* using log directory ‘/srv/hornik/tmp/CRAN_pretest/SHARK4R.Rcheck’ * using R Under development (unstable) (2026-03-09 r89580) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 21.1.8 (3+b1) Debian flang version 21.1.8 (3+b1) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * current time: 2026-03-09 10:13:17 UTC * checking for file ‘SHARK4R/DESCRIPTION’ ... OK * this is package ‘SHARK4R’ version ‘1.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [5s/8s] OK * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘SHARK4R’ can be installed ... [16s/16s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [4s/4s] OK * checking whether the package can be loaded with stated dependencies ... [4s/4s] OK * checking whether the package can be unloaded cleanly ... [4s/4s] OK * checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK * checking whether the namespace can be unloaded cleanly ... [4s/4s] OK * checking loading without being on the library search path ... [4s/4s] OK * checking whether startup messages can be suppressed ... [4s/4s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [23s/23s] OK * checking Rd files ... [1s/1s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [18s/18s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [15s/90s] ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [15s/89s] 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(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 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: /tmp/RtmpjqlWs9/working_dir/RtmpZ0nI9E/station.txt Using station.txt from SHARK4R bundle: /tmp/RtmpjqlWs9/working_dir/RtmpZ0nI9E/station.txt Using station.txt from SHARK4R bundle: /tmp/RtmpjqlWs9/working_dir/RtmpZ0nI9E/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: /tmp/RtmpjqlWs9/working_dir/RtmpZ0nI9E/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: /tmp/RtmpjqlWs9/working_dir/RtmpZ0nI9E/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: /tmp/RtmpjqlWs9/working_dir/RtmpZ0nI9E/shark_setup_1773051357 | | | 0% | |======================= | 33% | |=============================================== | 67%Saving _problems/test-worms_api_functions-162.R Retrieving WoRMS classification for 1 AphiaIDs. | | | 0% | |======================================================================| 100%Failed to retrieve classification for AphiaID 109604: (503) Service Unavailable - 109604 Saving _problems/test-worms_api_functions-168.R [ FAIL 2 | WARN 0 | SKIP 98 | PASS 418 ] ══ Skipped tests (98) ══════════════════════════════════════════════════════════ • On CRAN (98): '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:62:3', 'test-check_depth.R:79:3', '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:14:3', 'test-dyntaxa_api_functions.R:27:3', 'test-dyntaxa_api_functions.R:39:3', 'test-dyntaxa_api_functions.R:52:3', 'test-dyntaxa_api_functions.R:64:3', 'test-dyntaxa_api_functions.R:84:3', 'test-dyntaxa_api_functions.R:101:3', 'test-dyntaxa_api_functions.R:127:3', 'test-dyntaxa_api_functions.R:140:3', 'test-dyntaxa_api_functions.R:157:3', 'test-dyntaxa_api_functions.R:174:3', 'test-dyntaxa_api_functions.R:188:3', 'test-dyntaxa_api_functions.R:201:3', 'test-dyntaxa_api_functions.R:233:3', 'test-hab_api_functions.R:2:3', 'test-hab_api_functions.R:35:3', 'test-hab_api_functions.R:60:3', 'test-iRfcb_functions.R:3:3', 'test-iRfcb_functions.R:25:3', 'test-iRfcb_functions.R:62:3', 'test-iRfcb_functions.R:101:3', '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-nua_api_functions.R:49:3', 'test-nua_api_functions.R:63:3', 'test-nua_api_functions.R:76:3', '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:185:3', 'test-worms_api_functions.R:193:3', 'test-worms_api_functions.R:200:3', 'test-worms_api_functions.R:207:3', 'test-worms_api_functions.R:215:3', 'test-worms_api_functions.R:224:3', 'test-worms_api_functions.R:236:3', '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', 'test-xylookup.R:113:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-worms_api_functions.R:162:3'): deprecated match_worms_taxa_interactive works as expected ── Error in `value[[3L]](cond)`: Error retrieving WoRMS record for 'Dinophysis' after 3 attempts: (503) Service Unavailable - Dinophysis Backtrace: ▆ 1. ├─lifecycle::expect_deprecated(match_wormstaxa(test_names, ask = FALSE)) at test-worms_api_functions.R:162:3 2. │ └─testthat::expect_warning(...) 3. │ └─testthat:::expect_condition_matching_(...) 4. │ └─testthat:::quasi_capture(...) 5. │ ├─testthat (local) .capture(...) 6. │ │ └─base::withCallingHandlers(...) 7. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 8. └─SHARK4R::match_wormstaxa(test_names, ask = FALSE) 9. └─SHARK4R::match_worms_taxa(taxa_names = names, best_match_only = ask) 10. └─SHARK4R (local) fetch_single(q, max_retries) 11. └─base::tryCatch(...) 12. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 13. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14. └─value[[3L]](cond) ── Error ('test-worms_api_functions.R:166:3'): deprecated update_worms_taxonomy with deprecated argument works as expected ── Error in `dplyr::relocate(df_all, worms_hierarchy, .after = dplyr::last_col())`: Can't select columns that don't exist. x Column `worms_hierarchy` doesn't exist. Backtrace: ▆ 1. ├─lifecycle::expect_deprecated(lifecycle::expect_deprecated(update_worms_taxonomy(aphiaid = test_aphia_id))) at test-worms_api_functions.R:166:3 2. │ └─testthat::expect_warning(...) 3. │ └─testthat:::expect_condition_matching_(...) 4. │ └─testthat:::quasi_capture(...) 5. │ ├─testthat (local) .capture(...) 6. │ │ └─base::withCallingHandlers(...) 7. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 8. ├─lifecycle::expect_deprecated(update_worms_taxonomy(aphiaid = test_aphia_id)) 9. │ └─testthat::expect_warning(...) 10. │ └─testthat:::expect_condition_matching_(...) 11. │ └─testthat:::quasi_capture(...) 12. │ ├─testthat (local) .capture(...) 13. │ │ └─base::withCallingHandlers(...) 14. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 15. ├─SHARK4R::update_worms_taxonomy(aphiaid = test_aphia_id) 16. │ └─SHARK4R::add_worms_taxonomy(aphia_id) 17. │ └─SHARK4R::get_worms_classification(...) 18. │ ├─... %>% dplyr::relocate(aphia_id) 19. │ ├─dplyr::relocate(df_all, worms_hierarchy, .after = dplyr::last_col()) 20. │ └─dplyr:::relocate.data.frame(df_all, worms_hierarchy, .after = dplyr::last_col()) 21. │ └─dplyr:::eval_relocate(...) 22. │ └─tidyselect::eval_select(...) 23. │ └─tidyselect:::eval_select_impl(...) 24. │ ├─tidyselect:::with_subscript_errors(...) 25. │ │ └─base::withCallingHandlers(...) 26. │ └─tidyselect:::vars_select_eval(...) 27. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask) 28. │ └─tidyselect:::eval_c(expr, data_mask, context_mask) 29. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init) 30. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask) 31. │ └─tidyselect:::as_indices_sel_impl(...) 32. │ └─tidyselect:::as_indices_impl(...) 33. │ └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg) 34. │ └─vctrs::vec_as_location(...) 35. ├─dplyr::relocate(., aphia_id) 36. └─vctrs (local) ``() 37. └─vctrs:::stop_subscript_oob(...) 38. └─vctrs:::stop_subscript(...) 39. └─rlang::abort(...) [ FAIL 2 | WARN 0 | SKIP 98 | PASS 418 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [53s/123s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘quality_control.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘quality_control.Rmd’ --- re-building ‘retrieve_hab_data.Rmd’ using rmarkdown Quitting from retrieve_hab_data.Rmd:37-43 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `get_hab_list()`: ! Failed to download the HABs list. Status code:503 --- Backtrace: ▆ 1. └─SHARK4R::get_hab_list() ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'retrieve_hab_data.Rmd' failed with diagnostics: Failed to download the HABs list. Status code:503 --- failed re-building ‘retrieve_hab_data.Rmd’ --- re-building ‘retrieve_nordic_microalgae_data.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘retrieve_nordic_microalgae_data.Rmd’ --- re-building ‘retrieve_shark_data.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘retrieve_shark_data.Rmd’ --- re-building ‘retrieve_worms_data.Rmd’ using rmarkdown Quitting from retrieve_worms_data.Rmd:58-77 [unnamed-chunk-5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `value[[3L]]()`: ! Error retrieving WoRMS record for 'Scrippsiella' after 3 attempts: (500) Internal Server Error - Scrippsiella --- Backtrace: ▆ 1. └─SHARK4R::match_worms_taxa(...) 2. └─SHARK4R (local) fetch_single(q, max_retries) 3. └─base::tryCatch(...) 4. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 6. └─value[[3L]](cond) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'retrieve_worms_data.Rmd' failed with diagnostics: Error retrieving WoRMS record for 'Scrippsiella' after 3 attempts: (500) Internal Server Error - Scrippsiella --- failed re-building ‘retrieve_worms_data.Rmd’ SUMMARY: processing the following files failed: ‘retrieve_hab_data.Rmd’ ‘retrieve_worms_data.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [5s/5s] OK * checking HTML version of manual ... [6s/6s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs