip archive created successfully: D:/temp/2025_03_05_16_50_17_24433/RtmpAbFTDf/ifcb_zip_pngs/test_output.zip [==================================================] 100% Creating README file... Creating MANIFEST.txt... Creating zip archive... Zip archive created successfully: D:/temp/2025_03_05_16_50_17_24433/RtmpAbFTDf/ifcb_zip_pngs/test_output.zip D:\temp\2025_03_05_16_50_17_24433\RtmpAbFTDf/ifcb_zip_pngs/test_output.zip is larger than 1e-07 MB. Splitting the zip file into smaller parts... Successfully created 1 smaller zip files: D:/temp/2025_03_05_16_50_17_24433/RtmpAbFTDf/ifcb_zip_pngs/test_output_part_1.zip [==================================================] 100% Creating README file... Creating MANIFEST.txt... Creating zip archive... Zip archive created successfully: D:/temp/2025_03_05_16_50_17_24433/RtmpAbFTDf/ifcb_zip_pngs/test_output.zip [ FAIL 0 | WARN 0 | SKIP 23 | PASS 286 ] ══ Skipped tests (23) ══════════════════════════════════════════════════════════ • On CRAN (4): 'test-ifcb_download_test_data.R:10:3', 'test-ifcb_get_runtime.R:60:3', 'test-ifcb_is_diatom.R:6:3', 'test-ifcb_match_taxa_names.R:6:3' • Skipping Python-dependent tests: missing Python packages or running on CRAN. (19): 'test-ifcb_adjust_classes.R:3:3', 'test-ifcb_annotate_batch.R:3:3', 'test-ifcb_annotate_batch.R:65:3', 'test-ifcb_correct_annotation.R:3:3', 'test-ifcb_correct_annotation.R:68:3', 'test-ifcb_correct_annotation.R:124:3', 'test-ifcb_correct_annotation.R:184:3', 'test-ifcb_create_class2use.R:3:3', 'test-ifcb_create_empty_manual_file.R:3:3', 'test-ifcb_merge_manual.R:3:3', 'test-ifcb_merge_manual.R:63:3', 'test-ifcb_psd.R:3:3', 'test-ifcb_py_install.R:3:3', 'test-ifcb_py_install.R:33:3', 'test-ifcb_replace_mat_values.R:3:3', 'test-ifcb_replace_mat_values.R:40:3', 'test-ifcb_replace_mat_values.R:54:3', 'test-ifcb_replace_mat_values.R:78:3', 'test-ifcb_replace_mat_values.R:105:3' [ FAIL 0 | WARN 0 | SKIP 23 | PASS 286 ] > > proc.time() user system elapsed 17.81 1.95 22.46