• using R Under development (unstable) (2025-12-23 r89222 ucrt)
• using platform: x86_64-w64-mingw32
• R was compiled by     gcc.exe (GCC) 14.3.0     GNU Fortran (GCC) 14.3.0
• running under: Windows Server 2022 x64 (build 20348)
• using session charset: UTF-8
• checking for file 'BioTIMEr/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'BioTIMEr' version '0.3.0'
• 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 hidden files and directories ... OK
• checking for portable file names ... OK
• checking whether package 'BioTIMEr' can be installed ... OK See the install log for details.
• 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 ... [3s] OK
• checking whether the package can be loaded with stated dependencies ... [3s] OK
• checking whether the package can be unloaded cleanly ... [3s] OK
• checking whether the namespace can be loaded with stated dependencies ... [3s] OK
• checking whether the namespace can be unloaded cleanly ... [3s] OK
• checking loading without being on the library search path ... [3s] 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 ... [7s] 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 ... [5s] 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
• checking for unstated dependencies in 'tests' ... OK
• checking tests ... [22s] 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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [34s] 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
• checking PDF version of manual ... [20s] OK
• checking HTML version of manual ... [5s] OK
• DONE

Status: 3 ERRORs