BioC 3.3: CHECK report for IsoGeneGUI on windows2.bioconductor.org

Package: IsoGeneGUI

Version: 2.7.0

Command: rm -rf IsoGeneGUI.buildbin-libdir IsoGeneGUI.Rcheck && mkdir IsoGeneGUI.buildbin-libdir IsoGeneGUI.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IsoGeneGUI.buildbin-libdir IsoGeneGUI_2.7.0.tar.gz >IsoGeneGUI.Rcheck\00install.out 2>&1 && cp IsoGeneGUI.Rcheck\00install.out IsoGeneGUI-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=IsoGeneGUI.buildbin-libdir --install="check:IsoGeneGUI-install.out" --force-multiarch --no-vignettes --timings IsoGeneGUI_2.7.0.tar.gz

StartedAt: 2015-10-27 03:28:01 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:30:50 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 168.6 seconds

RetCode: 0

Status:  OK

CheckDir: IsoGeneGUI.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf IsoGeneGUI.buildbin-libdir IsoGeneGUI.Rcheck && mkdir IsoGeneGUI.buildbin-libdir IsoGeneGUI.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IsoGeneGUI.buildbin-libdir IsoGeneGUI_2.7.0.tar.gz >IsoGeneGUI.Rcheck\00install.out 2>&1 && cp IsoGeneGUI.Rcheck\00install.out IsoGeneGUI-install.out  && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=IsoGeneGUI.buildbin-libdir --install="check:IsoGeneGUI-install.out" --force-multiarch --no-vignettes --timings IsoGeneGUI_2.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/IsoGeneGUI.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IsoGeneGUI/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IsoGeneGUI' version '2.7.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'IsoGeneGUI' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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
* loading checks for arch 'i386'
** 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 whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** 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 whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* checking 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
CalcStat: no visible binding for '<<-' assignment to 'Direction'
CalcStat: no visible binding for global variable 'StatVal'
CalcStat: no visible binding for global variable 'Direction'
CalcStat: no visible binding for '<<-' assignment to 'E2Val'
CalcStat: no visible binding for '<<-' assignment to 'MVal'
CalcStat: no visible binding for '<<-' assignment to 'WilliamsVal'
CalcStat: no visible binding for '<<-' assignment to 'MarcusVal'
CalcStat: no visible binding for '<<-' assignment to 'ModMVal'
ChooseStat : on.Ok: no visible binding for '<<-' assignment to
  'statUsed'
ChooseStat : on.Cancel: no visible binding for '<<-' assignment to
  'statUsed'
ExactE2: no visible binding for global variable 'tt'
ExactE2 : Calc.Asymp: no visible binding for '<<-' assignment to
  'exprs2Asymp'
ExactE2 : Calc.Asymp: no visible binding for global variable 'exprs'
ExactE2 : Calc.Asymp: no visible binding for global variable
  'exprs2Asymp'
ExactE2 : Calc.Asymp: no visible binding for '<<-' assignment to
  'res.Asymp'
ExactE2 : Calc.Asymp: no visible binding for global variable 'dose'
ExactE2 : Calc.Asymp: no visible binding for '<<-' assignment to
  'pval.Asymp'
ExactE2 : Calc.Asymp: no visible binding for global variable
  'res.Asymp'
ExactE2 : Calc.Asymp: no visible binding for '<<-' assignment to
  'ProbeID'
ExactE2 : Calc.Asymp: no visible binding for '<<-' assignment to
  'Mu.Diff.Asymp'
ExactE2 : Calc.Asymp: no visible binding for '<<-' assignment to
  'E2Val.Asymp'
ExactE2 : Calc.Asymp: no visible binding for global variable 'ProbeID'
ExactE2 : Calc.Asymp: no visible binding for global variable
  'treeWidget'
ExactE2 : AdjustBut: no visible binding for global variable
  'E2Val.Asymp'
ExactE2 : AdjustBut: no visible binding for '<<-' assignment to
  'FDRval'
ExactE2 : AdjustBut: no visible binding for global variable 'res.Asymp'
ExactE2 : AdjustBut: no visible binding for global variable
  'treeWidget'
ExactE2 : AdjustBut: no visible binding for global variable 'FDRval'
ExactE2 : AdjustBut: no visible binding for global variable
  'pval.Asymp'
ExactE2 : AdjustBut: no visible binding for global variable
  'exprs2Asymp'
