IsoGeneGUI 2.4.0
Setia Pramana
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/IsoGeneGUI | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IsoGeneGUI_2.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/IsoGeneGUI.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘2.4.0’
* 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 ... [29s/28s] 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
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’
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’
doGORIC: no visible binding for global variable ‘tt’
doGORIC : OnOK: no visible binding for global variable ‘exprs’
doGORIC : OnOK: no visible binding for '<<-' assignment to
‘response.gene’
doGORIC : OnOK: no visible binding for global variable ‘dose’
doGORIC : OnOK: no visible binding for '<<-' assignment to ‘models’
doGORIC : OnOK: no visible binding for global variable ‘models’
doGORIC : OnOK: no visible binding for '<<-' assignment to
‘GORICoutput’
doGORIC : OnOK: no visible binding for '<<-' assignment to
‘modelSelected’
doGORIC : OnOK: no visible binding for global variable ‘GORICoutput’
doGORIC : OnOK: no visible binding for '<<-' assignment to
‘maxProbability’
doGORIC : OnOK: no visible binding for global variable ‘treeWidget’
doGORIC : OnOK: no visible binding for global variable ‘modelSelected’
doGORIC : OnOK: no visible binding for global variable ‘maxProbability’
doGORIC : saveResults: no visible binding for global variable
‘GORICoutput’
doGORIC : PlotAll : PlotAllModels: no visible binding for global
variable ‘GORICoutput’
doGORIC : PlotBest : PlotBestModel: no visible binding for global
variable ‘modelSelected’
doORCME: no visible binding for global variable ‘tt’
doORCME : calculateLambdaK: no visible binding for global variable
‘exprs’
doORCME : calculateLambdaK: no visible binding for global variable
‘dose’
doORCME : OnOK: no visible binding for global variable ‘exprs’
doORCME : OnOK: no visible binding for global variable ‘dose’
doORCME : OnOK: no visible binding for '<<-' assignment to
‘clusteringData’
doORCME : OnOK: no visible binding for '<<-' assignment to
‘ORCMEoutput’
doORCME : OnOK: no visible binding for global variable ‘clusteringData’
doORCME : OnOK: no visible binding for '<<-' assignment to ‘nClusters’
doORCME : OnOK: no visible binding for global variable ‘ORCMEoutput’
doORCME : OnOK: no visible binding for global variable ‘treeWidget’
doORCME : OnOK: no visible binding for global variable ‘nClusters’
doORCME : saveClusters: no visible binding for global variable
‘ORCMEoutput’
doORIClust: no visible binding for global variable ‘tt’
doORIClust : OnOK: no visible binding for global variable ‘exprs’
doORIClust : OnOK: no visible binding for '<<-' assignment to
‘oriccOutput’
doORIClust : OnOK: no visible binding for global variable ‘dose’
doORIClust : OnOK: no visible binding for global variable ‘oriccOutput’
doORIClust : OnOK: no visible binding for global variable ‘tt’
doORIClust : OnOK: no visible binding for '<<-' assignment to
‘nClustersORICC’
doORIClust : OnOK: no visible binding for global variable ‘treeWidget’
doORIClust : OnOK: no visible binding for global variable
‘nClustersORICC’
doORIClust : saveClusters: no visible binding for global variable
‘oriccOutput’
ExactE2: no visible binding for global variable ‘tt’
ExactE2 : Calc.Asymp: no visible binding for '<<-' assignment to
‘exprs2Asymp’
ExactE2 : Calc.Asymp: no visible binding for global variable ‘exprs’
ExactE2 : Calc.Asymp: no visible binding for global variable
‘exprs2Asymp’
ExactE2 : Calc.Asymp: no visible binding for '<<-' assignment to
‘res.Asymp’
ExactE2 : Calc.Asymp: no visible binding for global variable ‘dose’
ExactE2 : Calc.Asymp: no visible binding for '<<-' assignment to
‘pval.Asymp’
ExactE2 : Calc.Asymp: no visible binding for global variable
‘res.Asymp’
ExactE2 : Calc.Asymp: no visible binding for '<<-' assignment to
‘ProbeID’
ExactE2 : Calc.Asymp: no visible binding for '<<-' assignment to
‘Mu.Diff.Asymp’
ExactE2 : Calc.Asymp: no visible binding for '<<-' assignment to
‘E2Val.Asymp’
ExactE2 : Calc.Asymp: no visible binding for global variable ‘ProbeID’
ExactE2 : Calc.Asymp: no visible binding for global variable
‘treeWidget’
ExactE2 : AdjustBut: no visible binding for global variable
‘E2Val.Asymp’
ExactE2 : AdjustBut: no visible binding for '<<-' assignment to
‘FDRval’
ExactE2 : AdjustBut: no visible binding for global variable ‘res.Asymp’
ExactE2 : AdjustBut: no visible binding for global variable
‘treeWidget’
ExactE2 : AdjustBut: no visible binding for global variable ‘FDRval’
ExactE2 : AdjustBut: no visible binding for global variable
‘pval.Asymp’
ExactE2 : AdjustBut: no visible binding for global variable
‘exprs2Asymp’
ExactE2 : AdjustBut: no visible binding for global variable
‘Mu.Diff.Asymp’
ExactE2 : AdjustBut: no visible binding for '<<-' assignment to
‘Res.Asymtot’
ExactE2 : AdjustBut: no visible binding for global variable ‘ProbeID’
ExactE2 : AdjustBut: no visible binding for global variable
‘Res.Asymtot’
ExactE2 : AdjustBut: no visible binding for '<<-' assignment to
‘SigGenes.AsymptotE2’
ExactE2 : savesiggene: no visible binding for global variable
‘SigGenes.AsymptotE2’
ExactE2 : saveallgene: no visible binding for '<<-' assignment to
‘Pval.AllGenes.Asymp’
ExactE2 : saveallgene: no visible binding for global variable
‘Res.Asymtot’
ExactE2 : PlotBut : rankPlot: no visible binding for global variable
‘res.Asymp’
ExactE2 : PlotBut : rankPlot: no visible binding for global variable
‘pval.Asymp’
ExactE2 : PlotBut : rankPlot: no visible binding for global variable
‘exprs2Asymp’
ExactE2 : PlotBut : rankPlot: no visible binding for global variable
‘adjpBH’
ExactE2 : PlotBut : rankPlot: no visible binding for global variable
‘adjpBY’
ExactE2 : PlotBut : rankPlot: no visible binding for global variable
‘adjpSS’
ExactE2 : PlotBut : rankPlot: no visible binding for global variable
‘adjpSD’
ExactE2 : PlotBut : rankPlot: no visible binding for global variable
‘adjpHolm’
ExactE2 : PlotBut : rankPlot: no visible binding for global variable
‘adjpHoch’
ExactE2 : PlotBut : rankPlot: no visible binding for global variable
‘adjpBon’
ExactE2 : PlotBut : rankPlot: no visible binding for global variable
‘FDRval’
ExactE2 : PlotBut : rankPlot: no visible binding for global variable
‘result3’
ExactE2 : PlotBut : E2vsDiffPlot: no visible binding for global
variable ‘Mu.Diff.Asymp’
ExactE2 : PlotBut : E2vsDiffPlot: no visible binding for global
variable ‘res.Asymp’
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’
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’
Isoplot: no visible binding for global variable ‘tt’
Isoplot : OnOK: no visible binding for global variable ‘tt’
Isoplot : OnOK : plotIso: no visible binding for global variable ‘dose’
Isoplot : OnOK : plotIso: no visible binding for global variable
‘exprs’
Isoplot : OnOK: no visible binding for global variable ‘dose’
Isoplot : OnOK: no visible binding for global variable ‘exprs’
Isoplot : OnOK: no visible binding for '<<-' assignment to
‘genenameVal’
Isoplot : OnOK: no visible binding for global variable ‘genenameVal’
Isoplot : onCancel: no visible binding for global variable ‘tt’
IsoPlotSldr: no visible binding for '<<-' assignment to ‘statSAMplot’
IsoPlotSldr: no visible binding for global variable ‘statUsed’
IsoPlotSldr: no visible binding for '<<-' assignment to ‘pos’
IsoPlotSldr: no visible binding for '<<-' assignment to ‘AllFDR’
IsoPlotSldr: no visible binding for global variable ‘SAMRes’
IsoPlotSldr: no visible binding for global variable ‘statSAMplot’
IsoPlotSldr: no visible binding for '<<-' assignment to ‘Delta.table’
IsoPlotSldr: no visible binding for global variable ‘AllFDR’
IsoPlotSldr: no visible binding for global variable ‘Delta.table’
IsoPlotSldr: no visible binding for '<<-' assignment to ‘labelText’
IsoPlotSldr: no visible binding for global variable ‘labelText’
IsoPlotSldr : inputDelta: no visible binding for global variable
‘Delta.table’
IsoPlotSldr : inputDelta: no visible binding for '<<-' assignment to
‘pos’
IsoPlotSldr : inputDelta: no visible binding for '<<-' assignment to
‘delta.now’
IsoPlotSldr : showSigSAM: no visible binding for '<<-' assignment to
‘siggeneSAM’
IsoPlotSldr : showSigSAM: no visible binding for global variable
‘siggeneSAM’
IsoPlotSldr : showSigSAM: no visible binding for global variable
‘statSAMplot’
IsoPlotSldr : savegene: no visible binding for '<<-' assignment to
‘siggeneSAM’
IsoPlotSldr : saveAllgene: no visible binding for '<<-' assignment to
‘AllgeneSAM’
IsoPlotSldr : showDelta: no visible binding for global variable
‘Delta.table’
IsoPlotSldr : draw: no visible binding for '<<-' assignment to ‘pos’
IsoPlotSldr : draw: no visible binding for '<<-' assignment to
‘delta.now’
IsoPlotSldr : draw: no visible binding for global variable
‘Delta.table’
IsoPlotSldr : draw: no visible binding for global variable ‘pos’
IsoPlotSldr : draw: no visible binding for '<<-' assignment to
‘labelText’
IsoPlotSldr : draw: no visible binding for global variable ‘labelText’
IsoPlotSldr : draw: no visible binding for global variable ‘delta.now’
IsoPlotSldr : onExit: no visible binding for '<<-' assignment to
‘ReturnVal’
IsopvalPlot: no visible binding for global variable ‘tt’
IsopvalPlot : OnOK: no visible binding for global variable ‘tt’
IsopvalPlot : OnOK : plotIso: no visible binding for global variable
‘dose’
IsopvalPlot : OnOK : plotIso: no visible binding for global variable
‘exprs’
IsopvalPlot : OnOK : plotIso: no visible binding for global variable
‘SeedNum’
IsopvalPlot : OnOK: no visible binding for global variable ‘exprs’
IsoqqstatMOD: no visible binding for global variable ‘dose’
IsoqqstatMOD: no visible binding for global variable ‘exprs2SAM’
IsoqqstatMOD: no visible binding for global variable ‘fudgeVal’
IsoqqstatMOD: no visible binding for global variable ‘samPermute’
IsoqqstatMOD: no visible binding for global variable ‘NumPermval’
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’
loadDataSet: no visible binding for global variable ‘tt’
loadDataSet : OnOK: no visible binding for global variable ‘treeWidget’
loadDataSet : OnOK: no visible binding for global variable ‘tt’
loadDataSet : onCancel: no visible binding for '<<-' assignment to
‘ReturnVal’
loadDataSet : onCancel: no visible binding for global variable ‘tt’
openFile : getExprs: no visible binding for '<<-' assignment to
‘fileExprs’
openFile : getExprs: no visible binding for global variable ‘fileExprs’
openFile: no visible binding for '<<-' assignment to ‘fileDose’
openFile: no visible binding for '<<-' assignment to ‘fileExprs’
openFile: no visible binding for global variable ‘fileDose’
openFile: no visible binding for global variable ‘fileExprs’
openFile : OnOK: no visible binding for global variable ‘fileExprs’
openFile : OnOK: no visible binding for global variable ‘treeWidget’
openFile : onCancel: no visible binding for '<<-' assignment to
‘ReturnVal’
openFile : onCancel: no visible binding for global variable ‘tt’
orQAE2: no visible binding for global variable ‘tt’
orQAE2: no visible binding for global variable ‘exprs’
orQAE2 : Calc.orQA: no visible binding for global variable ‘exprs’
orQAE2 : Calc.orQA: no visible binding for global variable ‘dose’
orQAE2 : Calc.orQA: no visible binding for '<<-' assignment to
‘res.orQA’
orQAE2 : Calc.orQA: no visible binding for '<<-' assignment to
‘pval.orQA’
orQAE2 : Calc.orQA: no visible binding for global variable ‘res.orQA’
orQAE2 : Calc.orQA: no visible binding for '<<-' assignment to
‘ProbeID’
orQAE2 : Calc.orQA: no visible binding for '<<-' assignment to
‘Mu.Diff’
orQAE2 : Calc.orQA: no visible binding for global variable ‘ProbeID’
orQAE2 : Calc.orQA: no visible binding for global variable ‘treeWidget’
orQAE2 : AdjustBut: no visible binding for global variable ‘pval.orQA’
orQAE2 : AdjustBut: no visible binding for '<<-' assignment to ‘FDRval’
orQAE2 : AdjustBut: no visible binding for global variable ‘res.orQA’
orQAE2 : AdjustBut: no visible binding for global variable ‘treeWidget’
orQAE2 : AdjustBut: no visible binding for global variable ‘FDRval’
orQAE2 : AdjustBut: no visible binding for global variable ‘exprs2orqa’
orQAE2 : AdjustBut: no visible binding for '<<-' assignment to
‘Res.orQA’
orQAE2 : AdjustBut: no visible binding for global variable ‘ProbeID’
orQAE2 : AdjustBut: no visible binding for global variable ‘Mu.Diff’
orQAE2 : AdjustBut: no visible binding for global variable ‘Res.orQA’
orQAE2 : AdjustBut: no visible binding for '<<-' assignment to
‘SigGenes.orqaE2’
orQAE2 : AdjustBut: no visible binding for '<<-' assignment to
‘result3’
orQAE2 : AdjustBut: no visible binding for global variable ‘result3’
orQAE2 : savesiggene: no visible binding for global variable
‘SigGenes.orqaE2’
orQAE2 : saveallgene: no visible binding for '<<-' assignment to
‘Pval.AllGenes.orQA’
orQAE2 : saveallgene: no visible binding for global variable ‘Res.orQA’
orQAE2 : saveallgene: no visible binding for global variable
‘Pval.AllGenes.orQA’
orQAE2 : PlotBut : rankPlot: no visible binding for global variable
‘exprs2orqa’
orQAE2 : PlotBut : rankPlot: no visible binding for global variable
‘pval.orQA’
orQAE2 : PlotBut : rankPlot: no visible binding for global variable
‘adjpBHorqa’
orQAE2 : PlotBut : rankPlot: no visible binding for global variable
‘adjpBYorqa’
orQAE2 : PlotBut : rankPlot: no visible binding for global variable
‘adjpSSorqa’
orQAE2 : PlotBut : rankPlot: no visible binding for global variable
‘adjpSDorqa’
orQAE2 : PlotBut : rankPlot: no visible binding for global variable
‘adjpHolmorqa’
orQAE2 : PlotBut : rankPlot: no visible binding for global variable
‘adjpHochorqa’
orQAE2 : PlotBut : rankPlot: no visible binding for global variable
‘adjpBonorqa’
orQAE2 : PlotBut : rankPlot: no visible binding for global variable
‘FDRval’
orQAE2 : PlotBut : rankPlot: no visible binding for global variable
‘result3’
orQAE2 : PlotBut : PVALSvsDiffPlot: no visible binding for global
variable ‘Mu.Diff’
orQAE2 : PlotBut : PVALSvsDiffPlot: no visible binding for global
variable ‘pval.orQA’
Permutation: no visible binding for global variable ‘tt’
Permutation: no visible binding for '<<-' assignment to ‘SavefileName’
Permutation: no visible binding for global variable ‘SavefileName’
Permutation : Calc.Permut: no visible binding for global variable
‘asym’
Permutation : Calc.Permut: no visible binding for global variable
‘exprs’
Permutation : Calc.Permut: no visible binding for global variable
‘dose’
Permutation : Calc.Permut: no visible binding for global variable
‘SeedNum’
Permutation : Calc.Permut: no visible binding for global variable
‘treeWidget’
Permutation : Calc.Permut: no visible binding for global variable
‘fileRwd’
Permutation: no visible binding for '<<-' assignment to ‘PermuteText3’
Permutation: no visible binding for global variable ‘PermuteText3’
