Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2025-10-29 12:08 -0400 (Wed, 29 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4901
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4691
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4637
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 1919/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scDiagnostics 1.3.3  (landing page)
Anthony Christidis
Snapshot Date: 2025-10-28 13:45 -0400 (Tue, 28 Oct 2025)
git_url: https://git.bioconductor.org/packages/scDiagnostics
git_branch: devel
git_last_commit: 8d1892c
git_last_commit_date: 2025-10-27 14:00:16 -0400 (Mon, 27 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  YES
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  YES


CHECK results for scDiagnostics on kjohnson3

To the developers/maintainers of the scDiagnostics package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scDiagnostics.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: scDiagnostics
Version: 1.3.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scDiagnostics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scDiagnostics_1.3.3.tar.gz
StartedAt: 2025-10-28 21:52:52 -0400 (Tue, 28 Oct 2025)
EndedAt: 2025-10-28 21:57:51 -0400 (Tue, 28 Oct 2025)
EllapsedTime: 298.5 seconds
RetCode: 0
Status:   OK  
CheckDir: scDiagnostics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scDiagnostics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scDiagnostics_1.3.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/scDiagnostics.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scDiagnostics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scDiagnostics’ version ‘1.3.3’
* 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 ‘scDiagnostics’ 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:
  argumentCheck.Rd: SingleCellExperiment-class
  boxplotPCA.Rd: SingleCellExperiment-class
  calculateAveragePairwiseCorrelation.Rd: SingleCellExperiment-class
  calculateCellDistances.Rd: SingleCellExperiment-class
  calculateCellDistancesSimilarity.Rd: SingleCellExperiment-class
  calculateCellSimilarityPCA.Rd: SingleCellExperiment-class
  calculateCramerPValue.Rd: SingleCellExperiment-class
  calculateDiscriminantSpace.Rd: SingleCellExperiment-class
  calculateGraphIntegration.Rd: SingleCellExperiment-class
  calculateHotellingPValue.Rd: SingleCellExperiment-class
  calculateMMDPValue.Rd: SingleCellExperiment-class
  calculateSIRSpace.Rd: SingleCellExperiment-class
  calculateTopLoadingGeneShifts.Rd: SingleCellExperiment-class
  calculateVarImpOverlap.Rd: SingleCellExperiment-class
  calculateWassersteinDistance.Rd: SingleCellExperiment-class
  compareMarkers.Rd: SingleCellExperiment-class
  comparePCA.Rd: SingleCellExperiment-class
  comparePCASubspace.Rd: SingleCellExperiment-class
  convertColumnsToCharacter.Rd: SingleCellExperiment-class
  detectAnomaly.Rd: SingleCellExperiment-class
  downsampleSCE.Rd: SingleCellExperiment-class
  histQCvsAnnotation.Rd: SingleCellExperiment-class
  plotCellTypeMDS.Rd: SingleCellExperiment-class
  plotCellTypePCA.Rd: SingleCellExperiment-class
  plotGeneExpressionDimred.Rd: SingleCellExperiment-class
  plotGeneSetScores.Rd: SingleCellExperiment-class
  plotMarkerExpression.Rd: SingleCellExperiment-class
  plotPairwiseDistancesDensity.Rd: SingleCellExperiment-class
  plotQCvsAnnotation.Rd: SingleCellExperiment-class
  processPCA.Rd: SingleCellExperiment-class
  projectPCA.Rd: SingleCellExperiment-class
  projectSIR.Rd: SingleCellExperiment-class
  regressPC.Rd: SingleCellExperiment-class
  scDiagnostics-package.Rd: SingleCellExperiment-class
  selectCellTypes.Rd: SingleCellExperiment-class
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
calculateMMDPValue     17.246  0.059  17.419
plotCellTypeMDS        10.422  0.069  10.664
calculateCellDistances  5.869  0.242   6.209
calculateCramerPValue   3.947  1.378   5.391
compareMarkers          5.056  0.254   5.379
* 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-3.22-bioc/meat/scDiagnostics.Rcheck/00check.log’
for details.


Installation output

scDiagnostics.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘scDiagnostics’ ...
** this is package ‘scDiagnostics’ version ‘1.3.3’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (scDiagnostics)

Tests output

scDiagnostics.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(scDiagnostics)
> 
> test_check("scDiagnostics")
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
No data available to generate a heatmap for the specified parameters.
Computing MDS from expression data.
Data missing PCA - computing...
Computing PCA...
Using 231 highly variable genes for PCA computation
Data already has valid PCA - returning unchanged (503 cells)
Data missing PCA - computing...
Downsampling data from 1500 to 800 cells before PCA computation
Computing PCA...
Using 230 highly variable genes for PCA computation
Data already has valid PCA - returning unchanged (1500 cells)
[ FAIL 0 | WARN 45 | SKIP 0 | PASS 685 ]

[ FAIL 0 | WARN 45 | SKIP 0 | PASS 685 ]
> 
> proc.time()
   user  system elapsed 
133.085   6.087 137.776 

Example timings

scDiagnostics.Rcheck/scDiagnostics-Ex.timings

nameusersystemelapsed
boxplotPCA1.8100.0431.898
calculateAveragePairwiseCorrelation1.4010.0301.450
calculateCategorizationEntropy0.0160.0000.016
calculateCellDistances5.8690.2426.209
calculateCellDistancesSimilarity1.8970.0751.986
calculateCellSimilarityPCA0.7250.0360.800
calculateCramerPValue3.9471.3785.391
calculateDiscriminantSpace3.3650.0832.822
calculateGraphIntegration3.1860.1653.440
calculateHVGOverlap0.2580.0090.272
calculateHotellingPValue0.5510.0340.593
calculateMMDPValue17.246 0.05917.419
calculateSIRSpace3.5970.0333.672
calculateVarImpOverlap2.1170.0841.274
calculateWassersteinDistance1.9560.2042.180
compareMarkers5.0560.2545.379
comparePCA1.5310.0221.567
comparePCASubspace1.5060.0161.545
detectAnomaly4.3820.0764.550
histQCvsAnnotation0.4090.0050.443
plotCellTypeMDS10.422 0.06910.664
plotGeneExpressionDimred2.1610.0162.181
plotGeneSetScores1.7490.0031.771
plotMarkerExpression0.3000.0060.307
plotPairwiseDistancesDensity0.5840.0580.642
plotQCvsAnnotation0.1370.0020.139
processPCA1.0180.0131.046
projectPCA0.2350.0050.241
projectSIR0.6980.0110.719
qc_data0.0010.0000.001
query_data0.0000.0010.001
reference_data0.0000.0010.001
regressPC1.1200.0201.155