##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:iSEEu.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings iSEEu_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/iSEEu.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'iSEEu/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iSEEu' version '1.19.0'
* 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 whether package 'iSEEu' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... NOTE
Package in Depends field not imported from: 'iSEEhex'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  'iSEE:::.dataParamBoxOpen' 'iSEE:::.multiSelectHistory'
  'iSEE:::.noSelection' 'iSEE:::.organizationHeight'
  'iSEE:::.organizationWidth'
  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:
  AggregatedDotPlot.Rd: SummarizedExperiment-class, colData,
    ExperimentColorMap, Panel-class, .cacheCommonInfo,
    .refineParameters, .defineInterface, .defineDataInterface,
    .defineOutput, .panelColor, .fullName, .hideInterface,
    .createObservers, .generateOutput, ggplot, .renderOutput,
    .exportOutput, .definePanelTour, ComplexHeatmapPlot-class
  DynamicMarkerTable-class.Rd: rowData, RowTable-class, Table-class,
    Panel-class, .cacheCommonInfo, .refineParameters,
    .defineDataInterface, .panelColor, .fullName, .hideInterface,
    .createObservers, .generateTable, .definePanelTour
  DynamicReducedDimensionPlot-class.Rd: ColumnDotPlot-class,
    DotPlot-class, Panel-class, .cacheCommonInfo, .refineParameters,
    .defineDataInterface, .panelColor, .fullName, .createObservers,
    .generateDotPlotData, .multiSelectionInvalidated, .definePanelTour
  FeatureSetTable-class.Rd: SummarizedExperiment-class, Panel-class,
    .cacheCommonInfo, .refineParameters, .defineDataInterface,
    .panelColor, .fullName, .hideInterface, .defineOutput, datatable,
    .createObservers, .generateOutput, .renderOutput,
    .multiSelectionDimension, .multiSelectionCommands,
    .multiSelectionActive, .multiSelectionClear,
    .multiSelectionAvailable, .definePanelTour
  GeneSetTable-class.Rd: Panel-class, .defineDataInterface,
    .panelColor, .fullName, .hideInterface, .defineOutput, datatable,
    .createObservers, .generateOutput, .renderOutput,
    .multiSelectionDimension, .multiSelectionCommands,
    .multiSelectionActive, .multiSelectionClear,
    .multiSelectionAvailable
  LogFCLogFCPlot-class.Rd: RowDataPlot-class, rowData,
    RowDotPlot-class, DotPlot-class, Panel-class,
    SummarizedExperiment-class, .cacheCommonInfo, .refineParameters,
    .defineDataInterface, .panelColor, .allowableXAxisChoices,
    .allowableYAxisChoices, .hideInterface, .fullName,
    .createObservers, .generateDotPlotData, .prioritizeDotPlotData,
    .colorByNoneDotPlotField, .colorByNoneDotPlotScale,
    .generateDotPlot, ColumnDataPlot-class, ggplot, .definePanelTour,
    .getDotPlotColorHelp, RowDataPlot
  MAPlot-class.Rd: RowDataPlot-class, rowData, RowDotPlot-class,
    DotPlot-class, Panel-class, SummarizedExperiment-class,
    .cacheCommonInfo, .refineParameters, .defineDataInterface,
    .panelColor, .allowableXAxisChoices, .allowableYAxisChoices,
    .hideInterface, .fullName, .createObservers, .generateDotPlotData,
    .prioritizeDotPlotData, .colorByNoneDotPlotField,
    .colorByNoneDotPlotScale, .generateDotPlot, ColumnDataPlot-class,
    ggplot, .definePanelTour, .getDotPlotColorHelp, RowDataPlot
  MarkdownBoard-class.Rd: Panel-class, RowDataPlot-class,
    .defineDataInterface, .panelColor, .hideInterface, .fullName,
    .createObservers, .defineOutput, .renderOutput, .generateOutput,
    .exportOutput, .definePanelTour
  VolcanoPlot-class.Rd: RowDataPlot-class, RowDotPlot-class,
    DotPlot-class, Panel-class, rowData, SummarizedExperiment-class,
    .cacheCommonInfo, .refineParameters, .defineDataInterface,
    .panelColor, .allowableXAxisChoices, .allowableYAxisChoices,
    .hideInterface, .fullName, .createObservers, .generateDotPlotData,
    .prioritizeDotPlotData, .colorByNoneDotPlotField,
    .colorByNoneDotPlotScale, .generateDotPlot, ColumnDataPlot-class,
    ggplot, .definePanelTour, .getDotPlotColorHelp, RowDataPlot
  global-TableExtraFields.Rd: iSEE
  globals-PValuePattern.Rd: rowData, iSEE
  modeEmpty.Rd: iSEE
  modeGating.Rd: SummarizedExperiment, iSEE
  modeReducedDim.Rd: SingleCellExperiment, SingleCellExperiment-class,
    iSEE
  registerDEFields.Rd: Panel-class, SummarizedExperiment-class,
    rowData, iSEE
  registerFeatureSetCollections.Rd: SummarizedExperiment-class, iSEE,
    CharacterList-class, metadata, mcols
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 ... WARNING
Found the following significant warnings:

  Warning in .setOrganism("org.Mm.eg.db") : '.setOrganism' is deprecated.
  Warning in GeneSetTable(PanelId = 1L) : 'GeneSetTable' is deprecated.
  Warning in setPValuePattern(old) : 'setPValuePattern' is deprecated.
  Warning in .getIdentifierType() : '.getIdentifierType' is deprecated.
  Warning in .setOrganism("org.Mm.eg.db") : '.setOrganism' is deprecated.
  Warning in .getOrganism() : '.getOrganism' is deprecated.
  Warning in .getOrganism() : '.getOrganism' is deprecated.
  Warning in .getOrganism() : '.getOrganism' is deprecated.
  Warning in .getIdentifierType() : '.getIdentifierType' is deprecated.
  Warning in .getOrganism() : '.getOrganism' is deprecated.
  Warning in .getOrganism() : '.getOrganism' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
AggregatedDotPlot                 16.25   1.13   17.37
modeReducedDim                    14.53   0.73   15.47
DynamicReducedDimensionPlot-class  8.07   0.67    8.73
DynamicMarkerTable-class           6.69   0.61    7.29
* 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: 1 WARNING, 3 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/iSEEu.Rcheck/00check.log'
for details.