SHARK4R
Accessing and Validating Marine Environmental Data from 'SHARK' and Related Databases
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
Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | 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 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check History
OK 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 17, 2026
ERROR 11 OK · 0 NOTE · 0 WARNING · 3 ERROR · 0 FAILURE Mar 10, 2026
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.Rm ...[truncated]... ed: --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
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. > # > # ...[truncated]... :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
tests
Running 'spelling.R' [0s] Running 'testthat.R' [48s] 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 s ...[truncated]... :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