* using log directory 'd:/Rcompile/CRANpkg/local64/2.11/arrayImpute.Rcheck'
* using R version 2.11.1 Patched (2010-07-29 r52657)
* using session charset: ISO8859-1
* checking for file 'arrayImpute/DESCRIPTION' ... OK
* this is package 'arrayImpute' version '1.3'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'arrayImpute' 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
arrayImpute: no visible binding for '<<-' assignment to 'K'
arrayImpute: no visible binding for '<<-' assignment to 'Result.Save'
arrayImpute: no visible binding for '<<-' assignment to 'high.list'
arrayImpute: no visible binding for '<<-' assignment to
  'high.chip.list'
arrayImpute: no visible binding for '<<-' assignment to 'gene.location'
arrayImpute: no visible binding for '<<-' assignment to 'true.flag'
arrayImpute : geneListSelectRow.handler: no visible binding for '<<-'
  assignment to 'high.list'
arrayImpute : geneListSelectRow.handler: no visible binding for global
  variable 'high.list'
arrayImpute : geneListUnselectRow.handler: no visible binding for '<<-'
  assignment to 'high.list'
arrayImpute : geneListUnselectRow.handler: no visible binding for
  global variable 'high.list'
arrayImpute : chipListSelectRow.handler: no visible binding for '<<-'
  assignment to 'high.chip.list'
arrayImpute : chipListSelectRow.handler: no visible binding for global
  variable 'high.chip.list'
arrayImpute : chipListUnselectRow.handler: no visible binding for '<<-'
  assignment to 'high.chip.list'
arrayImpute : chipListUnselectRow.handler: no visible binding for
  global variable 'high.chip.list'
arrayImpute : showMissingList: no visible binding for global variable
  'geneList'
arrayImpute : showChipList: no visible binding for '<<-' assignment to
  'chip.name'
arrayImpute : showChipList: no visible binding for global variable
  'data.missing'
arrayImpute : showChipList: no visible binding for global variable
  'chip.name'
arrayImpute : showChipList: no visible binding for global variable
  'ChipList'
arrayImpute : removeMissingList: no visible binding for global variable
  'geneList'
arrayImpute : Mnu.read.file.handler : <anonymous>: no visible binding
  for '<<-' assignment to 'data.missing'
arrayImpute : Mnu.read.file.handler : <anonymous>: no visible binding
  for '<<-' assignment to 'exp.info.name'
arrayImpute : Mnu.read.file.handler : <anonymous>: no visible binding
  for global variable 'data.missing'
arrayImpute : Mnu.read.file.handler : <anonymous>: no visible binding
  for '<<-' assignment to 'AVE.impute'
arrayImpute : Mnu.read.file.handler : <anonymous>: no visible binding
  for global variable 'missing.I'
arrayImpute : Mnu.read.file.handler : <anonymous>: no visible binding
  for '<<-' assignment to 'missing.Name'
arrayImpute : Mnu.read.file.handler : <anonymous>: no visible binding
  for global variable 'missing.Name'
arrayImpute : Mnu.read.file.handler : <anonymous>: no visible binding
  for global variable 'AVE.impute'
arrayImpute : Mnu.read.file.handler : <anonymous>: no visible binding
  for global variable 'exp.info.name'
arrayImpute : Mnu.read.file.handler : <anonymous>: no visible binding
  for '<<-' assignment to 'Result.Save'
arrayImpute : Mnu.read.file.handler : <anonymous>: no visible binding
  for global variable 'Result.Save'
arrayImpute : Mnu.read.file.handler : <anonymous>: no visible binding
  for global variable 'new.text'
arrayImpute : Mnu.read.file.handler : <anonymous>: no visible binding
  for global variable 'outputText'
arrayImpute : Mnu.read.location.file.handler : <anonymous>: no visible
  binding for '<<-' assignment to 'gene.location'
arrayImpute : Mnu.read.location.file.handler : <anonymous>: no visible
  binding for '<<-' assignment to 'gene.location.o'
arrayImpute : Mnu.read.location.file.handler : <anonymous>: no visible
  binding for '<<-' assignment to 'exp.info.name'
arrayImpute : Mnu.read.location.file.handler : <anonymous>: no visible
  binding for global variable 'gene.location.o'
arrayImpute : missing.indicator: no visible binding for '<<-'
  assignment to 'missing.I'
arrayImpute : missing.indicator: no visible binding for '<<-'
  assignment to 'missing.Name'
arrayImpute : missing.indicator: no visible binding for global variable
  'missing.Name'
arrayImpute : missing.indicator: no visible binding for global variable
  'missing.I'
arrayImpute : missing.indicator: no visible binding for '<<-'
  assignment to 'missing.Name.temp'
arrayImpute : missing.indicator: no visible binding for '<<-'
  assignment to 'miss.temp'
arrayImpute : missing.indicator: no visible binding for '<<-'
  assignment to 'kNN.impute'
arrayImpute : missing.indicator: no visible binding for global variable
  'missing.Name.temp'
arrayImpute : missing.indicator: no visible binding for '<<-'
  assignment to 'LLS.impute'
arrayImpute : missing.indicator: no visible binding for '<<-'
  assignment to 'RLSP.impute'
arrayImpute : missing.indicator: no visible binding for '<<-'
  assignment to 'BPCA.impute'
arrayImpute : missing.indicator: no visible binding for '<<-'
  assignment to 'User1.impute'
arrayImpute : missing.indicator: no visible binding for '<<-'
  assignment to 'User2.impute'
arrayImpute : Mnu.save.result.handler: no visible binding for global
  variable 'kNN.impute'
arrayImpute : Mnu.save.result.handler: no visible binding for global
  variable 'data.missing'
arrayImpute : Mnu.save.result.handler: no visible binding for global
  variable 'LLS.impute'
arrayImpute : Mnu.save.result.handler: no visible binding for global
  variable 'RLSP.impute'
arrayImpute : Mnu.save.result.handler: no visible binding for global
  variable 'BPCA.impute'
arrayImpute : Mnu.exit.handler: no visible binding for global variable
  'main'
arrayImpute : Mnu.kNNimpute.handler: no visible binding for '<<-'
  assignment to 'Result.Save'
arrayImpute : Mnu.kNNimpute.handler: no visible binding for global
  variable 'Result.Save'
arrayImpute : Mnu.kNNimpute.handler: no visible binding for global
  variable 'new.text'
arrayImpute : Mnu.kNNimpute.handler: no visible binding for global
  variable 'outputText'
arrayImpute : Mnu.LLSimpute.handler: no visible binding for '<<-'
  assignment to 'pc.n.flag'
arrayImpute : Mnu.LLSimpute.handler: no visible binding for '<<-'
  assignment to 'Result.Save'
arrayImpute : Mnu.LLSimpute.handler: no visible binding for global
  variable 'Result.Save'
arrayImpute : Mnu.LLSimpute.handler: no visible binding for global
  variable 'new.text'
arrayImpute : Mnu.LLSimpute.handler: no visible binding for global
  variable 'outputText'
arrayImpute : Mnu.RLSPimpute.handler: no visible binding for '<<-'
  assignment to 'pc.n.flag'
arrayImpute : Mnu.RLSPimpute.handler: no visible binding for '<<-'
  assignment to 'Result.Save'
arrayImpute : Mnu.RLSPimpute.handler: no visible binding for global
  variable 'Result.Save'
arrayImpute : Mnu.RLSPimpute.handler: no visible binding for global
  variable 'new.text'
arrayImpute : Mnu.RLSPimpute.handler: no visible binding for global
  variable 'outputText'
arrayImpute : Mnu.BPCAimpute.handler: no visible binding for '<<-'
  assignment to 'Result.Save'
arrayImpute : Mnu.BPCAimpute.handler: no visible binding for global
