SHARK4R

Accessing and Validating Marine Environmental Data from 'SHARK' and Related Databases

v1.1.0 · Mar 9, 2026 · MIT + file LICENSE

Description

Provides functions to retrieve, process, analyze, and quality-control marine physical, chemical, and biological data. The main focus is on Swedish monitoring data available through the 'SHARK' database <https://shark.smhi.se/en/>, with additional API support for 'Nordic Microalgae' <https://nordicmicroalgae.org/>, 'Dyntaxa' <https://artfakta.se/>, World Register of Marine Species ('WoRMS') <https://www.marinespecies.org>, 'AlgaeBase' <https://www.algaebase.org>, OBIS 'xylookup' web service <https://iobis.github.io/xylookup/> and Intergovernmental Oceanographic Commission (IOC) - UNESCO databases on harmful algae <https://www.marinespecies.org/hab/> and toxins <https://toxins.hais.ioc-unesco.org/>.

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CRAN Check Status

3 ERROR

11 OK

Show all 14 flavors

Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	OK	480.7s
r-devel-linux-x86_64-debian-gcc	OK	288.1s
r-devel-linux-x86_64-fedora-clang	ERROR	743.6s
r-devel-linux-x86_64-fedora-gcc	OK	778.9s
r-devel-macos-arm64	OK	248s
r-devel-windows-x86_64	OK	472s
r-oldrel-macos-arm64	OK	232s
r-oldrel-macos-x86_64	OK	628s
r-oldrel-windows-x86_64	ERROR	664s
r-patched-linux-x86_64	OK	453.6s
r-release-linux-x86_64	ERROR	442s
r-release-macos-arm64	OK	237s
r-release-macos-x86_64	OK	579s
r-release-windows-x86_64	OK	476s

Check details (16 non-OK)

OK r-devel-linux-x86_64-debian-clang

OK r-devel-linux-x86_64-debian-gcc

ERROR r-devel-linux-x86_64-fedora-clang

re-building of vignette outputs

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
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘retrieve_hab_data.Rmd’

--- re-building ‘retrieve_nordic_microalgae_data.Rmd’ using rmarkdown

Quitting from retrieve_nordic_microalgae_data.Rmd:42-48 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `get_nua_taxa()`:
! Failed to retrieve options: 502
---
Backtrace:
    ▆
 1. └─SHARK4R::get_nua_taxa(unparsed = FALSE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'retrieve_nordic_microalgae_data.Rmd' failed with diagnostics:
Failed to retrieve options: 502
--- failed 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
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘retrieve_worms_data.Rmd’

SUMMARY: processing the following file failed:
  ‘retrieve_nordic_microalgae_data.Rmd’

Error: Vignette re-building failed.
Execution halted

OK r-devel-linux-x86_64-fedora-gcc

OK r-devel-macos-arm64

OK r-devel-windows-x86_64

OK r-oldrel-macos-arm64

OK r-oldrel-macos-x86_64

ERROR r-oldrel-windows-x86_64

re-building of vignette outputs

Error(s) in re-building vignettes:
--- re-building 'quality_control.Rmd' using rmarkdown

Quitting from quality_control.Rmd:123-126 [unnamed-chunk-10]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! {"title": "500 Internal Server Error"}
---
Backtrace:
    ▆
 1. └─SHARK4R::check_onland(chlorophyll_data)
 2.   └─SHARK4R::lookup_xy(...)
 3.     └─base::lapply(...)
 4.       └─SHARK4R (local) FUN(X[[i]], ...)
 5.         └─SHARK4R:::lookup_xy_chunk(msg)
 6.           └─SHARK4R:::service_call(url, msg)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'quality_control.Rmd' failed with diagnostics:
{"title": "500 Internal Server Error"}
--- failed re-building 'quality_control.Rmd'

--- re-building 'retrieve_hab_data.Rmd' using rmarkdown
--- finished re-building 'retrieve_hab_data.Rmd'

--- re-building 'retrieve_nordic_microalgae_data.Rmd' using rmarkdown
--- finished re-building 'retrieve_nordic_microalgae_data.Rmd'

--- re-building 'retrieve_shark_data.Rmd' using rmarkdown
--- finished re-building 'retrieve_shark_data.Rmd'

--- re-building 'retrieve_worms_data.Rmd' using rmarkdown
--- finished re-building 'retrieve_worms_data.Rmd'

SUMMARY: processing the following file failed:
  'quality_control.Rmd'

Error: Vignette re-building failed.
Execution halted

ERROR r-oldrel-windows-x86_64

tests

  Running 'spelling.R' [0s]
  Running 'testthat.R' [56s]
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")
  Saving _problems/test-check_depth-97.R
  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\2026_03_06_01_50_00_25361\Rtmp6Fjh65/station.txt
  Using station.txt from SHARK4R bundle: D:\temp\2026_03_06_01_50_00_25361\Rtmp6Fjh65/station.txt
  Using station.txt from SHARK4R bundle: D:\temp\2026_03_06_01_50_00_25361\Rtmp6Fjh65/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\2026_03_06_01_50_00_25361\Rtmp6Fjh65/station.txt
  WARNING: Some stations are outside the allowed distance limit
  # A tibble: 2 x 3
    station_name    distance_m OUT_OF_BOUNDS_RADIUS
    <chr>                <dbl>                <dbl>
  1 N7 OST NIDINGEN    222166.                 1200
  2 KA6                297717.                 1200
  # A tibble: 1 x 1
    station_name
    <chr>       
  1 STX         
  # A tibble: 2 x 3
    station_name distance_m OUT_OF_BOUNDS_RADIUS
    <chr>             <dbl>                <dbl>
  1 ST1               2509.                 1000
  2 ST2               6268.                 1000
  Using station.txt from SHARK4R bundle: D:\temp\2026_03_06_01_50_00_25361\Rtmp6Fjh65/station.txt
  WARNING: Unmatched stations found, check synonyms
  # A tibble: 1 x 1
    station_name
    <chr>       
  1 FAKE        
  WARNING: Some stations are outside the allowed distance limit
  # A tibble: 1 x 3
    station_name distance_m OUT_OF_BOUNDS_RADIUS
    <chr>             <dbl>                <dbl>
  1 ST2               6268.                 1000
  WARNING: Unmatched stations found, check synonyms
  # A tibble: 1 x 1
    station_name
    <chr>       
  1 FAKE        
  WARNING: Some stations are outside the allowed distance limit
  # A tibble: 1 x 3
    station_name distance_m OUT_OF_BOUNDS_RADIUS
    <chr>             <dbl>                <dbl>
  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\2026_03_06_01_50_00_25361\Rtmp6Fjh65\shark_setup_1772789679
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |=======================                                               |  33%
    |                                                                            
    |===============================================                       |  67%
    |                                                                            
    |======================================================================| 100%
  Retrieving WoRMS classification for 1 AphiaIDs.
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |======================================================================| 100%
  [ FAIL 1 | WARN 0 | SKIP 94 | PASS 419 ]
  
  ══ Skipped tests (94) ══════════════════════════════════════════════════════════
  • On CRAN (94): '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_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-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-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-check_depth.R:92:3'): check_depth works with SpatRaster bathymetry ──
  Error in `eval(expr, envir = NULL, enclos = env)`: {"title": "500 Internal Server Error"}
  Backtrace:
      ▆
   1. └─SHARK4R::check_depth(...) at test-check_depth.R:92:3
   2.   └─SHARK4R::lookup_xy(...)
   3.     └─base::lapply(...)
   4.       └─SHARK4R (local) FUN(X[[i]], ...)
   5.         └─SHARK4R:::lookup_xy_chunk(msg)
   6.           └─SHARK4R:::service_call(url, msg)
  
  [ FAIL 1 | WARN 0 | SKIP 94 | PASS 419 ]
  Error:
  ! Test failures.
  Execution halted

OK r-patched-linux-x86_64

ERROR r-release-linux-x86_64

re-building of vignette outputs

Error(s) in re-building vignettes:
  ...
--- re-building ‘quality_control.Rmd’ using rmarkdown

Quitting from quality_control.Rmd:123-126 [unnamed-chunk-10]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! {"title": "500 Internal Server Error"}
---
Backtrace:
    ▆
 1. └─SHARK4R::check_onland(chlorophyll_data)
 2.   └─SHARK4R::lookup_xy(...)
 3.     └─base::lapply(...)
 4.       └─SHARK4R (local) FUN(X[[i]], ...)
 5.         └─SHARK4R:::lookup_xy_chunk(msg)
 6.           └─SHARK4R:::service_call(url, msg)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'quality_control.Rmd' failed with diagnostics:
{"title": "500 Internal Server Error"}
--- failed re-building ‘quality_control.Rmd’

--- re-building ‘retrieve_hab_data.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished 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
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘retrieve_worms_data.Rmd’

SUMMARY: processing the following file failed:
  ‘quality_control.Rmd’

Error: Vignette re-building failed.
Execution halted

ERROR r-release-linux-x86_64

tests

  Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [34s/52s]
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")
  Saving _problems/test-check_depth-97.R
  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: /home/hornik/tmp/scratch/RtmpOyfQxj/station.txt
  Using station.txt from SHARK4R bundle: /home/hornik/tmp/scratch/RtmpOyfQxj/station.txt
  Using station.txt from SHARK4R bundle: /home/hornik/tmp/scratch/RtmpOyfQxj/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: /home/hornik/tmp/scratch/RtmpOyfQxj/station.txt
  WARNING: Some stations are outside the allowed distance limit
  # A tibble: 2 x 3
    station_name    distance_m OUT_OF_BOUNDS_RADIUS
    <chr>                <dbl>                <dbl>
  1 N7 OST NIDINGEN    222166.                 1200
  2 KA6                297717.                 1200
  # A tibble: 1 x 1
    station_name
    <chr>       
  1 STX         
  # A tibble: 2 x 3
    station_name distance_m OUT_OF_BOUNDS_RADIUS
    <chr>             <dbl>                <dbl>
  1 ST1               2509.                 1000
  2 ST2               6268.                 1000
  Using station.txt from SHARK4R bundle: /home/hornik/tmp/scratch/RtmpOyfQxj/station.txt
  WARNING: Unmatched stations found, check synonyms
  # A tibble: 1 x 1
    station_name
    <chr>       
  1 FAKE        
  WARNING: Some stations are outside the allowed distance limit
  # A tibble: 1 x 3
    station_name distance_m OUT_OF_BOUNDS_RADIUS
    <chr>             <dbl>                <dbl>
  1 ST2               6268.                 1000
  WARNING: Unmatched stations found, check synonyms
  # A tibble: 1 x 1
    station_name
    <chr>       
  1 FAKE        
  WARNING: Some stations are outside the allowed distance limit
  # A tibble: 1 x 3
    station_name distance_m OUT_OF_BOUNDS_RADIUS
    <chr>             <dbl>                <dbl>
  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: /home/hornik/tmp/scratch/RtmpOyfQxj/shark_setup_1772868462
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |=======================                                               |  33%
    |                                                                            
    |===============================================                       |  67%
    |                                                                            
    |======================================================================| 100%
  Retrieving WoRMS classification for 1 AphiaIDs.
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |======================================================================| 100%
  [ FAIL 1 | WARN 0 | SKIP 94 | PASS 419 ]
  
  ══ Skipped tests (94) ══════════════════════════════════════════════════════════
  • On CRAN (94): '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_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-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-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-check_depth.R:92:3'): check_depth works with SpatRaster bathymetry ──
  Error in `eval(expr, envir = NULL, enclos = env)`: {"title": "500 Internal Server Error"}
  Backtrace:
      ▆
   1. └─SHARK4R::check_depth(...) at test-check_depth.R:92:3
   2.   └─SHARK4R::lookup_xy(...)
   3.     └─base::lapply(...)
   4.       └─SHARK4R (local) FUN(X[[i]], ...)
   5.         └─SHARK4R:::lookup_xy_chunk(msg)
   6.           └─SHARK4R:::service_call(url, msg)
  
  [ FAIL 1 | WARN 0 | SKIP 94 | PASS 419 ]
  Error:
  ! Test failures.
  Execution halted

OK r-release-macos-arm64

OK r-release-macos-x86_64

OK r-release-windows-x86_64

Check History

ERROR 11 OK · 0 NOTE · 0 WARNING · 3 ERROR · 0 FAILURE Mar 9, 2026

ERROR r-devel-linux-x86_64-fedora-clang

re-building of vignette outputs

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
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘retrieve_hab_data.Rmd’

--- re-building ‘retrieve_nordic_microalgae_data.Rmd’ using rmarkdown

Quitting from retrieve_nordic_micr

ERROR r-release-linux-x86_64

tests

  Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [34s/52s]
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
  > 
  >

ERROR r-oldrel-windows-x86_64

tests

  Running 'spelling.R' [0s]
  Running 'testthat.R' [56s]
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
  > 
  > librar

Dependency Network

Version History

new 1.1.0 Mar 9, 2026