ExactE2 : AdjustBut: no visible binding for global variable
  'Mu.Diff.Asymp'
ExactE2 : AdjustBut: no visible binding for '<<-' assignment to
  'Res.Asymtot'
ExactE2 : AdjustBut: no visible binding for global variable 'ProbeID'
ExactE2 : AdjustBut: no visible binding for global variable
  'Res.Asymtot'
ExactE2 : AdjustBut: no visible binding for '<<-' assignment to
  'SigGenes.AsymptotE2'
ExactE2 : savesiggene: no visible binding for global variable
  'SigGenes.AsymptotE2'
ExactE2 : saveallgene: no visible binding for '<<-' assignment to
  'Pval.AllGenes.Asymp'
ExactE2 : saveallgene: no visible binding for global variable
  'Res.Asymtot'
ExactE2 : PlotBut : rankPlot: no visible binding for global variable
  'res.Asymp'
ExactE2 : PlotBut : rankPlot: no visible binding for global variable
  'pval.Asymp'
ExactE2 : PlotBut : rankPlot: no visible binding for global variable
  'exprs2Asymp'
ExactE2 : PlotBut : rankPlot: no visible binding for global variable
  'adjpBH'
ExactE2 : PlotBut : rankPlot: no visible binding for global variable
  'adjpBY'
ExactE2 : PlotBut : rankPlot: no visible binding for global variable
  'adjpSS'
ExactE2 : PlotBut : rankPlot: no visible binding for global variable
  'adjpSD'
ExactE2 : PlotBut : rankPlot: no visible binding for global variable
  'adjpHolm'
ExactE2 : PlotBut : rankPlot: no visible binding for global variable
  'adjpHoch'
ExactE2 : PlotBut : rankPlot: no visible binding for global variable
  'adjpBon'
ExactE2 : PlotBut : rankPlot: no visible binding for global variable
  'FDRval'
ExactE2 : PlotBut : rankPlot: no visible binding for global variable
  'result3'
ExactE2 : PlotBut : E2vsDiffPlot: no visible binding for global
  variable 'Mu.Diff.Asymp'
ExactE2 : PlotBut : E2vsDiffPlot: no visible binding for global
  variable 'res.Asymp'
IsoGeneGUI: no visible binding for '<<-' assignment to 'tt'
IsoGeneGUI: no visible binding for global variable 'tt'
IsoGeneGUI: no visible binding for '<<-' assignment to 'SeedNum'
IsoGeneGUI : <anonymous>: no visible binding for global variable
  'treeWidget'
IsoGeneGUI: no visible binding for '<<-' assignment to 'treeWidget'
IsoGeneGUI: no visible binding for global variable 'treeWidget'
IsoPlotSldr: no visible binding for '<<-' assignment to 'statSAMplot'
IsoPlotSldr: no visible binding for global variable 'statUsed'
IsoPlotSldr: no visible binding for '<<-' assignment to 'pos'
IsoPlotSldr: no visible binding for '<<-' assignment to 'AllFDR'
IsoPlotSldr: no visible binding for global variable 'SAMRes'
IsoPlotSldr: no visible binding for global variable 'statSAMplot'
IsoPlotSldr: no visible binding for '<<-' assignment to 'Delta.table'
IsoPlotSldr: no visible binding for global variable 'AllFDR'
IsoPlotSldr: no visible binding for global variable 'Delta.table'
IsoPlotSldr: no visible binding for '<<-' assignment to 'labelText'
IsoPlotSldr: no visible binding for global variable 'labelText'
IsoPlotSldr : inputDelta: no visible binding for global variable
  'Delta.table'
IsoPlotSldr : inputDelta: no visible binding for '<<-' assignment to
  'pos'
IsoPlotSldr : inputDelta: no visible binding for '<<-' assignment to
  'delta.now'
IsoPlotSldr : showSigSAM: no visible binding for '<<-' assignment to
  'siggeneSAM'
IsoPlotSldr : showSigSAM: no visible binding for global variable
  'siggeneSAM'
IsoPlotSldr : showSigSAM: no visible binding for global variable
  'statSAMplot'
IsoPlotSldr : savegene: no visible binding for '<<-' assignment to
  'siggeneSAM'
IsoPlotSldr : saveAllgene: no visible binding for '<<-' assignment to
  'AllgeneSAM'
IsoPlotSldr : showDelta: no visible binding for global variable
  'Delta.table'
IsoPlotSldr : draw: no visible binding for '<<-' assignment to 'pos'
IsoPlotSldr : draw: no visible binding for '<<-' assignment to
  'delta.now'
IsoPlotSldr : draw: no visible binding for global variable
  'Delta.table'
IsoPlotSldr : draw: no visible binding for global variable 'pos'
IsoPlotSldr : draw: no visible binding for '<<-' assignment to
  'labelText'
IsoPlotSldr : draw: no visible binding for global variable 'labelText'
IsoPlotSldr : draw: no visible binding for global variable 'delta.now'
IsoPlotSldr : onExit: no visible binding for '<<-' assignment to
