Multiple platform build/check report for BioC 3.22 - BUILD results for tRNAscanImport on lconway

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*

BUILD results for tRNAscanImport on lconway

To the developers/maintainers of the tRNAscanImport package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tRNAscanImport.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: tRNAscanImport

Version: 1.29.1

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data tRNAscanImport

StartedAt: 2025-09-19 18:56:30 -0400 (Fri, 19 Sep 2025)

EndedAt: 2025-09-19 18:57:36 -0400 (Fri, 19 Sep 2025)

EllapsedTime: 65.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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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 tRNAscanImport
###
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* checking for file ‘tRNAscanImport/DESCRIPTION’ ... OK
* preparing ‘tRNAscanImport’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘tRNAscanImport.Rmd’ using rmarkdown

Quitting from tRNAscanImport.Rmd:102-120 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.Call2()`:
! function '_new_DataFrame' not provided by package 'S4Vectors'
---
Backtrace:
     ▆
  1. ├─tRNA::gettRNAFeaturePlots(grl)
  2. └─tRNA::gettRNAFeaturePlots(grl)
  3.   └─base::lapply(...)
  4.     └─tRNA (local) FUN(X[[i]], ...)
  5.       ├─tRNA::gettRNASummary(x[[i]])
  6.       └─tRNA::gettRNASummary(x[[i]])
  7.         ├─Structstrings::getBasePairing(x$tRNA_str)
  8.         └─Structstrings::getBasePairing(x$tRNA_str)
  9.           └─Structstrings (local) .local(x, compress)
 10.             └─methods::as(x, "CompressedSplitDotBracketDataFrameList")
 11.               └─Structstrings (local) asMethod(object)
 12.                 └─Structstrings:::.get_pairing(from)
 13.                   └─S4Vectors::.Call2(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'tRNAscanImport.Rmd' failed with diagnostics:
function '_new_DataFrame' not provided by package 'S4Vectors'
--- failed re-building ‘tRNAscanImport.Rmd’

SUMMARY: processing the following file failed:
  ‘tRNAscanImport.Rmd’

Error: Vignette re-building failed.
Execution halted