• using R version 2.15.0 Patched (2012-05-19 r59366)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘HapEstXXR/DESCRIPTION’ ... OK
• this is package ‘HapEstXXR’ version ‘0.1-4’
• 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 whether package ‘HapEstXXR’ 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 whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace 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 ... NOTE
  maf: warning in matrix(0, nc = 9, nr = dim(geno)[2]): partial argument
  match of 'nr' to 'nrow'
  maf: warning in matrix(0, nc = 9, nr = dim(geno)[2]): partial argument
  match of 'nc' to 'ncol'
  msr.binomial.forward.adjusted: warning in matrix(out$newpat, nr =
  newdim[1], nc = newdim[2], byrow = F): partial argument match of 'nr'
  to 'nrow'
  msr.binomial.forward.adjusted: warning in matrix(out$newpat, nr =
  newdim[1], nc = newdim[2], byrow = F): partial argument match of 'nc'
  to 'ncol'
  msr.binomial.forward.unadjusted: warning in matrix(out$newpat, nr =
  newdim[1], nc = newdim[2], byrow = F): partial argument match of 'nr'
  to 'nrow'
  msr.binomial.forward.unadjusted: warning in matrix(out$newpat, nr =
  newdim[1], nc = newdim[2], byrow = F): partial argument match of 'nc'
  to 'ncol'
  msr.families.unadjusted: warning in matrix(out$newpat, nr = newdim[1],
  nc = newdim[2], byrow = F): partial argument match of 'nr' to 'nrow'
  msr.families.unadjusted: warning in matrix(out$newpat, nr = newdim[1],
  nc = newdim[2], byrow = F): partial argument match of 'nc' to 'ncol'
  msr.gaussian.forward.adjusted: warning in matrix(out$newpat, nr =
  newdim[1], nc = newdim[2], byrow = F): partial argument match of 'nr'
  to 'nrow'
  msr.gaussian.forward.adjusted: warning in matrix(out$newpat, nr =
  newdim[1], nc = newdim[2], byrow = F): partial argument match of 'nc'
  to 'ncol'
  msr.gaussian.forward.unadjusted: warning in matrix(out$newpat, nr =
  newdim[1], nc = newdim[2], byrow = F): partial argument match of 'nr'
  to 'nrow'
  msr.gaussian.forward.unadjusted: warning in matrix(out$newpat, nr =
  newdim[1], nc = newdim[2], byrow = F): partial argument match of 'nc'
  to 'ncol'
• 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 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-patched/Work/build/Packages/HapEstXXR/libs/HapEstXXR.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Object: ‘message.o’
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Object: ‘message.o’
  Found ‘stdout’, possibly from ‘stdout’ (C)
  Object: ‘message.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 ... [3s/3s] OK
• checking PDF version of manual ... OK
  NOTE: There were 2 notes.
  See
  ‘/home/hornik/tmp/R.check/r-patched/Work/PKGS/HapEstXXR.Rcheck/00check.log’
  for details.