Last updated on 2026-02-15 07:51:07 CET.
| Package | ERROR | OK |
|---|---|---|
| benthos | 2 | 12 |
| confidence | 14 | |
| litteR | 14 | |
| spcosa | 14 |
Current CRAN status: ERROR: 2, OK: 12
Version: 1.3-9
Check: examples
Result: ERROR
Running examples in ‘benthos-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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
Flavor: r-patched-linux-x86_64
Version: 1.3-9
Check: tests
Result: ERROR
Running ‘test-all.R’ [3s/3s]
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-patched-linux-x86_64
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
Flavor: r-patched-linux-x86_64
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
Flavor: r-oldrel-windows-x86_64
Version: 1.3-9
Check: tests
Result: ERROR
Running 'test-all.R' [4s]
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-oldrel-windows-x86_64
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
Flavor: r-oldrel-windows-x86_64
Current CRAN status: OK: 14
Current CRAN status: OK: 14
Current CRAN status: OK: 14
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