Movatterモバイル変換

################################################################################################################################################################## Running command:######   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:affylmGUI.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings affylmGUI_1.84.0.tar.gz###############################################################################################################################################################* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/affylmGUI.Rcheck’* using R version 4.5.2 (2025-10-31)* using platform: x86_64-apple-darwin20* R was compiled by    Apple clang version 14.0.0 (clang-1400.0.29.202)    GNU Fortran (GCC) 14.2.0* running under: macOS Monterey 12.7.6* using session charset: UTF-8* using option ‘--no-vignettes’* checking for file ‘affylmGUI/DESCRIPTION’ ... OK* this is package ‘affylmGUI’ version ‘1.84.0’* checking package namespace information ... OK* checking package dependencies ... OK* checking if this is a source package ... OK* checking if there is a namespace ... OK* checking for hidden files and directories ... OK* checking for portable file names ... OK* checking for sufficient/correct file permissions ... OK* checking whether package ‘affylmGUI’ 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 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 ... NOTEChooseCDF: no visible binding for global variable ‘.affylmGUIglobals’ChooseCDF : onOK: no visible binding for global variable  ‘.affylmGUIglobals’ChooseCDF : onCancel: no visible binding for global variable  ‘.affylmGUIglobals’ChooseCDF : <anonymous>: no visible binding for global variable  ‘.affylmGUIglobals’ChooseContrastParameterization: no visible binding for global variable  ‘affylmGUIenvironment’ChooseContrastParameterization: no visible binding for global variable  ‘.affylmGUIglobals’ChooseContrastParameterization : onOK: no visible binding for global  variable ‘.affylmGUIglobals’ChooseContrastParameterization : onCancel: no visible binding for  global variable ‘.affylmGUIglobals’ChooseContrastParameterization : <anonymous>: no visible binding for  global variable ‘.affylmGUIglobals’ChooseEbayesStatistic: no visible binding for global variable  ‘.affylmGUIglobals’ChooseEbayesStatistic : onOK: no visible binding for global variable  ‘.affylmGUIglobals’ChooseEbayesStatistic : onCancel: no visible binding for global  variable ‘.affylmGUIglobals’ChooseEbayesStatistic : <anonymous>: no visible binding for global  variable ‘.affylmGUIglobals’ComputeContrasts: no visible binding for global variable  ‘affylmGUIenvironment’ComputeLinearModelFit: no visible binding for global variable  ‘affylmGUIenvironment’ComputeLinearModelFit: no visible binding for global variable  ‘.affylmGUIglobals’DeleteContrastParameterization: no visible binding for global variable  ‘affylmGUIenvironment’DensityPlot: no visible binding for global variable  ‘affylmGUIenvironment’DensityPlot: no visible binding for global variable ‘.affylmGUIglobals’DensityPlot : plotFunction: no visible binding for global variable  ‘.affylmGUIglobals’DensityPlotAll: no visible binding for global variable  ‘affylmGUIenvironment’DensityPlotAll: no visible binding for global variable  ‘.affylmGUIglobals’DensityPlotAll : plotFunction: no visible binding for global variable  ‘.affylmGUIglobals’DensityPlotAll : plotFunction: no visible binding for global variable  ‘affylmGUIenvironment’ExportHTMLreport: no visible binding for global variable  ‘affylmGUIenvironment’ExportNormalizedExpressionValues: no visible binding for global  variable ‘affylmGUIenvironment’GetComponentsToExportInHTMLreport: no visible binding for global  variable ‘affylmGUIenvironment’GetComponentsToExportInHTMLreport: no visible binding for global  variable ‘.affylmGUIglobals’GetComponentsToExportInHTMLreport : onOK: no visible binding for global  variable ‘.affylmGUIglobals’GetComponentsToExportInHTMLreport : onCancel: no visible binding for  global variable ‘.affylmGUIglobals’GetComponentsToExportInHTMLreport : <anonymous>: no visible binding for  global variable ‘.affylmGUIglobals’GetContrast: no visible