  'ReturnVal'
IsoStat: no visible binding for '<<-' assignment to 'E2Val'
IsoStat: no visible binding for '<<-' assignment to 'SeE2Val'
IsoStat: no visible binding for '<<-' assignment to 'MVal'
IsoStat: no visible binding for '<<-' assignment to 'SeMVal'
IsoStat: no visible binding for '<<-' assignment to 'WilliamsVal'
IsoStat: no visible binding for '<<-' assignment to 'SeWilliamsVal'
IsoStat: no visible binding for '<<-' assignment to 'MarcusVal'
IsoStat: no visible binding for '<<-' assignment to 'SeMarcusVal'
IsoStat: no visible binding for '<<-' assignment to 'ModMVal'
IsoStat: no visible binding for '<<-' assignment to 'SeModMVal'
Isoplot: no visible binding for global variable 'tt'
Isoplot : OnOK: no visible binding for global variable 'tt'
Isoplot : OnOK : plotIso: no visible binding for global variable 'dose'
Isoplot : OnOK : plotIso: no visible binding for global variable
  'exprs'
Isoplot : OnOK: no visible binding for global variable 'dose'
Isoplot : OnOK: no visible binding for global variable 'exprs'
Isoplot : OnOK: no visible binding for '<<-' assignment to
  'genenameVal'
Isoplot : OnOK: no visible binding for global variable 'genenameVal'
Isoplot : onCancel: no visible binding for global variable 'tt'
IsopvalPlot: no visible binding for global variable 'tt'
IsopvalPlot : OnOK: no visible binding for global variable 'tt'
IsopvalPlot : OnOK : plotIso: no visible binding for global variable
  'dose'
IsopvalPlot : OnOK : plotIso: no visible binding for global variable
  'exprs'
IsopvalPlot : OnOK : plotIso: no visible binding for global variable
  'SeedNum'
IsopvalPlot : OnOK: no visible binding for global variable 'exprs'
IsoqqstatMOD: no visible binding for global variable 'dose'
IsoqqstatMOD: no visible binding for global variable 'exprs2SAM'
IsoqqstatMOD: no visible binding for global variable 'fudgeVal'
IsoqqstatMOD: no visible binding for global variable 'samPermute'
IsoqqstatMOD: no visible binding for global variable 'NumPermval'
Permutation: no visible binding for global variable 'tt'
Permutation: no visible binding for '<<-' assignment to 'SavefileName'
Permutation: no visible binding for global variable 'SavefileName'
Permutation : Calc.Permut: no visible binding for global variable
  'asym'
Permutation : Calc.Permut: no visible binding for global variable
  'exprs'
Permutation : Calc.Permut: no visible binding for global variable
  'dose'
Permutation : Calc.Permut: no visible binding for global variable
  'SeedNum'
Permutation : Calc.Permut: no visible binding for global variable
  'treeWidget'
Permutation : Calc.Permut: no visible binding for global variable
  'fileRwd'
Permutation: no visible binding for '<<-' assignment to 'PermuteText3'
Permutation: no visible binding for global variable 'PermuteText3'
Permutation: no visible binding for '<<-' assignment to 'PermuteText4'
Permutation: no visible binding for global variable 'PermuteText4'
Permutation: no visible binding for '<<-' assignment to 'pvalName'
Permutation: no visible binding for global variable 'pvalName'
Permutation : PermResBut: no visible binding for global variable
  'exprs2Perm'
Permutation : PermResBut: no visible binding for '<<-' assignment to
  'meandifPerm'
Permutation : PermResBut: no visible binding for global variable 'dose'
Permutation : PermResBut: no visible binding for global variable
  'meandifPerm'
Permutation : PermResBut: no visible binding for global variable
  'RawPval'
Permutation : PermResBut: no visible binding for '<<-' assignment to
  'FDRval'
Permutation : PermResBut: no visible binding for global variable
  'treeWidget'
Permutation : PermResBut: no visible binding for global variable
  'FDRval'
Permutation : PermResBut: no visible binding for global variable
  'matchID'
Permutation : PermResBut: no visible binding for global variable
  'Direction'
Permutation : PermResBut: no visible binding for global variable
  'ProbeID'
Permutation : savesiggene: no visible binding for global variable
  'listgene'
Permutation : saveallgene: no visible binding for global variable
  'listgene2'
Permutation : PlotBut: no visible binding for '<<-' assignment to
  'stat.list2'
