R Under development (unstable) (2025-11-19 r89040 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(SHARK4R) > > test_check("SHARK4R") All required fields present All recommended fields present All required fields present All required fields present All required fields present All required fields present All recommended fields present Common problems are e.g. '<', '>' signs, text labels, or malformed numbers. ERROR: Positions contain zeroes (0). Please check station coordinates with zero values! ERROR: Positions contain zeroes (0). Please check station coordinates with zero values! Parameter Total cover of all species (%), measurement(s) > 100% Parameter Total cover of all species (%), measurement(s) > 100% Parameter Cover (%), measurement(s) > 100% Parameter Cover (%), measurement(s) > 100% Parameter Cover, measurement(s) > 100% Parameter Cover, measurement(s) > 100% Parameter Cover class, measurement(s) > 10 Parameter Sediment deposition cover (%), measurement(s) > 100% Parameter Abundance class, measurement(s) > 10 Parameter BQIm, measurement(s) > 0 when Abundance = 0 Parameter Wet weight, measurement(s) violate logical assumption: should not be 0 No parameters from the logical rules are present in the dataset. Available parameters are: Total cover of all species, Cover, Cover class, Sediment deposition cover, Abundance class, Wet weight Parameter Wet weight, measurement(s) outside expected range: > 0 Parameter Wet weight, measurement(s) outside expected range: > 0 WARNING: TestParam1 ( TypeA ) exceeds extreme_upper in dataset WARNING: TestParam1 ( TypeA ) exceeds extreme_upper in dataset [1] "bacterial_production" WARNING: Bacterial carbon production ( Bacterioplankton ) exceeds extreme_upper in dataset [1] "bacterial_concentration" WARNING: Bacterial abundance ( Bacterioplankton ) exceeds extreme_upper in dataset [1] "bacterial_carbon" WARNING: Bacterial cell carbon content ( Bacterioplankton ) exceeds extreme_upper in dataset [1] "chlorophyll_conc" WARNING: Chlorophyll-a ( Chlorophyll ) exceeds extreme_upper in dataset [1] "picoplankton_abundance" WARNING: Abundance ( Picoplankton ) exceeds extreme_upper in dataset [1] "picoplankton_biovol" WARNING: Biovolume concentration ( Picoplankton ) exceeds extreme_upper in dataset [1] "picoplankton_carbon" WARNING: Carbon concentration ( Picoplankton ) exceeds extreme_upper in dataset [1] "picoplankton_counted" WARNING: # counted ( Picoplankton ) exceeds extreme_upper in dataset [1] "zooplankton_abund" WARNING: Abundance ( Zooplankton ) exceeds extreme_upper in dataset [1] "zooplankton_counted" WARNING: # counted ( Zooplankton ) exceeds extreme_upper in dataset [1] "zooplankton_length_mean" WARNING: Length (mean) ( Zooplankton ) exceeds extreme_upper in dataset [1] "zooplankton_length_median" WARNING: Length (median) ( Zooplankton ) exceeds extreme_upper in dataset [1] "zooplankton_wetweight" WARNING: Wet weight ( Zooplankton ) exceeds extreme_upper in dataset [1] "zooplankton_carbon" WARNING: Carbon content ( Zooplankton ) exceeds extreme_upper in dataset [1] "zooplankton_wetweight_volume" WARNING: Wet weight/volume ( Zooplankton ) exceeds extreme_upper in dataset [1] "zooplankton_wetweight_area" WARNING: Wet weight/area ( Zooplankton ) exceeds extreme_upper in dataset [1] "phytoplankton_abund" WARNING: Abundance ( Phytoplankton ) exceeds extreme_upper in dataset [1] "phytoplankton_biovol" WARNING: Biovolume concentration ( Phytoplankton ) exceeds extreme_upper in dataset [1] "phytoplankton_carbon" WARNING: Carbon concentration ( Phytoplankton ) exceeds extreme_upper in dataset [1] "phytoplankton_counted" WARNING: # counted ( Phytoplankton ) exceeds extreme_upper in dataset [1] "primaryproduction_carbonprod" WARNING: Carbon production ( Primary production ) exceeds extreme_upper in dataset [1] "primaryproduction_carbonprodlight" WARNING: Carbon prod in light ( Primary production ) exceeds extreme_upper in dataset [1] "primaryproduction_carbonprod_hour" WARNING: Carbon production/hour ( Primary production ) exceeds extreme_upper in dataset [1] "epibenthos_counted" WARNING: # counted ( Epibenthos ) exceeds extreme_upper in dataset [1] "epibenthos_dryweight" WARNING: Dry weight ( Epibenthos ) exceeds extreme_upper in dataset [1] "epibenthos_specdistr_maxdepth" WARNING: Species distribution max depth ( Epibenthos ) exceeds extreme_upper in dataset [1] "epibenthos_specdistr_mindepth" WARNING: Species distribution min depth ( Epibenthos ) exceeds extreme_upper in dataset [1] "harbourseal_counted" WARNING: # counted ( Harbour seal ) exceeds extreme_upper in dataset [1] "greyseal_counted" WARNING: # counted ( Grey seal ) exceeds extreme_upper in dataset [1] "zoobenthos_BQIm" WARNING: BQIm ( Zoobenthos ) exceeds extreme_upper in dataset [1] "zoobenthos_abund" WARNING: Abundance ( Zoobenthos ) exceeds extreme_upper in dataset [1] "zoobenthos_counted" WARNING: # counted ( Zoobenthos ) exceeds extreme_upper in dataset [1] "zoobenthos_wetweight" WARNING: Wet weight ( Zoobenthos ) exceeds extreme_upper in dataset [1] "ringedseal_calccounted" WARNING: Calculated # counted ( Ringed seal ) exceeds extreme_upper in dataset [1] "harbporp_positivemin" WARNING: Porpoise positive minutes ( Harbour Porpoise ) exceeds extreme_upper in dataset WARNING: TestParam1 ( TypeA ) exceeds extreme_upper in group WARNING: TestParam1 ( TypeA ) exceeds extreme_upper in dataset Using station.txt from SHARK4R bundle: D:\temp\2025_11_20_16_10_16_7012\RtmpW6f7os/station.txt Using station.txt from SHARK4R bundle: D:\temp\2025_11_20_16_10_16_7012\RtmpW6f7os/station.txt Using station.txt from SHARK4R bundle: D:\temp\2025_11_20_16_10_16_7012\RtmpW6f7os/station.txt Positions are not suspected to be nominal WARNING: Unmatched stations found, check synonyms WARNING: Unmatched stations found, check synonyms Using station.txt from SHARK4R bundle: D:\temp\2025_11_20_16_10_16_7012\RtmpW6f7os/station.txt WARNING: Some stations are outside the allowed distance limit # A tibble: 2 x 3 station_name distance_m OUT_OF_BOUNDS_RADIUS 1 N7 OST NIDINGEN 222166. 1200 2 KA6 297717. 1200 # A tibble: 1 x 1 station_name 1 STX # A tibble: 2 x 3 station_name distance_m OUT_OF_BOUNDS_RADIUS 1 ST1 2509. 1000 2 ST2 6268. 1000 Using station.txt from SHARK4R bundle: D:\temp\2025_11_20_16_10_16_7012\RtmpW6f7os/station.txt WARNING: Unmatched stations found, check synonyms # A tibble: 1 x 1 station_name 1 FAKE WARNING: Some stations are outside the allowed distance limit # A tibble: 1 x 3 station_name distance_m OUT_OF_BOUNDS_RADIUS 1 ST2 6268. 1000 WARNING: Unmatched stations found, check synonyms # A tibble: 1 x 1 station_name 1 FAKE WARNING: Some stations are outside the allowed distance limit # A tibble: 1 x 3 station_name distance_m OUT_OF_BOUNDS_RADIUS 1 ST2 6268. 1000 All stations found WARNING: Unmatched stations found, check synonyms Detected encoding 'ISO-8859-1' differs from specified 'utf_8'. Using detected encoding. Detected encoding 'ISO-8859-1' differs from specified 'utf_8'. Using detected encoding. Detected encoding 'ISO-8859-1' differs from specified 'utf_8'. Using detected encoding. Detected encoding 'ISO-8859-1' differs from specified 'utf_8'. Using detected encoding. Detected encoding 'ISO-8859-1' differs from specified 'utf_8'. Using detected encoding. Detected encoding 'ISO-8859-1' differs from specified 'utf_8'. Using detected encoding. Detected encoding 'ISO-8859-1' differs from specified 'utf_8'. Using detected encoding. Detected encoding 'ISO-8859-1' differs from specified 'utf_8'. Using detected encoding. Detected encoding 'ISO-8859-1' differs from specified 'utf_8'. Using detected encoding. Detected