Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMNOPQRS[T]UVWXYZ

This page was generated on 2025-09-20 12:05 -0400 (Sat, 20 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (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 2242/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tRNA 1.27.1  (landing page)
Felix GM Ernst
Snapshot Date: 2025-09-19 13:45 -0400 (Fri, 19 Sep 2025)
git_url: https://git.bioconductor.org/packages/tRNA
git_branch: devel
git_last_commit: df69575
git_last_commit_date: 2025-07-28 18:50:17 -0400 (Mon, 28 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


BUILD results for tRNA on lconway

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.

raw results


Summary

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 18:56:23 -0400 (Fri, 19 Sep 2025)
EndedAt: 2025-09-19 18:56:49 -0400 (Fri, 19 Sep 2025)
EllapsedTime: 26.2 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data tRNA
###
##############################################################################
##############################################################################


* 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