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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:single.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings single_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/single.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘single/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘single’ version ‘1.2.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘single’ 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... 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 ... NOTE
pileup_by_QUAL: no visible binding for global variable ‘count.y’
pileup_by_QUAL: no visible binding for global variable ‘count.x’
pileup_by_QUAL: no visible binding for global variable ‘nucleotide’
pileup_by_QUAL: no visible binding for global variable ‘QUAL’
single_consensus_byBarcode: no visible binding for global variable
  ‘readID’
single_consensus_byBarcode: no visible binding for global variable
  ‘bcID’
Undefined global functions or variables:
  QUAL bcID count.x count.y nucleotide readID
* checking Rd files ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘single-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: list_mismatches
> ### Title: Lists mismatches between two DNAstrings
> ### Aliases: list_mismatches
> 
> ### ** Examples
> 
> ref = Biostrings::DNAString("AAAA")
> seq = Biostrings::DNAString("AGAT")
> list_mismatches(ref,seq)
Error in `stringr::str_sub()`:
! `string` must be a vector, not a <DNAString> object.
Backtrace:
    ▆
 1. ├─single::list_mismatches(ref, seq)
 2. │ └─base::sapply(...)
 3. │   └─base::lapply(X = X, FUN = FUN, ...)
 4. │     └─single (local) FUN(X[[i]], ...)
 5. │       └─stringr::str_sub(ref, x)
 6. │         └─vctrs::vec_size_common(string = string, start = start, end = end)
 7. └─vctrs:::stop_scalar_type(`<fn>`(`<DNAStrng>`), "string", `<env>`)
 8.   └─vctrs:::stop_vctrs(...)
 9.     └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/single.Rcheck/00check.log’
for details.