• using R version 2.15.0 RC (2012-03-25 r58832)
• using platform: i386-apple-darwin9.8.0 (32-bit)
• using session charset: ASCII
• checking for file 'CNVassoc/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'CNVassoc' version '1.2'
• package encoding: latin1
• checking package namespace information ... OK
• checking package dependencies ... NOTE
  Packages suggested but not available for checking:
  'CGHcall' 'CGHregions' 'CNVtools'
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking whether package 'CNVassoc' 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
  getProbs.cghCall: no visible global function definition for
  'featureNames'
  getProbs.cghCall: no visible global function definition for
  'chromosomes'
  getProbs.cghCall: no visible global function definition for 'bpstart'
  getProbs.cghCall: no visible global function definition for 'bpend'
  getProbs.cghCall: no visible global function definition for 'calls'
  getProbs.cghCall: no visible global function definition for 'probloss'
  getProbs.cghCall: no visible global function definition for 'probnorm'
  getProbs.cghCall: no visible global function definition for 'probgain'
  getProbs.cghCall: no visible global function definition for 'probamp'
• 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 ... NOTE
  Error in .requirePackage(package) :
  unable to find required package 'CGHbase'
  Calls: <Anonymous> ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
  Execution halted
• checking data for ASCII and uncompressed saves ... OK
• checking sizes of PDF files under 'inst/doc' ... OK
• checking installed files from 'inst/doc' ... OK
• checking examples ... WARNING
  checking a package with encoding 'latin1' in an ASCII locale
  
  OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in 'inst/doc' ... OK
• checking running R code from vignettes ... WARNING
  Errors in running code in vignettes:
  when running code in 'CNVassoc_vignette.Rnw'
  ...
  > data(NeveCalled)
  
  > probs <- getProbs(NeveCalled)
  Loading required package: CGHbase
  Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
  there is no package called 'CGHbase'
  
  When sourcing 'CNVassoc_vignette.R':
  Error: unable to find required package 'CGHbase'
  Execution halted
  
• checking re-building of vignettes ... SKIPPED
• checking PDF version of manual ... OK
  WARNING: There were 2 warnings.
  NOTE: There were 3 notes.
  See
  '/Volumes/Tiger/Builds/Rdev-web/QA/Simon/packages/leopard-universal/results/2.15/CNVassoc.Rcheck/00check.log'
  for details.
• elapsed time (check, wall clock): 0:45