| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-20 12:06 -0400 (Sat, 20 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4814 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4603 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4547 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4553 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 2242/2333 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| tRNA 1.27.1 (landing page) Felix GM Ernst
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the tRNA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tRNA.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: tRNA |
| Version: 1.27.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data tRNA |
| StartedAt: 2025-09-19 17:58:31 -0400 (Fri, 19 Sep 2025) |
| EndedAt: 2025-09-19 17:58:40 -0400 (Fri, 19 Sep 2025) |
| EllapsedTime: 9.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data tRNA
###
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* checking for file ‘tRNA/DESCRIPTION’ ... OK
* preparing ‘tRNA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘tRNA.Rmd’ using rmarkdown
Quitting from tRNA.Rmd:72-76 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.Call2()`:
! function '_new_DataFrame' not provided by package 'S4Vectors'
---
Backtrace:
▆
1. ├─tRNA::gettRNAstructureGRanges(gr, structure = "anticodonLoop")
2. └─tRNA::gettRNAstructureGRanges(gr, structure = "anticodonLoop")
3. ├─tRNA::gettRNABasePairing(x)
4. └─tRNA::gettRNABasePairing(x)
5. ├─Structstrings::getBasePairing(strseq, return.sequence = with.nucleotides)
6. └─Structstrings::getBasePairing(strseq, return.sequence = with.nucleotides)
7. └─Structstrings (local) .local(x, compress)
8. └─methods::as(x, "CompressedSplitDotBracketDataFrameList")
9. └─Structstrings (local) asMethod(object)
10. └─Structstrings:::.get_pairing(from)
11. └─S4Vectors::.Call2(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'tRNA.Rmd' failed with diagnostics:
function '_new_DataFrame' not provided by package 'S4Vectors'
--- failed re-building ‘tRNA.Rmd’
SUMMARY: processing the following file failed:
‘tRNA.Rmd’
Error: Vignette re-building failed.
Execution halted