• using R version 4.5.2 Patched (2026-01-31 r89374)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.3.0-10) 14.3.0     GNU Fortran (Debian 14.3.0-10) 14.3.0
• running under: Debian GNU/Linux forky/sid
• 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 executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘benthos’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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/1s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the package can be unloaded cleanly ... [1s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
• checking loading without being on the library search path ... [1s/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 ... [8s/10s] OK
• checking Rd files ... [1s/1s] OK
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• 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 ... [0s/0s] 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 ... [1s/2s] 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
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [3s/4s] ERROR   Running ‘test-all.R’ [3s/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 ... [9s/14s] 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 ... [7s/10s] OK
• checking HTML version of manual ... [2s/4s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 3 ERRORs