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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:single.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings single_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/single.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘single/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘single’ version ‘1.10.0’
* 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 ... NOTE
License stub is invalid DCF.
* 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 ... 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 .load_package_gracefully("pwalign", "starting with BioC 3.19, ",  : 
  Could not load package pwalign. Is it installed?

  Note that starting with BioC 3.19, calling compareStrings() requires
  the pwalign package. Please install it with:

    BiocManager::install("pwalign")
Calls: list_mismatches ... <Anonymous> -> .call_fun_in_pwalign -> .load_package_gracefully
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘Analysis_FullCode.Rmd’ using rmarkdown
--- finished re-building ‘Analysis_FullCode.Rmd’

--- re-building ‘single.Rmd’ using rmarkdown

Quitting from single.Rmd:99-110 [evaluate model]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.load_package_gracefully()`:
! Could not load package pwalign. Is it installed?

  Note that starting with BioC 3.19, calling compareStrings() requires
  the pwalign package. Please install it with:

    BiocManager::install("pwalign")
---
Backtrace:
    ▆
 1. └─single::single_evaluate(...)
 2.   └─Biostrings::compareStrings(ref_seq, reads_aligned[i])
 3.     └─Biostrings:::.call_fun_in_pwalign("compareStrings", ...)
 4.       └─Biostrings:::.load_package_gracefully(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'single.Rmd' failed with diagnostics:
Could not load package pwalign. Is it installed?

  Note that starting with BioC 3.19, calling compareStrings() requires
  the pwalign package. Please install it with:

    BiocManager::install("pwalign")
--- failed re-building ‘single.Rmd’

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

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/single.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL single
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘single’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'single' is deprecated and will be removed from Bioconductor
  version 3.21
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'single' is deprecated and will be removed from Bioconductor
  version 3.21
** testing if installed package keeps a record of temporary installation path
* DONE (single)