Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2025-10-13 11:39 -0400 (Mon, 13 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 1904/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scDiagnostics 1.2.0  (landing page)
Anthony Christidis
Snapshot Date: 2025-10-09 13:40 -0400 (Thu, 09 Oct 2025)
git_url: https://git.bioconductor.org/packages/scDiagnostics
git_branch: RELEASE_3_21
git_last_commit: 1e9a005
git_last_commit_date: 2025-04-15 13:39:42 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for scDiagnostics on merida1

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: 1.2.0
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_1.2.0.tar.gz
StartedAt: 2025-10-10 09:52:07 -0400 (Fri, 10 Oct 2025)
EndedAt: 2025-10-10 10:06:45 -0400 (Fri, 10 Oct 2025)
EllapsedTime: 877.8 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/scDiagnostics.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘scDiagnostics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scDiagnostics’ version ‘1.2.0’
* 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
  calculateHotellingPValue.Rd: SingleCellExperiment-class
  calculateNearestNeighborProbabilities.Rd: SingleCellExperiment-class
  calculateSIRSpace.Rd: SingleCellExperiment-class
  calculateVarImpOverlap.Rd: SingleCellExperiment-class
  calculateWassersteinDistance.Rd: SingleCellExperiment-class
  compareCCA.Rd: SingleCellExperiment-class
  comparePCA.Rd: SingleCellExperiment-class
  comparePCASubspace.Rd: SingleCellExperiment-class
  detectAnomaly.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
  projectPCA.Rd: SingleCellExperiment-class
  projectSIR.Rd: SingleCellExperiment-class
  regressPC.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 ... NOTE
  'LazyDataCompression' is specified without 'LazyData'
* 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
calculateCellDistances                  29.845  0.835  34.884
plotCellTypeMDS                         24.929  0.422  27.742
calculateCramerPValue                   17.714  1.738  24.396
calculateCellDistancesSimilarity        14.532  0.504  17.625
calculateDiscriminantSpace              10.829  0.290  10.067
calculateVarImpOverlap                   8.736  0.167   5.219
calculateAveragePairwiseCorrelation      6.838  0.195   8.005
calculateSIRSpace                        6.657  0.114   7.260
boxplotPCA                               5.995  0.233   7.056
detectAnomaly                            5.437  0.188   7.409
regressPC                                5.207  0.108   5.940
calculateWassersteinDistance             4.728  0.123   5.149
plot.calculateWassersteinDistanceObject  4.133  0.126   5.378
* 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-3.21-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-x86_64/Resources/library’
* installing *source* package ‘scDiagnostics’ ...
** this is package ‘scDiagnostics’ version ‘1.2.0’
** using staged installation
** R
** data
** 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 RC (2025-06-05 r88288) -- "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.

> # 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")
[ FAIL 0 | WARN 27 | SKIP 0 | PASS 276 ]

[ FAIL 0 | WARN 27 | SKIP 0 | PASS 276 ]
> 
> proc.time()
   user  system elapsed 
270.072   9.929 281.301 

Example timings

scDiagnostics.Rcheck/scDiagnostics-Ex.timings

nameusersystemelapsed
boxplotPCA5.9950.2337.056
calculateAveragePairwiseCorrelation6.8380.1958.005
calculateCategorizationEntropy0.1360.0030.171
calculateCellDistances29.845 0.83534.884
calculateCellDistancesSimilarity14.532 0.50417.625
calculateCellSimilarityPCA3.7380.1204.860
calculateCramerPValue17.714 1.73824.396
calculateDiscriminantSpace10.829 0.29010.067
calculateHVGOverlap2.8100.0903.414
calculateHotellingPValue2.9010.0603.519
calculateNearestNeighborProbabilities3.8630.0584.510
calculateSIRSpace6.6570.1147.260
calculateVarImpOverlap8.7360.1675.219
calculateWassersteinDistance4.7280.1235.149
compareCCA2.5960.0762.919
comparePCA2.7790.0933.244
comparePCASubspace3.1700.1154.058
detectAnomaly5.4370.1887.409
histQCvsAnnotation2.1070.0382.769
plot.calculateWassersteinDistanceObject4.1330.1265.378
plotCellTypeMDS24.929 0.42227.742
plotCellTypePCA3.8950.1144.465
plotGeneExpressionDimred3.6390.0413.867
plotGeneSetScores3.2250.0333.485
plotMarkerExpression1.4840.0301.582
plotPairwiseDistancesDensity2.4090.1392.671
plotQCvsAnnotation0.7710.0200.854
projectPCA0.5940.0240.691
projectSIR2.3300.0292.602
qc_data0.0430.0100.056
query_data0.0370.0110.050
reference_data0.0810.0120.100
regressPC5.2070.1085.940