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This page was generated on 2025-08-01 12:10 -0400 (Fri, 01 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4534
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4517
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 2303/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
XNAString 1.17.1  (landing page)
Marianna Plucinska
Snapshot Date: 2025-07-31 13:25 -0400 (Thu, 31 Jul 2025)
git_url: https://git.bioconductor.org/packages/XNAString
git_branch: devel
git_last_commit: b20a70b
git_last_commit_date: 2025-07-07 12:39:25 -0400 (Mon, 07 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  ERROR    ERROR  skipped
palomino8Windows Server 2022 Datacenter / x64  ERROR    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  ERROR    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  ERROR    ERROR  skipped


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: 1.17.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data XNAString
StartedAt: 2025-07-31 19:09:30 -0400 (Thu, 31 Jul 2025)
EndedAt: 2025-07-31 19:12:03 -0400 (Thu, 31 Jul 2025)
EllapsedTime: 153.3 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 XNAString
###
##############################################################################
##############################################################################


* 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