* using log directory 'd:/Rcompile/CRANpkg/local64/2.11/arrayMissPattern.Rcheck'
* using R version 2.11.1 Patched (2010-07-29 r52657)
* using session charset: ISO8859-1
* 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 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 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 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 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