  variable 'Result.Save'
arrayImpute : Mnu.BPCAimpute.handler: no visible binding for global
  variable 'new.text'
arrayImpute : Mnu.BPCAimpute.handler: no visible binding for global
  variable 'outputText'
arrayImpute : Mnu.UserDef1.handler : <anonymous>: no visible binding
  for '<<-' assignment to 'User1.impute'
arrayImpute : Mnu.UserDef1.handler : <anonymous>: no visible binding
  for global variable 'User1.impute'
arrayImpute : Mnu.UserDef1.handler : <anonymous>: no visible binding
  for global variable 'data.missing'
arrayImpute : Mnu.UserDef1.handler : <anonymous>: no visible binding
  for '<<-' assignment to 'missing.Name'
arrayImpute : Mnu.UserDef1.handler : <anonymous>: no visible binding
  for global variable 'missing.Name.temp'
arrayImpute : Mnu.UserDef1.handler : <anonymous>: no visible binding
  for global variable 'AVE.impute'
arrayImpute : Mnu.UserDef1.handler : <anonymous>: no visible binding
  for global variable 'kNN.impute'
arrayImpute : Mnu.UserDef1.handler : <anonymous>: no visible binding
  for global variable 'LLS.impute'
arrayImpute : Mnu.UserDef1.handler : <anonymous>: no visible binding
  for global variable 'RLSP.impute'
arrayImpute : Mnu.UserDef1.handler : <anonymous>: no visible binding
  for global variable 'BPCA.impute'
arrayImpute : Mnu.UserDef1.handler : <anonymous>: no visible binding
  for global variable 'User2.impute'
arrayImpute : Mnu.UserDef1.handler : <anonymous>: no visible binding
  for global variable 'missing.Name'
arrayImpute : Mnu.UserDef2.handler : <anonymous>: no visible binding
  for '<<-' assignment to 'User2.impute'
arrayImpute : Mnu.UserDef2.handler : <anonymous>: no visible binding
  for global variable 'User2.impute'
arrayImpute : Mnu.UserDef2.handler : <anonymous>: no visible binding
  for global variable 'data.missing'
arrayImpute : Mnu.UserDef2.handler : <anonymous>: no visible binding
  for '<<-' assignment to 'missing.Name'
arrayImpute : Mnu.UserDef2.handler : <anonymous>: no visible binding
  for global variable 'missing.Name.temp'
arrayImpute : Mnu.UserDef2.handler : <anonymous>: no visible binding
  for global variable 'AVE.impute'
arrayImpute : Mnu.UserDef2.handler : <anonymous>: no visible binding
  for global variable 'kNN.impute'
arrayImpute : Mnu.UserDef2.handler : <anonymous>: no visible binding
  for global variable 'LLS.impute'
arrayImpute : Mnu.UserDef2.handler : <anonymous>: no visible binding
  for global variable 'RLSP.impute'
arrayImpute : Mnu.UserDef2.handler : <anonymous>: no visible binding
  for global variable 'BPCA.impute'
arrayImpute : Mnu.UserDef2.handler : <anonymous>: no visible binding
  for global variable 'User1.impute'
arrayImpute : Mnu.UserDef2.handler : <anonymous>: no visible binding
  for global variable 'missing.Name'
arrayImpute : subwindow: no visible binding for '<<-' assignment to
  'Method'
arrayImpute : subwindow : ok.handler: no visible binding for '<<-'
  assignment to 'K'
arrayImpute : subwindow : ok.handler: no visible binding for global
  variable 'KK'
arrayImpute : subwindow : ok.handler: no visible binding for global
  variable 'K'
arrayImpute : subwindow : ok.handler: no visible binding for global
  variable 'data.missing'
arrayImpute : subwindow : ok.handler: no visible binding for global
  variable 'k.input'
arrayImpute : subwindow : cancel.handler: no visible binding for global
  variable 'k.input'
arrayImpute : subwindow : check.handler: no visible binding for global
  variable 'Method'
arrayImpute : subwindow : check.handler : <anonymous>: no visible
  binding for '<<-' assignment to 'impute'
arrayImpute : subwindow : check.handler : <anonymous>: no visible
  binding for '<<-' assignment to 'exp.info.name'
arrayImpute : subwindow : check.handler : <anonymous>: no visible
  binding for global variable 'impute'
arrayImpute : subwindow : check.handler : <anonymous>: no visible
  binding for global variable 'data.missing'
arrayImpute : subwindow : check.handler : <anonymous>: no visible
  binding for '<<-' assignment to 'kNN.impute'
arrayImpute : subwindow : check.handler : <anonymous>: no visible
  binding for '<<-' assignment to 'BPCA.impute'
arrayImpute : subwindow : check.handler : <anonymous>: no visible
  binding for '<<-' assignment to 'LLS.impute'
arrayImpute : subwindow : check.handler : <anonymous>: no visible
  binding for '<<-' assignment to 'RLSP.impute'
arrayImpute : subwindow : check.handler : <anonymous>: no visible
  binding for '<<-' assignment to 'missing.Name'
arrayImpute : subwindow : check.handler : <anonymous>: no visible
  binding for global variable 'missing.Name.temp'
arrayImpute : subwindow : check.handler : <anonymous>: no visible
  binding for global variable 'AVE.impute'
arrayImpute : subwindow : check.handler : <anonymous>: no visible
  binding for global variable 'kNN.impute'
arrayImpute : subwindow : check.handler : <anonymous>: no visible
  binding for global variable 'LLS.impute'
arrayImpute : subwindow : check.handler : <anonymous>: no visible
  binding for global variable 'RLSP.impute'
arrayImpute : subwindow : check.handler : <anonymous>: no visible
  binding for global variable 'BPCA.impute'
arrayImpute : subwindow : check.handler : <anonymous>: no visible
  binding for global variable 'User1.impute'
arrayImpute : subwindow : check.handler : <anonymous>: no visible
  binding for global variable 'User2.impute'
arrayImpute : subwindow : check.handler : <anonymous>: no visible
  binding for global variable 'missing.Name'
arrayImpute : subwindow : check.handler: no visible binding for global
  variable 'k.input'
arrayImpute : subwindow: no visible binding for '<<-' assignment to
  'k.input'
arrayImpute : subwindow: no visible binding for '<<-' assignment to
  'KK'
arrayImpute : subwindow: no visible binding for global variable 'KK'
arrayImpute : subwindow: no visible binding for global variable
  'k.input'
arrayImpute : kNNimpute: no visible binding for '<<-' assignment to
  'kNNimpute.temp'
arrayImpute : kNNimpute: no visible binding for global variable
  'data.missing'
arrayImpute : kNNimpute: no visible binding for '<<-' assignment to
  'kNN.impute'
arrayImpute : kNNimpute: no visible binding for global variable
  'kNNimpute.temp'
arrayImpute : kNNimpute: no visible binding for '<<-' assignment to
  'missing.Name'
arrayImpute : kNNimpute: no visible binding for global variable
  'missing.Name.temp'
arrayImpute : kNNimpute: no visible binding for global variable
  'AVE.impute'
arrayImpute : kNNimpute: no visible binding for global variable
  'kNN.impute'
arrayImpute : kNNimpute: no visible binding for global variable
  'LLS.impute'
arrayImpute : kNNimpute: no visible binding for global variable
  'RLSP.impute'
arrayImpute : kNNimpute: no visible binding for global variable
  'BPCA.impute'
arrayImpute : kNNimpute: no visible binding for global variable
  'User1.impute'
arrayImpute : kNNimpute: no visible binding for global variable
  'User2.impute'
arrayImpute : kNNimpute: no visible binding for global variable
  'missing.Name'
arrayImpute : LSimpute: no visible binding for '<<-' assignment to
  'LLS.impute'
arrayImpute : LSimpute: no visible binding for global variable