binding for global variable ‘.affylmGUIglobals’GetContrast: no visible binding for global variable  ‘affylmGUIenvironment’GetContrast : onOK: no visible binding for global variable  ‘.affylmGUIglobals’GetContrast : onCancel: no visible binding for global variable  ‘.affylmGUIglobals’GetContrast : <anonymous>: no visible binding for global variable  ‘.affylmGUIglobals’GetContrastNamesForHeatDiagram: no visible binding for global variable  ‘.affylmGUIglobals’GetContrastNamesForHeatDiagram : onOK: no visible binding for global  variable ‘.affylmGUIglobals’GetContrastNamesForHeatDiagram : onCancel: no visible binding for  global variable ‘.affylmGUIglobals’GetContrastNamesForHeatDiagram : <anonymous>: no visible binding for  global variable ‘.affylmGUIglobals’GetContrastParameterizationName: no visible binding for global variable  ‘.affylmGUIglobals’GetContrastParameterizationName : onOK: no visible binding for global  variable ‘.affylmGUIglobals’GetContrastParameterizationName : onCancel: no visible binding for  global variable ‘.affylmGUIglobals’GetContrastParameterizationName : <anonymous>: no visible binding for  global variable ‘.affylmGUIglobals’GetContrasts: no visible binding for global variable  ‘affylmGUIenvironment’GetDEcutoff: no visible binding for global variable ‘.affylmGUIglobals’GetDEcutoff : onOK: no visible binding for global variable  ‘.affylmGUIglobals’GetDEcutoff : onCancel: no visible binding for global variable  ‘.affylmGUIglobals’GetDEcutoff : <anonymous>: no visible binding for global variable  ‘.affylmGUIglobals’GetGeneLabelsOptions: no visible binding for global variable  ‘.affylmGUIglobals’GetGeneLabelsOptions : onOK: no visible binding for global variable  ‘.affylmGUIglobals’GetGeneLabelsOptions : onCancel: no visible binding for global variable  ‘.affylmGUIglobals’GetGeneLabelsOptions : <anonymous>: no visible binding for global  variable ‘.affylmGUIglobals’GetJpegOrPngParams: no visible binding for global variable  ‘.affylmGUIglobals’GetJpegOrPngParams : onOK: no visible binding for global variable  ‘.affylmGUIglobals’GetJpegOrPngParams : onCancel: no visible binding for global variable  ‘.affylmGUIglobals’GetJpegOrPngParams : <anonymous>: no visible binding for global  variable ‘.affylmGUIglobals’GetJpegOrPngX11Params: no visible binding for global variable  ‘.affylmGUIglobals’GetJpegOrPngX11Params : onOK: no visible binding for global variable  ‘.affylmGUIglobals’GetJpegOrPngX11Params : onCancel: no visible binding for global  variable ‘.affylmGUIglobals’GetJpegOrPngX11Params : <anonymous>: no visible binding for global  variable ‘.affylmGUIglobals’GetLogPLMDataChoice: no visible binding for global variable  ‘.affylmGUIglobals’GetLogPLMDataChoice : onCancel: no visible binding for global variable  ‘.affylmGUIglobals’GetLogPLMDataChoice : onOK: no visible binding for global variable  ‘.affylmGUIglobals’GetLogPLMDataChoice : <anonymous>: no visible binding for global  variable ‘.affylmGUIglobals’GetMultipleContrasts: no visible binding for global variable  ‘.affylmGUIglobals’GetMultipleContrasts: no visible binding for global variable  ‘affylmGUIenvironment’GetMultipleContrasts : onOK: no visible binding for global variable  ‘.affylmGUIglobals’GetMultipleContrasts : onCancel: no visible binding for global variable  ‘.affylmGUIglobals’GetMultipleContrasts : <anonymous>: no visible binding for global  variable ‘.affylmGUIglobals’GetNormalizationMethod: no visible binding for global variable  ‘.affylmGUIglobals’GetNormalizationMethod : onCancel: no visible binding for global  variable ‘.affylmGUIglobals’GetNormalizationMethod : onOK: no visible binding for global variable  ‘.affylmGUIglobals’GetNormalizationMethod : <anonymous>: no visible binding for global  variable ‘.affylmGUIglobals’GetPValueCutoff: no visible binding for global variable  ‘.affylmGUIglobals’GetPValueCutoff : onOK: no visible binding for global variable  ‘.affylmGUIglobals’GetPValueCutoff : onCancel: no visible binding for global variable  ‘.affylmGUIglobals’GetPValueCutoff : <anonymous>: no visible binding for global variable  ‘.affylmGUIglobals’GetParameterizationName: no visible binding for global variable  ‘.affylmGUIglobals’GetParameterizationName : onOK: no visible binding for global variable  ‘.affylmGUIglobals’GetParameterizationName : onCancel: no visible binding for global  variable ‘.affylmGUIglobals’GetParameterizationName : <anonymous>: no visible binding for global  variable ‘.affylmGUIglobals’GetPlotLabels: no visible binding for global variable  ‘.affylmGUIglobals’GetPlotLabels : onOK: no visible binding for global variable  ‘.affylmGUIglobals’GetPlotLabels : onCancel: no visible binding for global variable  ‘.affylmGUIglobals’GetPlotLabels : <anonymous>: no visible binding for global variable  ‘.affylmGUIglobals’GetPlotSize: no visible binding for global variable ‘.affylmGUIglobals’GetPlotSize : onOK: no visible binding for global variable  ‘.affylmGUIglobals’GetPlotSize : onCancel: no visible binding for global variable  ‘.affylmGUIglobals’GetPlotSize : <anonymous>: no visible binding for global variable  ‘.affylmGUIglobals’GetPlotTitle: no visible binding for global variable  ‘.affylmGUIglobals’GetPlotTitle : onOK: no visible binding for global variable  ‘.affylmGUIglobals’GetPlotTitle : onCancel: no visible binding for global variable  ‘.affylmGUIglobals’GetPlotTitle : <anonymous>: no visible binding for global variable  ‘.affylmGUIglobals’GetResidualTypeChoice: no visible binding for global variable  ‘.affylmGUIglobals’GetResidualTypeChoice : onCancel: no visible binding for global  variable ‘.affylmGUIglobals’GetResidualTypeChoice : onOK: no visible binding for global variable  ‘.affylmGUIglobals’GetResidualTypeChoice : <anonymous>: no visible binding for global  variable ‘.affylmGUIglobals’GetSetNames: no visible binding for global variable ‘.affylmGUIglobals’GetSetNames : onOK: no visible binding for global variable  ‘.affylmGUIglobals’GetSetNames : onCancel: no visible binding for global variable  ‘.affylmGUIglobals’GetSetNames : <anonymous>: no visible binding for global variable  ‘.affylmGUIglobals’GetSlideNum: no visible binding for global variable  ‘affylmGUIenvironment’GetSlideNum: no visible binding for global variable ‘.affylmGUIglobals’GetSlideNum : onOK: no visible binding for global variable  ‘.affylmGUIglobals’GetSlideNum : onCancel: no visible binding for global variable  ‘.affylmGUIglobals’GetSlideNum : <anonymous>: no visible binding for global variable  ‘.affylmGUIglobals’GetSlideNums: no visible binding for global variable  ‘affylmGUIenvironment’GetSlideNums: no visible binding for global variable  ‘.affylmGUIglobals’GetSlideNums : onOK: no visible binding for global variable  ‘.affylmGUIglobals’GetSlideNums : onCancel: no visible binding for global variable  ‘.affylmGUIglobals’GetSlideNums : <anonymous>: no visible binding for global variable  ‘.affylmGUIglobals’GetWhichProbes: no visible binding for global variable  ‘.affylmGUIglobals’GetWhichProbes : onCancel: no visible binding for global variable  ‘.affylmGUIglobals’GetWhichProbes : onOK: no visible binding for global variable  ‘.affylmGUIglobals’GetWhichProbes : <anonymous>: no visible binding for global variable  ‘.affylmGUIglobals’GetWtAreaParams: no visible binding for global variable  ‘.affylmGUIglobals’GetWtAreaParams : onOK: no visible binding for global variable  ‘affylmGUIenvironment’GetWtAreaParams : onOK: no visible binding for global variable  ‘.affylmGUIglobals’GetWtAreaParams : onCancel: no visible binding for global variable  ‘.affylmGUIglobals’GetWtAreaParams : <anonymous>: no visible binding for global variable  ‘.affylmGUIglobals’GetWtFlagParams: no visible binding for global variable  ‘.affylmGUIglobals’GetWtFlagParams : onOK: no visible binding for global variable  ‘.affylmGUIglobals’GetWtFlagParams : onCancel: no visible binding for global variable  ‘.affylmGUIglobals’GetWtFlagParams : <anonymous>: no visible binding for global variable  ‘.affylmGUIglobals’GetWtFlagParams: no visible binding for global variable  ‘affylmGUIenvironment’GetlimmaDataSetName: no visible binding for global variable  ‘affylmGUIenvironment’GetlimmaDataSetName: no visible binding for global variable  ‘.affylmGUIglobals’GetlimmaDataSetName : onOK: no visible binding for global variable  ‘affylmGUIenvironment’GetlimmaDataSetName : <anonymous>: no visible binding