Last updated on 2025-12-17 19:50:04 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.1 | 0.33 | 3.08 | 3.41 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.1 | 24.09 | 354.65 | 378.74 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.1 | 61.00 | 779.02 | 840.02 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.1 | 62.00 | 781.80 | 843.80 | ERROR | |
| r-devel-windows-x86_64 | 1.0.1 | 34.00 | 459.00 | 493.00 | OK | |
| r-patched-linux-x86_64 | 1.0.1 | 32.61 | 493.77 | 526.38 | OK | |
| r-release-linux-x86_64 | 1.0.1 | 32.96 | 500.18 | 533.14 | OK | |
| r-release-macos-arm64 | 1.0.1 | OK | ||||
| r-release-macos-x86_64 | 1.0.1 | 22.00 | 406.00 | 428.00 | OK | |
| r-release-windows-x86_64 | 1.0.1 | 34.00 | 496.00 | 530.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.1 | 7.00 | 296.00 | 303.00 | OK | |
| r-oldrel-macos-x86_64 | 1.0.1 | 24.00 | 437.00 | 461.00 | OK | |
| r-oldrel-windows-x86_64 | 1.0.1 | 48.00 | 625.00 | 673.00 | OK |
Version: 1.0.1
Check: package dependencies
Result: ERROR
Package required but not available: ‘taxize’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.1
Check: examples
Result: ERROR
Running examples in ‘EcoCleanR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ec_geographic_map
> ### Title: Map view of occurrence data points
> ### Aliases: ec_geographic_map
>
> ### ** Examples
>
> data <- data.frame(
+ scientificName = "Mexacanthina lugubris",
+ decimalLongitude = c(-117, -117.8, -116.9),
+ decimalLatitude = c(32.9, 33.5, 31.9),
+ temperature_mean = c(12, 13, 14),
+ temperature_min = c(9, 6, 10),
+ temperature_max = c(14, 16, 18)
+ )
> ec_geographic_map(data,
+ latitude = "decimalLatitude",
+ longitude = "decimalLongitude"
+ )
The geodata server is temporary out of service for maintenance. It should be back on 20 December.
Error: unable to find an inherited method for function ‘crop’ for signature ‘x = "NULL"’
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [144s/459s]
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(EcoCleanR)
>
> test_check("EcoCleanR")
== 1 queries ===============
Retrieving data for taxon 'Mexacanthina lugubris'
✔ Found: Mexacanthina lugubris
== Results =================
• Total: 1
• Found: 1
• Not Found: 0
Suggested threshold at 96th percentile: 8801832
Extracting BO_sstmean...
Imputation iteration 1
Imputation iteration 2
No more missing values to impute.
The geodata server is temporary out of service for maintenance. It should be back on 20 December.
Saving _problems/test-data_cleaning-294.R
The geodata server is temporary out of service for maintenance. It should be back on 20 December.
Saving _problems/test-data_cleaning-329.R
[ FAIL 2 | WARN 0 | SKIP 3 | PASS 30 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• Skipping ec_flag_non_east_atlantic test - big shape files required to load
for it (1): 'test-data_cleaning.R:417:3'
• Skipping ec_flag_non_west_atlantic test - big shape files required to load
for it (1): 'test-data_cleaning.R:438:3'
• Skipping ec_flag_non_west_pacific test - big shape files required to load for
it (1): 'test-data_cleaning.R:459:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-data_cleaning.R:290:3'): ec_geographic_map_w_flag works ────────
Error: unable to find an inherited method for function 'crop' for signature 'x = "NULL"'
Backtrace:
▆
1. └─EcoCleanR::ec_geographic_map_w_flag(...) at test-data_cleaning.R:290:3
2. └─terra::crop(x = world_map, y = geographic_extent)
3. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
── Error ('test-data_cleaning.R:326:3'): ec_geographic_map works ───────────────
Error: unable to find an inherited method for function 'crop' for signature 'x = "NULL"'
Backtrace:
▆
1. └─EcoCleanR::ec_geographic_map(...) at test-data_cleaning.R:326:3
2. └─terra::crop(x = world_map, y = geographic_extent)
3. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
[ FAIL 2 | WARN 0 | SKIP 3 | PASS 30 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘data_cleaning.Rmd’ using rmarkdown
Quitting from data_cleaning.Rmd:68-73 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unable to find an inherited method for function 'crop' for signature 'x = "NULL"'
---
Backtrace:
▆
1. └─EcoCleanR::ec_geographic_map(...)
