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This page was generated on 2025-08-09 12:09 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1871/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scater 1.37.0  (landing page)
Alan O'Callaghan
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/scater
git_branch: devel
git_last_commit: aaaa4b0
git_last_commit_date: 2025-04-15 10:58:25 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    ERROR    OK  


CHECK results for scater on lconway

To the developers/maintainers of the scater package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scater.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: scater
Version: 1.37.0
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_1.37.0.tar.gz
StartedAt: 2025-08-08 23:48:05 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 23:56:12 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 487.4 seconds
RetCode: 0
Status:   OK  
CheckDir: scater.Rcheck
Warnings: 0

Command output

##############################################################################
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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_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/scater.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.37.0’
* 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    9.412  0.431   8.301
plotRLE           7.753  0.271   8.065
runMultiUMAP      5.566  0.052   5.637
projectReducedDim 4.928  0.085   5.042
* 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.


Installation output

scater.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘scater’ ...
** this is package ‘scater’ version ‘1.37.0’
** 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)

Tests output

scater.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
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 0 | SKIP 0 | PASS 822 ]
> 
> proc.time()
   user  system elapsed 
205.906   5.068 212.283 

Example timings

scater.Rcheck/scater-Ex.timings

nameusersystemelapsed
accessors1.5550.0381.607
annotateBMFeatures0.0000.0010.000
bootstraps0.2300.0040.235
defunct000
getExplanatoryPCs1.2990.0291.333
getVarianceExplained0.3720.0100.383
ggsce1.7700.0821.867
nexprs0.2780.0040.284
plotColData3.3330.1043.391
plotDots1.7860.0391.843
plotExplanatoryPCs0.9600.0220.989
plotExplanatoryVariables0.6160.0140.635
plotExpression4.7330.1214.815
plotGroupedHeatmap0.6410.0280.677
plotHeatmap0.5620.0150.583
plotHighestExprs1.7000.0341.746
plotPlatePosition1.0120.0331.052
plotRLE7.7530.2718.065
plotReducedDim9.4120.4318.301
plotRowData0.5490.0130.563
plotScater2.6650.2212.901
plot_reddim3.0910.0783.195
projectReducedDim4.9280.0855.042
retrieveCellInfo0.3790.0120.395
retrieveFeatureInfo0.4420.0240.470
runColDataPCA0.6410.0090.655
runMDS0.4850.0120.501
runMultiUMAP5.5660.0525.637
runNMF0.4310.0090.442
runPCA0.5880.0070.597
runTSNE0.9890.0321.027
runUMAP3.9650.0384.020
toSingleCellExperiment000