* using log directory ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/STRMPS.Rcheck’ * using R Under development (unstable) (2025-02-25 r87824) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-14 (Debian 14.2.0-16) 14.2.0 GNU Fortran (Debian 14.2.0-16) 14.2.0 * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * 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 ... OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/STRMPS-00install.html' for details. * checking package directory ... OK * checking for future file timestamps ... 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 ... [10s/11s] OK * checking whether the package can be loaded with stated dependencies ... [11s/12s] OK * checking whether the package can be unloaded cleanly ... [10s/11s] OK * checking whether the namespace can be loaded with stated dependencies ... [10s/12s] OK * checking whether the namespace can be unloaded cleanly ... [11s/15s] OK * checking loading without being on the library search path ... [10s/11s] 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 ... [44s/51s] OK * checking Rd files ... [0s/1s] 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 ... [3s/4s] 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 ... [10s/13s] ERROR Running examples in ‘STRMPS-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### 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 ... [82s/95s] 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 ... [5s/6s] OK * checking HTML version of manual ... [1s/2s] OK * checking for non-standard things in the check directory ... OK * DONE Status: 2 ERRORs