* using log directory 'd:/Rcompile/CRANpkg/local/4.6/longreadvqs.Rcheck'
* using R Under development (unstable) (2025-10-10 r88914 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'longreadvqs/DESCRIPTION' ... OK
* this is package 'longreadvqs' version '0.1.3'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'longreadvqs' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [5s] OK
* checking whether the package can be loaded with stated dependencies ... [5s] OK
* checking whether the package can be unloaded cleanly ... [5s] OK
* checking whether the namespace can be loaded with stated dependencies ... [5s] OK
* checking whether the namespace can be unloaded cleanly ... [5s] OK
* checking loading without being on the library search path ... [5s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [19s] OK
* checking Rd files ... [1s] OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [6s] ERROR
Running examples in 'longreadvqs-Ex.R' failed
The error most likely occurred in:

> ### Name: AAcompare
> ### Title: Comparing viral quasispecies diversity metrics at amino acid
> ###   level
> ### Aliases: AAcompare
> 
> ### ** Examples
> 
> ## Locate input FASTA files-----------------------------------------------------------------------
> sample1filepath <- system.file("extdata", "s1.fasta", package = "longreadvqs")
> sample2filepath <- system.file("extdata", "s2.fasta", package = "longreadvqs")
> 
> ## Prepare data for viral quasispecies comparison between two samples-----------------------------
> set.seed(123)
> sample1 <- vqsassess(sample1filepath, pct = 5, samsize = 50, label = "sample1")
Error in (function (cond)  : 
  error in evaluating the argument 'pattern' in selecting a method for function 'nmismatch': pairwiseAlignment() has moved from Biostrings to the pwalign package, and is
  formally defunct in Biostrings >= 2.77.1. Please call
  pwalign::pairwiseAlignment() to get rid of this error.
Calls: vqsassess ... pairwiseAlignment -> .call_fun_in_pwalign -> .Defunct
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [34s] ERROR
Error(s) in re-building vignettes:
--- re-building 'longreadvqs-vignette.Rmd' using rmarkdown

Quitting from longreadvqs-vignette.Rmd:44-47 [cmd0]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! error in evaluating the argument 'pattern' in selecting a method for function 'nmismatch': pairwiseAlignment() has moved from Biostrings to the pwalign package, and is
  formally defunct in Biostrings >= 2.77.1. Please call
  pwalign::pairwiseAlignment() to get rid of this error.
---
Backtrace:
    ▆
 1. ├─longreadvqs::vqssub(sample1, pct = 10, label = "sample1")
 2. │ ├─Biostrings::nmismatch(pairwiseAlignment(hapre$seqs, hapre$seqs[1]))
 3. │ └─Biostrings::pairwiseAlignment(hapre$seqs, hapre$seqs[1])
 4. │   └─Biostrings:::.call_fun_in_pwalign("pairwiseAlignment", ...)
 5. │     └─base::.Defunct(msg = wmsg(msg))
 6. │       └─base::stop(...)
 7. └─base (local) `<fn>`(`<dfnctErr>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

SUMMARY: processing the following file failed:
  'longreadvqs-vignette.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [19s] OK
* checking HTML version of manual ... [2s] OK
* DONE
Status: 2 ERRORs