• using R Under development (unstable) (2012-05-19 r59366)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘graphComp/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘graphComp’ version ‘1.0’
• checking package namespace information ... OK
• checking package dependencies ... NOTE
  Packages suggested but not available for checking:
  ‘genefilter’ ‘hgu95av2.db’
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking whether package ‘graphComp’ 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 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 ... NOTE
  compGraphs.vis: no visible binding for global variable ‘Colors’
  compGraphs.vis: no visible binding for global variable ‘cexx’
• 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 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.
  The following files look like leftovers/mistakes:
  ‘references.log’
  Please remove them from your package.
  The following directories should probably not be installed:
  ‘fig’
  
  Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
  or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
• checking examples ... [1s/1s] OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... [3s/3s] WARNING
  Errors in running code in vignettes:
  when running code in ‘graphComp.Rnw’
  ...
  
  > dim(ALL_B)
  Features Samples
  12625 95
  
  > library(genefilter)
  
  When sourcing ‘graphComp.R’:
  Error: there is no package called ‘genefilter’
  Execution halted
  
• checking re-building of vignette PDFs ... NOTE
  Error in re-building vignettes:
  ...
  
  Attaching package: ‘BiocGenerics’
  
  The following object(s) are masked from ‘package:stats’:
  
  xtabs
  
  The following object(s) are masked from ‘package:base’:
  
  Filter, Find, Map, Position, Reduce, anyDuplicated, cbind,
  colnames, duplicated, eval, get, intersect, lapply, mapply, mget,
  order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int,
  rownames, sapply, setdiff, table, tapply, union, unique
  
  Welcome to Bioconductor
  
  Vignettes contain introductory material; view with
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")', and for packages 'citation("pkgname")'.
  
  
  Error: processing vignette 'graphComp.Rnw' failed with diagnostics:
  chunk 3 (label = nspfil)
  Error in library(genefilter) : there is no package called ‘genefilter’
  Execution halted
  
• checking PDF version of manual ... OK
  WARNING: There was 1 warning.
  NOTE: There were 4 notes.
  See
  ‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/graphComp.Rcheck/00check.log’
  for details.