  'LLS.impute'
arrayImpute : LSimpute: no visible binding for '<<-' assignment to
  'missing.Name'
arrayImpute : LSimpute: no visible binding for global variable
  'missing.Name.temp'
arrayImpute : LSimpute: no visible binding for global variable
  'AVE.impute'
arrayImpute : LSimpute: no visible binding for global variable
  'kNN.impute'
arrayImpute : LSimpute: no visible binding for global variable
  'RLSP.impute'
arrayImpute : LSimpute: no visible binding for global variable
  'BPCA.impute'
arrayImpute : LSimpute: no visible binding for global variable
  'User1.impute'
arrayImpute : LSimpute: no visible binding for global variable
  'User2.impute'
arrayImpute : LSimpute: no visible binding for global variable
  'missing.Name'
arrayImpute : LSimpute: no visible binding for '<<-' assignment to
  'LS.flag'
arrayImpute : RLSPimpute: no visible binding for '<<-' assignment to
  'RLSP.impute'
arrayImpute : RLSPimpute: no visible binding for global variable
  'data.missing'
arrayImpute : RLSPimpute: no visible binding for global variable
  'RLSP.impute'
arrayImpute : RLSPimpute: no visible binding for '<<-' assignment to
  'missing.Name'
arrayImpute : RLSPimpute: no visible binding for global variable
  'missing.Name.temp'
arrayImpute : RLSPimpute: no visible binding for global variable
  'AVE.impute'
arrayImpute : RLSPimpute: no visible binding for global variable
  'kNN.impute'
arrayImpute : RLSPimpute: no visible binding for global variable
  'LLS.impute'
arrayImpute : RLSPimpute: no visible binding for global variable
  'BPCA.impute'
arrayImpute : RLSPimpute: no visible binding for global variable
  'User1.impute'
arrayImpute : RLSPimpute: no visible binding for global variable
  'User2.impute'
arrayImpute : RLSPimpute: no visible binding for global variable
  'missing.Name'
arrayImpute : RLSPimpute: no visible binding for '<<-' assignment to
  'RLSP.flag'
arrayImpute : BPCAfill: no visible binding for '<<-' assignment to
  'BPCA.impute'
arrayImpute : BPCAfill: no visible binding for '<<-' assignment to
  'missing.Name'
arrayImpute : BPCAfill: no visible binding for global variable
  'missing.Name.temp'
arrayImpute : BPCAfill: no visible binding for global variable
  'AVE.impute'
arrayImpute : BPCAfill: no visible binding for global variable
  'kNN.impute'
arrayImpute : BPCAfill: no visible binding for global variable
  'LLS.impute'
arrayImpute : BPCAfill: no visible binding for global variable
  'RLSP.impute'
arrayImpute : BPCAfill: no visible binding for global variable
  'BPCA.impute'
arrayImpute : BPCAfill: no visible binding for global variable
  'User1.impute'
arrayImpute : BPCAfill: no visible binding for global variable
  'User2.impute'
arrayImpute : BPCAfill: no visible binding for global variable
  'missing.Name'
arrayImpute: no visible binding for '<<-' assignment to 'main'
arrayImpute: no visible binding for global variable 'main'
arrayImpute: no visible binding for '<<-' assignment to 'geneList'
arrayImpute: no visible binding for global variable 'geneList'
arrayImpute: no visible binding for '<<-' assignment to 'ChipList'
arrayImpute: no visible binding for global variable 'ChipList'
arrayImpute: no visible binding for '<<-' assignment to 'outputText'
arrayImpute: no visible binding for global variable 'outputText'
arrayImpute: no visible binding for '<<-' assignment to 'new.text'
Found possibly global 'T' or 'F' in the following function:
  arrayImpute
* 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: 'gtkCListNew' is deprecated.
  Warning: 'method' 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