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###
### Running command:
###
###   /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_2.25.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.24-bioc/meat/iSEE.Rcheck’
* using R version 4.6.0 Patched (2026-05-01 r89994)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-05-19 02:10:01 UTC
* using option ‘--no-vignettes’
* checking for file ‘iSEE/DESCRIPTION’ ... OK
* this is package ‘iSEE’ version ‘2.25.0’
* 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 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 ... WARNING
Found the following significant warnings:

  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.24-bioc/meat/iSEE.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL iSEE
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘iSEE’ ...
** this is package ‘iSEE’ version ‘2.25.0’
** 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 (iSEE)

R version 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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(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: Seqinfo
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
> 
> test_check("iSEE")
Loading required package: scRNAseq
Loading required package: scater
Loading required package: scuttle
Loading required package: ggplot2
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
downloading 1 resources
retrieving 1 resource

loading from cache
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
downloading 1 resources
retrieving 1 resource

loading from cache
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
downloading 1 resources
retrieving 1 resource

loading from cache
Warning in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE,  :
  You're computing too large a percentage of total singular values, use a standard svd instead.
Class: ExperimentColorMap
assays(5): counts tophat_counts cufflinks_fpkm cufflinks_fpkm rsem_tpm
colData(1): passes_qc_checks_s
rowData(0):
all_discrete(0):
all_continuous(0):
global_discrete(1)
global_continuous(1)
[ FAIL 0 | WARN 5 | SKIP 2 | PASS 1486 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_zzz.R:3:1'
• waiting for a fix to the SCE itself (1): 'test_clean.R:100:5'

[ FAIL 0 | WARN 5 | SKIP 2 | PASS 1486 ]
Warning messages:
1: In .library_size_factors(assay(x, assay.type), ...) :
  'librarySizeFactors' is deprecated.
Use 'scrapper::centerSizeFactors' instead.
See help("Deprecated")
2: In .local(x, ...) : 'normalizeCounts' is deprecated.
Use 'scrapper::normalizeCounts' instead.
See help("Deprecated")
> 
> proc.time()
   user  system elapsed 
 23.899   1.011  26.371