Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 |
Package 1079/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
limmaGUI 1.81.0 (landing page) Gordon Smyth
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the limmaGUI package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/limmaGUI.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: limmaGUI |
Version: 1.81.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:limmaGUI.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings limmaGUI_1.81.0.tar.gz |
StartedAt: 2024-06-10 04:33:21 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 04:35:37 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 136.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: limmaGUI.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:limmaGUI.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings limmaGUI_1.81.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/limmaGUI.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'limmaGUI/DESCRIPTION' ... OK * this is package 'limmaGUI' version '1.81.0' * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'limmaGUI' can be installed ... OK * checking installed package size ... NOTE installed size is 7.6Mb sub-directories of 1Mb or more: doc 6.8Mb * 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 code 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 whether startup messages can be suppressed ... 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 AboutNormalization: no visible binding for global variable '.limmaGUIglobals' ChooseContrastsParameterization: no visible binding for global variable 'limmaGUIenvironment' ChooseContrastsParameterization: no visible binding for global variable 'ParameterizationNamesVec' ChooseContrastsParameterization: no visible binding for global variable 'parameterizationIndex' ChooseContrastsParameterization: no visible binding for global variable '.limmaGUIglobals' ChooseContrastsParameterization : onOK: no visible binding for global variable '.limmaGUIglobals' ChooseContrastsParameterization : onCancel: no visible binding for global variable '.limmaGUIglobals' ChooseContrastsParameterization : <anonymous>: no visible binding for global variable '.limmaGUIglobals' ChooseEbayesStatistic: no visible binding for global variable '.limmaGUIglobals' ChooseEbayesStatistic : onOK: no visible binding for global variable '.limmaGUIglobals' ChooseEbayesStatistic : onCancel: no visible binding for global variable '.limmaGUIglobals' ChooseEbayesStatistic : <anonymous>: no visible binding for global variable '.limmaGUIglobals' ChooseParameterization: no visible binding for global variable 'limmaGUIenvironment' ChooseParameterization: no visible binding for global variable '.limmaGUIglobals' ChooseParameterization : onOK: no visible binding for global variable '.limmaGUIglobals' ChooseParameterization : onCancel: no visible binding for global variable '.limmaGUIglobals' ChooseParameterization : <anonymous>: no visible binding for global variable '.limmaGUIglobals' ChoosePlotSymbolByClicking: no visible binding for global variable '.limmaGUIglobals' ChoosePlotSymbolByClicking : LeftClick: no visible binding for global variable '.limmaGUIglobals' ChoosePlotSymbolByClicking : onCancel: no visible binding for global variable '.limmaGUIglobals' ChoosePlotSymbolByClicking : <anonymous>: no visible binding for global variable '.limmaGUIglobals' ChooseSpotType: no visible binding for global variable '.limmaGUIglobals' ChooseSpotType : onOK: no visible binding for global variable '.limmaGUIglobals' ChooseSpotType : onCancel: no visible binding for global variable '.limmaGUIglobals' ChooseSpotType : <anonymous>: no visible binding for global variable '.limmaGUIglobals' ComputeContrasts: no visible binding for global variable 'limmaGUIenvironment' ComputeContrasts: no visible binding for global variable '.limmaGUIglobals' ComputeContrasts: no visible global function definition for 'ebayes' ComputeLinearModelFit: no visible binding for global variable 'limmaGUIenvironment' ComputeLinearModelFit: no visible binding for global variable '.limmaGUIglobals' ComputeLinearModelFit : GetDupCor: no visible binding for global variable '.limmaGUIglobals' ComputeLinearModelFit : GetDupCor : onOK: no visible binding for global variable '.limmaGUIglobals' ComputeLinearModelFit : GetDupCor : onCancel: no visible binding for global variable '.limmaGUIglobals' ComputeLinearModelFit : GetDupCor : <anonymous>: no visible binding for global variable '.limmaGUIglobals' ComputeLinearModelFit: no visible global function definition for 'ebayes' CreateNewParameterization: no visible binding for global variable 'limmaGUIenvironment' CreateNewParameterization: no visible binding for global variable '.limmaGUIglobals' CreateTreeAndList: no visible binding for global variable 'limmaGUIenvironment' CreateTreeAndList: no visible binding for global variable '.limmaGUIglobals' DeleteContrastsParameterization: no visible binding for global variable 'limmaGUIenvironment' DeleteContrastsParameterization: no visible binding for global variable '.limmaGUIglobals' DeleteParameterization: no visible binding for global variable 'limmaGUIenvironment' DeleteParameterization: no visible binding for global variable '.limmaGUIglobals' DupCorBoxPlot: no visible binding for global variable 'limmaGUIenvironment' DupCorBoxPlot: no visible binding for global variable '.limmaGUIglobals' ExportAvalues: no visible binding for global variable 'limmaGUIenvironment' ExportHTMLreport: no visible binding for global variable 'limmaGUIenvironment' ExportHTMLreport: no visible binding for global variable '.limmaGUIglobals' ExportHTMLreport: no visible global function definition for 'toptable' ExportMvalues: no visible binding for global variable 'limmaGUIenvironment' GetBackgroundCorrectionMethod: no visible binding for global variable '.limmaGUIglobals' GetBackgroundCorrectionMethod: no visible binding for global variable 'limmaGUIenvironment' GetBackgroundCorrectionMethod : onOK: no visible binding for global variable '.limmaGUIglobals' GetBackgroundCorrectionMethod : onOK: no visible binding for global variable 'limmaGUIenvironment' GetBackgroundCorrectionMethod : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetBetweenArrayNormalizationMethod: no visible binding for global variable '.limmaGUIglobals' GetBetweenArrayNormalizationMethod: no visible binding for global variable 'limmaGUIenvironment' GetBetweenArrayNormalizationMethod : onOK: no visible binding for global variable 'limmaGUIenvironment' GetBetweenArrayNormalizationMethod : onOK: no visible binding for global variable '.limmaGUIglobals' GetBetweenArrayNormalizationMethod : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetCoef: no visible binding for global variable 'limmaGUIenvironment' GetCoef: no visible binding for global variable '.limmaGUIglobals' GetCoef : onOK: no visible binding for global variable '.limmaGUIglobals' GetCoef : onCancel: no visible binding for global variable '.limmaGUIglobals' GetCoef : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetComponentsToExportInHTMLreport: no visible binding for global variable 'limmaGUIenvironment' GetComponentsToExportInHTMLreport: no visible binding for global variable '.limmaGUIglobals' GetComponentsToExportInHTMLreport : onOK: no visible binding for global variable '.limmaGUIglobals' GetComponentsToExportInHTMLreport : onCancel: no visible binding for global variable '.limmaGUIglobals' GetComponentsToExportInHTMLreport : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetContrastsParameterizationName: no visible binding for global variable '.limmaGUIglobals' GetContrastsParameterizationName : onOK: no visible binding for global variable '.limmaGUIglobals' GetContrastsParameterizationName : onCancel: no visible binding for global variable '.limmaGUIglobals' GetContrastsParameterizationName : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetContrastsParameterizationNames: no visible binding for global variable 'limmaGUIenvironment' GetDEcutoff: no visible binding for global variable '.limmaGUIglobals' GetDEcutoff : onOK: no visible binding for global variable '.limmaGUIglobals' GetDEcutoff : onCancel: no visible binding for global variable '.limmaGUIglobals' GetDEcutoff : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetDesignOrContrasts: no visible binding for global variable 'limmaGUIenvironment' GetDesignOrContrasts: no visible binding for global variable '.limmaGUIglobals' GetDesignOrContrasts : GetDesignOrContrastsTable: no visible binding for global variable '.limmaGUIglobals' GetDesignOrContrasts : GetDesignOrContrastsTable : onOK: no visible binding for global variable 'limmaGUIenvironment' GetDesignOrContrasts : GetDesignOrContrastsTable : onOK: no visible binding for global variable '.limmaGUIglobals' GetDesignOrContrasts : GetDesignOrContrastsTable : onCancel: no visible binding for global variable '.limmaGUIglobals' GetDesignOrContrasts : GetDesignOrContrastsTable : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetDesignOrContrasts : OnAdvanced: no visible binding for global variable 'limmaGUIenvironment' GetDesignOrContrasts : OnAdvanced: no visible binding for global variable '.limmaGUIglobals' GetDesignOrContrasts : onOK: no visible binding for global variable '.limmaGUIglobals' GetDesignOrContrasts : onCancel: no visible binding for global variable '.limmaGUIglobals' GetDesignOrContrasts : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetGeneLabelsOptions: no visible binding for global variable '.limmaGUIglobals' GetGeneLabelsOptions : onOK: no visible binding for global variable '.limmaGUIglobals' GetGeneLabelsOptions : onCancel: no visible binding for global variable '.limmaGUIglobals' GetGeneLabelsOptions : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetGenePixFlagWeightings: no visible binding for global variable '.limmaGUIglobals' GetGenePixFlagWeightings : onOK: no visible binding for global variable '.limmaGUIglobals' GetGenePixFlagWeightings : onCancel: no visible binding for global variable '.limmaGUIglobals' GetGenePixFlagWeightings : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetImageAnalysisColumnHeadings: no visible binding for global variable '.limmaGUIglobals' GetImageAnalysisColumnHeadings : onOK: no visible binding for global variable '.limmaGUIglobals' GetImageAnalysisColumnHeadings : onCancel: no visible binding for global variable '.limmaGUIglobals' GetImageAnalysisColumnHeadings : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetImageProcessingFileType: no visible binding for global variable '.limmaGUIglobals' GetImageProcessingFileType: no visible binding for global variable 'limmaGUIenvironment' GetImageProcessingFileType : onOther: no visible binding for global variable '.limmaGUIglobals' GetImageProcessingFileType : onOK: no visible binding for global variable '.limmaGUIglobals' GetImageProcessingFileType : onCancel: no visible binding for global variable '.limmaGUIglobals' GetImageProcessingFileType : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetJpegOrPngParams: no visible binding for global variable '.limmaGUIglobals' GetJpegOrPngParams : onOK: no visible binding for global variable '.limmaGUIglobals' GetJpegOrPngParams : onCancel: no visible binding for global variable '.limmaGUIglobals' GetJpegOrPngParams : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetJpegOrPngX11Params: no visible binding for global variable '.limmaGUIglobals' GetJpegOrPngX11Params : onOK: no visible binding for global variable '.limmaGUIglobals' GetJpegOrPngX11Params : onCancel: no visible binding for global variable '.limmaGUIglobals' GetJpegOrPngX11Params : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetLowessType: no visible binding for global variable '.limmaGUIglobals' GetLowessType : onOK: no visible binding for global variable '.limmaGUIglobals' GetLowessType : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetNEWxlim: no visible binding for global variable '.limmaGUIglobals' GetNEWxlim : onOK: no visible binding for global variable '.limmaGUIglobals' GetNEWxlim : onCancel: no visible binding for global variable '.limmaGUIglobals' GetNEWxlim : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetNormexpOffsetValue: no visible binding for global variable '.limmaGUIglobals' GetNormexpOffsetValue : onOK: no visible binding for global variable '.limmaGUIglobals' GetNormexpOffsetValue : onCancel: no visible binding for global variable '.limmaGUIglobals' GetNormexpOffsetValue : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetNumParametersNoTargets: no visible binding for global variable 'limmaGUIenvironment' GetNumParametersNoTargets: no visible binding for global variable '.limmaGUIglobals' GetNumParametersNoTargets : onOK: no visible binding for global variable 'limmaGUIenvironment' GetNumParametersNoTargets : onOK: no visible binding for global variable '.limmaGUIglobals' GetNumParametersNoTargets : onCancel: no visible binding for global variable '.limmaGUIglobals' GetNumParametersNoTargets : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetPValueCutoff: no visible binding for global variable '.limmaGUIglobals' GetPValueCutoff : onOK: no visible binding for global variable '.limmaGUIglobals' GetPValueCutoff : onCancel: no visible binding for global variable '.limmaGUIglobals' GetPValueCutoff : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetParameterNames: no visible binding for global variable 'limmaGUIenvironment' GetParameterizationName: no visible binding for global variable '.limmaGUIglobals' GetParameterizationName : onOK: no visible binding for global variable '.limmaGUIglobals' GetParameterizationName : onCancel: no visible binding for global variable '.limmaGUIglobals' GetParameterizationName : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetParametersAndOrContrasts: no visible binding for global variable 'limmaGUIenvironment' GetParametersAndOrContrasts: no visible binding for global variable '.limmaGUIglobals' GetParametersAndOrContrasts : onOK: no visible binding for global variable '.limmaGUIglobals' GetParametersAndOrContrasts : onCancel: no visible binding for global variable '.limmaGUIglobals' GetParametersAndOrContrasts : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetPlotLabels: no visible binding for global variable '.limmaGUIglobals' GetPlotLabels : onOK: no visible binding for global variable '.limmaGUIglobals' GetPlotLabels : onCancel: no visible binding for global variable '.limmaGUIglobals' GetPlotLabels : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetPlotSize: no visible binding for global variable '.limmaGUIglobals' GetPlotSize : onOK: no visible binding for global variable '.limmaGUIglobals' GetPlotSize : onCancel: no visible binding for global variable '.limmaGUIglobals' GetPlotSize : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetPlotTitle: no visible binding for global variable '.limmaGUIglobals' GetPlotTitle : onOK: no visible binding for global variable '.limmaGUIglobals' GetPlotTitle : onCancel: no visible binding for global variable '.limmaGUIglobals' GetPlotTitle : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetReducedDuplicateSpacing: no visible binding for global variable 'limmaGUIenvironment' GetSlideNum: no visible binding for global variable 'limmaGUIenvironment' GetSlideNum: no visible binding for global variable '.limmaGUIglobals' GetSlideNum : onOK: no visible binding for global variable '.limmaGUIglobals' GetSlideNum : onCancel: no visible binding for global variable '.limmaGUIglobals' GetSlideNum : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetSpotTypesForLinearModel: no visible binding for global variable 'limmaGUIenvironment' GetSpotTypesForLinearModel: no visible binding for global variable '.limmaGUIglobals' GetSpotTypesForLinearModel : onOK: no visible binding for global variable '.limmaGUIglobals' GetSpotTypesForLinearModel : onCancel: no visible binding for global variable '.limmaGUIglobals' GetSpotTypesForLinearModel : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetSpotTypesIncludedNames: no visible binding for global variable 'limmaGUIenvironment' GetWithinArrayNormalizationMethod: no visible binding for global variable '.limmaGUIglobals' GetWithinArrayNormalizationMethod: no visible binding for global variable 'limmaGUIenvironment' GetWithinArrayNormalizationMethod : onOK: no visible binding for global variable 'limmaGUIenvironment' GetWithinArrayNormalizationMethod : onOK: no visible binding for global variable '.limmaGUIglobals' GetWithinArrayNormalizationMethod : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetWtAreaParams: no visible binding for global variable '.limmaGUIglobals' GetWtAreaParams : onOK: no visible binding for global variable 'limmaGUIenvironment' GetWtAreaParams : onOK: no visible binding for global variable '.limmaGUIglobals' GetWtAreaParams : onCancel: no visible binding for global variable '.limmaGUIglobals' GetWtAreaParams : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetlimmaDataSetName: no visible binding for global variable 'limmaGUIenvironment' GetlimmaDataSetName: no visible binding for global variable '.limmaGUIglobals' GetlimmaDataSetName : onOK: no visible binding for global variable 'limmaGUIenvironment' GetlimmaDataSetName : <anonymous>: no visible binding for global variable '.limmaGUIglobals' GetlmFitMethod: no visible binding for global variable '.limmaGUIglobals' GetlmFitMethod: no visible binding for global variable 'limmaGUIenvironment' GetlmFitMethod : onOK: no visible binding for global variable 'limmaGUIenvironment' GetlmFitMethod : onOK: no visible binding for global variable '.limmaGUIglobals' GetlmFitMethod : <anonymous>: no visible binding for global variable '.limmaGUIglobals' HTMLplotUsingFunction: no visible binding for global variable '.HTML.file' HTMLplotUsingFunction: no visible binding for global variable 'gif' HeatDiagramDialog: no visible binding for global variable '.limmaGUIglobals' HeatDiagramDialog : onOK: no visible binding for global variable '.limmaGUIglobals' HeatDiagramDialog : onCancel: no visible binding for global variable '.limmaGUIglobals' HeatDiagramDialog : <anonymous>: no visible binding for global variable '.limmaGUIglobals' HeatDiagramPlot: no visible binding for global variable 'limmaGUIenvironment' HeatDiagramPlot: no visible binding for global variable '.limmaGUIglobals' HowManyDups: no visible binding for global variable 'limmaGUIenvironment' HowManyDups: no visible binding for global variable '.limmaGUIglobals' HowManyDups : onOK: no visible binding for global variable 'limmaGUIenvironment' HowManyDups : onOK: no visible binding for global variable '.limmaGUIglobals' HowManyDups : onCancel: no visible binding for global variable '.limmaGUIglobals' HowManyDups : <anonymous>: no visible binding for global variable '.limmaGUIglobals' ImageArrayPlot: no visible binding for global variable 'limmaGUIenvironment' ImageArrayPlot: no visible binding for global variable '.limmaGUIglobals' ImageArrayPlotDialog: no visible binding for global variable 'limmaGUIenvironment' ImageArrayPlotDialog: no visible binding for global variable '.limmaGUIglobals' ImageArrayPlotDialog : onOK: no visible binding for global variable '.limmaGUIglobals' ImageArrayPlotDialog : onCancel: no visible binding for global variable '.limmaGUIglobals' ImageArrayPlotDialog : <anonymous>: no visible binding for global variable '.limmaGUIglobals' ImportMA: no visible binding for global variable 'limmaGUIenvironment' ImportMA: no visible binding for global variable '.limmaGUIglobals' ImportMADialog: no visible binding for global variable '.limmaGUIglobals' ImportMADialog : onOK: no visible binding for global variable '.limmaGUIglobals' ImportMADialog : onCancel: no visible binding for global variable '.limmaGUIglobals' ImportMADialog : <anonymous>: no visible binding for global variable '.limmaGUIglobals' InitNewParameterization: no visible binding for global variable 'limmaGUIenvironment' InitNewParameterization: no visible binding for global variable '.limmaGUIglobals' LogOddsPlot: no visible binding for global variable 'limmaGUIenvironment' LogOddsPlot: no visible binding for global variable '.limmaGUIglobals' MAPlot: no visible binding for global variable 'limmaGUIenvironment' MAPlot: no visible binding for global variable '.limmaGUIglobals' MAPlotAvg: no visible binding for global variable 'limmaGUIenvironment' MAPlotAvg: no visible binding for global variable '.limmaGUIglobals' MAPlotAvg : plotAvgMA: no visible binding for global variable 'limmaGUIenvironment' MBoxPlot: no visible binding for global variable 'limmaGUIenvironment' MBoxPlot: no visible binding for global variable '.limmaGUIglobals' MMPlot: no visible binding for global variable 'limmaGUIenvironment' MMPlot: no visible binding for global variable '.limmaGUIglobals' NewLimmaFile: no visible binding for global variable 'limmaGUIenvironment' NormalizeNow: no visible binding for global variable 'limmaGUIenvironment' NormalizeNow: no visible binding for global variable '.limmaGUIglobals' OpenALimmaFile: no visible binding for global variable 'limmaGUIenvironment' OpenGALFile: no visible binding for global variable 'limmaGUIenvironment' OpenGALandTargetsandSpotTypesfiles : onOK: no visible binding for global variable 'limmaGUIenvironment' OpenSpotTypesFile: no visible binding for global variable 'limmaGUIenvironment' OpenTargetsFile: no visible binding for global variable 'limmaGUIenvironment' PlotOptions: no visible binding for global variable '.limmaGUIglobals' PlotOptions : onOK: no visible binding for global variable '.limmaGUIglobals' PlotOptions : <anonymous>: no visible binding for global variable '.limmaGUIglobals' PrintTipGroupMAPlot: no visible binding for global variable 'limmaGUIenvironment' PrintTipGroupMAPlot: no visible binding for global variable '.limmaGUIglobals' QQTplot: no visible binding for global variable 'limmaGUIenvironment' QQTplot: no visible binding for global variable '.limmaGUIglobals' ReadImageProcessingFiles: no visible binding for global variable 'limmaGUIenvironment' ReadImageProcessingFiles: no visible binding for global variable '.limmaGUIglobals' SaveAsLimmaFile: no visible binding for global variable 'limmaGUIenvironment' SaveAsLimmaFile: no visible binding for global variable '.limmaGUIglobals' SaveLimmaFile: no visible binding for global variable 'limmaGUIenvironment' SaveLimmaFile: no visible binding for global variable '.limmaGUIglobals' SelectPlotSymbols: no visible binding for global variable '.limmaGUIglobals' SelectPlotSymbols : onBrowse: no visible binding for global variable '.limmaGUIglobals' SelectPlotSymbols : onOK: no visible binding for global variable '.limmaGUIglobals' SelectPlotSymbols : onCancel: no visible binding for global variable '.limmaGUIglobals' SelectPlotSymbols : <anonymous>: no visible binding for global variable '.limmaGUIglobals' SetLayoutParameters: no visible binding for global variable 'limmaGUIenvironment' SetLayoutParameters: no visible binding for global variable '.limmaGUIglobals' SetLayoutParameters : GetFromGAL: no visible binding for global variable 'limmaGUIenvironment' SetLayoutParameters : onOK: no visible binding for global variable 'limmaGUIenvironment' SetLayoutParameters : onOK: no visible binding for global variable '.limmaGUIglobals' SetLayoutParameters : onCancel: no visible binding for global variable '.limmaGUIglobals' SetLayoutParameters : <anonymous>: no visible binding for global variable '.limmaGUIglobals' SetWD: no visible binding for global variable '.limmaGUIglobals' TclRequire: no visible binding for global variable '.limmaGUIglobals' TclRequire : onDestroy: no visible binding for global variable '.limmaGUIglobals' TclRequire : onOK: no visible binding for global variable '.limmaGUIglobals' TclRequire : onOK: no visible binding for global variable 'limmaGUIenvironment' UpDownOrBoth: no visible binding for global variable '.limmaGUIglobals' UpDownOrBoth : onOK: no visible binding for global variable '.limmaGUIglobals' UpDownOrBoth : <anonymous>: no visible binding for global variable '.limmaGUIglobals' UpdateSpotTypesStatus: no visible binding for global variable 'limmaGUIenvironment' VennDiagramPlot: no visible binding for global variable 'limmaGUIenvironment' VennDiagramPlot: no visible binding for global variable '.limmaGUIglobals' ViewDesignOrContrastsMatrixAsPairs: no visible binding for global variable 'limmaGUIenvironment' ViewDesignOrContrastsMatrixAsPairs: no visible binding for global variable '.limmaGUIglobals' ViewDesignOrContrastsMatrixAsPairs : onOK: no visible binding for global variable '.limmaGUIglobals' ViewDesignOrContrastsMatrixAsPairs : <anonymous>: no visible binding for global variable '.limmaGUIglobals' ViewDesignOrContrastsMatrixInTable: no visible binding for global variable 'limmaGUIenvironment' ViewDesignOrContrastsMatrixInTable: no visible binding for global variable '.limmaGUIglobals' ViewDesignOrContrastsMatrixInTable : onClose: no visible binding for global variable '.limmaGUIglobals' ViewDesignOrContrastsMatrixInTable : <anonymous>: no visible