* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/dowser.Rcheck’
* using R Under development (unstable) (2024-05-02 r86508)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    clang version 18.1.5
    flang-new version 18.1.5
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘dowser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dowser’ version ‘2.1.0’
* 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 ‘dowser’ can be installed ... [93s/280s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/dowser-00install.html' for details.
* 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 ... [22s/45s] OK
* checking whether the package can be loaded with stated dependencies ... [22s/50s] OK
* checking whether the package can be unloaded cleanly ... [21s/45s] OK
* checking whether the namespace can be loaded with stated dependencies ... [21s/39s] OK
* checking whether the namespace can be unloaded cleanly ... [23s/38s] OK
* checking loading without being on the library search path ... [22s/26s] OK
* checking whether startup messages can be suppressed ... [22s/27s] 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 ... [129s/136s] 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 ... [24s/25s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [31s/32s] ERROR
Running examples in ‘dowser-Ex.R’ failed
The error most likely occurred in:

> ### Name: maskCodons
> ### Title: 'maskCodons' Masks codons split by insertions
> ### Aliases: maskCodons
> 
> ### ** Examples
> 
> s = "ATCATCATC..."
> q = "ATCTTTATCATC"
> print(maskCodons(1,q,s,TRUE))
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 pairwiseAlignment() requires
  the pwalign package. Please install it with:

    BiocManager::install("pwalign")
Calls: print ... <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 ... [271s/280s] OK
* checking PDF version of manual ... [11s/12s] 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