Permutation : PlotBut: no visible binding for '<<-' assignment to
  'twosd.pvalmat'
Permutation : PlotBut: no visible binding for global variable
  'twosided.RawPval'
Permutation : PlotBut: no visible binding for global variable
  'twosd.pvalmat'
Permutation : PlotBut: no visible binding for global variable
  'stat.list2'
Permutation : PlotBut : rankPlot: no visible binding for global
  variable 'twosd.pvalmat'
Permutation : PlotBut : rankPlot: no visible binding for global
  variable 'matchID'
Permutation : PlotBut : rankPlot: no visible binding for global
  variable 'linecd'
Permutation : PlotBut : rankPlot: no visible binding for global
  variable 'FDRval'
Permutation : PlotBut : E2vsDiffPlot: no visible binding for global
  variable 'meandifPerm'
PermuteSAM: no visible binding for global variable 'tt'
PermuteSAM: no visible binding for '<<-' assignment to 'samPermute'
PermuteSAM: no visible binding for global variable 'samPermute'
PermuteSAM : ShowSEplot: no visible binding for global variable 'exprs'
PermuteSAM : ShowSEplot: no visible binding for global variable
  'matchIDtemp'
PermuteSAM : ShowSEplot: no visible binding for global variable 'dose'
PermuteSAM : ShowSEplot: no visible binding for '<<-' assignment to
  'matchIDtemp'
PermuteSAM: no visible binding for '<<-' assignment to 'SavefileName'
PermuteSAM: no visible binding for global variable 'SavefileName'
PermuteSAM : Calc.PermutSAM: no visible binding for '<<-' assignment to
  'rbVal2'
PermuteSAM : Calc.PermutSAM: no visible binding for '<<-' assignment to
  'fudgeVal'
PermuteSAM : Calc.PermutSAM: no visible binding for global variable
  'samPermute'
PermuteSAM : Calc.PermutSAM: no visible binding for global variable
  'rbVal2'
PermuteSAM : Calc.PermutSAM: no visible binding for '<<-' assignment to
  'exprs2SAM'
PermuteSAM : Calc.PermutSAM: no visible binding for global variable
  'exprs'
PermuteSAM : Calc.PermutSAM: no visible binding for '<<-' assignment to
  'matchID'
PermuteSAM : Calc.PermutSAM: no visible binding for global variable
  'exprs2SAM'
PermuteSAM : Calc.PermutSAM: no visible binding for global variable
  'dose'
PermuteSAM : Calc.PermutSAM: no visible binding for global variable
  'SeedNum'
PermuteSAM : Calc.PermutSAM: no visible binding for global variable
  'fudgeVal'
PermuteSAM : Calc.PermutSAM: no visible binding for global variable
  'treeWidget'
PermuteSAM : Calc.PermutSAM: no visible binding for '<<-' assignment to
  'DirectionSAM'
PermuteSAM : Calc.PermutSAM: no visible binding for '<<-' assignment to
  'MeanDiffSAM'
PermuteSAM : Calc.PermutSAM: no visible binding for global variable
  'MeanDiffSAM'
PermuteSAM : Calc.PermutSAM: no visible binding for global variable
  'fileRwd'
PermuteSAM: no visible binding for '<<-' assignment to 'PermuteText1'
PermuteSAM: no visible binding for global variable 'PermuteText1'
PermuteSAM: no visible binding for '<<-' assignment to 'PermuteText2'
PermuteSAM: no visible binding for global variable 'PermuteText2'
PermuteSAM: no visible binding for '<<-' assignment to 'pvalName'
PermuteSAM: no visible binding for global variable 'pvalName'
PermuteSAM : onCancel: no visible binding for global variable
  'SAMRes.temp'
PermuteSAM : onCancel: no visible binding for global variable
  'exprs2SAM.temp'
PermuteSAM : onCancel: no visible binding for global variable
  'samPermute'
PermuteSAM : onOK: no visible binding for global variable 'SAMRes.temp'
PermuteSAM : onOK: no visible binding for global variable
  'exprs2SAM.temp'
PermuteSAM : onOK: no visible binding for global variable 'samPermute'
PlotFPDlt: no visible binding for '<<-' assignment to 'AllFDR'
PlotFPDlt: no visible binding for global variable 'SAMRes'
PlotFPDlt: no visible binding for global variable 'statUsed'
PlotFPDlt: no visible binding for global variable 'AllFDR'
PlotFPDlt : plotFPD: no visible binding for global variable 'SAMRes'
PlotFdrDlt: no visible binding for '<<-' assignment to 'AllFDR'
PlotFdrDlt: no visible binding for global variable 'SAMRes'
PlotFdrDlt: no visible binding for global variable 'statUsed'
PlotFdrDlt: no visible binding for global variable 'AllFDR'
PlotSigDlt: no visible binding for '<<-' assignment to 'AllFDR'
