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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_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CatsCradle.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 ‘1.0.1’
* 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 ... WARNING
Codoc mismatches from Rd file 'aggregateGeneExpression.Rd':
aggregateGeneExpression
  Code: function(f, neighbourhoods, self = FALSE, verbose = TRUE,
                 returnType = "Seurat")
  Docs: function(f, neighbourhoods, verbose = TRUE, returnType =
                 "Seurat")
  Argument names in code not in docs:
    self
  Mismatches in argument names:
    Position: 3 Code: self Docs: verbose
    Position: 4 Code: verbose Docs: returnType

Codoc mismatches from Rd file 'nbhdsAsEdgesToNbhdsAsList.Rd':
nbhdsAsEdgesToNbhdsAsList
  Code: function(cells, neighbourhoods, self = FALSE)
  Docs: function(cells, neighbourhoods)
  Argument names in code not in docs:
    self

* 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                32.059  0.348  32.999
computeNBHDVsCTObject               26.066  0.239  27.095
getObjectSubsetClusteringPValue     22.561  0.939  24.354
aggregateGeneExpression             19.999  0.570  20.646
predictAnnotation                   13.882  0.753  14.900
computeGraphEmbedding               13.994  0.155  14.520
predictAnnotationAllGenes           12.054  0.500  13.064
transposeObject                     12.456  0.093  12.720
predictGeneAnnotationImpl            9.487  0.353  10.177
cullEdges                            9.305  0.534   9.939
edgeCutoffsByPercentile              8.619  0.614   9.272
edgeLengthPlot                       8.696  0.461   9.381
edgeCutoffsByWatershed               8.544  0.570   9.163
edgeCutoffsByZScore                  8.446  0.509   9.034
edgeCutoffsByClustering              8.467  0.472   8.981
edgeLengthsAndCellTypePairs          8.268  0.370   8.700
performLigandReceptorAnalysis        6.263  2.274   8.671
collapseExtendedNBHDs                7.888  0.079   7.998
geneSetsVsGeneClustersPValueMatrix   7.730  0.189   7.950
combinatorialSpheres                 7.773  0.125   8.072
runGeometricClusteringTrials         7.705  0.169   8.010
medianComplementPValue               7.753  0.090   8.007
getObjectSubsetClusteringStatistics  7.695  0.114   8.319
getNearbyGenes                       7.584  0.091   7.881
getAverageExpressionMatrix           7.353  0.081   7.502
getAverageExpressionDF               7.251  0.059   7.339
desymmetriseNN                       6.975  0.079   7.098
tagRowAndColNames                    6.953  0.080   7.241
getGeneClusterAveragesPerCell        6.792  0.095   6.971
annotateGeneAsVector                 6.535  0.226   6.791
getGeneNeighbors                     6.679  0.080   6.884
getClusterOrder                      6.603  0.075   6.904
meanZPerClusterOnUMAP                6.518  0.085   6.863
meanGeneClusterOnCellUMAP            6.382  0.095   7.165
meanZPerCluster                      6.350  0.059   6.541
getNearestNeighbourLists             6.341  0.053   6.479
symmetriseNN                         6.212  0.092   6.441
symmetryCheckNN                      6.174  0.062   6.415
* 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 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/CatsCradle.Rcheck/00check.log’
for details.

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### Running command:
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###   /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)