Last updated on 2025-12-26 12:49:48 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 | 7.99 | 169.03 | 177.02 | 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 | 12.27 | 209.99 | 222.26 | 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 |
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