binding for global variable '.limmaGUIglobals' ViewExistingContrastsParameterization: no visible binding for global variable 'limmaGUIenvironment' ViewExistingContrastsParameterization: no visible binding for global variable '.limmaGUIglobals' ViewExistingParameterization: no visible binding for global variable 'limmaGUIenvironment' ViewExistingParameterization: no visible binding for global variable '.limmaGUIglobals' ViewRNATargets: no visible binding for global variable 'limmaGUIenvironment' ViewRNATargets: no visible binding for global variable '.limmaGUIglobals' ViewRNATargets : onClose: no visible binding for global variable '.limmaGUIglobals' ViewRNATargets : <anonymous>: no visible binding for global variable '.limmaGUIglobals' ViewSpotTypes: no visible binding for global variable 'limmaGUIenvironment' ViewSpotTypes: no visible binding for global variable '.limmaGUIglobals' ViewSpotTypes : onUpdate: no visible binding for global variable 'limmaGUIenvironment' ViewSpotTypes : onUpdate: no visible binding for global variable '.limmaGUIglobals' ViewSpotTypes : onClose: no visible binding for global variable '.limmaGUIglobals' ViewSpotTypes : <anonymous>: no visible binding for global variable '.limmaGUIglobals' WithinBetweenOrBoth: no visible binding for global variable '.limmaGUIglobals' WithinBetweenOrBoth : onOK: no visible binding for global variable '.limmaGUIglobals' WithinBetweenOrBoth : <anonymous>: no visible binding for global variable '.limmaGUIglobals' chooseDir: no visible binding for global variable '.limmaGUIglobals' ebayesBoxPlots: no visible binding for global variable 'limmaGUIenvironment' ebayesBoxPlots: no visible binding for global variable '.limmaGUIglobals' ebayesBoxPlots: no visible binding for global variable 'limmaDataSetNameText' evalRcode: no visible binding for global variable '.limmaGUIglobals' evalRcode : runOverall: no visible binding for global variable '.limmaGUIglobals' evalRcode : runOverall: no visible binding for global variable 'limmaGUIenvironment' initGlobals: no visible binding for global variable 'limmaGUIenvironment' initGlobals: no visible binding for '<<-' assignment to 'NEOffsetDefault' initGlobals: no visible binding for global variable 'NEOffsetDefault' limmaGUI: no visible binding for global variable 'limmaGUIenvironment' limmaGUI: no visible binding for global variable '.limmaGUIglobals' limmaGUI : <anonymous>: no visible binding for global variable '.limmaGUIglobals' onDestroy: no visible binding for global variable 'limmaGUIenvironment' onExit: no visible binding for global variable 'limmaGUIenvironment' onExit: no visible binding for global variable '.limmaGUIglobals' plotMAColorCoded: no visible binding for global variable 'limmaGUIenvironment' plotMAColorCoded: no visible binding for global variable '.limmaGUIglobals' showGAL: no visible binding for global variable 'limmaGUIenvironment' showGAL: no visible binding for global variable '.limmaGUIglobals' showTopTable: no visible binding for global variable 'limmaGUIenvironment' showTopTable: no visible binding for global variable '.limmaGUIglobals' showTopTable : onOK: no visible binding for global variable '.limmaGUIglobals' showTopTable : onCancel: no visible binding for global variable '.limmaGUIglobals' showTopTable : <anonymous>: no visible binding for global variable '.limmaGUIglobals' showTopTable: no visible global function definition for 'toptable' Undefined global functions or variables: .HTML.file .limmaGUIglobals NEOffsetDefault ParameterizationNamesVec ebayes gif limmaDataSetNameText limmaGUIenvironment parameterizationIndex toptable * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking sizes of PDF files under 'inst/doc' ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... NONE * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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 'F:/biocbuild/bbs-3.20-bioc/meat/limmaGUI.Rcheck/00check.log' for details.
limmaGUI.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL limmaGUI ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'limmaGUI' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** 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 (limmaGUI)