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) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 11:58:40 -0400 (Wed, 16 Oct 2019).
| Package 838/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| IsoGeneGUI 2.20.0 Setia Pramana
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: IsoGeneGUI |
| Version: 2.20.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:IsoGeneGUI.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings IsoGeneGUI_2.20.0.tar.gz |
| StartedAt: 2019-10-16 02:37:52 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:40:34 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 162.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: IsoGeneGUI.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:IsoGeneGUI.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings IsoGeneGUI_2.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/IsoGeneGUI.Rcheck’ * using R version 3.6.1 (2019-07-05) * 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 ‘2.20.0’ * 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 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 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 ... 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-3.9-bioc/meat/IsoGeneGUI.Rcheck/00check.log’ for details.
IsoGeneGUI.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL IsoGeneGUI ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘IsoGeneGUI’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (IsoGeneGUI)
IsoGeneGUI.Rcheck/IsoGeneGUI-Ex.timings
| name | user | system | elapsed | |
| IsoGeneGUI-package | 0 | 0 | 0 | |
| IsoGeneGUI | 0 | 0 | 0 | |
| IsoGeneGUIHelp | 0 | 0 | 0 | |