Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-17 13:06:28 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for IsoGeneGUI on tokay2


To the developers/maintainers of the IsoGeneGUI package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IsoGeneGUI.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 964/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IsoGeneGUI 2.30.0  (landing page)
Setia Pramana
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/IsoGeneGUI
git_branch: RELEASE_3_14
git_last_commit: 55c03bf
git_last_commit_date: 2021-10-26 11:56:33 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: IsoGeneGUI
Version: 2.30.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:IsoGeneGUI.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings IsoGeneGUI_2.30.0.tar.gz
StartedAt: 2022-01-16 22:46:41 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 22:49:47 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 185.8 seconds
RetCode: 0
Status:   OK  
CheckDir: IsoGeneGUI.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:IsoGeneGUI.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings IsoGeneGUI_2.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/IsoGeneGUI.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '2.30.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* 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
* 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 '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 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'
ExactE2Val : pval: no visible global function definition for 'pbeta'
IsoGeneGUI: no visible binding for '<<-' assignment to 'tt'
IsoGeneGUI: no visible binding for global variable 'tt'
IsoGeneGUI: no visible binding for '<<-' assignment to 'SeedNum'
IsoGeneGUI : <anonymous>: no visible binding for global variable
  'treeWidget'
IsoGeneGUI: no visible binding for '<<-' assignment to 'treeWidget'
IsoGeneGUI: no visible binding for global variable 'treeWidget'
IsoGeneGUIHelp: no visible binding for global variable 'window'
IsoGeneGUIHelp: no visible global function definition for 'browseURL'
IsoGeneGUIVignette: no visible binding for global variable 'window'
IsoPlot.mod: no visible global function definition for '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 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'
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 '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
  '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
  '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 '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
  '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
  '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 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'
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 '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 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", "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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/IsoGeneGUI.Rcheck/00check.log'
for details.



Installation output

IsoGeneGUI.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch IsoGeneGUI
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
* 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
* DONE (IsoGeneGUI)
Making 'packages.html' ... done

Tests output


Example timings

IsoGeneGUI.Rcheck/IsoGeneGUI-Ex.timings

nameusersystemelapsed
IsoGeneGUI-package000
IsoGeneGUI000
IsoGeneGUIHelp000