* using log directory 'd:/Rcompile/CRANpkg/local/2.8/arrayImpute.Rcheck' * using R version 2.8.1 beta (2008-12-12 r47183) * 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 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 : : no visible binding for '<<-' assignment to 'data.missing' arrayImpute : Mnu.read.file.handler : : no visible binding for '<<-' assignment to 'exp.info.name' arrayImpute : Mnu.read.file.handler : : no visible binding for global variable 'data.missing' arrayImpute : Mnu.read.file.handler : : no visible binding for '<<-' assignment to 'AVE.impute' arrayImpute : Mnu.read.file.handler : : no visible binding for global variable 'missing.I' arrayImpute : Mnu.read.file.handler : : no visible binding for '<<-' assignment to 'missing.Name' arrayImpute : Mnu.read.file.handler : : no visible binding for global variable 'missing.Name' arrayImpute : Mnu.read.file.handler : : no visible binding for global variable 'AVE.impute' arrayImpute : Mnu.read.file.handler : : no visible binding for global variable 'exp.info.name' arrayImpute : Mnu.read.file.handler : : no visible binding for '<<-' assignment to 'Result.Save' arrayImpute : Mnu.read.file.handler : : no visible binding for global variable 'Result.Save' arrayImpute : Mnu.read.file.handler : : no visible binding for global variable 'new.text' arrayImpute : Mnu.read.file.handler : : no visible binding for global variable 'outputText' arrayImpute : Mnu.read.location.file.handler : : no visible binding for '<<-' assignment to 'gene.location' arrayImpute : Mnu.read.location.file.handler : : no visible binding for '<<-' assignment to 'gene.location.o' arrayImpute : Mnu.read.location.file.handler : : no visible binding for '<<-' assignment to 'exp.info.name' arrayImpute : Mnu.read.location.file.handler : : 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 : : no visible binding for '<<-' assignment to 'User1.impute' arrayImpute : Mnu.UserDef1.handler : : no visible binding for global variable 'User1.impute' arrayImpute : Mnu.UserDef1.handler : : no visible binding for global variable 'data.missing' arrayImpute : Mnu.UserDef1.handler : : no visible binding for '<<-' assignment to 'missing.Name' arrayImpute : Mnu.UserDef1.handler : : no visible binding for global variable 'missing.Name.temp' arrayImpute : Mnu.UserDef1.handler : : no visible binding for global variable 'AVE.impute' arrayImpute : Mnu.UserDef1.handler : : no visible binding for global variable 'kNN.impute' arrayImpute : Mnu.UserDef1.handler : : no visible binding for global variable 'LLS.impute' arrayImpute : Mnu.UserDef1.handler : : no visible binding for global variable 'RLSP.impute' arrayImpute : Mnu.UserDef1.handler : : no visible binding for global variable 'BPCA.impute' arrayImpute : Mnu.UserDef1.handler : : no visible binding for global variable 'User2.impute' arrayImpute : Mnu.UserDef1.handler : : no visible binding for global variable 'missing.Name' arrayImpute : Mnu.UserDef2.handler : : no visible binding for '<<-' assignment to 'User2.impute' arrayImpute : Mnu.UserDef2.handler : : no visible binding for global variable 'User2.impute' arrayImpute : Mnu.UserDef2.handler : : no visible binding for global variable 'data.missing' arrayImpute : Mnu.UserDef2.handler : : no visible binding for '<<-' assignment to 'missing.Name' arrayImpute : Mnu.UserDef2.handler : : no visible binding for global variable 'missing.Name.temp' arrayImpute : Mnu.UserDef2.handler : : no visible binding for global variable 'AVE.impute' arrayImpute : Mnu.UserDef2.handler : : no visible binding for global variable 'kNN.impute' arrayImpute : Mnu.UserDef2.handler : : no visible binding for global variable 'LLS.impute' arrayImpute : Mnu.UserDef2.handler : : no visible binding for global variable 'RLSP.impute' arrayImpute : Mnu.UserDef2.handler : : no visible binding for global variable 'BPCA.impute' arrayImpute : Mnu.UserDef2.handler : : no visible binding for global variable 'User1.impute' arrayImpute : Mnu.UserDef2.handler : : 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 : : no visible binding for '<<-' assignment to 'impute' arrayImpute : subwindow : check.handler : : no visible binding for '<<-' assignment to 'exp.info.name' arrayImpute : subwindow : check.handler : : no visible binding for global variable 'impute' arrayImpute : subwindow : check.handler : : no visible binding for global variable 'data.missing' arrayImpute : subwindow : check.handler : : no visible binding for '<<-' assignment to 'kNN.impute' arrayImpute : subwindow : check.handler : : no visible binding for '<<-' assignment to 'BPCA.impute' arrayImpute : subwindow : check.handler : : no visible binding for '<<-' assignment to 'LLS.impute' arrayImpute : subwindow : check.handler : : no visible binding for '<<-' assignment to 'RLSP.impute' arrayImpute : subwindow : check.handler : : no visible binding for '<<-' assignment to 'missing.Name' arrayImpute : subwindow : check.handler : : no visible binding for global variable 'missing.Name.temp' arrayImpute : subwindow : check.handler : : no visible binding for global variable 'AVE.impute' arrayImpute : subwindow : check.handler : : no visible binding for global variable 'kNN.impute' arrayImpute : subwindow : check.handler : : no visible binding for global variable 'LLS.impute' arrayImpute : subwindow : check.handler : : no visible binding for global variable 'RLSP.impute' arrayImpute : subwindow : check.handler : : no visible binding for global variable 'BPCA.impute' arrayImpute : subwindow : check.handler : : no visible binding for global variable 'User1.impute' arrayImpute : subwindow : check.handler : : no visible binding for global variable 'User2.impute' arrayImpute : subwindow : check.handler : : 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 cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * creating arrayImpute-Ex.R ... 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. * creating arrayImpute-manual.tex ... OK * checking arrayImpute-manual.tex using pdflatex ... OK