• 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 ‘rtfbs/DESCRIPTION’ ... OK
• this is package ‘rtfbs’ version ‘0.2’
• 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 ... NOTE
  Found the following hidden files and directories:
  tests/.Rhistory
  These were most likely included in error. See section ‘Package
  structure’ in the ‘Writing R Extensions’ manual.
• checking whether package ‘rtfbs’ can be installed ... OK
• checking installed package size ... NOTE
  installed size is 6.2Mb
  sub-directories of 1Mb or more:
  libs 5.2Mb
• 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 ... 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 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/rtfbs/libs/rtfbs.so’:
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Objects: ‘rph_phyloP.o’, ‘msa.o’, ‘fit_column.o’, ‘indel_mod.o’,
  ‘motif.o’, ‘tfbs.o’, ‘gap_patterns.o’, ‘sufficient_stats.o’,
  ‘bed.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_tfbs.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’ ... OK
• checking examples ... [6s/6s] OK
• checking for unstated dependencies in tests ... OK
• checking tests ... [11s/11s] OK
  Running ‘build_mm.R’ [1s/1s]
  Running ‘calc_fdr.R’ [2s/2s]
  Running ‘gcContent_ms.R’ [0s/0s]
  Running ‘groupByGC_ms.R’ [1s/1s]
  Running ‘makeFdrPlot.R’ [2s/2s]
  Running ‘output_sites.R’ [2s/2s]
  Running ‘read_ms.R’ [1s/1s]
  Running ‘read_pwm.R’ [0s/1s]
  Running ‘score_ms.R’ [2s/2s]
  Running ‘simulate_ms.R’ [1s/1s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... [3s/3s] OK
• checking re-building of vignette PDFs ... [4s/5s] OK
• checking PDF version of manual ... OK
  NOTE: There were 3 notes.
  See
  ‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/rtfbs.Rcheck/00check.log’
  for details.