2. └─terra::crop(x = world_map, y = geographic_extent)
3. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'data_cleaning.Rmd' failed with diagnostics:
unable to find an inherited method for function 'crop' for signature 'x = "NULL"'
--- failed re-building ‘data_cleaning.Rmd’
--- re-building ‘data_merging.Rmd’ using rmarkdown
Quitting from data_merging.Rmd:141-147 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unable to find an inherited method for function 'crop' for signature 'x = "NULL"'
---
Backtrace:
▆
1. └─EcoCleanR::ec_geographic_map(Mixdb.occ, "decimalLatitude", longitude = "decimalLongitude")
2. └─terra::crop(x = world_map, y = geographic_extent)
3. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'data_merging.Rmd' failed with diagnostics:
unable to find an inherited method for function 'crop' for signature 'x = "NULL"'
--- failed re-building ‘data_merging.Rmd’
SUMMARY: processing the following files failed:
‘data_cleaning.Rmd’ ‘data_merging.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.1
Check: examples
Result: ERROR
Running examples in ‘EcoCleanR-Ex.R’ failed
The error most likely occurred in:
> ### Name: ec_geographic_map
> ### Title: Map view of occurrence data points
> ### Aliases: ec_geographic_map
>
> ### ** Examples
>
> data <- data.frame(
+ scientificName = "Mexacanthina lugubris",
+ decimalLongitude = c(-117, -117.8, -116.9),
+ decimalLatitude = c(32.9, 33.5, 31.9),
+ temperature_mean = c(12, 13, 14),
+ temperature_min = c(9, 6, 10),
+ temperature_max = c(14, 16, 18)
+ )
> ec_geographic_map(data,
+ latitude = "decimalLatitude",
+ longitude = "decimalLongitude"
+ )
The geodata server is temporary out of service for maintenance. It should be back on 20 December.
Error: unable to find an inherited method for function ‘crop’ for signature ‘x = "NULL"’
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.0.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [4m/11m]
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(EcoCleanR)
>
> test_check("EcoCleanR")
== 1 queries ===============
Retrieving data for taxon 'Mexacanthina lugubris'
✔ Found: Mexacanthina lugubris
== Results =================
• Total: 1
• Found: 1
• Not Found: 0
Suggested threshold at 96th percentile: 8801832
Extracting BO_sstmean...
Imputation iteration 1
Imputation iteration 2
No more missing values to impute.
The geodata server is temporary out of service for maintenance. It should be back on 20 December.
Saving _problems/test-data_cleaning-294.R
The geodata server is temporary out of service for maintenance. It should be back on 20 December.
Saving _problems/test-data_cleaning-329.R
[ FAIL 2 | WARN 0 | SKIP 3 | PASS 30 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• Skipping ec_flag_non_east_atlantic test - big shape files required to load
for it (1): 'test-data_cleaning.R:417:3'
• Skipping ec_flag_non_west_atlantic test - big shape files required to load
for it (1): 'test-data_cleaning.R:438:3'
• Skipping ec_flag_non_west_pacific test - big shape files required to load for
it (1): 'test-data_cleaning.R:459:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-data_cleaning.R:290:3'): ec_geographic_map_w_flag works ────────
Error: unable to find an inherited method for function 'crop' for signature 'x = "NULL"'
Backtrace:
▆
1. └─EcoCleanR::ec_geographic_map_w_flag(...) at test-data_cleaning.R:290:3
2. └─terra::crop(x = world_map, y = geographic_extent)
3. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
── Error ('test-data_cleaning.R:326:3'): ec_geographic_map works ───────────────
Error: unable to find an inherited method for function 'crop' for signature 'x = "NULL"'
Backtrace:
▆
1. └─EcoCleanR::ec_geographic_map(...) at test-data_cleaning.R:326:3
2. └─terra::crop(x = world_map, y = geographic_extent)
3. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
[ FAIL 2 | WARN 0 | SKIP 3 | PASS 30 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘data_cleaning.Rmd’ using rmarkdown
Quitting from data_cleaning.Rmd:68-73 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unable to find an inherited method for function 'crop' for signature 'x = "NULL"'
---
Backtrace:
▆
1. └─EcoCleanR::ec_geographic_map(...)
2. └─terra::crop(x = world_map, y = geographic_extent)
3. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'data_cleaning.Rmd' failed with diagnostics:
unable to find an inherited method for function 'crop' for signature 'x = "NULL"'
--- failed re-building ‘data_cleaning.Rmd’
--- re-building ‘data_merging.Rmd’ using rmarkdown
Quitting from data_merging.Rmd:141-147 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unable to find an inherited method for function 'crop' for signature 'x = "NULL"'
---
Backtrace:
▆
1. └─EcoCleanR::ec_geographic_map(Mixdb.occ, "decimalLatitude", longitude = "decimalLongitude")
2. └─terra::crop(x = world_map, y = geographic_extent)
3. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'data_merging.Rmd' failed with diagnostics:
unable to find an inherited method for function 'crop' for signature 'x = "NULL"'
--- failed re-building ‘data_merging.Rmd’
SUMMARY: processing the following files failed:
‘data_cleaning.Rmd’ ‘data_merging.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.0.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [255s/536s]
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(EcoCleanR)
>
> test_check("EcoCleanR")
== 1 queries ===============
Retrieving data for taxon 'Mexacanthina lugubris'
✔ Found: Mexacanthina lugubris
== Results =================
• Total: 1
• Found: 1
• Not Found: 0
Suggested threshold at 96th percentile: 8801832
Extracting BO_sstmean...
Imputation iteration 1
Imputation iteration 2
No more missing values to impute.
The geodata server is temporary out of service for maintenance. It should be back on 20 December.
Saving _problems/test-data_cleaning-294.R
The geodata server is temporary out of service for maintenance. It should be back on 20 December.
Saving _problems/test-data_cleaning-329.R
[ FAIL 2 | WARN 0 | SKIP 3 | PASS 30 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• Skipping ec_flag_non_east_atlantic test - big shape files required to load
for it (1): 'test-data_cleaning.R:417:3'
• Skipping ec_flag_non_west_atlantic test - big shape files required to load
for it (1): 'test-data_cleaning.R:438:3'
• Skipping ec_flag_non_west_pacific test - big shape files required to load for
it (1): 'test-data_cleaning.R:459:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-data_cleaning.R:290:3'): ec_geographic_map_w_flag works ────────
Error: unable to find an inherited method for function 'crop' for signature 'x = "NULL"'
Backtrace:
▆
1. └─EcoCleanR::ec_geographic_map_w_flag(...) at test-data_cleaning.R:290:3
2. └─terra::crop(x = world_map, y = geographic_extent)
3. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
── Error ('test-data_cleaning.R:326:3'): ec_geographic_map works ───────────────
Error: unable to find an inherited method for function 'crop' for signature 'x = "NULL"'
Backtrace:
▆
1. └─EcoCleanR::ec_geographic_map(...) at test-data_cleaning.R:326:3
2. └─terra::crop(x = world_map, y = geographic_extent)
3. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
[ FAIL 2 | WARN 0 | SKIP 3 | PASS 30 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc