CRAN Package Check Results for Package BioTIMEr

Last updated on 2025-12-28 01:48:34 CET.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	0.3.0	12.65	255.72	268.37	OK
r-devel-linux-x86_64-debian-gcc	0.3.0	7.24	173.65	180.89	OK
r-devel-linux-x86_64-fedora-clang	0.3.0	22.00	387.61	409.61	OK
r-devel-linux-x86_64-fedora-gcc	0.3.0	22.00	607.83	629.83	OK
r-devel-windows-x86_64	0.3.0	14.00	158.00	172.00	ERROR
r-patched-linux-x86_64	0.3.0	13.13	209.11	222.24	OK
r-release-linux-x86_64	0.3.0	11.04	210.14	221.18	OK
r-release-macos-arm64	0.3.0	3.00	35.00	38.00	OK
r-release-macos-x86_64	0.3.0	10.00	287.00	297.00	OK
r-release-windows-x86_64	0.3.0	13.00	203.00	216.00	OK
r-oldrel-macos-arm64	0.3.0	3.00	70.00	73.00	OK
r-oldrel-macos-x86_64	0.3.0	10.00	279.00	289.00	OK
r-oldrel-windows-x86_64	0.3.0	19.00	254.00	273.00	OK

Check Details

Version: 0.3.0
Check: examples
Result: ERROR Running examples in 'BioTIMEr-Ex.R' failed The error most likely occurred in: > ### Name: getAlphaMetrics > ### Title: Alpha diversity metrics > ### Aliases: getAlphaMetrics > > ### ** Examples > > # Mean and sd values of the metrics for several resamplings > gridding(BTsubset_meta, BTsubset_data) |> + resampling(measure = "BIOMASS", resamps = 2) |> + getAlphaMetrics(measure = "BIOMASS") |> + dplyr::summarise( + dplyr::across( + .cols = !resamp, + .fns = c(mean = mean, sd = sd)), + .by = c(assemblageID, YEAR)) |> + tidyr::pivot_longer( + col = dplyr::contains("_"), + names_to = c("metric", "stat"), + names_sep = "_", + names_transform = as.factor) |> + tidyr::pivot_wider(names_from = stat) |> + head(10) OK: all SL studies have 1 grid cell Warning: NA values found and removed. Only a subset of `x` is used. Error in `[.data.table`(x, j = `:=`(minsamp, data.table::uniqueN(SAMPLE_DESC)), : attempt access index 20/20 in VECTOR_ELT Calls: head ... resampling.default -> resampling_internal -> [ -> [.data.table Execution halted Flavor: r-devel-windows-x86_64

Version: 0.3.0
Check: tests
Result: ERROR Running 'testthat.R' [21s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > test_check("BioTIMEr") Loading required package: BioTIMEr Starting 2 test processes. > test-gridding.R: OK: all SL studies have 1 grid cell > test-gridding.R: OK: all SL studies have 1 grid cell > test-resampling.R: OK: all SL studies have 1 grid cell > test-gridding.R: OK: all SL studies have 1 grid cell > test-resampling.R: OK: all SL studies have 1 grid cell > test-gridding.R: OK: all SL studies have 1 grid cell > test-resampling.R: OK: all SL studies have 1 grid cell > test-gridding.R: OK: all SL studies have 1 grid cell > test-resampling.R: OK: all SL studies have 1 grid cell Saving _problems/test-resampling-10.R Saving _problems/test-resampling-11.R Saving _problems/test-resampling-37.R Saving _problems/test-resampling-46.R Saving _problems/test-resampling-60.R Saving _problems/test-resampling-85.R > test-gridding.R: OK: all SL studies have 1 grid cell > test-resampling_abundance.R: OK: all SL studies have 1 grid cell > test-resampling_abundance_biomass.R: OK: all SL studies have 1 grid cell > test-resampling_abundance_biomass_conservative.R: OK: all SL studies have 1 grid cell > test-resampling_biomass.R: OK: all SL studies have 1 grid cell [ FAIL 6 | WARN 5 | SKIP 20 | PASS 65 ] ══ Skipped tests (20) ══════════════════════════════════════════════════════════ • On CRAN (20): 'test-metrics.R:59:3', 'test-metrics.R:82:3', 'test-metrics.R:95:3', 'test-metrics.R:107:3', 'test-metrics.R:120:3', 'test-workflow_alpha.R:3:3', 'test-workflow_beta.R:3:3', 'test-slopes.R:3:3', 'test-plots.R:4:3', 'test-scales.R:35:3', 'test-resampling.R:101:3', 'test-gridding.R:75:3', 'test-gridding.R:82:3', 'test-gridding.R:89:3', 'test-resampling_abundance.R:11:3', 'test-resampling_abundance_biomass.R:11:3', 'test-resampling_abundance_biomass_conservative.R:11:3', 'test-resampling_core.R:91:3', 'test-resampling_core.R:164:3', 'test-resampling_biomass.R:11:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-resampling.R:10:3'): resampling returns an object of same class as meta ── Expected `resdf <- resampling(test_df, measure = "BIOMASS")` not to throw any errors. Actually got a <simpleError> with message: attempt access index 20/20 in VECTOR_ELT ── Error ('test-resampling.R:11:3'): resampling returns an object of same class as meta ── Error in `eval(code, test_env)`: object 'resdf' not found Backtrace: ▆ 1. └─testthat::expect_s3_class(resdf, "data.frame") at test-resampling.R:11:3 2. └─testthat::quasi_label(enquo(object)) 3. └─rlang::eval_bare(expr, quo_get_env(quo)) ── Failure ('test-resampling.R:34:3'): gridded object passed to resampling is not changed by reference ── Expected `{ ... }` not to throw any errors. Actually got a <simpleError> with message: attempt access index 20/20 in VECTOR_ELT ── Failure ('test-resampling.R:40:3'): gridded object passed to resampling is not changed by reference ── Expected `{ ... }` not to throw any errors. Actually got a <simpleError> with message: attempt access index 20/20 in VECTOR_ELT ── Failure ('test-resampling.R:53:3'): gridded object passed to resampling is not changed by reference ── Expected `{ ... }` not to throw any errors. Actually got a <simpleError> with message: attempt access index 20/20 in VECTOR_ELT ── Error ('test-resampling.R:82:3'): resampling correctly excludes 1 year long studies ── Error in ``[.data.table`(x, j = `:=`(minsamp, data.table::uniqueN(SAMPLE_DESC)), keyby = c("assemblageID", "YEAR"))`: attempt access index 20/20 in VECTOR_ELT Backtrace: ▆ 1. ├─testthat::expect_warning(resampling(test_df_1y, "BIOMASS"), regexp = "Some 1-year-long studies were removed.") at test-resampling.R:82:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─BioTIMEr::resampling(test_df_1y, "BIOMASS") 8. └─BioTIMEr:::resampling.default(test_df_1y, "BIOMASS") 9. └─BioTIMEr:::resampling_internal(...) 10. ├─...[] 11. └─data.table:::`[.data.table`(...) [ FAIL 6 | WARN 5 | SKIP 20 | PASS 65 ] Deleting unused snapshots: 'plots/themebiotime-plot.svg', 'scales/color-continuous-cool-false.svg', 'scales/color-continuous-cool-true.svg', 'scales/color-continuous-gradient-false.svg', 'scales/color-continuous-gradient-true.svg', 'scales/color-continuous-realms-false.svg', 'scales/color-continuous-realms-true.svg', 'scales/color-continuous-warm-false.svg', 'scales/color-continuous-warm-true.svg', 'scales/color-cool-false-false.svg', 'scales/color-cool-false-true.svg', 'scales/color-cool-true-false.svg', 'scales/color-cool-true-true.svg', 'scales/color-gradient-false-false.svg', 'scales/color-gradient-false-true.svg', 'scales/color-gradient-true-false.svg', 'scales/color-gradient-true-true.svg', 'scales/color-realms-false-false.svg', …, 'scales/fill-warm-true-false.svg', and 'scales/fill-warm-true-true.svg' Error: ! Test failures. Execution halted Flavor: r-devel-windows-x86_64

Version: 0.3.0
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building 'introduction.qmd' using html processing file: introduction.qmd Error in `[.data.table`: ! attempt access index 20/20 in VECTOR_ELT Backtrace: ▆ 1. ├─BioTIMEr::resampling(...) 2. └─BioTIMEr:::resampling.default(...) 3. └─BioTIMEr:::resampling_internal(...) 4. ├─...[] 5. └─data.table:::`[.data.table`(...) Quitting from introduction.qmd:286-295 [resampling_ex1] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 20/20 in VECTOR_ELT --- Backtrace: ▆ 1. ├─BioTIMEr::resampling(...) 2. └─BioTIMEr:::resampling.default(...) 3. └─BioTIMEr:::resampling_internal(...) 4. ├─...[] 5. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Execution halted Error: processing vignette 'introduction.qmd' failed with diagnostics: ! Error running quarto CLI from R. Caused by error in `quarto_render()`: ✖ Error returned by quarto CLI. ----------------------------- processing file: introduction.qmd Error in `[.data.table`: ! attempt access index 20/20 in VECTOR_ELT Backtrace: ▆ 1. ├─BioTIMEr::resampling(...) 2. └─BioTIMEr:::resampling.default(...) 3. └─BioTIMEr:::resampling_internal(...) 4. ├─...[] 5. └─data.table:::`[.data.table`(...) Quitting from introduction.qmd:286-295 [resampling_ex1] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 20/20 in VECTOR_ELT --- Backtrace: ▆ 1. ├─BioTIMEr::resampling(...) 2. └─BioTIMEr:::resampling.default(...) 3. └─BioTIMEr:::resampling_internal(...) 4. ├─...[] 5. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Execution halted Caused by error: ! System command 'quarto.exe' failed --- failed re-building 'introduction.qmd' SUMMARY: processing the following file failed: 'introduction.qmd' Error: Vignette re-building failed. Execution halted Flavor: r-devel-windows-x86_64