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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CatsCradle.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CatsCradle_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CatsCradle.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* 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 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
randomiseNodeIndices                32.337  0.360  34.459
computeNBHDVsCTObject               26.376  0.280  28.177
getObjectSubsetClusteringPValue     22.186  0.921  25.270
aggregateGeneExpression             20.452  0.591  22.309
predictAnnotation                   13.933  0.666  15.784
computeGraphEmbedding               13.959  0.151  14.809
transposeObject                     12.481  0.133  13.257
predictAnnotationAllGenes           12.149  0.393  13.261
predictGeneAnnotationImpl            9.962  0.318  10.906
cullEdges                            9.494  0.482  10.435
edgeLengthPlot                       8.756  0.580   9.747
edgeCutoffsByWatershed               8.780  0.536   9.802
edgeCutoffsByPercentile              8.752  0.558   9.970
edgeCutoffsByClustering              8.719  0.477   9.687
edgeCutoffsByZScore                  8.557  0.488   9.365
edgeLengthsAndCellTypePairs          8.568  0.393   9.462
performLigandReceptorAnalysis        6.093  2.090   8.563
collapseExtendedNBHDs                8.046  0.095   8.552
combinatorialSpheres                 7.859  0.124   8.334
runGeometricClusteringTrials         7.761  0.118   8.230
geneSetsVsGeneClustersPValueMatrix   7.669  0.180   8.314
medianComplementPValue               7.749  0.082   8.198
getNearbyGenes                       7.630  0.086   8.177
getObjectSubsetClusteringStatistics  7.430  0.111   7.997
getAverageExpressionMatrix           7.378  0.093   8.001
getAverageExpressionDF               7.191  0.064   7.512
desymmetriseNN                       6.962  0.091   7.376
annotateGeneAsVector                 6.742  0.274   7.374
tagRowAndColNames                    6.914  0.056   7.325
getGeneClusterAveragesPerCell        6.554  0.097   7.274
getClusterOrder                      6.493  0.074   6.877
getGeneNeighbors                     6.461  0.072   6.820
meanGeneClusterOnCellUMAP            6.384  0.074   6.786
meanZPerClusterOnUMAP                6.379  0.071   6.928
getNearestNeighbourLists             6.379  0.050   6.761
meanZPerCluster                      6.280  0.058   6.744
symmetriseNN                         6.143  0.076   6.509
symmetryCheckNN                      6.071  0.072   6.669
* 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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/CatsCradle.Rcheck/00check.log’
for details.

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CatsCradle
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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)