• using R version 2.9.1 Patched (2009-06-30 r48877)
• using session charset: UTF-8
• checking for file 'arrayMissPattern/DESCRIPTION' ... OK
• this is package 'arrayMissPattern' version '1.3'
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking whether package 'arrayMissPattern' can be installed ... OK
• checking package directory ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking DESCRIPTION meta-information ... NOTE
  Non-standard license specification:
  GPL version 2 or newer
  Standardizable: TRUE
  Standardized license specification:
  GPL (>= 2)
• 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 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
  arrayMissPattern: no visible binding for '<<-' assignment to
  ‘Result.Save’
  arrayMissPattern: no visible binding for '<<-' assignment to
  ‘high.list’
  arrayMissPattern: no visible binding for '<<-' assignment to
  ‘high.chip.list’
  arrayMissPattern: no visible binding for '<<-' assignment to
  ‘gene.location’
  arrayMissPattern: no visible binding for '<<-' assignment to
  ‘true.flag’
  arrayMissPattern : geneListSelectRow.handler: no visible binding for
  '<<-' assignment to ‘high.list’
  arrayMissPattern : geneListSelectRow.handler: no visible binding for
  global variable ‘high.list’
  arrayMissPattern : geneListUnselectRow.handler: no visible binding for
  '<<-' assignment to ‘high.list’
  arrayMissPattern : geneListUnselectRow.handler: no visible binding for
  global variable ‘high.list’
  arrayMissPattern : chipListSelectRow.handler: no visible binding for
  '<<-' assignment to ‘high.chip.list’
  arrayMissPattern : chipListSelectRow.handler: no visible binding for
  global variable ‘high.chip.list’
  arrayMissPattern : chipListUnselectRow.handler: no visible binding for
  '<<-' assignment to ‘high.chip.list’
  arrayMissPattern : chipListUnselectRow.handler: no visible binding for
  global variable ‘high.chip.list’
  arrayMissPattern : showMissingList: no visible binding for global
  variable ‘geneList’
  arrayMissPattern : showChipList: no visible binding for '<<-'
  assignment to ‘chip.name’
  arrayMissPattern : showChipList: no visible binding for global variable
  ‘data.missing’
  arrayMissPattern : showChipList: no visible binding for global variable
  ‘chip.name’
  arrayMissPattern : showChipList: no visible binding for global variable
  ‘ChipList’
  arrayMissPattern : removeMissingList: no visible binding for global
  variable ‘geneList’
  arrayMissPattern : Mnu.read.file.handler : <anonymous>: no visible
  binding for '<<-' assignment to ‘data.missing’
  arrayMissPattern : Mnu.read.file.handler : <anonymous>: no visible
  binding for '<<-' assignment to ‘exp.info.name’
  arrayMissPattern : Mnu.read.file.handler : <anonymous>: no visible
  binding for global variable ‘data.missing’
  arrayMissPattern : Mnu.read.file.handler : <anonymous>: no visible
  binding for '<<-' assignment to ‘missing.pattern’
  arrayMissPattern : Mnu.read.file.handler : <anonymous>: no visible
  binding for global variable ‘exp.info.name’
  arrayMissPattern : Mnu.read.file.handler : <anonymous>: no visible
  binding for global variable ‘new.text’
  arrayMissPattern : Mnu.read.file.handler : <anonymous>: no visible
  binding for global variable ‘outputText’
  arrayMissPattern : Mnu.read.grid.file.handler : <anonymous>: no visible
  binding for '<<-' assignment to ‘gene.location’
  arrayMissPattern : Mnu.read.grid.file.handler : <anonymous>: no visible
  binding for '<<-' assignment to ‘exp.info.name’
  arrayMissPattern : Mnu.read.grid.file.handler : <anonymous>: no visible
  binding for global variable ‘gene.location’
  arrayMissPattern : Mnu.read.grid.file.handler : <anonymous>: no visible
  binding for '<<-' assignment to ‘y’
  arrayMissPattern : Mnu.read.grid.file.handler : <anonymous>: no visible
  binding for global variable ‘exp.info.name’
  arrayMissPattern : Mnu.read.grid.file.handler : <anonymous>: no visible
  binding for global variable ‘new.text’
  arrayMissPattern : Mnu.read.grid.file.handler : <anonymous>: no visible
  binding for global variable ‘outputText’
  arrayMissPattern : Mnu.read.block.file.handler : <anonymous>: no
  visible binding for '<<-' assignment to ‘gene.block’
  arrayMissPattern : Mnu.read.block.file.handler : <anonymous>: no
  visible binding for '<<-' assignment to ‘exp.info.name’
  arrayMissPattern : Mnu.read.block.file.handler : <anonymous>: no
  visible binding for global variable ‘exp.info.name’
  arrayMissPattern : Mnu.read.block.file.handler : <anonymous>: no
  visible binding for global variable ‘new.text’
  arrayMissPattern : Mnu.read.block.file.handler : <anonymous>: no
  visible binding for global variable ‘outputText’
  arrayMissPattern : Mnu.exit.handler: no visible binding for global
  variable ‘main’
  arrayMissPattern : missing.indicator: no visible binding for '<<-'
  assignment to ‘missing.I’
  arrayMissPattern : missing.indicator: no visible binding for '<<-'
  assignment to ‘missing.Name’
  arrayMissPattern : missing.indicator: no visible binding for global
  variable ‘missing.Name’
  arrayMissPattern : missing.indicator: no visible binding for global
  variable ‘missing.I’
  arrayMissPattern : missing.indicator: no visible binding for '<<-'
  assignment to ‘missing.Name.temp’
  arrayMissPattern : missing.indicator: no visible binding for '<<-'
  assignment to ‘miss.temp’
  arrayMissPattern : Mnu.Missing.rates.chip.handler: no visible binding
  for global variable ‘data.missing’
  arrayMissPattern : Mnu.Missing.rates.gene.handler: no visible binding
  for global variable ‘data.missing’
  arrayMissPattern : Mnu.Missing.rates.block.handler: no visible binding
  for global variable ‘gene.block’
  arrayMissPattern : Mnu.Missing.rates.block.handler: no visible binding
  for global variable ‘data.missing’
  arrayMissPattern : Mnu.Missing.pattern1.handler: no visible binding for
  global variable ‘data.missing’
  arrayMissPattern : Mnu.Missing.pattern2.handler: no visible binding for
  global variable ‘gene.block’
  arrayMissPattern : Mnu.Missing.pattern2.handler: no visible binding for
  global variable ‘missing.pattern’
  arrayMissPattern : Mnu.Missing.pattern2.handler: no visible binding for
  global variable ‘x’
  arrayMissPattern : Mnu.Missing.pattern2.handler: no visible binding for
  global variable ‘y’
  arrayMissPattern : Mnu.Missing.pattern2.handler: no visible binding for
  global variable ‘data.missing’
  arrayMissPattern : Mnu.Missing.pattern2.handler: no visible binding for
  global variable ‘gene.location’
  arrayMissPattern : Mnu.Missing.pattern.chip.handler: no visible binding
  for global variable ‘high.chip.list’
  arrayMissPattern : Mnu.Missing.pattern.chip.handler: no visible binding
  for global variable ‘gene.block’
  arrayMissPattern : Mnu.Missing.pattern.chip.handler: no visible binding
  for global variable ‘gene.location’
  arrayMissPattern : Mnu.Missing.pattern.chip.handler: no visible binding
  for global variable ‘data.missing’
  arrayMissPattern : Mnu.Missing.pattern.chip.handler: no visible binding
  for global variable ‘x’
  arrayMissPattern : Mnu.Missing.pattern.chip.handler: no visible binding
  for global variable ‘y’
  arrayMissPattern : Mnu.Missing.pattern.chip.handler: no visible binding
  for global variable ‘chip.name’
  arrayMissPattern : Mnu.Missing.pattern.intensity.handler: no visible
  binding for global variable ‘data.missing’
  arrayMissPattern : Mnu.Ripley.K.handler: no visible binding for global
  variable ‘data.missing’
  arrayMissPattern : Mnu.Ripley.K.handler: no visible binding for global
  variable ‘gene.location’
  arrayMissPattern : Mnu.Ripley.K.handler: no visible binding for global
  variable ‘chip.name’
  arrayMissPattern : Mnu.Ripley.K.handler: no visible binding for global
  variable ‘new.text’
  arrayMissPattern : Mnu.Ripley.K.handler: no visible binding for global
  variable ‘outputText’
  arrayMissPattern: no visible binding for '<<-' assignment to ‘main’
  arrayMissPattern: no visible binding for global variable ‘main’
  arrayMissPattern: no visible binding for '<<-' assignment to ‘ChipList’
  arrayMissPattern: no visible binding for global variable ‘ChipList’
  arrayMissPattern: no visible binding for '<<-' assignment to
  ‘outputText’
  arrayMissPattern: no visible binding for global variable ‘outputText’
  arrayMissPattern: no visible binding for '<<-' assignment to ‘new.text’
  Found possibly global 'T' or 'F' in the following function:
  arrayMissPattern
• checking Rd files ... OK
• checking Rd files against version 2 parser ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking examples ... WARNING
  Found the following significant warnings:
  Warning: 'gtkCListNew' is deprecated.
  Warning: 'method' is deprecated.
  Warning: 'method' is deprecated.
  Deprecated functions may be defunct as soon as of the next release of R.
  See ?Deprecated.
• checking PDF version of manual ... OK