• using R version 2.15.0 (2012-03-30)
• using platform: i686-pc-linux-gnu (32-bit)
• 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 if there is a namespace ... NOTE
  As from R 2.14.0 all packages need a namespace.
  One will be generated on installation, but it is better to handcraft a
  NAMESPACE file: R CMD build will produce a suitable starting point.
  CRAN requires a NAMESPACE file for all submissions.
• checking for executable files ... OK
• checking whether package ‘stepwise’ can be installed ... OK
• checking installed package size ... 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 whether the package can be unloaded cleanly ... 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 Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking compiled code ... NOTE
  File ‘/home/hornik/tmp/R.check/r-release/Work/build/Packages/stepwise/libs/stepwise.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Object: ‘init.o’
  Found ‘printf’, possibly from ‘printf’ (C)
  Objects: ‘MaxChi.o’, ‘Phylpro.o’, ‘init.o’
  Found ‘putchar’, possibly from ‘putchar’ (C)
  Object: ‘init.o’
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Objects: ‘MaxChi.o’, ‘Phylpro.o’, ‘init.o’
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Object: ‘init.o’
  Found ‘stdout’, possibly from ‘stdout’ (C)
  Objects: ‘MaxChi.o’, ‘Phylpro.o’, ‘init.o’
  
  Compiled code should not call functions which might terminate R nor
  write to stdout/stderr instead of to the console.
  
  See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
• checking examples ... ERROR
  Running examples in ‘stepwise-Ex.R’ failed
  The error most likely occurred in:
  
  > ### 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