Multiple platform build/check report for BioC 3.22 - BUILD results for Structstrings on nebbiolo2

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"	4816
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4605
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4549
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4560
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 Structstrings on nebbiolo2

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

Version: 1.25.1

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 Structstrings

StartedAt: 2025-09-22 20:18:16 -0400 (Mon, 22 Sep 2025)

EndedAt: 2025-09-22 20:18:37 -0400 (Mon, 22 Sep 2025)

EllapsedTime: 21.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 Structstrings
###
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* checking for file ‘Structstrings/DESCRIPTION’ ... OK
* preparing ‘Structstrings’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Structstrings.Rmd’ using rmarkdown

Quitting from Structstrings.Rmd:105-109 [base_pairing]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `if (!is.null(value) && (nrx != lv)) ...`:
! missing value where TRUE/FALSE needed
---
Backtrace:
     ▆
  1. ├─Structstrings::getBasePairing(dbs)
  2. └─Structstrings::getBasePairing(dbs)
  3.   └─Structstrings (local) .local(x, compress)
  4.     └─methods::as(x, "CompressedSplitDotBracketDataFrameList")
  5.       └─Structstrings (local) asMethod(object)
  6.         └─Structstrings:::.get_pairing(from)
  7.           └─Structstrings:::.convert_char_type_to_character(ans@unlistData)
  8.             ├─methods (local) `$<-`(`*tmp*`, "character", value = `<chr>`)
  9.             └─S4Vectors (local) `$<-`(`*tmp*`, "character", value = `<chr>`)
 10.               ├─methods (local) `[[<-`(`*tmp*`, name, value = `<chr>`)
 11.               └─S4Vectors (local) `[[<-`(`*tmp*`, name, value = `<chr>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Structstrings.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘Structstrings.Rmd’

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

Error: Vignette re-building failed.
Execution halted