IsoGeneGUI 2.9.0
Setia Pramana
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IsoGeneGUI | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings IsoGeneGUI_2.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/IsoGeneGUI.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 ‘2.9.0’
* 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
‘/home/biocbuild/bbs-3.4-bioc/meat/IsoGeneGUI.Rcheck/00check.log’
for details.