Last updated on 2026-01-29 10:51:46 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.3.4 | 61.14 | 435.26 | 496.40 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 2.3.4 | 41.40 | 390.74 | 432.14 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.3.4 | 124.00 | 718.51 | 842.51 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 2.3.4 | 108.00 | 681.12 | 789.12 | OK | |
| r-devel-windows-x86_64 | 2.3.4 | 69.00 | 441.00 | 510.00 | OK | |
| r-patched-linux-x86_64 | 2.3.4 | 60.76 | 408.45 | 469.21 | ERROR | |
| r-release-linux-x86_64 | 2.3.4 | 58.68 | 410.81 | 469.49 | OK | |
| r-release-macos-arm64 | 2.3.4 | OK | ||||
| r-release-macos-x86_64 | 2.3.4 | 46.00 | 504.00 | 550.00 | OK | |
| r-release-windows-x86_64 | 2.3.4 | 70.00 | 464.00 | 534.00 | OK | |
| r-oldrel-macos-arm64 | 2.3.4 | NOTE | ||||
| r-oldrel-macos-x86_64 | 2.3.4 | 47.00 | 496.00 | 543.00 | NOTE | |
| r-oldrel-windows-x86_64 | 2.3.4 | 86.00 | 600.00 | 686.00 | NOTE |
Version: 2.3.4
Check: relative paths in package URLs
Result: NOTE
Found the following (possibly) invalid URLs:
URL: ../reference/index.html
From: inst/doc/myTAI.html
URL: ../reference/index.html
From: inst/doc/tai-gallery.html
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 2.3.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘myTAI.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘myTAI.Rmd’
--- re-building ‘other-strata.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- 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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘phylo-expression-object.Rmd’
--- re-building ‘phylostratigraphy.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘phylostratigraphy.Rmd’
--- re-building ‘tai-breaker.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘tai-breaker.Rmd’
--- re-building ‘tai-gallery.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘tai-gallery.Rmd’
--- re-building ‘tai-stats.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘tai-stats.Rmd’
--- re-building ‘tai-transform.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘tai-transform.Rmd’
--- re-building ‘taxonomy.Rmd’ using rmarkdown
Quitting from taxonomy.Rmd:225-229 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `dplyr::filter()`:
ℹ In argument: `name == organism`.
Caused by error:
! `..1` must be of size 1, not size 0.
---
Backtrace:
▆
1. ├─global taxonomy(organism = "Arabidopsis thaliana", db = "ncbi", output = "taxid")
2. │ ├─dplyr::select(...)
3. │ ├─dplyr::filter(tax_hierarchy, name == organism)
4. │ └─dplyr:::filter.data.frame(tax_hierarchy, name == organism)
5. │ └─dplyr:::filter_rows(.data, dots, by)
6. │ └─dplyr:::filter_eval(...)
7. │ ├─base::withCallingHandlers(...)
8. │ └─mask$eval_all_filter(dots, env_filter)
9. │ └─dplyr (local) eval()
10. └─dplyr:::dplyr_internal_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'taxonomy.Rmd' failed with diagnostics:
ℹ In argument: `name == organism`.
Caused by error:
! `..1` must be of size 1, not size 0.
--- failed re-building ‘taxonomy.Rmd’
SUMMARY: processing the following file failed:
‘taxonomy.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64
Version: 2.3.4
Check: installed package size
Result: NOTE
installed size is 11.1Mb
sub-directories of 1Mb or more:
doc 6.1Mb
libs 3.5Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64