* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/CleanBSequences.Rcheck’
* using R Under development (unstable) (2025-02-22 r87796)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘CleanBSequences/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CleanBSequences’ version ‘2.3.0’
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CleanBSequences’ can be installed ... [14s/14s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/CleanBSequences-00install.html' for details.
* checking package 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 ... 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 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/19s] 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 examples ... ERROR
Running examples in ‘CleanBSequences-Ex.R’ failed
The error most likely occurred in:

> ### Name: DNAStringSetOPR
> ### Title: Curing of biological sequences
> ### Aliases: DNAStringSetOPR
> 
> ### ** Examples
> 
> SEQs = readDNAStringSet(system.file("sequences","SeqInputOPR.fasta", package = "CleanBSequences"))
> PrimerR= DNAString ("GACTGCGTACCATGC")
> DNAStringSetOPR (SEQs,PrimerR)
DNAStringSet object of length 2:
    width seq                                               names               
[1]   116 GCCTCGCCTCCCTCTTTGATCAG...CCTTTGCAATCTTCACAAGGTGG 170522-033_K03_11...
[2]   113 GTCTACTCGATCGTGATCCGGTA...CCTTTGCAATCTTCACAAGGTGG 170522-033_C05_15...
Local PairwiseAlignmentsSingleSubject (1 of 2)
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'table' in selecting a method for function 'match': object 'DNA_AND_RNA_COLORED_LETTERS' not found
Calls: DNAStringSetOPR ... add_colors.DNA -> vapply -> FUN -> match -> .handleSimpleError -> h
Execution halted
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR