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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_1.4.0.tar.gz
###
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* 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 ‘1.4.0’
* 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
  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                  74.374  0.171  96.698
plotCellTypeMDS                     64.059  0.334  81.993
calculateCramerPValue               28.758  0.109  38.107
compareMarkers                      21.144  0.119  24.954
calculateCellDistances              19.652  0.369  23.789
detectAnomaly                       16.308  0.051  17.049
calculateSIRSpace                   14.403  0.072  18.426
calculateDiscriminantSpace          12.242  0.093  14.414
calculateGraphIntegration           11.825  0.114  18.388
calculateCellDistancesSimilarity     9.547  0.125  13.872
calculateWassersteinDistance         8.355  0.476  12.665
calculateHotellingPValue             8.460  0.013  11.877
plotGeneSetScores                    8.429  0.036   9.243
plotGeneExpressionDimred             8.349  0.037  11.361
boxplotPCA                           7.579  0.439  10.818
calculateAveragePairwiseCorrelation  6.081  0.165   7.518
regressPC                            5.380  0.016   5.784
comparePCA                           5.215  0.036   8.980
comparePCASubspace                   5.040  0.008   6.150
calculateVarImpOverlap               4.527  0.015   5.169
calculateCellSimilarityPCA           3.152  0.007   5.013
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/scDiagnostics.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL scDiagnostics
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘scDiagnostics’ ...
** this is package ‘scDiagnostics’ version ‘1.4.0’
** 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)

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")
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
'magick' package is suggested to install to give better rasterization.

Set `ht_opt$message = FALSE` to turn off this message.
'magick' package is suggested to install to give better rasterization.

Set `ht_opt$message = FALSE` to turn off this message.
'magick' package is suggested to install to give better rasterization.

Set `ht_opt$message = FALSE` to turn off this message.
No data available to generate a heatmap for the specified parameters.
'magick' package is suggested to install to give better rasterization.

Set `ht_opt$message = FALSE` to turn off this message.
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 237 highly variable genes for PCA computation
Data already has valid PCA - returning unchanged (1500 cells)
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 685 ]
> 
> proc.time()
   user  system elapsed 
558.802   5.585 714.232