Gordon Smyth
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/limmaGUI |
| git_branch: RELEASE_3_17 |
| git_last_commit: e03b89c |
| git_last_commit_date: 2023-04-25 09:40:17 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:05 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 1064/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| limmaGUI 1.76.0 (landing page) Gordon Smyth
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the limmaGUI package: - 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: 1.76.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:limmaGUI.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings limmaGUI_1.76.0.tar.gz |
| StartedAt: 2023-10-18 03:42:40 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 03:44:25 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 105.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: limmaGUI.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:limmaGUI.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings limmaGUI_1.76.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/limmaGUI.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘limmaGUI/DESCRIPTION’ ... OK
* this is package ‘limmaGUI’ version ‘1.76.0’
* 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 ‘limmaGUI’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.5Mb
sub-directories of 1Mb or more:
doc 6.7Mb
* 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 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/limmaGUI.Rcheck/00check.log’
for details.
limmaGUI.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL limmaGUI ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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)