Permutation: no visible binding for '<<-' assignment to ‘PermuteText4’
Permutation: no visible binding for global variable ‘PermuteText4’
Permutation: no visible binding for '<<-' assignment to ‘pvalName’
Permutation: no visible binding for global variable ‘pvalName’
Permutation : PermResBut: no visible binding for global variable
‘exprs2Perm’
Permutation : PermResBut: no visible binding for '<<-' assignment to
‘meandifPerm’
Permutation : PermResBut: no visible binding for global variable ‘dose’
Permutation : PermResBut: no visible binding for global variable
‘meandifPerm’
Permutation : PermResBut: no visible binding for global variable
‘RawPval’
Permutation : PermResBut: no visible binding for '<<-' assignment to
‘FDRval’
Permutation : PermResBut: no visible binding for global variable
‘treeWidget’
Permutation : PermResBut: no visible binding for global variable
‘FDRval’
Permutation : PermResBut: no visible binding for global variable
‘matchID’
Permutation : PermResBut: no visible binding for global variable
‘Direction’
Permutation : PermResBut: no visible binding for global variable
‘ProbeID’
Permutation : savesiggene: no visible binding for global variable
‘listgene’
Permutation : saveallgene: no visible binding for global variable
‘listgene2’
Permutation : PlotBut: no visible binding for '<<-' assignment to
‘stat.list2’
Permutation : PlotBut: no visible binding for '<<-' assignment to
‘twosd.pvalmat’
Permutation : PlotBut: no visible binding for global variable
‘twosided.RawPval’
Permutation : PlotBut: no visible binding for global variable
‘twosd.pvalmat’
Permutation : PlotBut: no visible binding for global variable
‘stat.list2’
Permutation : PlotBut : rankPlot: no visible binding for global
variable ‘twosd.pvalmat’
Permutation : PlotBut : rankPlot: no visible binding for global
variable ‘matchID’
Permutation : PlotBut : rankPlot: no visible binding for global
variable ‘linecd’
Permutation : PlotBut : rankPlot: no visible binding for global
variable ‘FDRval’
Permutation : PlotBut : E2vsDiffPlot: no visible binding for global
variable ‘meandifPerm’
PermuteSAM: no visible binding for global variable ‘tt’
PermuteSAM: no visible binding for '<<-' assignment to ‘samPermute’
PermuteSAM: no visible binding for global variable ‘samPermute’
PermuteSAM : ShowSEplot: no visible binding for global variable ‘exprs’
PermuteSAM : ShowSEplot: no visible binding for global variable
‘matchIDtemp’
PermuteSAM : ShowSEplot: no visible binding for global variable ‘dose’
PermuteSAM : ShowSEplot: no visible binding for '<<-' assignment to
‘matchIDtemp’
PermuteSAM: no visible binding for '<<-' assignment to ‘SavefileName’
PermuteSAM: no visible binding for global variable ‘SavefileName’
PermuteSAM : Calc.PermutSAM: no visible binding for '<<-' assignment to
‘rbVal2’
PermuteSAM : Calc.PermutSAM: no visible binding for '<<-' assignment to
‘fudgeVal’
PermuteSAM : Calc.PermutSAM: no visible binding for global variable
‘samPermute’
PermuteSAM : Calc.PermutSAM: no visible binding for global variable
‘rbVal2’
PermuteSAM : Calc.PermutSAM: no visible binding for '<<-' assignment to
‘exprs2SAM’
PermuteSAM : Calc.PermutSAM: no visible binding for global variable
‘exprs’
PermuteSAM : Calc.PermutSAM: no visible binding for '<<-' assignment to
‘matchID’
PermuteSAM : Calc.PermutSAM: no visible binding for global variable
‘exprs2SAM’
PermuteSAM : Calc.PermutSAM: no visible binding for global variable
‘dose’
PermuteSAM : Calc.PermutSAM: no visible binding for global variable
‘SeedNum’
PermuteSAM : Calc.PermutSAM: no visible binding for global variable
‘fudgeVal’
PermuteSAM : Calc.PermutSAM: no visible binding for global variable
‘treeWidget’
