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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:CatsCradle.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CatsCradle_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/CatsCradle.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CatsCradle/DESCRIPTION’ ... OK
* this is package ‘CatsCradle’ version ‘1.0.0’
* 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 ‘CatsCradle’ 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 ... NOTE
edgeLengthPlot: no visible binding for global variable ‘cellTypePair’
edgeLengthPlot: no visible binding for global variable ‘cutoff’
make.getExample : getExample: no visible binding for global variable
  ‘seuratGenes’
make.getExample : getExample: no visible binding for global variable
  ‘seuratCells’
make.getExample : getExample: no visible binding for global variable
  ‘xeniumCells’
make.getExample : getExample: no visible binding for global variable
  ‘moransI’
make.getExample : getExample: no visible binding for global variable
  ‘moransILigandReceptor’
make.getExample : getExample: no visible binding for global variable
  ‘humanLRN’
make.getExample : getExample: no visible binding for global variable
  ‘mouseLRN’
meanGeneClusterOnCellUMAP: no visible binding for global variable
  ‘UMAP_1’
meanGeneClusterOnCellUMAP: no visible binding for global variable
  ‘UMAP_2’
Undefined global functions or variables:
  UMAP_1 UMAP_2 cellTypePair cutoff humanLRN moransI
  moransILigandReceptor mouseLRN seuratCells seuratGenes xeniumCells
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'getFeatureZScores.Rd'
  ‘features’
Documented arguments not in \usage in Rd file 'getFeatureZScores.Rd':
  ‘featurs’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 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
computeNBHDVsCTObject               22.192  0.104  22.340
randomiseNodeIndices                20.759  0.123  20.764
getObjectSubsetClusteringPValue     18.511  0.095  18.483
aggregateGeneExpression             14.776  0.324  15.032
transposeObject                     12.190  0.040  12.074
computeGraphEmbedding               11.754  0.088  11.864
predictAnnotation                   10.511  0.076  10.519
predictAnnotationAllGenes            9.621  0.052   9.652
predictGeneAnnotationImpl            8.129  0.040   8.094
runGeometricClusteringTrials         7.192  0.056   7.172
medianComplementPValue               7.131  0.072   7.128
geneSetsVsGeneClustersPValueMatrix   6.976  0.204   7.105
combinatorialSpheres                 7.077  0.052   7.052
getObjectSubsetClusteringStatistics  7.003  0.124   7.052
getNearbyGenes                       7.031  0.048   7.001
desymmetriseNN                       6.335  0.555   6.814
getAverageExpressionDF               6.583  0.059   6.565
getAverageExpressionMatrix           6.511  0.080   6.584
tagRowAndColNames                    6.481  0.044   6.447
getGeneClusterAveragesPerCell        6.206  0.104   6.231
getGeneNeighbors                     6.254  0.040   6.218
meanZPerClusterOnUMAP                6.228  0.048   6.199
meanGeneClusterOnCellUMAP            6.201  0.044   6.171
symmetriseNN                         6.145  0.060   6.127
meanZPerCluster                      6.149  0.012   6.083
getClusterOrder                      6.066  0.044   6.031
symmetryCheckNN                      6.093  0.008   6.022
getNearestNeighbourLists             5.948  0.096   6.013
edgeCutoffsByWatershed               5.520  0.203   5.735
cullEdges                            5.559  0.008   5.580
edgeCutoffsByPercentile              5.298  0.140   5.451
edgeLengthPlot                       5.202  0.195   5.410
annotateGeneAsVector                 5.213  0.147   5.404
edgeCutoffsByClustering              5.015  0.323   5.351
edgeCutoffsByZScore                  5.069  0.252   5.332
edgeLengthsAndCellTypePairs          5.144  0.100   5.255
* 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 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/CatsCradle.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL CatsCradle
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* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘CatsCradle’ ...
** 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 (CatsCradle)