• using R version 2.10.0 Patched (2009-11-22 r50534)
• using session charset: UTF-8
• checking for file 'stepwise/DESCRIPTION' ... OK
• this is package 'stepwise' version '0.2-4'
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking whether package 'stepwise' can be installed ... OK
• checking package directory ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking R 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 for unstated 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 ... OK
• 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 data for non-ASCII characters ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking for portable use of $BLAS_LIBS ... OK
• checking examples ... ERROR
  Running examples in 'stepwise-Ex.R' failed.
  The error most likely occurred in:
  
  > ### * phylpro
  >
  > flush(stderr()); flush(stdout())
  >
  > ### Name: phylpro
  > ### Title: Stepwise detection of recombination breakpoints using Phylpro
  > ### Aliases: phylpro
  > ### Keywords: htest
  >
  > ### ** Examples
  > demo(phylpro)
  
  
  demo(phylpro)
  ---- ~~~~~~~
  
  > inputFile<-system.file("data", "simulinfile", package = "stepwise")
  
  > breaks<-c(548, 735, 832)
  
  > WinHalfWidth<-30
  
  > permReps<-10
  
  > b<-phylpro(inputFile, breaks, WinHalfWidth, permReps)
  
  > summary.phylpro(b)
  Error in siteChisqs[1] <- object$corrs[1] : replacement has length zero
  Calls: demo ... source -> eval.with.vis -> eval.with.vis -> summary.phylpro
  Execution halted