* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/STRMPS.Rcheck’
* using R Under development (unstable) (2025-02-28 r87848)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    clang version 20.1.0-rc3
    flang version 20.1.0-rc3
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘STRMPS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘STRMPS’ version ‘0.6.8’
* 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 ‘STRMPS’ can be installed ... [78s/105s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/STRMPS-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/30s] OK
* checking whether the package can be loaded with stated dependencies ... [23s/29s] OK
* checking whether the package can be unloaded cleanly ... [24s/32s] OK
* checking whether the namespace can be loaded with stated dependencies ... [22s/27s] OK
* checking whether the namespace can be unloaded cleanly ... [24s/32s] OK
* checking loading without being on the library search path ... [23s/29s] 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 ... [105s/132s] 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 ... [25s/30s] ERROR
Running examples in ‘STRMPS-Ex.R’ failed
The error most likely occurred in:

> ### Name: findStutter,stringCoverageGenotypeList-method
> ### Title: Find stutters
> ### Aliases: findStutter,stringCoverageGenotypeList-method
> 
> ### ** Examples
> 
> # The object returned by merging a stringCoverageList-Object
> # and a genotypeList-Object.
> data("stringCoverageGenotypeList")
> 
> stutterList <- findStutter(stringCoverageGenotypeList)
Error in unlist(substitutionMatrix, substitutionMatrix) : 
  'recursive' must be a length-1 vector
Calls: findStutter ... mpi.XStringSet.pairwiseAlignment -> XStringSet.pairwiseAlignment -> array -> unlist
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [254s/354s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘STRMPSworkflow.Rmd’ using rmarkdown

Quitting from lines 169-174 [unnamed-chunk-14] (STRMPSworkflow.Rmd)
Error: processing vignette 'STRMPSworkflow.Rmd' failed with diagnostics:
'recursive' must be a length-1 vector
--- failed re-building ‘STRMPSworkflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [10s/13s] 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: 2 ERRORs