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This page was generated on 2025-08-04 12:13 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4536
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4517
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 1882/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scDiagnostics 1.3.0  (landing page)
Anthony Christidis
Snapshot Date: 2025-08-03 13:25 -0400 (Sun, 03 Aug 2025)
git_url: https://git.bioconductor.org/packages/scDiagnostics
git_branch: devel
git_last_commit: e9987c5
git_last_commit_date: 2025-04-15 13:39:42 -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  NO, package depends on 'bluster' which is only available as a source package that needs compilation
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    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for scDiagnostics on taishan

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: 1.3.0
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_1.3.0.tar.gz
StartedAt: 2025-08-01 10:53:14 -0000 (Fri, 01 Aug 2025)
EndedAt: 2025-08-01 11:08:09 -0000 (Fri, 01 Aug 2025)
EllapsedTime: 895.7 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_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/scDiagnostics.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scDiagnostics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scDiagnostics’ version ‘1.3.0’
* 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                       62.975  0.142  86.682
calculateCramerPValue                 26.995  1.190  46.369
calculateCellDistances                19.110  0.409  23.720
calculateCellDistancesSimilarity       8.950  0.051  13.371
calculateHotellingPValue               8.531  0.102  12.065
calculateDiscriminantSpace             6.025  0.076   8.853
calculateNearestNeighborProbabilities  5.228  0.052  10.581
calculateVarImpOverlap                 4.756  0.003   5.643
calculateAveragePairwiseCorrelation    4.303  0.071   5.859
calculateSIRSpace                      2.963  0.008   5.955
* 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-3.22-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-4.5.0/site-library’
* installing *source* package ‘scDiagnostics’ ...
** this is package ‘scDiagnostics’ version ‘1.3.0’
** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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 
244.687   3.740 327.320 

Example timings

scDiagnostics.Rcheck/scDiagnostics-Ex.timings

nameusersystemelapsed
boxplotPCA3.0690.0524.584
calculateAveragePairwiseCorrelation4.3030.0715.859
calculateCategorizationEntropy0.0110.0040.015
calculateCellDistances19.110 0.40923.720
calculateCellDistancesSimilarity 8.950 0.05113.371
calculateCellSimilarityPCA2.8040.0554.458
calculateCramerPValue26.995 1.19046.369
calculateDiscriminantSpace6.0250.0768.853
calculateHVGOverlap1.7040.0363.033
calculateHotellingPValue 8.531 0.10212.065
calculateNearestNeighborProbabilities 5.228 0.05210.581
calculateSIRSpace2.9630.0085.955
calculateVarImpOverlap4.7560.0035.643
calculateWassersteinDistance3.0740.2124.863
compareCCA1.4460.0151.932
comparePCA1.4350.0051.886
comparePCASubspace1.6880.0081.970
detectAnomaly3.4090.0274.921
histQCvsAnnotation0.7530.0001.515
plot.calculateWassersteinDistanceObject2.4470.1623.061
plotCellTypeMDS62.975 0.14286.682
plotCellTypePCA2.6220.0833.107
plotGeneExpressionDimred1.8390.0163.252
plotGeneSetScores1.5040.0001.673
plotMarkerExpression0.6690.0000.883
plotPairwiseDistancesDensity1.5550.0312.188
plotQCvsAnnotation0.2830.0000.285
projectPCA0.4050.0000.535
projectSIR1.1060.0042.063
qc_data0.0250.0040.029
query_data0.0270.0000.027
reference_data0.0600.0000.061
regressPC2.5240.0082.622