for global  variable ‘.affylmGUIglobals’HeatDiagramDialog: no visible binding for global variable  ‘.affylmGUIglobals’HeatDiagramDialog : onOK: no visible binding for global variable  ‘.affylmGUIglobals’HeatDiagramDialog : onCancel: no visible binding for global variable  ‘.affylmGUIglobals’HeatDiagramDialog : <anonymous>: no visible binding for global variable  ‘.affylmGUIglobals’HeatDiagramPlot: no visible binding for global variable  ‘affylmGUIenvironment’ImageArrayPlot: no visible binding for global variable  ‘affylmGUIenvironment’ImageArrayPlot: no visible binding for global variable  ‘.affylmGUIglobals’ImageArrayPlot : plotFunction: no visible binding for global variable  ‘.affylmGUIglobals’ImageQualityResidualPlot: no visible binding for global variable  ‘affylmGUIenvironment’ImageQualityResidualPlot: no visible binding for global variable  ‘.affylmGUIglobals’ImageQualityResidualPlot : plotFunction: no visible binding for global  variable ‘.affylmGUIglobals’ImageQualityWeightPlot: no visible binding for global variable  ‘affylmGUIenvironment’ImageQualityWeightPlot: no visible binding for global variable  ‘.affylmGUIglobals’ImageQualityWeightPlot : plotFunction: no visible binding for global  variable ‘.affylmGUIglobals’IntensityHistogram: no visible binding for global variable  ‘affylmGUIenvironment’IntensityHistogram: no visible binding for global variable  ‘.affylmGUIglobals’IntensityHistogram : plotFunction: no visible binding for global  variable ‘.affylmGUIglobals’IntensityHistogramAll: no visible binding for global variable  ‘affylmGUIenvironment’IntensityHistogramAll: no visible binding for global variable  ‘.affylmGUIglobals’IntensityHistogramAll : plotFunction: no visible binding for global  variable ‘.affylmGUIglobals’LogOddsPlot: no visible binding for global variable  ‘affylmGUIenvironment’NUSEPlotAll: no visible binding for global variable  ‘affylmGUIenvironment’NUSEPlotAll: no visible binding for global variable ‘.affylmGUIglobals’NUSEPlotAll : plotFunction: no visible binding for global variable  ‘.affylmGUIglobals’NewLimmaFile: no visible binding for global variable  ‘affylmGUIenvironment’NormalizeNow: no visible binding for global variable  ‘affylmGUIenvironment’NormalizeNow: no visible binding for global variable  ‘.affylmGUIglobals’NormalizedIntensityBoxPlot: no visible binding for global variable  ‘affylmGUIenvironment’NormalizedIntensityBoxPlot: no visible binding for global variable  ‘.affylmGUIglobals’NormalizedIntensityBoxPlot : plotFunction: no visible binding for  global variable ‘.affylmGUIglobals’OpenALimmaFile: no visible binding for global variable  ‘affylmGUIenvironment’OpenCDFFile: no visible binding for global variable  ‘affylmGUIenvironment’OpenCDFandTargetsfiles : onOK: no visible binding for global variable  ‘affylmGUIenvironment’OpenCDFandTargetsfiles: no visible binding for global variable  ‘affylmGUIenvironment’OpenTargetsFile: no visible binding for global variable  ‘affylmGUIenvironment’PlotOptions: no visible binding for global variable ‘.affylmGUIglobals’PlotOptions : onOK: no visible binding for global variable  ‘.affylmGUIglobals’PlotOptions : <anonymous>: no visible binding for global variable  ‘.affylmGUIglobals’QQTplot: no visible binding for global variable ‘affylmGUIenvironment’RLEPlotAll: no visible binding for global variable  ‘affylmGUIenvironment’RLEPlotAll: no visible binding for global variable ‘.affylmGUIglobals’RLEPlotAll : plotFunction: no visible binding for global variable  ‘.affylmGUIglobals’RNADegradationPlotAll: no visible binding for global variable  ‘affylmGUIenvironment’RNADegradationPlotAll: no visible binding for global variable  ‘.affylmGUIglobals’RNADegradationPlotAll : plotFunction: no visible binding for global  variable ‘.affylmGUIglobals’RawIntensityBoxPlot: no visible binding for global variable  ‘affylmGUIenvironment’RawIntensityBoxPlot: no visible binding for global variable  ‘.affylmGUIglobals’RawIntensityBoxPlot : plotFunction: no visible binding for global  variable ‘.affylmGUIglobals’Resize: no visible binding for '<<-' assignment to ‘LocalHScale’Resize: no visible binding for '<<-' assignment to ‘LocalVScale’Resize: no visible binding