• 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 ‘phyclust/DESCRIPTION’ ... OK
• this is package ‘phyclust’ version ‘0.1-11’
• 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 ‘phyclust’ 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
  chkdim.Add.fun: no visible binding for global variable ‘RRstar’
  get.deriBigMatB.fun: no visible binding for global variable ‘k’
  get.fullBB.fun: no visible binding for global variable ‘medBB.cs’
  get.fullBB.fun: no visible binding for global variable ‘subPI.cs’
  get.matD.matEI.fun: no visible binding for global variable ‘y’
  get.matD.matEI.fun: no visible binding for global variable ‘mu’
  get.matD.matEI.fun: no visible binding for global variable ‘a’
  get.matD.matEI.fun: no visible binding for global variable ‘xRD.post’
  get.matD.matEI.fun: no visible binding for global variable ‘x.post’
  get.matD.matEI.fun: no visible binding for global variable ‘xRD’
  get.matD.matEI.fun: no visible binding for global variable ‘x’
  get.matD.matEI.fun: no visible binding for global variable ‘post’
  get.matD.matEI.fun: no visible binding for global variable ‘v’
  get.matD.matEI.fun: no visible binding for global variable ‘nreps’
  get.matD.matEI.fun: no visible binding for global variable ‘CC’
  get.matD.matEI.fun: no visible binding for global variable ‘subPI’
  get.matD.matEI.fun: no visible binding for global variable ‘BB’
  get.matD.matEI.fun: no visible binding for global variable ‘p.cscn.FD’
  get.matD.matEI.fun: no visible binding for global variable ‘x.adj’
  get.medBB.skip.fun: no visible binding for global variable ‘subPI.cn’
  get.medBB.skip.fun: no visible binding for global variable ‘preBB.cn’
  get.medBB.skip.fun: no visible binding for global variable ‘indexBB.cn’
  get.preBB.skip.fun: no visible binding for global variable ‘subPI.cs’
  getBigMatB.fun: no visible binding for global variable ‘BB.cs’
  getBigMatB.fun: no visible binding for global variable ‘subPI.cs’
  getI13.fun: no visible binding for global variable ‘y’
  getPIstar.fun: no visible binding for global variable ‘BB.cs’
  getPIstar.fun: no visible binding for global variable ‘subPI.cs’
  getcut.fun: no visible binding for global variable ‘nhap’
  haplo.score.RD.unphased.fun: no visible binding for global variable
  ‘Y.vec’
  haplo.score.RD.unphased.fun: no visible binding for global variable
  ‘Geno’
  haplo.score.RD.unphased.fun: no visible global function definition for
  ‘haplo.em’
  haplo.score.RD.unphased.fun: no visible global function definition for
  ‘haplo.em.control’
  haplo.score.RD.unphased.fun: no visible binding for global variable
  ‘nhap’
  haplo.score.RD.unphased.fun: no visible binding for global variable
  ‘digit’
  haplo.score.RD.unphased.fun: no visible global function definition for
  ‘Ginv’
• 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 compilation flags in Makevars ... 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/phyclust/libs/phyclust.so’:
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Objects: ‘seq-gen/progress.o’, ‘seq-gen/seq-gen.o’
  Found ‘stdout’, possibly from ‘stdout’ (C)
  Objects: ‘paml_baseml/baseml.o’, ‘paml_baseml/tools.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 sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking examples ... [0s/0s] OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... [0s/0s] OK
• checking re-building of vignette PDFs ... [3s/4s] OK
• checking PDF version of manual ... OK
  NOTE: There were 2 notes.
  See
  ‘/home/hornik/tmp/R.check/r-patched/Work/PKGS/phyclust.Rcheck/00check.log’
  for details.