Gordon Smyth
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/affylmGUI |
| Branch: RELEASE_3_9 |
| Last Commit: cecdfae |
| Last Changed Date: 2019-05-02 11:53:02 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:45:01 -0400 (Wed, 16 Oct 2019).
| Package 31/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| affylmGUI 1.58.0 Gordon Smyth
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: affylmGUI |
| Version: 1.58.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:affylmGUI.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings affylmGUI_1.58.0.tar.gz |
| StartedAt: 2019-10-16 00:26:36 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 00:29:46 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 189.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: affylmGUI.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:affylmGUI.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings affylmGUI_1.58.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/affylmGUI.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘affylmGUI/DESCRIPTION’ ... OK * this is package ‘affylmGUI’ version ‘1.58.0’ * 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 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 ChooseCDF: 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 :: 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 : : 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 : : 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 : : 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 : : 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 : : 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 : : 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 : : 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 : : 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 : : 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 : : 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 : : 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 : : 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 : : 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 : : 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 : : 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 : : 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 : : 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 : : 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 : : 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 : : 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 : : 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 : : 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 : : 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 : : 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 : : 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 : : no visible binding for global variable ‘.affylmGUIglobals’ HTMLplotUsingFunction: no visible binding for global variable ‘.HTML.file’ 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 : : 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 : : 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 : : 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 : : 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 : : 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’ toptable2: no visible global function definition for ‘ebayes’ Undefined global functions or variables: .HTML.file .affylmGUIglobals LocalHScale LocalVScale affylmGUIenvironment ebayes * 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 in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.9-bioc/meat/affylmGUI.Rcheck/00check.log’ for details.
affylmGUI.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL affylmGUI ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘affylmGUI’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ‘affylmGUI.Rnw’ ‘extract.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 (affylmGUI)