IsoGeneGUI 1.3.1
Setia Pramana
| Snapshot Date: 2011-03-17 11:16:30 -0700 (Thu, 17 Mar 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IsoGeneGUI | | Last Changed Rev: 50725 / Revision: 53825 | | Last Changed Date: 2010-11-06 14:29:12 -0700 (Sat, 06 Nov 2010) |
| lamb1 | Linux (openSUSE 11.3) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.6) / i386 | OK | [ WARNINGS ] | OK |
* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/IsoGeneGUI.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'IsoGeneGUI/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IsoGeneGUI' version '1.3.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'IsoGeneGUI' can be installed ... WARNING
Found the following significant warnings:
Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
See '/Users/biocbuild/bbs-2.8-bioc/meat/IsoGeneGUI.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated 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
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
'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 : 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'
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'
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'
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 binding for global variable 'dose'
Isoplot : OnOK: no visible binding for global variable 'dose'
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 binding for global variable
'dose'
IsopvalPlot : OnOK : plotIso: no visible binding for global variable
'SeedNum'
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
'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
'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 '<<-' 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'
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'
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'
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'
SEPlot: no visible binding for global variable 'SeModMVal'
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'
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 : 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 '<<-' 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 '<<-' assignment to
'MeanDiffSAM'
browse2 : OnOK: no visible binding for global variable 'dose'
browse2 : OnOK: no visible binding for global variable 'treeWidget'
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'
getExprs: no visible binding for '<<-' assignment to 'fileExprs'
getExprs: no visible binding for global variable 'fileExprs'
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: 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 'treeWidget'
openFile : onCancel: no visible binding for '<<-' assignment to
'ReturnVal'
openFile : 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'
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.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 : onCancel: no visible binding for global variable 'tt'
* 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 examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running 'isogenegui_unit_tests.R'
OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There was 1 warning, see
'/Users/biocbuild/bbs-2.8-bioc/meat/IsoGeneGUI.Rcheck/00check.log'
for details
* installing *source* package 'IsoGeneGUI' ...
** R
** inst
** preparing package for lazy loading
Loading Tcl/Tk interface ... done
Loading required package: Iso
Iso 0.0-8
Note: This package now has a NAMESPACE.
Loading required package: affy
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation("pkgname")'.
Loading required package: ff
Loading required package: tools
Loading required package: bit
Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
Loading package bit1.1-6
package:bit (c) 2008/2009 Jens Oehlschlaegel (GPL-2)
creators: bit bitwhich
coercion: as.logical as.integer as.bit as.bitwhich which
operator: ! & | xor != ==
querying: print length any all min max range sum summary
bit access: length<- [ [<- [[ [[<-
for more help type ?bit
Attaching package: 'bit'
The following object(s) are masked from 'package:base':
xor
Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
Loading package ff2.2-1
- getOption("fftempdir")=="/tmp/RtmpTO9p4T"
- getOption("ffextension")=="ff"
- getOption("ffdrop")==TRUE
- getOption("fffinonexit")==TRUE
- getOption("ffpagesize")==65536
- getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes
- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system
Attaching package ff
Attaching package: 'ff'
The following object(s) are masked from 'package:utils':
write.csv, write.csv2
The following object(s) are masked from 'package:base':
is.factor, is.ordered
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Iso 0.0-8
Note: This package now has a NAMESPACE.
Warning messages:
1: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
2: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
* DONE (IsoGeneGUI)