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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4750
palomino8	Windows Server 2022 Datacenter	x64	4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six"	4525
lconway	macOS 12.7.1 Monterey	x86_64	4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"	4550
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"	4491
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4455
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 LinTInd on lconway

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

Version: 1.13.0

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

StartedAt: 2025-05-21 17:15:06 -0400 (Wed, 21 May 2025)

EndedAt: 2025-05-21 17:15:35 -0400 (Wed, 21 May 2025)

EllapsedTime: 28.5 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 LinTInd
###
##############################################################################
##############################################################################


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

Quitting from tutorial.Rmd:70-73 [find indels and generate array-form strings]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `checkForRemoteErrors()`:
! one node produced an error: error in evaluating the argument 'subject' in selecting a method for function 'matchPattern': 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. └─LinTInd::FindIndel(...)
 2.   └─parallel::parLapply(cl, data$Read.Seq, find_barcode)
 3.     ├─base::do.call(...)
 4.     └─parallel::clusterApply(...)
 5.       └─parallel:::staticClusterApply(cl, fun, length(x), argfun)
 6.         └─parallel:::checkForRemoteErrors(val)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
one node produced an error: error in evaluating the argument 'subject' in selecting a method for function 'matchPattern': 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 ‘tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted