• using R version 2.11.0 Under development (unstable) (2010-01-14 r50981)
• using session charset: UTF-8
• 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 for executable files ... OK
• checking whether package 'arrayImpute' 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 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 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