PlotSigDlt: no visible binding for global variable 'SAMRes'
PlotSigDlt: no visible binding for global variable 'statUsed'
PlotSigDlt: no visible binding for global variable 'AllFDR'
SEPlot: no visible binding for global variable 'SeModMVal'
SaveGraph: no visible global function definition for 'x'
SaveGraph: no visible binding for global variable 'buttonFramePlot'
SaveGraph: no visible binding for global variable 'CopyToClip'
SaveGraph: no visible binding for global variable 'img'
Setseed : OnOK: no visible binding for '<<-' assignment to 'SeedNum'
Setseed : OnOK: no visible binding for global variable 'SeedNum'
Setseed : OnOK: no visible binding for global variable 'tt'
UserPlot : onCancel: no visible binding for '<<-' assignment to
  'ReturnVal'
UserPlotting: no visible binding for '<<-' assignment to 'ExactPval.E2'
UserPlotting: no visible binding for global variable 'pval.Asymp'
UserPlotting: no visible binding for '<<-' assignment to 'FoldChange'
UserPlotting: no visible binding for global variable 'Mu.Diff.Asymp'
UserPlotting: no visible binding for '<<-' assignment to 'E2.value'
UserPlotting: no visible binding for global variable 'E2Val.Asymp'
UserPlotting: no visible binding for global variable 'E2Val'
UserPlotting: no visible binding for '<<-' assignment to 'Marcus.value'
UserPlotting: no visible binding for global variable 'MarcusVal'
UserPlotting: no visible binding for '<<-' assignment to
  'ModifiedM.value'
UserPlotting: no visible binding for global variable 'ModMVal'
UserPlotting: no visible binding for '<<-' assignment to 'M.value'
UserPlotting: no visible binding for global variable 'MVal'
UserPlotting: no visible binding for '<<-' assignment to
  'Williams.value'
UserPlotting: no visible binding for global variable 'WilliamsVal'
UserPlotting: no visible binding for '<<-' assignment to
  'twosided.RawPval'
UserPlotting: no visible binding for global variable 'RawPval'
UserPlotting: no visible binding for '<<-' assignment to
  'PermutationPval.E2'
UserPlotting: no visible binding for global variable 'twosided.RawPval'
UserPlotting: no visible binding for '<<-' assignment to
  'PermutationPval.Williams'
UserPlotting: no visible binding for '<<-' assignment to
  'PermutationPval.Marcus'
UserPlotting: no visible binding for '<<-' assignment to
  'PermutationPval.M'
UserPlotting: no visible binding for '<<-' assignment to
  'PermutationPval.ModM'
UserPlotting: no visible binding for global variable 'meandifPerm'
UserPlotting: no visible binding for global variable 'dose'
UserPlotting: no visible binding for global variable 'exprs2Perm'
UserPlotting: no visible binding for global variable 'SAMRes'
UserPlotting: no visible binding for global variable 'MeanDiffSAM'
UserPlotting: no visible binding for global variable 'exprs2SAM'
UserPlotting: no visible binding for '<<-' assignment to 'SAM.M.value'
UserPlotting: no visible binding for '<<-' assignment to 'SAM.E2.value'
UserPlotting: no visible binding for '<<-' assignment to
  'SAM.Marcus.value'
UserPlotting: no visible binding for '<<-' assignment to
  'SAM.Williams.value'
UserPlotting: no visible binding for '<<-' assignment to
  'SAM.ModifiedM.value'
UserPlotting: no visible binding for '<<-' assignment to 'M.q.value'
UserPlotting: no visible binding for '<<-' assignment to 'E2.q.value'
UserPlotting: no visible binding for '<<-' assignment to
  'Marcus.q.value'
UserPlotting: no visible binding for '<<-' assignment to
  'Williams.q.value'
UserPlotting: no visible binding for '<<-' assignment to
  'ModifiedM.q.value'
browse : OnOK: no visible binding for '<<-' assignment to 'pvalName'
browse : OnOK: no visible binding for global variable 'pvalName'
browse : OnOK: no visible binding for global variable 'exprs'
browse : OnOK: no visible binding for '<<-' assignment to 'StatVal'
browse : OnOK: no visible binding for global variable 'dose'
browse : OnOK: no visible binding for global variable 'treeWidget'
browse2 : OnOK: no visible binding for '<<-' assignment to 'pvalName'
browse2 : OnOK: no visible binding for global variable 'pvalName'
browse2 : OnOK: no visible binding for global variable 'exprs'
