• using R Under development (unstable) (2012-08-14 r60253)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘bams/DESCRIPTION’ ... OK
• this is package ‘bams’ version ‘1.2’
• checking package namespace information ... OK
• checking package dependencies ... NOTE
  Package suggested but not available for checking: ‘gada’
• 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:
  vignettes/.Rhistory
  These were most likely included in error. See section ‘Package
  structure’ in the ‘Writing R Extensions’ manual.
• checking whether package ‘bams’ 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
  exportData: no visible binding for global variable ‘neuroblastoma’
  geom_tallrect : draw_groups: no visible global function definition for
  ‘coord_transform’
  run.cghseg : <anonymous> : <anonymous>: no visible binding for global
  variable ‘begin’
  run.smoothers: no visible binding for global variable ‘annotation’
  runglad: no visible binding for global variable ‘position’
  runglad: no visible binding for global variable ‘logratio’
  runglad: no visible binding for global variable ‘chromosome’
• 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’ ... OK
• checking examples ... NONE
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... OK
• checking re-building of vignette PDFs ... OK
• checking PDF version of manual ... OK
  NOTE: There were 3 notes.
  See
  ‘/data/blackswan/ripley/R/packages/tests-devel/bams.Rcheck/00check.log’
  for details.