• using R Under development (unstable) (2012-08-11 r60235)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘rphast/DESCRIPTION’ ... OK
• this is package ‘rphast’ version ‘1.3’
• 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 whether package ‘rphast’ can be installed ... OK
• checking installed package size ... NOTE
  installed size is 8.7Mb
  sub-directories of 1Mb or more:
  doc 1.0Mb
  extdata 2.3Mb
  libs 5.0Mb
• 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 loading without being on the library search path ... 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 ... NOTE
  S3 methods shown with full name in documentation object 'as.data.frame.feat':
  ‘as.data.frame.feat’
  
  S3 methods shown with full name in documentation object 'as.list.tm':
  ‘as.list.tm’
  
  S3 methods shown with full name in documentation object 'density.feat':
  ‘density.feat’
  
  S3 methods shown with full name in documentation object 'dim.feat':
  ‘dim.feat’
  
  S3 methods shown with full name in documentation object 'dim.msa':
  ‘dim.msa’
  
  S3 methods shown with full name in documentation object 'hist.feat':
  ‘hist.feat’
  
  S3 methods shown with full name in documentation object 'names.msa':
  ‘names.msa’
  
  S3 methods shown with full name in documentation object 'plot.altmodel.tm':
  ‘plot.altmodel.tm’
  
  S3 methods shown with full name in documentation object 'plot.feat':
  ‘plot.feat’
  
  S3 methods shown with full name in documentation object 'plot.gene':
  ‘plot.gene’
  
  S3 methods shown with full name in documentation object 'plot.msa':
  ‘plot.msa’
  
  S3 methods shown with full name in documentation object 'plot.rate.matrix':
  ‘plot.rate.matrix’
  
  S3 methods shown with full name in documentation object 'plot.tm':
  ‘plot.tm’
  
  S3 methods shown with full name in documentation object 'plot.track':
  ‘plot.track’
  
  S3 methods shown with full name in documentation object 'print.feat':
  ‘print.feat’
  
  S3 methods shown with full name in documentation object 'print.msa':
  ‘print.msa’
  
  S3 methods shown with full name in documentation object 'print.tm':
  ‘print.tm’
  
  S3 methods shown with full name in documentation object 'range.feat':
  ‘range.feat’
  
  S3 methods shown with full name in documentation object 'range.track':
  ‘range.track’
  
  S3 methods shown with full name in documentation object 'simulate.msa':
  ‘simulate.msa’
  
  S3 methods shown with full name in documentation object 'sort.feat':
  ‘sort.feat’
  
  S3 methods shown with full name in documentation object 'split.by.feature.msa':
  ‘split.by.feature.msa’
  
  S3 methods shown with full name in documentation object 'split.feat':
  ‘split.feat’
  
  S3 methods shown with full name in documentation object 'summary.feat':
  ‘summary.feat’
  
  S3 methods shown with full name in documentation object 'summary.msa':
  ‘summary.msa’
  
  S3 methods shown with full name in documentation object 'summary.tm':
  ‘summary.tm’
  
  S3 methods shown with full name in documentation object 'summary.tree':
  ‘summary.tree’
  
  S3 methods shown with full name in documentation object 'unique.feat':
  ‘unique.feat’
  
  The \usage entries for S3 methods should use the \method markup and not
  their full name.
  See the chapter ‘Writing R documentation files’ in the ‘Writing R
  Extensions’ manual.
• 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 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-devel/Work/build/Packages/rphast/libs/rphast.so’:
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Object: ‘dgamma.o’
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Objects: ‘rph_phyloP.o’, ‘msa.o’, ‘fit_column.o’, ‘indel_mod.o’,
  ‘motif.o’, ‘gap_patterns.o’, ‘sufficient_stats.o’, ‘matrix.o’,
  ‘bed.o’, ‘eigen.o’, ‘rph_phyloFit.o’, ‘phast_cons.o’,
  ‘tree_model.o’, ‘misc.o’, ‘maf.o’, ‘hmm.o’, ‘category_map.o’,
  ‘stringsplus.o’, ‘multi_msa.o’, ‘markov_matrix.o’,
  ‘fit_feature.o’, ‘phylo_hmm.o’, ‘phylo_fit.o’
  Found ‘stdout’, possibly from ‘stdout’ (C)
  Objects: ‘rph_phyloP.o’, ‘rph_msa.o’, ‘rph_phyloFit.o’,
  ‘phast_cons.o’, ‘misc.o’, ‘maf.o’, ‘maf_block.o’, ‘rph_hmm.o’,
  ‘rph_tree_model.o’, ‘phylo_p.o’, ‘rph_gff.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’ ... NOTE
  The following files are already in R: ‘Sweave.sty’
  Please remove them from your package.
• checking examples ... [25s/25s] OK
• checking for unstated dependencies in tests ... OK
• checking tests ... [49s/49s] OK
  Running ‘feat.examples.R’ [1s/1s]
  Running ‘hmm.examples.R’ [2s/2s]
  Running ‘msa.examples.R’ [7s/7s]
  Running ‘phastCons.examples.R’ [14s/14s]
  Running ‘phyloFit.examples.R’ [5s/5s]
  Running ‘phyloP.examples.R’ [16s/16s]
  Running ‘plot.examples.R’ [2s/2s]
  Running ‘treeModel.examples.R’ [1s/1s]
  Running ‘trees.examples.R’ [0s/0s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... [32s/32s] OK
• checking re-building of vignette PDFs ... [34s/38s] OK
• checking PDF version of manual ... OK
  NOTE: There were 4 notes.
  See
  ‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/rphast.Rcheck/00check.log’
  for details.