browse2 : OnOK: no visible binding for '<<-' assignment to
  'MeanDiffSAM'
browse2 : OnOK: no visible binding for global variable 'dose'
browse2 : OnOK: no visible binding for global variable 'treeWidget'
doGORIC: no visible binding for global variable 'tt'
doGORIC : OnOK: no visible binding for global variable 'exprs'
doGORIC : OnOK: no visible binding for '<<-' assignment to
  'response.gene'
doGORIC : OnOK: no visible binding for global variable 'dose'
doGORIC : OnOK: no visible binding for '<<-' assignment to 'models'
doGORIC : OnOK: no visible binding for global variable 'models'
doGORIC : OnOK: no visible binding for '<<-' assignment to
  'GORICoutput'
doGORIC : OnOK: no visible binding for '<<-' assignment to
  'modelSelected'
doGORIC : OnOK: no visible binding for global variable 'GORICoutput'
doGORIC : OnOK: no visible binding for '<<-' assignment to
  'maxProbability'
doGORIC : OnOK: no visible binding for global variable 'treeWidget'
doGORIC : OnOK: no visible binding for global variable 'modelSelected'
doGORIC : OnOK: no visible binding for global variable 'maxProbability'
doGORIC : saveResults: no visible binding for global variable
  'GORICoutput'
doGORIC : PlotAll : PlotAllModels: no visible binding for global
  variable 'GORICoutput'
doGORIC : PlotBest : PlotBestModel: no visible binding for global
  variable 'modelSelected'
doORCME: no visible binding for global variable 'tt'
doORCME : calculateLambdaK: no visible binding for global variable
  'exprs'
doORCME : calculateLambdaK: no visible binding for global variable
  'dose'
doORCME : OnOK: no visible binding for global variable 'exprs'
doORCME : OnOK: no visible binding for global variable 'dose'
doORCME : OnOK: no visible binding for '<<-' assignment to
  'clusteringData'
doORCME : OnOK: no visible binding for '<<-' assignment to
  'ORCMEoutput'
doORCME : OnOK: no visible binding for global variable 'clusteringData'
doORCME : OnOK: no visible binding for '<<-' assignment to 'nClusters'
doORCME : OnOK: no visible binding for global variable 'ORCMEoutput'
doORCME : OnOK: no visible binding for global variable 'treeWidget'
doORCME : OnOK: no visible binding for global variable 'nClusters'
doORCME : saveClusters: no visible binding for global variable
  'ORCMEoutput'
doORIClust: no visible binding for global variable 'tt'
doORIClust : OnOK: no visible binding for global variable 'exprs'
doORIClust : OnOK: no visible binding for '<<-' assignment to
  'oriccOutput'
doORIClust : OnOK: no visible binding for global variable 'dose'
doORIClust : OnOK: no visible binding for global variable 'oriccOutput'
doORIClust : OnOK: no visible binding for global variable 'tt'
doORIClust : OnOK: no visible binding for '<<-' assignment to
  'nClustersORICC'
doORIClust : OnOK: no visible binding for global variable 'treeWidget'
doORIClust : OnOK: no visible binding for global variable
  'nClustersORICC'
doORIClust : saveClusters: no visible binding for global variable
  'oriccOutput'
exit: no visible binding for global variable 'tt'
get.ResSAM: no visible binding for global variable 'delta.now'
get.ResSAM: no visible binding for global variable 'AllFDR'
get.ResSAM: no visible binding for global variable 'SAMRes'
get.ResSAM: no visible binding for global variable 'statSAMplot'
get.ResSAM: no visible binding for global variable 'exprs2SAM'
get.ResSAM: no visible binding for global variable 'MeanDiffSAM'
get.ResSAM: no visible binding for global variable 'DirectionSAM'
getDose: no visible binding for '<<-' assignment to 'fileDose'
getDose: no visible binding for global variable 'fileDose'
loadDataSet: no visible binding for global variable 'tt'
loadDataSet : OnOK: no visible binding for global variable 'treeWidget'
loadDataSet : OnOK: no visible binding for global variable 'tt'
loadDataSet : onCancel: no visible binding for '<<-' assignment to
  'ReturnVal'
loadDataSet : onCancel: no visible binding for global variable 'tt'
openFile : getExprs: no visible binding for '<<-' assignment to
  'fileExprs'
openFile : getExprs: no visible binding for global variable 'fileExprs'
openFile: no visible binding for '<<-' assignment to 'fileDose'
openFile: no visible binding for '<<-' assignment to 'fileExprs'
