BioC 3.5: CHECK report for IsoGeneGUI on toluca2

Package: IsoGeneGUI

Version: 2.11.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IsoGeneGUI_2.11.0.tar.gz

StartedAt: 2017-04-23 05:39:33 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 05:42:52 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 198.7 seconds

RetCode: 0

Status:  OK

CheckDir: IsoGeneGUI.Rcheck

Warnings: 0

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IsoGeneGUI_2.11.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/IsoGeneGUI.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IsoGeneGUI/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IsoGeneGUI’ version ‘2.11.0’
* 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 for sufficient/correct file permissions ... 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
* 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
CVPlot: no visible global function definition for ‘par’
CVPlot: no visible global function definition for ‘plot’
CVPlot: no visible global function definition for ‘axis’
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 global function definition for
  ‘na.exclude’
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 global function definition for
  ‘par’
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 global function definition for
  ‘densCols’
ExactE2 : PlotBut : rankPlot: no visible global function definition for
  ‘plot’
ExactE2 : PlotBut : rankPlot: no visible binding for global variable
  ‘exprs2Asymp’
ExactE2 : PlotBut : rankPlot: no visible global function definition for
  ‘lines’
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 global function definition for
  ‘abline’
ExactE2 : PlotBut : rankPlot: no visible binding for global variable
  ‘FDRval’
ExactE2 : PlotBut : rankPlot: no visible binding for global variable
  ‘result3’
ExactE2 : PlotBut : rankPlot: no visible global function definition for
  ‘legend’
ExactE2 : PlotBut : E2vsDiffPlot: no visible global function definition
  for ‘par’
ExactE2 : PlotBut : E2vsDiffPlot: no visible binding for global
  variable ‘Mu.Diff.Asymp’
ExactE2 : PlotBut : E2vsDiffPlot: no visible binding for global
  variable ‘res.Asymp’
ExactE2 : PlotBut : E2vsDiffPlot: no visible global function definition
  for ‘densCols’
ExactE2 : PlotBut : E2vsDiffPlot: no visible global function definition
  for ‘plot’
ExactE2Val : pval: no visible global function definition for ‘pbeta’
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’
IsoGeneGUIHelp: no visible binding for global variable ‘window’
IsoGeneGUIHelp: no visible global function definition for ‘browseURL’
IsoGeneGUIVignette: no visible binding for global variable ‘window’
IsoPlot.mod: no visible global function definition for ‘plot’
IsoPlot.mod: no visible global function definition for ‘points’
IsoPlot.mod: no visible global function definition for ‘lines’
IsoPlot.mod: no visible global function definition for ‘axis’
IsoPlot.mod: no visible global function definition for ‘legend’
IsoPlot.mod: no visible global function definition for ‘title’
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 : inputDelta: no visible global function definition for
  ‘na.exclude’
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 : SaveGraph: no visible global function definition for
  ‘dev.off’
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 global function definition for
  ‘par’
Isoplot : OnOK : plotIso: no visible binding for global variable ‘dose’
Isoplot : OnOK : plotIso: no visible binding for global variable
  ‘exprs’
Isoplot : OnOK : plotIso: no visible global function definition for
  ‘title’
Isoplot : OnOK: no visible binding for global variable ‘dose’
Isoplot : OnOK: no visible binding for global variable ‘exprs’
Isoplot : OnOK: no visible global function definition for ‘na.omit’
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 global function definition for
  ‘par’
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 global function definition for ‘na.omit’
IsopvalPlot : OnOK: no visible binding for global variable ‘exprs’
IsopvaluePlot: no visible global function definition for ‘hist’
IsopvaluePlot: no visible global function definition for ‘density’
IsopvaluePlot: no visible global function definition for ‘abline’
IsopvaluePlot: no visible global function definition for ‘lines’
IsopvaluePlot: no visible global function definition for ‘title’
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 global function definition for
  ‘na.exclude’
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 global function definition
  for ‘par’
