* using log directory ‘/data/gannet/ripley/R/packages/tests-ATLAS/brolgar.Rcheck’ * using R Under development (unstable) (2023-04-26 r84330) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc-13 (GCC) 13.1.0 GNU Fortran (GCC) 13.1.0 * running under: Fedora Linux 36 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘brolgar/DESCRIPTION’ ... OK * this is package ‘brolgar’ version ‘1.0.0’ * 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 ‘brolgar’ can be installed ... [13s/16s] 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking startup messages can be suppressed ... 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 ... [15s/18s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... 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 ... 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 ... [20s/22s] ERROR Running examples in ‘brolgar-Ex.R’ failed The error most likely occurred in: > ### Name: keys_near.data.frame > ### Title: Return keys nearest to a given statistics or summary. > ### Aliases: keys_near.data.frame > > ### ** Examples > > heights %>% + key_slope(height_cm ~ year) %>% + keys_near(key = country, + var = .slope_year) # A tibble: 6 × 5 country .slope_year stat stat_value stat_diff 1 Austria 0.0695 q_75 0.0690 0.000515 2 Burundi 0.321 max 0.321 0 3 Eritrea -0.102 min -0.102 0 4 Mali 0.0401 med 0.0403 0.000120 5 Spain 0.0404 med 0.0403 0.000120 6 Tajikistan 0.0199 q_25 0.0205 0.000632 > # Specify your own list of summaries > l_ranges <- list(min = b_min, + range_diff = b_range_diff, + max = b_max, + iqr = b_iqr) > > heights %>% + key_slope(formula = height_cm ~ year) %>% + keys_near(key = country, + var = .slope_year, + funs = l_ranges) Error in `mutate()`: ℹ In argument: `range_diff = (function (x, ...) ...`. Caused by error in `b_range()`: ! formal argument "na.rm" matched by multiple actual arguments Backtrace: ▆ 1. ├─heights %>% key_slope(formula = height_cm ~ year) %>% ... 2. ├─brolgar::keys_near(., key = country, var = .slope_year, funs = l_ranges) 3. ├─brolgar:::keys_near.data.frame(...) 4. │ └─... %>% ... 5. ├─dplyr::mutate(., stat = factor(x = stat, levels = names(funs))) 6. ├─dplyr::ungroup(.) 7. ├─dplyr::top_n(., -top_n, wt = stat_diff) 8. │ └─dplyr::filter(...) 9. ├─dplyr::group_by(., stat) 10. ├─dplyr::mutate(...) 11. ├─tidyr::pivot_longer(...) 12. ├─dplyr::select(...) 13. ├─dplyr::mutate_at(...) 14. │ ├─dplyr::mutate(.tbl, !!!funs) 15. │ └─dplyr:::mutate.data.frame(.tbl, !!!funs) 16. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by) 17. │ ├─base::withCallingHandlers(...) 18. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns) 19. │ └─mask$eval_all_mutate(quo) 20. │ └─dplyr (local) eval() 21. ├─brolgar (local) ``(.slope_year) 22. │ ├─base::diff(b_range(x, na.rm = TRUE, ...)) 23. │ └─brolgar::b_range(x, na.rm = TRUE, ...) 24. └─base::.handleSimpleError(...) 25. └─dplyr (local) h(simpleError(msg, call)) 26. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘spelling.R’ Running ‘testthat.R’ [28s/31s] [29s/33s] ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(brolgar) > > test_check("brolgar") Attaching package: 'dplyr' The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Attaching package: 'tsibble' The following objects are masked from 'package:base': intersect, setdiff, union [ FAIL 5 | WARN 3 | SKIP 5 | PASS 269 ] ══ Skipped tests ═══════════════════════════════════════════════════════════════ • On CRAN (5) ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-b-funs.R:21:3'): b functions return non NA value ─────────────── Error in `b_range(x, na.rm = TRUE, ...)`: formal argument "na.rm" matched by multiple actual arguments Backtrace: ▆ 1. ├─testthat::expect_equal(b_range_diff(vec), 4) at test-b-funs.R:21:2 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─brolgar::b_range_diff(vec) 5. ├─base::diff(b_range(x, na.rm = TRUE, ...)) 6. └─brolgar::b_range(x, na.rm = TRUE, ...) ── Failure ('test-features-brolgar.R:5:3'): feat_brolgar returns the right names ── names(wages_brolgar) (`actual`) not equal to c(...) (`expected`). actual | expected [1] "id" | "id" [1] - "min" [2] - "max" [3] - "median" [4] - "mean" [5] - "q25" [6] - "q75" [7] - "range1" [8] - "range2" [9] - "range_diff" [10] ... ... ... and 16 more ... ── Failure ('test-features-brolgar.R:37:3'): feat_brolgar returns the right dimensions ── dim(wages_brolgar) (`actual`) not equal to c(888, 26) (`expected`). `actual`: 888 1 `expected`: 888 26 ── Failure ('test-features-ranges.R:5:3'): feat_ranges returns the right names ── names(wages_ranges) (`actual`) not equal to c("id", "min", "max", "range_diff", "iqr") (`expected`). `actual`: "id" `expected`: "id" "min" "max" "range_diff" "iqr" ── Failure ('test-features-ranges.R:10:3'): feat_ranges returns the right dimensions ── dim(wages_ranges) (`actual`) not equal to c(888, 5) (`expected`). `actual`: 888 1 `expected`: 888 5 [ FAIL 5 | WARN 3 | SKIP 5 | PASS 269 ] Deleting unused snapshots: • facet-sample/gg-facet-sample-alt.svg • facet-sample/gg-facet-sample.svg • facet-strata/gg-facet-strata-along.svg • facet-strata/gg-facet-strata.svg Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [178s/215s] ERROR Error(s) in re-building vignettes: --- re-building ‘exploratory-modelling.Rmd’ using rmarkdown --- finished re-building ‘exploratory-modelling.Rmd’ --- re-building ‘finding-features.Rmd’ using rmarkdown --- finished re-building ‘finding-features.Rmd’ --- re-building ‘getting-started.Rmd’ using rmarkdown Quitting from lines 89-96 (getting-started.Rmd) Error: processing vignette 'getting-started.Rmd' failed with diagnostics: Problem while computing aesthetics. ℹ Error occurred in the 1st layer. Caused by error: ! object 'range_diff' not found --- failed re-building ‘getting-started.Rmd’ --- re-building ‘id-interesting-obs.Rmd’ using rmarkdown Quitting from lines 93-104 (id-interesting-obs.Rmd) Error: processing vignette 'id-interesting-obs.Rmd' failed with diagnostics: ℹ In argument: `range_diff = (function (x, ...) ...`. Caused by error in `b_range()`: ! formal argument "na.rm" matched by multiple actual arguments --- failed re-building ‘id-interesting-obs.Rmd’ --- re-building ‘longitudinal-data-structures.Rmd’ using rmarkdown --- finished re-building ‘longitudinal-data-structures.Rmd’ --- re-building ‘mixed-effects-models.Rmd’ using rmarkdown --- finished re-building ‘mixed-effects-models.Rmd’ --- re-building ‘visualisation-gallery.Rmd’ using rmarkdown --- finished re-building ‘visualisation-gallery.Rmd’ SUMMARY: processing the following files failed: ‘getting-started.Rmd’ ‘id-interesting-obs.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [8s/13s] OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 3 ERRORs See ‘/data/gannet/ripley/R/packages/tests-ATLAS/brolgar.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 6:38.66, 303.30 + 22.30