Last updated on 2026-04-29 00:53:37 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.3.5 | 67.83 | 434.96 | 502.79 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.3.5 | 39.60 | 357.45 | 397.05 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.3.5 | 99.00 | 742.94 | 841.94 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 2.3.5 | 131.00 | 778.53 | 909.53 | OK | |
| r-devel-windows-x86_64 | 2.3.5 | 80.00 | 443.00 | 523.00 | OK | |
| r-patched-linux-x86_64 | 2.3.5 | 53.05 | 415.55 | 468.60 | OK | |
| r-release-linux-x86_64 | 2.3.5 | 35.62 | 406.66 | 442.28 | OK | |
| r-release-macos-arm64 | 2.3.5 | 17.00 | 112.00 | 129.00 | OK | |
| r-release-macos-x86_64 | 2.3.5 | 49.00 | 1471.00 | 1520.00 | OK | |
| r-release-windows-x86_64 | 2.3.5 | 74.00 | 433.00 | 507.00 | OK | |
| r-oldrel-macos-arm64 | 2.3.5 | 16.00 | 173.00 | 189.00 | OK | |
| r-oldrel-macos-x86_64 | 2.3.5 | 48.00 | 359.00 | 407.00 | OK | |
| r-oldrel-windows-x86_64 | 2.3.5 | 94.00 | 646.00 | 740.00 | OK |
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. │ └─taxize:::process_children_ids(...)
6. │ └─eval(fxn)(input, ...)
7. │ └─ritis::terms(sci_com[i], what = searchtype, ...)
8. │ └─base::lapply(query, fun, wt = wt, raw = raw, ...)
9. │ └─ritis (local) FUN(X[[i]], ...)
10. │ └─ritis:::itis_GET(path, list(srchKey = x), wt, ...)
11. │ └─cli$get(query = args)
12. │ └─private$make_request(rr, mock)
13. │ └─crul:::crul_fetch(opts)
14. │ └─curl::curl_fetch_memory(x$url$url, handle = x$url$handle)
15. └─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-gcc