Permutation : PlotBut : rankPlot: no visible binding for global
  variable ‘twosd.pvalmat’
Permutation : PlotBut : rankPlot: no visible global function definition
  for ‘densCols’
Permutation : PlotBut : rankPlot: no visible global function definition
  for ‘plot’
Permutation : PlotBut : rankPlot: no visible binding for global
  variable ‘matchID’
Permutation : PlotBut : rankPlot: no visible global function definition
  for ‘lines’
Permutation : PlotBut : rankPlot: no visible binding for global
  variable ‘linecd’
Permutation : PlotBut : rankPlot: no visible global function definition
  for ‘abline’
Permutation : PlotBut : rankPlot: no visible binding for global
  variable ‘FDRval’
Permutation : PlotBut : rankPlot: no visible global function definition
  for ‘legend’
Permutation : PlotBut : E2vsDiffPlot: no visible global function
  definition for ‘par’
Permutation : PlotBut : E2vsDiffPlot: no visible binding for global
  variable ‘meandifPerm’
Permutation : PlotBut : E2vsDiffPlot: no visible global function
  definition for ‘densCols’
Permutation : PlotBut : E2vsDiffPlot: no visible global function
  definition for ‘plot’
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’
Plot2 : SaveGraph: no visible global function definition for ‘dev.off’
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 global function definition for ‘par’
PlotFPDlt : plotFPD: no visible global function definition for ‘plot’
PlotFPDlt : plotFPD: no visible global function definition for ‘lines’
PlotFPDlt : plotFPD: no visible global function definition for ‘legend’
PlotFPDlt : plotFPD: no visible binding for global variable ‘SAMRes’
PlotFPDlt : plotFPD: no visible global function definition for ‘title’
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’
PlotFdrDlt : plotFdrD: no visible global function definition for ‘par’
PlotFdrDlt : plotFdrD: no visible global function definition for ‘plot’
PlotFdrDlt : plotFdrD: no visible global function definition for
  ‘lines’
PlotFdrDlt : plotFdrD: no visible global function definition for
  ‘abline’
PlotFdrDlt : plotFdrD: no visible global function definition for
  ‘legend’
PlotFdrDlt : plotFdrD: no visible global function definition for
  ‘title’
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’
PlotSigDlt : plotSigD: no visible global function definition for ‘par’
PlotSigDlt : plotSigD: no visible global function definition for ‘plot’
PlotSigDlt : plotSigD: no visible global function definition for
  ‘lines’
PlotSigDlt : plotSigD: no visible global function definition for
  ‘title’
SEPlot: no visible global function definition for ‘par’
SEPlot: no visible global function definition for ‘densCols’
SEPlot: no visible global function definition for ‘plot’
SEPlot: no visible global function definition for ‘abline’
SEPlot: no visible global function definition for ‘density’
SEPlot: no visible binding for global variable ‘SeModMVal’
SaveGraph: no visible global function definition for ‘postscript’
SaveGraph: no visible global function definition for ‘x’
SaveGraph: no visible global function definition for ‘dev.off’
SaveGraph: no visible global function definition for ‘jpeg’
SaveGraph: no visible global function definition for ‘png’
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 : OnOK : Userplot: no visible global function definition for
  ‘par’
UserPlot : OnOK : Userplot: no visible global function definition for
  ‘densCols’
UserPlot : OnOK : Userplot: no visible global function definition for
  ‘plot’
UserPlot : OnOK : Userplot: no visible global function definition for
  ‘title’
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 global function
  definition for ‘par’
doGORIC : PlotAll : PlotAllModels: no visible binding for global
  variable ‘GORICoutput’
doGORIC : PlotAll : PlotAllModels: no visible global function
  definition for ‘barplot’
doGORIC : PlotAll: no visible global function definition for ‘par’
doGORIC : PlotBest : PlotBestModel: no visible global function
  definition for ‘par’
doGORIC : PlotBest : PlotBestModel: no visible global function
  definition for ‘boxplot’
doGORIC : PlotBest : PlotBestModel: no visible binding for global
  variable ‘modelSelected’
doGORIC : PlotBest : PlotBestModel: no visible global function
  definition for ‘points’
doGORIC : PlotModel : PlotSelectedModel: no visible global function
  definition for ‘par’
doGORIC : PlotModel : PlotSelectedModel: no visible global function
  definition for ‘boxplot’
doGORIC : PlotModel : PlotSelectedModel: no visible global function
  definition for ‘points’
