Last updated on 2026-02-03 14:51:22 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.3-9 | 5.87 | 77.77 | 83.64 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.3-9 | 4.15 | 53.60 | 57.75 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.3-9 | 9.00 | 97.70 | 106.70 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 1.3-9 | 10.00 | 106.80 | 116.80 | ERROR | |
| r-devel-windows-x86_64 | 1.3-9 | 10.00 | 96.00 | 106.00 | OK | |
| r-patched-linux-x86_64 | 1.3-9 | 5.73 | 70.82 | 76.55 | OK | |
| r-release-linux-x86_64 | 1.3-9 | 4.93 | 70.16 | 75.09 | OK | |
| r-release-macos-arm64 | 1.3-9 | OK | ||||
| r-release-macos-x86_64 | 1.3-9 | 4.00 | 86.00 | 90.00 | OK | |
| r-release-windows-x86_64 | 1.3-9 | 8.00 | 94.00 | 102.00 | OK | |
| r-oldrel-macos-arm64 | 1.3-9 | OK | ||||
| r-oldrel-macos-x86_64 | 1.3-9 | 4.00 | 89.00 | 93.00 | OK | |
| r-oldrel-windows-x86_64 | 1.3-9 | 12.00 | 118.00 | 130.00 | OK |
Version: 1.3-9
Check: examples
Result: ERROR
Running examples in ‘benthos-Ex.R’ failed
The error most likely occurred in:
> ### Name: ambi
> ### Title: AZTI Marine Biotic Index (AMBI)
> ### Aliases: ambi ambi_ has_ambi has_ambi_
>
> ### ** Examples
>
> ambi(
+ taxon = c("Euspira pulchella", "Nephtys cirrosa"),
+ count = c(4, 6)
+ )
Error:
! `filter_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `filter()` instead.
ℹ See vignette('programming') for more help
Backtrace:
▆
1. ├─benthos::ambi(...)
2. │ └─benthos::ambi_(.data, lazy(taxon), lazy(count), lazy(group))
3. │ └─d %>% select_(~GROUP, ~COUNT) %>% filter_(~!is.na(GROUP))
4. └─dplyr::filter_(., ~!is.na(GROUP))
5. └─dplyr:::lazy_defunct("filter")
6. └─lifecycle::deprecate_stop(...)
7. └─lifecycle:::deprecate_stop0(msg)
8. └─rlang::cnd_signal(...)
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.3-9
Check: tests
Result: ERROR
Running ‘test-all.R’
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
> library(testthat)
> library(benthos)
> test_check("benthos")
Saving _problems/test-indicators-208.R
Saving _problems/test-indicators-243.R
[ FAIL 2 | WARN 0 | SKIP 1 | PASS 139 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-indicators.R:436:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-indicators.R:201:5'): 'AMBI-index' has been correctly implemented ──
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: `filter_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `filter()` instead.
ℹ See vignette('programming') for more help
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-indicators.R:201:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─benthos::ambi(...)
5. │ └─benthos::ambi_(.data, lazy(taxon), lazy(count), lazy(group))
6. │ └─d %>% select_(~GROUP, ~COUNT) %>% filter_(~!is.na(GROUP))
7. └─dplyr::filter_(., ~!is.na(GROUP))
8. └─dplyr:::lazy_defunct("filter")
9. └─lifecycle::deprecate_stop(...)
10. └─lifecycle:::deprecate_stop0(msg)
11. └─rlang::cnd_signal(...)
── Error ('test-indicators.R:236:5'): 'ITI-index' has been correctly implemented ──
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: `filter_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `filter()` instead.
ℹ See vignette('programming') for more help
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-indicators.R:236:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─benthos::iti(...)
5. │ └─benthos::iti_(.data, lazy(taxon), lazy(count), lazy(group))
6. │ └─d %>% select_(~GROUP, ~COUNT) %>% filter_(~!is.na(GROUP))
7. └─dplyr::filter_(., ~!is.na(GROUP))
8. └─dplyr:::lazy_defunct("filter")
9. └─lifecycle::deprecate_stop(...)
10. └─lifecycle:::deprecate_stop0(msg)
11. └─rlang::cnd_signal(...)
[ FAIL 2 | WARN 0 | SKIP 1 | PASS 139 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.3-9
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘benthos.Rmd’ using rmarkdown
Quitting from benthos.Rmd:664-667 [unnamed-chunk-50]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/lifecycle_error_deprecated>
Error:
! `filter_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `filter()` instead.
ℹ See vignette('programming') for more help
---
Backtrace:
▆
1. ├─d %>% ambi(taxon = TAXON, count = COUNT)
2. ├─benthos::ambi(., taxon = TAXON, count = COUNT)
3. │ └─benthos::ambi_(.data, lazy(taxon), lazy(count), lazy(group))
4. │ └─d %>% select_(~GROUP, ~COUNT) %>% filter_(~!is.na(GROUP))
5. └─dplyr::filter_(., ~!is.na(GROUP))
6. └─dplyr:::lazy_defunct("filter")
7. └─lifecycle::deprecate_stop(...)
8. └─lifecycle:::deprecate_stop0(msg)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'benthos.Rmd' failed with diagnostics:
`filter_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `filter()` instead.
ℹ See vignette('programming') for more help
--- failed re-building ‘benthos.Rmd’
SUMMARY: processing the following file failed:
‘benthos.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.3-9
Check: tests
Result: ERROR
Running ‘test-all.R’ [5s/12s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
> library(testthat)
> library(benthos)
> test_check("benthos")
Saving _problems/test-indicators-208.R
Saving _problems/test-indicators-243.R
[ FAIL 2 | WARN 0 | SKIP 1 | PASS 139 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-indicators.R:436:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-indicators.R:201:5'): 'AMBI-index' has been correctly implemented ──
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: `filter_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `filter()` instead.
ℹ See vignette('programming') for more help
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-indicators.R:201:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─benthos::ambi(...)
5. │ └─benthos::ambi_(.data, lazy(taxon), lazy(count), lazy(group))
6. │ └─d %>% select_(~GROUP, ~COUNT) %>% filter_(~!is.na(GROUP))
7. └─dplyr::filter_(., ~!is.na(GROUP))
8. └─dplyr:::lazy_defunct("filter")
9. └─lifecycle::deprecate_stop(...)
10. └─lifecycle:::deprecate_stop0(msg)
11. └─rlang::cnd_signal(...)
── Error ('test-indicators.R:236:5'): 'ITI-index' has been correctly implemented ──
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: `filter_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `filter()` instead.
ℹ See vignette('programming') for more help
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-indicators.R:236:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─benthos::iti(...)
5. │ └─benthos::iti_(.data, lazy(taxon), lazy(count), lazy(group))
6. │ └─d %>% select_(~GROUP, ~COUNT) %>% filter_(~!is.na(GROUP))
7. └─dplyr::filter_(., ~!is.na(GROUP))
8. └─dplyr:::lazy_defunct("filter")
9. └─lifecycle::deprecate_stop(...)
10. └─lifecycle:::deprecate_stop0(msg)
11. └─rlang::cnd_signal(...)
[ FAIL 2 | WARN 0 | SKIP 1 | PASS 139 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc