Last updated on 2026-03-07 04:50:22 CET.
| Package | ERROR | OK |
|---|---|---|
| iRfcb | 14 | |
| SHARK4R | 1 | 13 |
Current CRAN status: OK: 14
Current CRAN status: ERROR: 1, OK: 13
Version: 1.0.3
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [26s/45s]
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: /tmp/RtmpMYxFm1/station.txt
Using station.txt from SHARK4R bundle: /tmp/RtmpMYxFm1/station.txt
Using station.txt from SHARK4R bundle: /tmp/RtmpMYxFm1/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/RtmpMYxFm1/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: /tmp/RtmpMYxFm1/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: /tmp/RtmpMYxFm1/shark_setup_1772803179
|
| | 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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.3
Check: re-building of vignette outputs
Result: ERROR
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
Flavor: r-devel-linux-x86_64-debian-gcc