* using log directory 'd:/Rcompile/CRANpkg/local/4.4/benthos.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'benthos/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'benthos' version '1.3-9'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'benthos' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s] OK
* checking whether the package can be unloaded cleanly ... [1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s] OK
* checking whether the namespace can be unloaded cleanly ... [2s] OK
* checking loading without being on the library search path ... [1s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [6s] OK
* checking Rd files ... [1s] OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... [1s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [2s] 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
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [5s] 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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [11s] 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

* checking PDF version of manual ... [24s] OK
* checking HTML version of manual ... [6s] OK
* DONE
Status: 3 ERRORs