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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iSEE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iSEE_2.19.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/iSEE.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iSEE/DESCRIPTION’ ... OK
* this is package ‘iSEE’ version ‘2.19.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘iSEE’ 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 ... NOTE
Unexported object imported by a ':::' call: ‘S4Vectors:::selectSome’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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:
  ColumnDataPlot-class.Rd: colData, SummarizedExperiment-class
  ColumnDataTable-class.Rd: colData, SummarizedExperiment-class
  ColumnDotPlot-class.Rd: SummarizedExperiment-class, ggplot, colData
  ColumnTable-class.Rd: SummarizedExperiment-class, datatable
  ComplexHeatmapPlot-class.Rd: SummarizedExperiment-class, Heatmap,
    colData, columnAnnotation, rowData, rowAnnotation
  DotPlot-class.Rd: SummarizedExperiment-class, ggplot, rowData,
    colData, brushedPoints
  FeatureAssayPlot-class.Rd: assay, SummarizedExperiment-class, colData
  Panel-class.Rd: updateObject
  ReducedDimensionPlot-class.Rd: reducedDims,
    SingleCellExperiment-class
  RowDataPlot-class.Rd: rowData, SummarizedExperiment-class
  RowDataTable-class.Rd: rowData, SummarizedExperiment-class
  RowDotPlot-class.Rd: SummarizedExperiment-class, ggplot, rowData
  RowTable-class.Rd: SummarizedExperiment-class, datatable
  SampleAssayPlot-class.Rd: assay, SummarizedExperiment-class, colData
  Table-class.Rd: datatable, SummarizedExperiment-class
  addCustomLabelsCommands.Rd: ggplot
  addLabelCentersCommands.Rd: ggplot
  addMultiSelectionCommands.Rd: ggplot
  aes-utils.Rd: ggplot
  cache-utils.Rd: SummarizedExperiment-class, DataFrame-class, rowData,
    colData, ggplot, datatable
  checkColormapCompatibility.Rd: SingleCellExperiment-class
  cleanDataset.Rd: SummarizedExperiment-class, assay, rowData, colData,
    selectInput, SingleCellExperiment-class, reducedDims
  conditional-utils.Rd: conditionalPanel
  createCustomDimnamesModalObservers.Rd: SummarizedExperiment-class
  createCustomPanels.Rd: ggplot, SummarizedExperiment-class,
    selectInput, textInput, numericInput, checkboxInput
  createLandingPage.Rd: SummarizedExperiment,
    SummarizedExperiment-class, renderUI
  createProtectedParameterObservers.Rd: observeEvent
  extractAssaySubmatrix.Rd: SummarizedExperiment-class
  filterDTColumn.Rd: datatable
  hidden-inputs.Rd: selectInput
  iSEE.Rd: SummarizedExperiment-class, shinyApp, runApp
  interface-generics.Rd: SummarizedExperiment-class
  interface-wrappers.Rd: selectInput, hidden
  jitterPoints.Rd: offsetX
  labs-utils.Rd: ggplot
  lassoPoints.Rd: brushedPoints, in.out
  metadata-plot-generics.Rd: SummarizedExperiment-class, colData,
    rowData
  multi-select-generics.Rd: SummarizedExperiment-class
  observer-generics.Rd: SummarizedExperiment-class
  output-generics.Rd: plotOutput, dataTableOutput, tagList,
    SummarizedExperiment-class, renderPlot, ggplot
  plot-generics.Rd: SummarizedExperiment-class, ggplot,
    scale_color_manual
  processMultiSelections.Rd: SummarizedExperiment-class
  registerAppOptions.Rd: SummarizedExperiment-class
  retrieveOutput.Rd: SummarizedExperiment-class
  setCachedCommonInfo.Rd: SummarizedExperiment-class, int_metadata
  setup-generics.Rd: SummarizedExperiment-class, int_metadata,
    SingleCellExperiment-class
  single-select-generics.Rd: selectInput, checkboxInput
  synchronizeAssays.Rd: SingleCellExperiment-class
  table-generics.Rd: datatable, SummarizedExperiment-class
  visual-parameters-generics.Rd: SummarizedExperiment-class, colData
Please provide package anchors for all Rd \link{} targets not in the
package 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 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/iSEE.Rcheck/00check.log’
for details.