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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scater.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scater_1.38.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/scater.Rcheck’
* using R version 4.5.2 Patched (2025-11-05 r88990)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scater/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scater’ version ‘1.38.0’
* 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 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
.handle_truncval: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
* 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
  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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
plotReducedDim    23.771  0.397  23.580
plotExpression    14.552  0.203  14.738
plotRLE           14.086  0.311  14.576
plot_reddim       10.007  0.147  11.520
plotColData        9.097  0.218   9.297
runMultiUMAP       7.567  0.050   7.951
projectReducedDim  6.751  0.050   7.331
plotScater         5.862  0.175   6.895
ggsce              5.373  0.100   5.508
plotDots           4.955  0.049   5.027
runUMAP            4.746  0.039   5.022
* 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-3.22-bioc/meat/scater.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scater
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘scater’ ...
** this is package ‘scater’ version ‘1.38.0’
** 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 (scater)

R version 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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.

> 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 1 | SKIP 0 | PASS 822 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 822 ]
> 
> proc.time()
   user  system elapsed 
389.385   4.991 435.823