PermuteSAM : Calc.PermutSAM: no visible binding for '<<-' assignment to
‘DirectionSAM’
PermuteSAM : Calc.PermutSAM: no visible binding for '<<-' assignment to
‘MeanDiffSAM’
PermuteSAM : Calc.PermutSAM: no visible binding for global variable
‘MeanDiffSAM’
PermuteSAM : Calc.PermutSAM: no visible binding for global variable
‘fileRwd’
PermuteSAM: no visible binding for '<<-' assignment to ‘PermuteText1’
PermuteSAM: no visible binding for global variable ‘PermuteText1’
PermuteSAM: no visible binding for '<<-' assignment to ‘PermuteText2’
PermuteSAM: no visible binding for global variable ‘PermuteText2’
PermuteSAM: no visible binding for '<<-' assignment to ‘pvalName’
PermuteSAM: no visible binding for global variable ‘pvalName’
PermuteSAM : onCancel: no visible binding for global variable
‘SAMRes.temp’
PermuteSAM : onCancel: no visible binding for global variable
‘exprs2SAM.temp’
PermuteSAM : onCancel: no visible binding for global variable
‘samPermute’
PermuteSAM : onOK: no visible binding for global variable ‘SAMRes.temp’
PermuteSAM : onOK: no visible binding for global variable
‘exprs2SAM.temp’
PermuteSAM : onOK: no visible binding for global variable ‘samPermute’
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’
PlotFPDlt: no visible binding for '<<-' assignment to ‘AllFDR’
PlotFPDlt: no visible binding for global variable ‘SAMRes’
PlotFPDlt: no visible binding for global variable ‘statUsed’
PlotFPDlt: no visible binding for global variable ‘AllFDR’
PlotFPDlt : plotFPD: no visible binding for global variable ‘SAMRes’
plotORCME: no visible binding for global variable ‘tt’
plotORCME: no visible binding for global variable ‘nClusters’
plotORCME: no visible binding for global variable ‘dose’
plotORCME : OnOK : plotClusters: no visible binding for global variable
‘clusteringData’
plotORCME : OnOK : plotClusters: no visible binding for global variable
‘ORCMEoutput’
plotORCME : onCancel: no visible binding for global variable ‘tt’
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’
samplot2: no visible binding for global variable ‘SAMRes’
samplot2: no visible binding for global variable ‘statSAMplot’
samplot2: no visible binding for global variable ‘Delta.table’
samplot2: no visible binding for global variable ‘pos’
save.result: no visible binding for '<<-' assignment to ‘fileXls’
save.result: no visible binding for global variable ‘fileXls’
save.result: no visible binding for '<<-' assignment to ‘SavefileName’
save.result: no visible binding for global variable ‘SavefileName’
save.result : saveSigGene: no visible binding for global variable
‘fileXls2’
save.result : saveSigGene: no visible binding for global variable
‘fileRwd’
save.result.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’
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’
saveDir: no visible binding for '<<-' assignment to ‘SaveDirName’
saveDir: no visible binding for global variable ‘SaveDirName’
SaveGraph: no visible global function definition for ‘x’
SaveGraph: no visible binding for global variable ‘buttonFramePlot’
SaveGraph: no visible binding for global variable ‘CopyToClip’
SaveGraph: no visible binding for global variable ‘img’
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’
SEPlot: no visible binding for global variable ‘SeModMVal’
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’
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’
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’
* 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 ... [15s/14s] 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-3.1-bioc/meat/IsoGeneGUI.Rcheck/00check.log’
for details.
* installing *source* package ‘IsoGeneGUI’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (IsoGeneGUI)