Multiple platform build/check report for BioC 3.22 - BUILD results for XNAString 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"	4902
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4692
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4638
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 XNAString on lconway

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

Version: 1.18.0

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

StartedAt: 2025-11-03 19:16:00 -0500 (Mon, 03 Nov 2025)

EndedAt: 2025-11-03 19:18:45 -0500 (Mon, 03 Nov 2025)

EllapsedTime: 164.8 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data XNAString
###
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* checking for file ‘XNAString/DESCRIPTION’ ... OK
* preparing ‘XNAString’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘XNAString_vignette.Rmd’ using rmarkdown

Quitting from XNAString_vignette.Rmd:648-658 [unnamed-chunk-34]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! error in evaluating the argument 'x' in selecting a method for function 'start': pattern() has moved from Biostrings to the pwalign package, and is formally
  defunct in Biostrings >= 2.77.1. Please call pwalign::pattern() to get rid of
  this error.
---
Backtrace:
    ▆
 1. ├─XNAString::XNAStringToHelm(obj)
 2. │ ├─base::paste(...)
 3. │ └─XNAString::siRNA_HELM(xnastring_obj)
 4. │   ├─Biostrings::start(Biostrings::pattern(pa))
 5. │   └─Biostrings::pattern(pa)
 6. │     └─Biostrings:::.call_fun_in_pwalign("pattern", ...)
 7. │       └─base::.Defunct(msg = wmsg(msg))
 8. │         └─base::stop(...)
 9. └─base (local) `<fn>`(`<dfnctErr>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'XNAString_vignette.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'start': pattern() has moved from Biostrings to the pwalign package, and is formally
  defunct in Biostrings >= 2.77.1. Please call pwalign::pattern() to get rid of
  this error.
--- failed re-building ‘XNAString_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted