############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iSEEtree.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iSEEtree_1.1.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/iSEEtree.Rcheck’ * using R Under development (unstable) (2025-03-02 r87868) * 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 ‘iSEEtree/DESCRIPTION’ ... OK * this is package ‘iSEEtree’ version ‘1.1.4’ * package encoding: UTF-8 * 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 ‘iSEEtree’ 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 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 .create_visual_box_for_abund_plot: no visible global function definition for ‘.getEncodedName’ .create_visual_box_for_abund_plot: no visible global function definition for ‘.addSpecificTour’ .create_visual_box_for_abund_plot: no visible global function definition for ‘collapseBox’ .create_visual_box_for_abund_plot: no visible global function definition for ‘.selectInput.iSEE’ .create_visual_box_for_abund_plot: no visible global function definition for ‘.checkboxInput.iSEE’ .create_visual_box_for_abunddens_plot: no visible global function definition for ‘.getEncodedName’ .create_visual_box_for_abunddens_plot: no visible global function definition for ‘.addSpecificTour’ .create_visual_box_for_abunddens_plot: no visible global function definition for ‘collapseBox’ .create_visual_box_for_abunddens_plot: no visible global function definition for ‘.selectInput.iSEE’ .create_visual_box_for_abunddens_plot: no visible global function definition for ‘.checkboxInput.iSEE’ .create_visual_box_for_abunddens_plot: no visible global function definition for ‘.radioButtons.iSEE’ .create_visual_box_for_abunddens_plot: no visible global function definition for ‘.conditionalOnRadio’ .create_visual_box_for_graph: no visible global function definition for ‘.getEncodedName’ .create_visual_box_for_graph: no visible global function definition for ‘.addSpecificTour’ .create_visual_box_for_graph: no visible global function definition for ‘collapseBox’ .create_visual_box_for_graph: no visible global function definition for ‘.selectInput.iSEE’ .create_visual_box_for_graph: no visible global function definition for ‘.checkboxInput.iSEE’ .create_visual_box_for_graph: no visible global function definition for ‘.checkboxGroupInput.iSEE’ .create_visual_box_for_graph: no visible global function definition for ‘.conditionalOnCheckGroup’ .create_visual_box_for_loading_plot: no visible global function definition for ‘.getEncodedName’ .create_visual_box_for_loading_plot: no visible global function definition for ‘.addSpecificTour’ .create_visual_box_for_loading_plot: no visible global function definition for ‘collapseBox’ .create_visual_box_for_loading_plot: no visible global function definition for ‘.selectInput.iSEE’ .create_visual_box_for_loading_plot: no visible global function definition for ‘.checkboxInput.iSEE’ .create_visual_box_for_prev_plot: no visible global function definition for ‘.getEncodedName’ .create_visual_box_for_prev_plot: no visible global function definition for ‘collapseBox’ .create_visual_box_for_rda: no visible global function definition for ‘.getEncodedName’ .create_visual_box_for_rda: no visible global function definition for ‘.addSpecificTour’ .create_visual_box_for_rda: no visible global function definition for ‘collapseBox’ .create_visual_box_for_rda: no visible global function definition for ‘.checkboxGroupInput.iSEE’ .create_visual_box_for_rda: no visible global function definition for ‘.selectInput.iSEE’ .create_visual_box_for_rda: no visible global function definition for ‘.conditionalOnCheckGroup’ .create_visual_box_for_rda: no visible global function definition for ‘.sliderInput.iSEE’ .create_visual_box_for_rda: no visible global function definition for ‘.numericInput.iSEE’ .create_visual_box_for_rda: no visible global function definition for ‘.checkboxInput.iSEE’ .create_visual_box_for_rda: no visible global function definition for ‘.conditionalOnCheckSolo’ .create_visual_box_for_scree_plot: no visible global function definition for ‘.getEncodedName’ .create_visual_box_for_scree_plot: no visible global function definition for ‘.addSpecificTour’ .create_visual_box_for_scree_plot: no visible global function definition for ‘collapseBox’ .create_visual_box_for_scree_plot: no visible global function definition for ‘.checkboxInput.iSEE’ .create_visual_box_for_tree: no visible global function definition for ‘.getEncodedName’ .create_visual_box_for_tree: no visible global function definition for ‘.addSpecificTour’ .create_visual_box_for_tree: no visible global function definition for ‘collapseBox’ .create_visual_box_for_tree: no visible global function definition for ‘.selectInput.iSEE’ .create_visual_box_for_tree: no visible global function definition for ‘.checkboxInput.iSEE’ .create_visual_box_for_tree: no visible global function definition for ‘.checkboxGroupInput.iSEE’ .create_visual_box_for_tree: no visible global function definition for ‘.conditionalOnCheckGroup’ .createObservers,AbundanceDensityPlot: no visible global function definition for ‘.getEncodedName’ .createObservers,AbundanceDensityPlot: no visible global function definition for ‘.createProtectedParameterObservers’ .createObservers,AbundanceDensityPlot: no visible global function definition for ‘.createUnprotectedParameterObservers’ .createObservers,AbundancePlot: no visible global function definition for ‘.getEncodedName’ .createObservers,AbundancePlot: no visible global function definition for ‘.createProtectedParameterObservers’ .createObservers,AbundancePlot: no visible global function definition for ‘.createUnprotectedParameterObservers’ .createObservers,GraphPlot: no visible global function definition for ‘.getEncodedName’ .createObservers,GraphPlot: no visible global function definition for ‘.createProtectedParameterObservers’ .createObservers,GraphPlot: no visible global function definition for ‘.createUnprotectedParameterObservers’ .createObservers,LoadingPlot: no visible global function definition for ‘.getEncodedName’ .createObservers,LoadingPlot: no visible global function definition for ‘.createProtectedParameterObservers’ .createObservers,LoadingPlot: no visible global function definition for ‘.createUnprotectedParameterObservers’ .createObservers,PrevalencePlot: no visible global function definition for ‘.getEncodedName’ .createObservers,PrevalencePlot: no visible global function definition for ‘.createProtectedParameterObservers’ .createObservers,PrevalencePlot: no visible global function definition for ‘.createUnprotectedParameterObservers’ .createObservers,RDAPlot: no visible global function definition for ‘.getEncodedName’ .createObservers,RDAPlot: no visible global function definition for ‘.createProtectedParameterObservers’ .createObservers,RDAPlot: no visible global function definition for ‘.createUnprotectedParameterObservers’ .createObservers,ScreePlot: no visible global function definition for ‘.getEncodedName’ .createObservers,ScreePlot: no visible global function definition for ‘.createProtectedParameterObservers’ .createObservers,ScreePlot: no visible global function definition for ‘.createUnprotectedParameterObservers’ .createObservers,TreePlot: no visible global function definition for ‘.getEncodedName’ .createObservers,TreePlot: no visible global function definition for ‘.createProtectedParameterObservers’ .createObservers,TreePlot: no visible global function definition for ‘.createUnprotectedParameterObservers’ .defineDataInterface,AbundanceDensityPlot: no visible global function definition for ‘.getEncodedName’ .defineDataInterface,AbundanceDensityPlot: no visible global function definition for ‘.selectInput.iSEE’ .defineDataInterface,AbundanceDensityPlot: no visible global function definition for ‘.numericInput.iSEE’ .defineDataInterface,AbundanceDensityPlot: no visible global function definition for ‘.checkboxInput.iSEE’ .defineDataInterface,AbundanceDensityPlot: no visible global function definition for ‘.radioButtons.iSEE’ .defineDataInterface,AbundanceDensityPlot: no visible global function definition for ‘.conditionalOnRadio’ .defineDataInterface,AbundancePlot: no visible global function definition for ‘.getEncodedName’ .defineDataInterface,AbundancePlot: no visible global function definition for ‘.checkboxInput.iSEE’ .defineDataInterface,AbundancePlot: no visible global function definition for ‘.radioButtons.iSEE’ .defineDataInterface,AbundancePlot: no visible global function definition for ‘.conditionalOnRadio’ .defineDataInterface,AbundancePlot: no visible global function definition for ‘.selectInput.iSEE’ .defineDataInterface,ColumnTreePlot: no visible global function definition for ‘.getEncodedName’ .defineDataInterface,ColumnTreePlot: no visible global function definition for ‘.selectInput.iSEE’ .defineDataInterface,GraphPlot: no visible global function definition for ‘.getEncodedName’ .defineDataInterface,GraphPlot: no visible global function definition for ‘.selectInput.iSEE’ .defineDataInterface,GraphPlot: no visible global function definition for ‘.checkboxInput.iSEE’ .defineDataInterface,LoadingPlot: no visible global function definition for ‘.getEncodedName’ .defineDataInterface,LoadingPlot: no visible global function definition for ‘.selectInput.iSEE’ .defineDataInterface,LoadingPlot: no visible global function definition for ‘.numericInput.iSEE’ .defineDataInterface,PrevalencePlot: no visible global function definition for ‘.getEncodedName’ .defineDataInterface,PrevalencePlot: no visible global function definition for ‘.selectInput.iSEE’ .defineDataInterface,PrevalencePlot: no visible global function definition for ‘.sliderInput.iSEE’ .defineDataInterface,PrevalencePlot: no visible global function definition for ‘.checkboxInput.iSEE’ .defineDataInterface,PrevalencePlot: no visible global function definition for ‘.conditionalOnCheckSolo’ .defineDataInterface,RDAPlot: no visible global function definition for ‘.getEncodedName’ .defineDataInterface,RDAPlot: no visible global function definition for ‘.selectInput.iSEE’ .defineDataInterface,RDAPlot: no visible global function definition for ‘.sliderInput.iSEE’ .defineDataInterface,RDAPlot: no visible global function definition for ‘.checkboxInput.iSEE’ .defineDataInterface,RowTreePlot: no visible global function definition for ‘.getEncodedName’ .defineDataInterface,RowTreePlot: no visible global function definition for ‘.selectInput.iSEE’ .defineDataInterface,ScreePlot: no visible global function definition for ‘.getEncodedName’ .defineDataInterface,ScreePlot: no visible global function definition for ‘.selectInput.iSEE’ .defineDataInterface,ScreePlot: no visible global function definition for ‘.numericInput.iSEE’ .defineDataInterface,ScreePlot: no visible global function definition for ‘.checkboxInput.iSEE’ .defineDataInterface,TreePlot: no visible global function definition for ‘.getEncodedName’ .defineDataInterface,TreePlot: no visible global function definition for ‘.checkboxInput.iSEE’ .defineDataInterface,TreePlot: no visible global function definition for ‘.sliderInput.iSEE’ .defineOutput,AbundanceDensityPlot: no visible global function definition for ‘.getEncodedName’ .defineOutput,AbundanceDensityPlot: no visible global function definition for ‘.panelColor’ .defineOutput,AbundancePlot: no visible global function definition for ‘.getEncodedName’ .defineOutput,AbundancePlot: no visible global function definition for ‘.panelColor’ .defineOutput,GraphPlot: no visible global function definition for ‘.getEncodedName’ .defineOutput,GraphPlot: no visible global function definition for ‘.panelColor’ .defineOutput,LoadingPlot: no visible global function definition for ‘.getEncodedName’ .defineOutput,LoadingPlot: no visible global function definition for ‘.panelColor’ .defineOutput,PrevalencePlot: no visible global function definition for ‘.getEncodedName’ .defineOutput,PrevalencePlot: no visible global function definition for ‘.panelColor’ .defineOutput,RDAPlot: no visible global function definition for ‘.getEncodedName’ .defineOutput,RDAPlot: no visible global function definition for ‘.panelColor’ .defineOutput,ScreePlot: no visible global function definition for ‘.getEncodedName’ .defineOutput,ScreePlot: no visible global function definition for ‘.panelColor’ .defineOutput,TreePlot: no visible global function definition for ‘.getEncodedName’ .defineOutput,TreePlot: no visible global function definition for ‘.panelColor’ .definePanelTour,AbundanceDensityPlot: no visible global function definition for ‘.getEncodedName’ .definePanelTour,AbundanceDensityPlot: no visible global function definition for ‘.getPanelColor’ .definePanelTour,AbundanceDensityPlot: no visible global function definition for ‘.addTourStep’ .definePanelTour,AbundancePlot: no visible global function definition for ‘.getEncodedName’ .definePanelTour,AbundancePlot: no visible global function definition for ‘.getPanelColor’ .definePanelTour,AbundancePlot: no visible global function definition for ‘.addTourStep’ .definePanelTour,GraphPlot: no visible global function definition for ‘.getEncodedName’ .definePanelTour,GraphPlot: no visible global function definition for ‘.getPanelColor’ .definePanelTour,GraphPlot: no visible global function definition for ‘.fullName’ .definePanelTour,GraphPlot: no visible global function definition for ‘.addTourStep’ .definePanelTour,LoadingPlot: no visible global function definition for ‘.getEncodedName’ .definePanelTour,LoadingPlot: no visible global function definition for ‘.getPanelColor’ .definePanelTour,LoadingPlot: no visible global function definition for ‘.addTourStep’ .definePanelTour,PrevalencePlot: no visible global function definition for ‘.getEncodedName’ .definePanelTour,PrevalencePlot: no visible global function definition for ‘.getPanelColor’ .definePanelTour,PrevalencePlot: no visible global function definition for ‘.addTourStep’ .definePanelTour,RDAPlot: no visible global function definition for ‘.getEncodedName’ .definePanelTour,RDAPlot: no visible global function definition for ‘.getPanelColor’ .definePanelTour,RDAPlot: no visible global function definition for ‘.addTourStep’ .definePanelTour,ScreePlot: no visible global function definition for ‘.getEncodedName’ .definePanelTour,ScreePlot: no visible global function definition for ‘.getPanelColor’ .definePanelTour,ScreePlot: no visible global function definition for ‘.addTourStep’ .definePanelTour,TreePlot: no visible global function definition for ‘.getEncodedName’ .definePanelTour,TreePlot: no visible global function definition for ‘.getPanelColor’ .definePanelTour,TreePlot: no visible global function definition for ‘.fullName’ .definePanelTour,TreePlot: no visible global function definition for ‘.addTourStep’ .exportOutput,AbundanceDensityPlot: no visible global function definition for ‘.generateOutput’ .exportOutput,AbundanceDensityPlot: no visible global function definition for ‘.getEncodedName’ .exportOutput,AbundancePlot: no visible global function definition for ‘.generateOutput’ .exportOutput,AbundancePlot: no visible global function definition for ‘.getEncodedName’ .exportOutput,GraphPlot: no visible global function definition for ‘.generateOutput’ .exportOutput,GraphPlot: no visible global function definition for ‘.getEncodedName’ .exportOutput,LoadingPlot: no visible global function definition for ‘.generateOutput’ .exportOutput,LoadingPlot: no visible global function definition for ‘.getEncodedName’ .exportOutput,PrevalencePlot: no visible global function definition for ‘.generateOutput’ .exportOutput,PrevalencePlot: no visible global function definition for ‘.getEncodedName’ .exportOutput,RDAPlot: no visible global function definition for ‘.generateOutput’ .exportOutput,RDAPlot: no visible global function definition for ‘.getEncodedName’ .exportOutput,ScreePlot: no visible global function definition for ‘.generateOutput’ .exportOutput,ScreePlot: no visible global function definition for ‘.getEncodedName’ .exportOutput,TreePlot: no visible global function definition for ‘.generateOutput’ .exportOutput,TreePlot: no visible global function definition for ‘.getEncodedName’ .generateOutput,AbundanceDensityPlot: no visible global function definition for ‘.processMultiSelections’ .generateOutput,AbundanceDensityPlot: no visible global function definition for ‘.textEval’ .generateOutput,AbundancePlot: no visible global function definition for ‘.processMultiSelections’ .generateOutput,AbundancePlot: no visible global function definition for ‘.textEval’ .generateOutput,ColumnGraphPlot: no visible global function definition for ‘.processMultiSelections’ .generateOutput,ColumnGraphPlot: no visible global function definition for ‘.textEval’ .generateOutput,ColumnTreePlot: no visible global function definition for ‘.processMultiSelections’ .generateOutput,ColumnTreePlot: no visible global function definition for ‘.textEval’ .generateOutput,LoadingPlot: no visible global function definition for ‘.processMultiSelections’ .generateOutput,LoadingPlot: no visible global function definition for ‘.textEval’ .generateOutput,PrevalencePlot: no visible global function definition for ‘.processMultiSelections’ .generateOutput,PrevalencePlot: no visible global function definition for ‘.textEval’ .generateOutput,RDAPlot: no visible global function definition for ‘.processMultiSelections’ .generateOutput,RDAPlot: no visible global function definition for ‘.textEval’ .generateOutput,RowGraphPlot: no visible global function definition for ‘.processMultiSelections’ .generateOutput,RowGraphPlot: no visible global function definition for ‘.textEval’ .generateOutput,RowTreePlot: no visible global function definition for ‘.processMultiSelections’ .generateOutput,RowTreePlot: no visible global function definition for ‘.textEval’ .generateOutput,ScreePlot: no visible global function definition for ‘.textEval’ .renderOutput,AbundanceDensityPlot: no visible global function definition for ‘.getEncodedName’ .renderOutput,AbundanceDensityPlot: no visible global function definition for ‘.retrieveOutput’ .renderOutput,AbundancePlot: no visible global function definition for ‘.getEncodedName’ .renderOutput,AbundancePlot: no visible global function definition for ‘.retrieveOutput’ .renderOutput,GraphPlot: no visible global function definition for ‘.getEncodedName’ .renderOutput,GraphPlot: no visible global function definition for ‘.retrieveOutput’ .renderOutput,LoadingPlot: no visible global function definition for ‘.getEncodedName’ .renderOutput,LoadingPlot: no visible global function definition for ‘.retrieveOutput’ .renderOutput,PrevalencePlot: no visible global function definition for ‘.getEncodedName’ .renderOutput,PrevalencePlot: no visible global function definition for ‘.retrieveOutput’ .renderOutput,RDAPlot: no visible global function definition for ‘.getEncodedName’ .renderOutput,RDAPlot: no visible global function definition for ‘.retrieveOutput’ .renderOutput,ScreePlot: no visible global function definition for ‘.getEncodedName’ .renderOutput,ScreePlot: no visible global function definition for ‘.retrieveOutput’ .renderOutput,TreePlot: no visible global function definition for ‘.getEncodedName’ .renderOutput,TreePlot: no visible global function definition for ‘.retrieveOutput’ initialize,AbundanceDensityPlot: no visible global function definition for ‘.emptyDefault’ initialize,AbundancePlot: no visible global function definition for ‘.emptyDefault’ initialize,GraphPlot: no visible global function definition for ‘.emptyDefault’ initialize,LoadingPlot: no visible global function definition for ‘.emptyDefault’ initialize,PrevalencePlot: no visible global function definition for ‘.emptyDefault’ initialize,RDAPlot: no visible global function definition for ‘.emptyDefault’ initialize,ScreePlot: no visible global function definition for ‘.emptyDefault’ initialize,TreePlot: no visible global function definition for ‘.emptyDefault’ Undefined global functions or variables: .addSpecificTour .addTourStep .checkboxGroupInput.iSEE .checkboxInput.iSEE .conditionalOnCheckGroup .conditionalOnCheckSolo .conditionalOnRadio .createProtectedParameterObservers .createUnprotectedParameterObservers .emptyDefault .fullName .generateOutput .getEncodedName .getPanelColor .numericInput.iSEE .panelColor .processMultiSelections .radioButtons.iSEE .retrieveOutput .selectInput.iSEE .sliderInput.iSEE .textEval collapseBox * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: iSEE.Rd: SummarizedExperiment-class, Panel-class, ExperimentColorMap-class, shinyApp Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. Unknown package ‘SingleSummarizedExperiment’ in Rd xrefs * 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 files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ 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 * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/iSEEtree.Rcheck/00check.log’ for details.