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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iSEEu.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iSEEu_1.19.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/iSEEu.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-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 Monterey 12.7.6
* 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 ...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 ‘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                 11.457  0.931  12.453
modeReducedDim                     9.675  0.445  10.177
DynamicReducedDimensionPlot-class  4.919  0.408   5.351
* 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
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/iSEEu.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL iSEEu
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘iSEEu’ ...
** 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 (iSEEu)

R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(iSEEu)
Loading required package: iSEE
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Loading required package: SingleCellExperiment
Loading required package: iSEEhex
> 
> test_check("iSEEu")
Loading required package: scuttle
Loading required package: ggplot2
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 262 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 262 ]
> 
> proc.time()
   user  system elapsed 
 41.507   3.869  53.114