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This page was generated on 2025-09-22 11:42 -0400 (Mon, 22 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4549
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4581
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: 2025-09-18 13:40 -0400 (Thu, 18 Sep 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 kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: scDiagnostics
Version: 1.2.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:scDiagnostics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scDiagnostics_1.2.0.tar.gz
StartedAt: 2025-09-19 14:24:41 -0000 (Fri, 19 Sep 2025)
EndedAt: 2025-09-19 14:37:35 -0000 (Fri, 19 Sep 2025)
EllapsedTime: 774.5 seconds
RetCode: 0
Status:   OK  
CheckDir: scDiagnostics.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:scDiagnostics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scDiagnostics_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/scDiagnostics.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* 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 loading without being on the library search path ... 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
plotCellTypeMDS                       101.030  0.129 101.313
calculateCramerPValue                  34.853  1.517  36.455
calculateCellDistances                 24.779  1.115  25.191
calculateCellDistancesSimilarity        9.326  0.183   8.808
calculateHotellingPValue                8.050  0.020   8.092
calculateNearestNeighborProbabilities   6.634  0.056   6.707
calculateDiscriminantSpace              6.226  0.115   4.781
calculateVarImpOverlap                  5.003  0.108   3.075
* 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/scDiagnostics.Rcheck/00check.log’
for details.


Installation output

scDiagnostics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL scDiagnostics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 0 | SKIP 0 | PASS 276 ]
> 
> proc.time()
   user  system elapsed 
304.344   6.152 300.281 

Example timings

scDiagnostics.Rcheck/scDiagnostics-Ex.timings

nameusersystemelapsed
boxplotPCA3.5290.5554.091
calculateAveragePairwiseCorrelation4.4010.0844.493
calculateCategorizationEntropy0.0140.0000.015
calculateCellDistances24.779 1.11525.191
calculateCellDistancesSimilarity9.3260.1838.808
calculateCellSimilarityPCA2.8270.0712.192
calculateCramerPValue34.853 1.51736.455
calculateDiscriminantSpace6.2260.1154.781
calculateHVGOverlap1.6670.0201.691
calculateHotellingPValue8.0500.0208.092
calculateNearestNeighborProbabilities6.6340.0566.707
calculateSIRSpace3.9760.0324.017
calculateVarImpOverlap5.0030.1083.075
calculateWassersteinDistance2.9170.1553.079
compareCCA1.4390.0081.451
comparePCA1.4530.0041.461
comparePCASubspace1.7020.0201.726
detectAnomaly3.2470.0582.604
histQCvsAnnotation0.7570.0000.759
plot.calculateWassersteinDistanceObject2.6370.0882.732
plotCellTypeMDS101.030 0.129101.313
plotCellTypePCA2.8260.1002.933
plotGeneExpressionDimred1.6970.0161.717
plotGeneSetScores1.4110.0121.426
plotMarkerExpression0.6940.0000.696
plotPairwiseDistancesDensity1.8900.0361.929
plotQCvsAnnotation0.2880.0000.289
projectPCA0.4290.0040.434
projectSIR2.0250.0122.040
qc_data0.0290.0000.029
query_data0.0270.0000.027
reference_data0.0600.0000.061
regressPC2.3940.0122.414