openFile: no visible binding for global variable 'fileDose'
openFile: no visible binding for global variable 'fileExprs'
openFile : OnOK: no visible binding for global variable 'fileExprs'
openFile : OnOK: no visible binding for global variable 'treeWidget'
openFile : onCancel: no visible binding for '<<-' assignment to
  'ReturnVal'
openFile : onCancel: no visible binding for global variable 'tt'
orQAE2: no visible binding for global variable 'tt'
orQAE2: no visible binding for global variable 'exprs'
orQAE2 : Calc.orQA: no visible binding for global variable 'exprs'
orQAE2 : Calc.orQA: no visible binding for global variable 'dose'
orQAE2 : Calc.orQA: no visible binding for '<<-' assignment to
  'res.orQA'
orQAE2 : Calc.orQA: no visible binding for '<<-' assignment to
  'pval.orQA'
orQAE2 : Calc.orQA: no visible binding for global variable 'res.orQA'
orQAE2 : Calc.orQA: no visible binding for '<<-' assignment to
  'ProbeID'
orQAE2 : Calc.orQA: no visible binding for '<<-' assignment to
  'Mu.Diff'
orQAE2 : Calc.orQA: no visible binding for global variable 'ProbeID'
orQAE2 : Calc.orQA: no visible binding for global variable 'treeWidget'
orQAE2 : AdjustBut: no visible binding for global variable 'pval.orQA'
orQAE2 : AdjustBut: no visible binding for '<<-' assignment to 'FDRval'
orQAE2 : AdjustBut: no visible binding for global variable 'res.orQA'
orQAE2 : AdjustBut: no visible binding for global variable 'treeWidget'
orQAE2 : AdjustBut: no visible binding for global variable 'FDRval'
orQAE2 : AdjustBut: no visible binding for global variable 'exprs2orqa'
orQAE2 : AdjustBut: no visible binding for '<<-' assignment to
  'Res.orQA'
orQAE2 : AdjustBut: no visible binding for global variable 'ProbeID'
orQAE2 : AdjustBut: no visible binding for global variable 'Mu.Diff'
orQAE2 : AdjustBut: no visible binding for global variable 'Res.orQA'
orQAE2 : AdjustBut: no visible binding for '<<-' assignment to
  'SigGenes.orqaE2'
orQAE2 : AdjustBut: no visible binding for '<<-' assignment to
  'result3'
orQAE2 : AdjustBut: no visible binding for global variable 'result3'
orQAE2 : savesiggene: no visible binding for global variable
  'SigGenes.orqaE2'
orQAE2 : saveallgene: no visible binding for '<<-' assignment to
  'Pval.AllGenes.orQA'
orQAE2 : saveallgene: no visible binding for global variable 'Res.orQA'
orQAE2 : saveallgene: no visible binding for global variable
  'Pval.AllGenes.orQA'
orQAE2 : PlotBut : rankPlot: no visible binding for global variable
  'exprs2orqa'
orQAE2 : PlotBut : rankPlot: no visible binding for global variable
  'pval.orQA'
orQAE2 : PlotBut : rankPlot: no visible binding for global variable
  'adjpBHorqa'
orQAE2 : PlotBut : rankPlot: no visible binding for global variable
  'adjpBYorqa'
orQAE2 : PlotBut : rankPlot: no visible binding for global variable
  'adjpSSorqa'
orQAE2 : PlotBut : rankPlot: no visible binding for global variable
  'adjpSDorqa'
orQAE2 : PlotBut : rankPlot: no visible binding for global variable
  'adjpHolmorqa'
orQAE2 : PlotBut : rankPlot: no visible binding for global variable
  'adjpHochorqa'
orQAE2 : PlotBut : rankPlot: no visible binding for global variable
  'adjpBonorqa'
orQAE2 : PlotBut : rankPlot: no visible binding for global variable
  'FDRval'
orQAE2 : PlotBut : rankPlot: no visible binding for global variable
  'result3'
orQAE2 : PlotBut : PVALSvsDiffPlot: no visible binding for global
  variable 'Mu.Diff'
orQAE2 : PlotBut : PVALSvsDiffPlot: no visible binding for global
  variable 'pval.orQA'
plotORCME: no visible binding for global variable 'tt'
plotORCME: no visible binding for global variable 'nClusters'
plotORCME: no visible binding for global variable 'dose'
plotORCME : OnOK : plotClusters: no visible binding for global variable
  'clusteringData'
plotORCME : OnOK : plotClusters: no visible binding for global variable
  'ORCMEoutput'
plotORCME : onCancel: no visible binding for global variable 'tt'
samplot2: no visible binding for global variable 'SAMRes'
samplot2: no visible binding for global variable 'statSAMplot'
samplot2: no visible binding for global variable 'Delta.table'
samplot2: no visible binding for global variable 'pos'
