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### Running command:
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###   /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_1.35.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/scater.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scater/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scater’ version ‘1.35.0’
* 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 ... 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:
  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
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/scater.Rcheck/00check.log’
for details.