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### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:scater.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings scater_1.39.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/scater.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-25 07:31:40 UTC
* checking for file ‘scater/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scater’ version ‘1.39.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘scater’ 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 loading without being on the library search path ... 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
plotXY: no visible global function definition for ‘colnmames’
Undefined global functions or variables:
  colnmames
* 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:
  accessors.Rd: SingleCellExperiment
  annotateBMFeatures.Rd: SingleCellExperiment,
    SingleCellExperiment-class, DataFrame-class, rowData
  bootstraps.Rd: SingleCellExperiment
  getExplanatoryPCs.Rd: SingleCellExperiment-class
  getVarianceExplained.Rd: SummarizedExperiment-class, DataFrame-class,
    BiocParallelParam-class
  ggsce.Rd: ggplot, SingleCellExperiment-class, aes
  nexprs.Rd: SummarizedExperiment-class, BiocParallelParam-class,
    DelayedMatrix-class
  plotColData.Rd: SingleCellExperiment-class, geom_hex, ggplot
  plotDots.Rd: SingleCellExperiment-class, colData,
    correctGroupSummary, ggplot
  plotExpression.Rd: geom_hex
  plotGroupedHeatmap.Rd: SingleCellExperiment-class, colData,
    correctGroupSummary
  plotHeatmap.Rd: SingleCellExperiment-class
  plotHighestExprs.Rd: ggplot
  plotRLE.Rd: BiocParallelParam-class, DelayedArray
  plotReducedDim.Rd: geom_hex
  plotRowData.Rd: ggplot
  plotScater.Rd: SingleCellExperiment-class, facet_wrap, ggplot
  plotXY.Rd: geom_hex, ggplot
  plot_reddim.Rd: reducedDims, ggplot
  projectReducedDim.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class
  retrieveCellInfo.Rd: SingleCellExperiment-class, DataFrame-class,
    colData, assay, altExps
  retrieveFeatureInfo.Rd: SingleCellExperiment-class, DataFrame-class,
    rowData, assay
  runColDataPCA.Rd: SingleCellExperiment-class,
    BiocSingularParam-class, BiocParallelParam-class
  runMDS.Rd: SummarizedExperiment-class, SingleCellExperiment-class,
    reducedDims, reducedDim, altExp
  runMultiUMAP.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class, reducedDims, altExps
  runNMF.Rd: SummarizedExperiment-class, SingleCellExperiment-class,
    reducedDims, reducedDim, altExp
  runPCA.Rd: SummarizedExperiment-class, SingleCellExperiment-class,
    BiocSingularParam-class, BiocParallelParam-class, reducedDims,
    bsparam, reducedDim, altExp
  runTSNE.Rd: SummarizedExperiment-class, SingleCellExperiment-class,
    MulticoreParam-class, findKNN, BiocNeighborParam-class,
    BiocParallelParam-class, reducedDims, reducedDim, altExp
  runUMAP.Rd: SummarizedExperiment-class, SingleCellExperiment-class,
    MulticoreParam-class, findKNN, BiocNeighborParam-class,
    BiocParallelParam-class, reducedDims, reducedDim, altExp
  scater-plot-args.Rd: ggplot, DataFrame-class
  toSingleCellExperiment.Rd: SingleCellExperiment
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.
  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.
  Warning in .local(x, ...) : 'perCellQCMetrics' is deprecated.
  Warning in .local(x, ...) : 'perCellQCMetrics' is deprecated.
  Warning in .local(x, ...) : 'perCellQCMetrics' 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.
  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.
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
plotReducedDim    11.989  0.269  10.477
plotRLE            7.802  0.148   7.950
projectReducedDim  7.908  0.012   7.965
plot_reddim        7.663  0.003   9.485
runMultiUMAP       6.570  0.016   6.793
plotExpression     5.951  0.172   6.040
runUMAP            5.927  0.002   5.929
plotScater         4.485  0.015   5.426
plotXY             3.764  0.009   7.483
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.24-bioc/meat/scater.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL scater
###
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* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
* installing *source* package ‘scater’ ...
** this is package ‘scater’ version ‘1.39.4’
** 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 (scater)

R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(scater)
Loading required package: SingleCellExperiment
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: scuttle
Loading required package: ggplot2
> 
> test_check("scater")
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Loading required package: S4Arrays
Loading required package: abind

Attaching package: 'S4Arrays'

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

    abind

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

    rowsum

Loading required package: SparseArray

Attaching package: 'DelayedArray'

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

    apply, scale, sweep

[ FAIL 0 | WARN 72 | SKIP 0 | PASS 822 ]

[ FAIL 0 | WARN 72 | SKIP 0 | PASS 822 ]
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 
246.552   1.711 251.710