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 : calculateLambdaK: no visible global function definition for
  ‘par’
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 : OnOK: no visible global function definition for ‘plot’
doORIClust : OnOK: no visible global function definition for
  ‘rasterImage’
doORIClust : OnOK: no visible global function definition for ‘x11’
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’
getDose: no visible global function definition for ‘read.table’
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’
onHelpIsoGene: no visible binding for global variable ‘window’
onHelpIsoGene: no visible global function definition for ‘help’
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 global function definition for ‘read.table’
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 global function definition for
  ‘na.exclude’
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 global function definition for
  ‘par’
orQAE2 : PlotBut : rankPlot: no visible global function definition for
  ‘plot’
orQAE2 : PlotBut : rankPlot: no visible binding for global variable
  ‘exprs2orqa’
orQAE2 : PlotBut : rankPlot: no visible global function definition for
  ‘lines’
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 global function definition for
  ‘abline’
orQAE2 : PlotBut : rankPlot: no visible binding for global variable
  ‘FDRval’
orQAE2 : PlotBut : rankPlot: no visible binding for global variable
  ‘result3’
orQAE2 : PlotBut : rankPlot: no visible global function definition for
  ‘legend’
orQAE2 : PlotBut : PVALSvsDiffPlot: no visible global function
  definition for ‘par’
orQAE2 : PlotBut : PVALSvsDiffPlot: no visible binding for global
  variable ‘Mu.Diff’
orQAE2 : PlotBut : PVALSvsDiffPlot: no visible binding for global
  variable ‘pval.orQA’
orQAE2 : PlotBut : PVALSvsDiffPlot: no visible global function
  definition for ‘densCols’
orQAE2 : PlotBut : PVALSvsDiffPlot: no visible global function
  definition for ‘plot’
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 global function definition
  for ‘par’
plotORCME : OnOK : plotClusters: no visible binding for global variable
  ‘clusteringData’
plotORCME : OnOK : plotClusters: no visible binding for global variable
  ‘ORCMEoutput’
plotORCME : OnOK: no visible global function definition for ‘na.omit’
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’
samplot2: no visible global function definition for ‘par’
samplot2: no visible global function definition for ‘plot’
samplot2: no visible global function definition for ‘abline’
samplot2: no visible global function definition for ‘points’
samplot2: no visible global function definition for ‘legend’
samplot2: no visible global function definition for ‘title’
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’
xfudge: no visible global function definition for ‘quantile’
xfudge: no visible binding for global variable ‘mad’
xfudge : xcv: no visible global function definition for ‘var’
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 abline adjpBH adjpBHorqa adjpBY adjpBYorqa
  adjpBon adjpBonorqa adjpHoch adjpHochorqa adjpHolm adjpHolmorqa
  adjpSD adjpSDorqa adjpSS adjpSSorqa asym axis barplot boxplot
  browseURL buttonFramePlot clusteringData dataSet delta.now densCols
  density dev.off dose exprs exprs2Asymp exprs2Perm exprs2SAM
  exprs2SAM.temp exprs2orqa fileDose fileExprs fileRwd fileXls fileXls2
  fudgeVal genenameVal help hist img jpeg labelText legend linecd lines
  listgene listgene2 mad matchID matchIDtemp maxProbability meandifPerm
  modelSelected models nClusters nClustersORICC na.exclude na.omit
  oriccOutput par pbeta plot png points pos postscript pval.Asymp
  pval.orQA pvalName quantile rasterImage rbVal2 read.table res.Asymp
  res.orQA result3 samPermute siggeneSAM stat.list2 statSAMplot
  statUsed title treeWidget tt twosd.pvalmat twosided.RawPval var
  window x x11
Consider adding
  importFrom("grDevices", "densCols", "dev.off", "jpeg", "png",
             "postscript", "x11")
  importFrom("graphics", "abline", "axis", "barplot", "boxplot", "hist",
             "legend", "lines", "par", "plot", "points", "rasterImage",
             "title")
  importFrom("stats", "density", "mad", "na.exclude", "na.omit", "pbeta",
             "quantile", "var", "window")
  importFrom("utils", "browseURL", "help", "read.table")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/IsoGeneGUI.Rcheck/00check.log’
for details.

* 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
* DONE (IsoGeneGUI)

name	user	system	elapsed
IsoGeneGUI-package	0.000	0.001	0.000
IsoGeneGUI	0.000	0.000	0.001
IsoGeneGUIHelp	0.000	0.001	0.001