for global variable ‘LocalHScale’Resize: no visible binding for global variable ‘LocalVScale’SaveAsLimmaFile: no visible binding for global variable  ‘affylmGUIenvironment’SaveAsLimmaFile: no visible binding for global variable  ‘.affylmGUIglobals’SaveLimmaFile: no visible binding for global variable  ‘affylmGUIenvironment’SaveLimmaFile: no visible binding for global variable  ‘.affylmGUIglobals’SetWD: no visible binding for global variable ‘.affylmGUIglobals’TclRequire: no visible binding for global variable ‘.affylmGUIglobals’TclRequire : onDestroy: no visible binding for global variable  ‘.affylmGUIglobals’TclRequire : onOK: no visible binding for global variable  ‘.affylmGUIglobals’TclRequire : onOK: no visible binding for global variable  ‘affylmGUIenvironment’UpDownOrBoth: no visible binding for global variable  ‘.affylmGUIglobals’UpDownOrBoth : onOK: no visible binding for global variable  ‘.affylmGUIglobals’UpDownOrBoth : <anonymous>: no visible binding for global variable  ‘.affylmGUIglobals’VennDiagramPlot: no visible binding for global variable  ‘affylmGUIenvironment’ViewContrastsMatrixAsPairs: no visible binding for global variable  ‘affylmGUIenvironment’ViewContrastsMatrixInTable: no visible binding for global variable  ‘affylmGUIenvironment’ViewExistingContrastParameterization: no visible binding for global  variable ‘affylmGUIenvironment’ViewRNATargets: no visible binding for global variable  ‘affylmGUIenvironment’ViewRNATargets: no visible binding for global variable  ‘.affylmGUIglobals’ViewRNATargets : onClose: no visible binding for global variable  ‘.affylmGUIglobals’ViewRNATargets : <anonymous>: no visible binding for global variable  ‘.affylmGUIglobals’affyPlotMA: no visible binding for global variable  ‘affylmGUIenvironment’affyPlotMA: no visible binding for global variable ‘.affylmGUIglobals’affyPlotMA : plotFunction: no visible binding for global variable  ‘.affylmGUIglobals’affyPlotMAcontrast: no visible binding for global variable  ‘affylmGUIenvironment’affylmGUI: no visible binding for global variable  ‘affylmGUIenvironment’affylmGUI: no visible binding for global variable ‘.affylmGUIglobals’affylmGUI : <anonymous>: no visible binding for global variable  ‘.affylmGUIglobals’chooseDir: no visible binding for global variable ‘.affylmGUIglobals’evalRcode: no visible binding for global variable ‘.affylmGUIglobals’evalRcode : runOverall: no visible binding for global variable  ‘.affylmGUIglobals’evalRcode : runOverall: no visible binding for global variable  ‘affylmGUIenvironment’generalPlotFunction: no visible binding for global variable  ‘.affylmGUIglobals’generalPlotFunction: no visible binding for global variable  ‘affylmGUIenvironment’initGlobals: no visible binding for global variable  ‘affylmGUIenvironment’onDestroy: no visible binding for global variable  ‘affylmGUIenvironment’onExit: no visible binding for global variable ‘affylmGUIenvironment’onExit: no visible binding for global variable ‘.affylmGUIglobals’showTopTable: no visible binding for global variable  ‘affylmGUIenvironment’showTopTable : onOK: no visible binding for global variable  ‘affylmGUIenvironment’Undefined global functions or variables:  .affylmGUIglobals LocalHScale LocalVScale affylmGUIenvironment* checking Rd files ... OK* checking Rd metadata ... OK* checking Rd cross-references ... NOTEFound the following Rd file(s) with Rd \link{} targets missing packageanchors:  affylmGU-package.Rd: limma-packagePlease provide package anchors for all Rd \link{} targets not in thepackage itself and the base packages.* 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 ... OK* 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* DONEStatus: 2 NOTEsSee  ‘/Users/biocbuild/bbs-3.22-bioc/meat/affylmGUI.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL affylmGUI###############################################################################################################################################################* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’* installing *source* package ‘affylmGUI’ ...** this is package ‘affylmGUI’ version ‘1.84.0’** 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 (affylmGUI)