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CHECK report for IsoGeneGUI on tokay2

This page was generated on 2019-10-16 12:24:04 -0400 (Wed, 16 Oct 2019).

Package 838/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IsoGeneGUI 2.20.0
Setia Pramana
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/IsoGeneGUI
Branch: RELEASE_3_9
Last Commit: 712e2e3
Last Changed Date: 2019-05-02 11:53:14 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: IsoGeneGUI
Version: 2.20.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IsoGeneGUI.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings IsoGeneGUI_2.20.0.tar.gz
StartedAt: 2019-10-16 04:40:28 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:43:55 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 207.4 seconds
RetCode: 0
Status:  OK  
CheckDir: IsoGeneGUI.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IsoGeneGUI.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings IsoGeneGUI_2.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/IsoGeneGUI.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '2.20.0'
* 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
* 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 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 : : 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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:/Users/biocbuild/bbs-3.9-bioc/meat/IsoGeneGUI.Rcheck/00check.log'
for details.

Installation output

IsoGeneGUI.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/IsoGeneGUI_2.20.0.tar.gz && rm -rf IsoGeneGUI.buildbin-libdir && mkdir IsoGeneGUI.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IsoGeneGUI.buildbin-libdir IsoGeneGUI_2.20.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL IsoGeneGUI_2.20.0.zip && rm IsoGeneGUI_2.20.0.tar.gz IsoGeneGUI_2.20.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2556k  100 2556k    0     0  23.6M      0 --:--:-- --:--:-- --:--:-- 25.2M

install for i386

* installing *source* package 'IsoGeneGUI' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'IsoGeneGUI'
    finding HTML links ... done
    IsoGeneGUI-package                      html  
    IsoGeneGUI                              html  
    IsoGeneGUIHelp                          html  
** building package indices
** installing vignettes
   'IsoGeneGUI.Rnw' 
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'IsoGeneGUI' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IsoGeneGUI' as IsoGeneGUI_2.20.0.zip
* DONE (IsoGeneGUI)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'IsoGeneGUI' successfully unpacked and MD5 sums checked

Tests output

Example timings

IsoGeneGUI.Rcheck/examples_i386/IsoGeneGUI-Ex.timings

nameusersystemelapsed
IsoGeneGUI-package000
IsoGeneGUI000
IsoGeneGUIHelp000

IsoGeneGUI.Rcheck/examples_x64/IsoGeneGUI-Ex.timings

nameusersystemelapsed
IsoGeneGUI-package000
IsoGeneGUI000
IsoGeneGUIHelp000