save.result: no visible binding for '<<-' assignment to 'fileXls'
save.result: no visible binding for global variable 'fileXls'
save.result: no visible binding for '<<-' assignment to 'SavefileName'
save.result: no visible binding for global variable 'SavefileName'
save.result : saveSigGene: no visible binding for global variable
  'fileXls2'
save.result : saveSigGene: no visible binding for global variable
  'fileRwd'
save.result.ORCME: no visible binding for '<<-' assignment to 'fileXls'
save.result.ORCME: no visible binding for global variable 'fileXls'
save.result.ORCME: no visible binding for '<<-' assignment to
  'SavefileName'
save.result.ORCME: no visible binding for global variable
  'SavefileName'
save.result.ORCME : saveSigGene: no visible binding for global variable
  'fileXls2'
save.result.ORCME : saveSigGene: no visible binding for global variable
  'fileRwd'
save.result.ORICC: no visible binding for '<<-' assignment to
  'SavefileName'
save.result.ORICC: no visible binding for global variable
  'SavefileName'
save.result.ORICC : saveSigGene: no visible binding for global variable
  'fileRwd'
save.result.mult: no visible binding for '<<-' assignment to
  'SaveDirName'
save.result.mult: no visible binding for global variable 'SaveDirName'
save.result.mult: no visible binding for '<<-' assignment to
  'SavefileName'
save.result.mult: no visible binding for global variable 'SavefileName'
save.result.mult : saveSigGenes: no visible binding for global variable
  'DirName'
save.result.mult : saveSigGenes: no visible binding for global variable
  'fileRwd'
saveDir: no visible binding for '<<-' assignment to 'SaveDirName'
saveDir: no visible binding for global variable 'SaveDirName'
saveXls: no visible binding for '<<-' assignment to 'fileXls2'
saveXls: no visible binding for global variable 'fileXls'
saveXls: no visible binding for '<<-' assignment to 'fileXls'
saveXls: no visible binding for global variable 'fileXls2'
savingRwd: no visible binding for '<<-' assignment to 'SavefileName'
savingRwd: no visible binding for global variable 'SavefileName'
showdata: no visible binding for global variable 'tt'
showdata: no visible binding for global variable 'dataSet'
showdata : OnOK: no visible binding for global variable 'dose'
showdata : OnOK: no visible binding for global variable 'exprs'
showdata : onCancel: no visible binding for global variable 'tt'
Undefined global functions or variables:
  AllFDR CopyToClip Delta.table DirName Direction DirectionSAM E2Val
  E2Val.Asymp FDRval GORICoutput MVal MarcusVal MeanDiffSAM ModMVal
  Mu.Diff Mu.Diff.Asymp NumPermval ORCMEoutput PermuteText1
  PermuteText2 PermuteText3 PermuteText4 ProbeID Pval.AllGenes.orQA
  RawPval Res.Asymtot Res.orQA SAMRes SAMRes.temp SaveDirName
  SavefileName SeModMVal SeedNum SigGenes.AsymptotE2 SigGenes.orqaE2
  StatVal WilliamsVal adjpBH adjpBHorqa adjpBY adjpBYorqa adjpBon
  adjpBonorqa adjpHoch adjpHochorqa adjpHolm adjpHolmorqa adjpSD
  adjpSDorqa adjpSS adjpSSorqa asym buttonFramePlot clusteringData
  dataSet delta.now dose exprs exprs2Asymp exprs2Perm exprs2SAM
  exprs2SAM.temp exprs2orqa fileDose fileExprs fileRwd fileXls fileXls2
  fudgeVal genenameVal img labelText linecd listgene listgene2 matchID
  matchIDtemp maxProbability meandifPerm modelSelected models nClusters
  nClustersORICC oriccOutput pos pval.Asymp pval.orQA pvalName rbVal2
  res.Asymp res.orQA result3 samPermute siggeneSAM stat.list2
  statSAMplot statUsed treeWidget tt twosd.pvalmat twosided.RawPval x
* 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 for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [5s] OK
** running examples for arch 'x64' ... [5s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'c:/biocbld/bbs-3.3-bioc/meat/IsoGeneGUI.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'IsoGeneGUI' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'IsoGeneGUI' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IsoGeneGUI' as IsoGeneGUI_2.7.0.zip
* DONE (IsoGeneGUI)

name	user	system	elapsed
IsoGeneGUI-package	0	0	0
IsoGeneGUI	0	0	0
IsoGeneGUIHelp	0	0	0

name	user	system	elapsed
IsoGeneGUI-package	0	0	0
IsoGeneGUI	0	0	0
IsoGeneGUIHelp	0	0	0