encoding 'ISO-8859-1' differs from specified 'utf_8'. Using detected encoding. Detected encoding 'ISO-8859-1' differs from specified 'utf_8'. Using detected encoding. Detected encoding 'ISO-8859-1' differs from specified 'utf_8'. Using detected encoding. Products and scripts already exist in: D:\temp\2025_11_20_16_10_16_7012\RtmpW6f7os\shark_setup_1763651652 3 names, 0 without matches, 0 with multiple matches 3 names, 0 without matches, 0 with multiple matches Retrieving WoRMS classification for 1 AphiaIDs. | | | 0% | |======================================================================| 100% [ FAIL 0 | WARN 0 | SKIP 92 | PASS 405 ] ══ Skipped tests (92) ══════════════════════════════════════════════════════════ • On CRAN (92): 'test-algaebase_api_functions.R:13:3', 'test-check_codes.R:2:3', 'test-check_codes.R:13:3', 'test-check_codes.R:24:3', 'test-check_depth.R:2:3', 'test-check_depth.R:64:3', 'test-check_fields.R:253:3', 'test-check_onland.R:6:3', 'test-check_onland.R:17:3', 'test-check_onland.R:33:3', 'test-check_onland.R:47:3', 'test-check_onland.R:63:3', 'test-dyntaxa_api_functions.R:13:3', 'test-dyntaxa_api_functions.R:25:3', 'test-dyntaxa_api_functions.R:36:3', 'test-dyntaxa_api_functions.R:48:3', 'test-dyntaxa_api_functions.R:59:3', 'test-dyntaxa_api_functions.R:78:3', 'test-dyntaxa_api_functions.R:94:3', 'test-dyntaxa_api_functions.R:119:3', 'test-dyntaxa_api_functions.R:131:3', 'test-dyntaxa_api_functions.R:147:3', 'test-dyntaxa_api_functions.R:163:3', 'test-dyntaxa_api_functions.R:176:3', 'test-dyntaxa_api_functions.R:188:3', 'test-dyntaxa_api_functions.R:219:3', 'test-hab_api_functions.R:2:3', 'test-hab_api_functions.R:35:3', 'test-iRfcb_functions.R:3:3', 'test-iRfcb_functions.R:25:3', 'test-iRfcb_functions.R:61:3', 'test-iRfcb_functions.R:100:3', 'test-nua_api_functions.R:5:3', 'test-nua_api_functions.R:16:3', 'test-nua_api_functions.R:27:3', 'test-nua_api_functions.R:38:3', 'test-plankton_toolbox.R:21:3', 'test-plankton_toolbox.R:33:3', 'test-plankton_toolbox.R:43:3', 'test-plankton_toolbox.R:54:3', 'test-plankton_toolbox.R:71:3', 'test-plankton_toolbox.R:83:3', 'test-plankton_toolbox.R:94:3', 'test-plankton_toolbox.R:105:3', 'test-plankton_toolbox.R:116:3', 'test-plankton_toolbox.R:137:3', 'test-read_delivery_template.R:2:3', 'test-read_delivery_template.R:28:3', 'test-read_delivery_template.R:44:3', 'test-read_delivery_template.R:53:3', 'test-shark_api_functions.R:4:3', 'test-shark_api_functions.R:21:3', 'test-shark_api_functions.R:55:3', 'test-shark_api_functions.R:82:3', 'test-shark_api_functions.R:106:3', 'test-shark_api_functions.R:126:3', 'test-shark_api_functions.R:140:3', 'test-shark_api_functions.R:157:3', 'test-shark_api_functions.R:169:3', 'test-shark_api_functions.R:180:3', 'test-shark_api_functions.R:201:3', 'test-shark_api_functions.R:238:3', 'test-util.R:60:3', 'test-util.R:90:3', 'test-util.R:133:3', 'test-util.R:197:3', 'test-util.R:212:3', 'test-worms_api_functions.R:9:3', 'test-worms_api_functions.R:27:3', 'test-worms_api_functions.R:38:3', 'test-worms_api_functions.R:58:3', 'test-worms_api_functions.R:70:3', 'test-worms_api_functions.R:77:3', 'test-worms_api_functions.R:89:3', 'test-worms_api_functions.R:101:3', 'test-worms_api_functions.R:113:3', 'test-worms_api_functions.R:120:3', 'test-worms_api_functions.R:140:3', 'test-worms_api_functions.R:190:3', 'test-worms_api_functions.R:198:3', 'test-worms_api_functions.R:205:3', 'test-worms_api_functions.R:212:3', 'test-worms_api_functions.R:220:3', 'test-worms_api_functions.R:229:3', 'test-worms_api_functions.R:241:3', 'test-xylookup.R:6:3', 'test-xylookup.R:18:3', 'test-xylookup.R:34:3', 'test-xylookup.R:44:3', 'test-xylookup.R:60:3', 'test-xylookup.R:81:3', 'test-xylookup.R:101:3' [ FAIL 0 | WARN 0 | SKIP 92 | PASS 405 ] > > proc.time() user system elapsed 27.45 7.98 31.56