Last updated on 2026-04-09 08:50:22 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.3.5 | 62.91 | 417.81 | 480.72 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 2.3.5 | 43.78 | 337.66 | 381.44 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.3.5 | 109.00 | 730.83 | 839.83 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 2.3.5 | 131.00 | 740.92 | 871.92 | OK | |
| r-devel-macos-arm64 | 2.3.5 | 17.00 | 113.00 | 130.00 | OK | |
| r-devel-windows-x86_64 | 2.3.5 | 80.00 | 406.00 | 486.00 | ERROR | |
| r-patched-linux-x86_64 | 2.3.5 | 57.58 | 411.40 | 468.98 | OK | |
| r-release-linux-x86_64 | 2.3.5 | 53.64 | 400.88 | 454.52 | OK | |
| r-release-macos-arm64 | 2.3.5 | 16.00 | 173.00 | 189.00 | OK | |
| r-release-macos-x86_64 | 2.3.5 | 48.00 | 359.00 | 407.00 | OK | |
| r-release-windows-x86_64 | 2.3.5 | 63.00 | 411.00 | 474.00 | OK | |
| r-oldrel-macos-arm64 | 2.3.5 | 15.00 | 177.00 | 192.00 | NOTE | |
| r-oldrel-macos-x86_64 | 2.3.5 | 47.00 | 429.00 | 476.00 | NOTE | |
| r-oldrel-windows-x86_64 | 2.3.5 | 83.00 | 564.00 | 647.00 | NOTE |
Version: 2.3.5
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘myTAI.Rmd’ using rmarkdown
--- finished re-building ‘myTAI.Rmd’
--- re-building ‘other-strata.Rmd’ using rmarkdown
--- finished re-building ‘other-strata.Rmd’
--- re-building ‘phylo-expression-object.Rmd’ using rmarkdown
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 0%
|
|======================================================================| 100%
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
--- finished re-building ‘phylo-expression-object.Rmd’
--- re-building ‘phylostratigraphy.Rmd’ using rmarkdown
--- finished re-building ‘phylostratigraphy.Rmd’
--- re-building ‘tai-breaker.Rmd’ using rmarkdown
--- finished re-building ‘tai-breaker.Rmd’
--- re-building ‘tai-gallery.Rmd’ using rmarkdown
--- finished re-building ‘tai-gallery.Rmd’
--- re-building ‘tai-stats.Rmd’ using rmarkdown
--- finished re-building ‘tai-stats.Rmd’
--- re-building ‘tai-transform.Rmd’ using rmarkdown
--- finished re-building ‘tai-transform.Rmd’
--- re-building ‘taxonomy.Rmd’ using rmarkdown
Quitting from taxonomy.Rmd:307-311 [unnamed-chunk-13]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [www.itis.gov]:
Operation too slow. Less than 1 bytes/sec transferred the last 600 seconds
---
Backtrace:
▆
1. ├─global taxonomy(organism = "Arabidopsis", db = "itis", output = "children")
2. │ ├─base::as.data.frame(taxize::children(organism, db = db)[[1]])
3. │ ├─taxize::children(organism, db = db)
4. │ └─taxize:::children.default(organism, db = db)
5. │ ├─stats::setNames(children(id, ...), sci_id)
6. │ ├─taxize::children(id, ...)
7. │ └─taxize:::children.tsn(id, ...)
8. │ └─base::lapply(sci_id, fun)
9. │ └─taxize (local) FUN(X[[i]], ...)
10. │ └─ritis::hierarchy_down(y, ...)
11. │ └─ritis:::itis_GET(...)
12. │ └─cli$get(query = args)
13. │ └─private$make_request(rr, mock)
14. │ └─crul:::crul_fetch(opts)
15. │ └─curl::curl_fetch_memory(x$url$url, handle = x$url$handle)
16. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'taxonomy.Rmd' failed with diagnostics:
Timeout was reached [www.itis.gov]:
Operation too slow. Less than 1 bytes/sec transferred the last 600 seconds
--- failed re-building ‘taxonomy.Rmd’
SUMMARY: processing the following file failed:
‘taxonomy.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 2.3.5
Check: examples
Result: ERROR
Running examples in 'myTAI-Ex.R' failed
The error most likely occurred in:
> ### Name: diagnose_test_robustness
> ### Title: Diagnose Test Robustness
> ### Aliases: diagnose_test_robustness
>
> ### ** Examples
>
> # Diagnose flatline test robustness
> p <- example_phyex_set
> robustness <- diagnose_test_robustness(stat_flatline_test,
+ p |> select_genes(p@gene_ids[1:30]),
+ sample_sizes=c(10,20),
+ plot_result=FALSE,
+ num_reps=2)
Computing: [========================================] 100% (done)
Warning in dgamma(c(0.018427722665775, 0.018427722665775, 0.018427722665775, :
NaNs produced
Error in `purrr::map()`:
ℹ In index: 1.
Caused by error in `if (ks_result$p.value > max_p_fit_v) ...`:
! missing value where TRUE/FALSE needed
Backtrace:
▆
1. ├─myTAI::diagnose_test_robustness(...)
2. │ ├─purrr::map_dbl(...)
3. │ │ └─purrr:::map_("double", .x, .f, ..., .progress = .progress)
4. │ │ └─purrr:::vctrs_vec_compat(.x, .purrr_user_env)
5. │ └─purrr::map(rep(sample_sizes, each = num_reps), f)
6. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
7. │ ├─purrr:::with_indexed_errors(...)
8. │ │ └─base::withCallingHandlers(...)
9. │ ├─purrr:::call_with_cleanup(...)
10. │ └─myTAI (local) .f(.x[[i]], ...)
11. │ └─myTAI (local) test(phyex_set, custom_null_txis = null_txis, ..., plot_result = FALSE)
12. │ └─myTAI:::stat_generic_conservation_test(...)
13. │ └─fitting_dist@fitting_function(null_sample)
14. └─base::.handleSimpleError(...)
15. └─purrr (local) h(simpleError(msg, call))
16. └─cli::cli_abort(...)
17. └─rlang::abort(...)
Execution halted
Flavor: r-devel-windows-x86_64
Version: 2.3.5
Check: installed package size
Result: NOTE
installed size is 11.0Mb
sub-directories of 1Mb or more:
doc 6.1Mb
libs 3.4Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64