* using log directory 'd:/RCompile/CRANincoming/R-devel/BOLDconnectR.Rcheck'
* using R Under development (unstable) (2026-07-22 r90289 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.3.0
    GNU Fortran (GCC) 14.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* current time: 2026-07-23 14:31:06 UTC
* checking for file 'BOLDconnectR/DESCRIPTION' ... OK
* this is package 'BOLDconnectR' version '1.0.1'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [11s] OK
* 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 'BOLDconnectR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [13s] OK
* checking whether the package can be loaded with stated dependencies ... [12s] OK
* checking whether the package can be unloaded cleanly ... [12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s] OK
* checking whether the namespace can be unloaded cleanly ... [13s] OK
* checking loading without being on the library search path ... [13s] 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 ... [59s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [19s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [30s] ERROR
Error(s) in re-building vignettes:
--- re-building 'boldconnectr_workflow.Rmd' using rmarkdown

Quitting from boldconnectr_workflow.Rmd:121-132 [align-data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.local()`:
! unused argument (validRN = FALSE)
---
Backtrace:
    ▆
 1. ├─BOLDconnectR::bold.analyze.align(...)
 2. │ └─msa_dna_string_obj %>% data.frame(.) %>% ...
 3. ├─dplyr::rename(., aligned_seq = ".")
 4. └─base::data.frame(.)
 5.   ├─base::as.data.frame(x[[i]], optional = TRUE, validRN = FALSE)
 6.   └─S4Vectors::as.data.frame.Vector(x[[i]], optional = TRUE, validRN = FALSE)
 7.     ├─BiocGenerics::as.data.frame(...)
 8.     └─Biostrings::as.data.frame(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'boldconnectr_workflow.Rmd' failed with diagnostics:
unused argument (validRN = FALSE)
--- failed re-building 'boldconnectr_workflow.Rmd'

SUMMARY: processing the following file failed:
  'boldconnectr_workflow.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [28s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR