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### Running command:
###
###   /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_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/CatsCradle.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* 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 ‘1.3.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ... 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 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
annotateGeneAsVector                51.822  0.604  52.663
computeNBHDVsCTObject               20.979  0.206  21.310
randomiseNodeIndices                16.840  0.363  17.309
getObjectSubsetClusteringPValue     15.051  0.938  16.083
transposeObject                     12.391  0.100  12.549
aggregateGeneExpression             12.096  0.330  12.493
computeGraphEmbedding               11.013  0.109  11.179
predictAnnotation                    9.999  0.878  10.939
predictAnnotationAllGenes            9.123  0.389   9.566
predictGeneAnnotationImpl            7.532  0.209   7.781
runGeometricClusteringTrials         6.948  0.154   7.140
medianComplementPValue               6.873  0.079   6.983
getObjectSubsetClusteringStatistics  6.680  0.120   6.831
getNearbyGenes                       6.610  0.052   6.680
combinatorialSpheres                 6.574  0.074   6.676
geneSetsVsGeneClustersPValueMatrix   6.546  0.078   6.680
tagRowAndColNames                    6.537  0.076   6.648
getAverageExpressionMatrix           6.301  0.076   6.425
getAverageExpressionDF               6.289  0.073   6.409
desymmetriseNN                       6.194  0.166   6.399
symmetryCheckNN                      6.217  0.057   6.295
symmetriseNN                         6.154  0.114   6.301
meanZPerCluster                      6.164  0.056   6.246
getNearestNeighbourLists             6.157  0.056   6.236
meanGeneClusterOnCellUMAP            6.112  0.076   6.217
meanZPerClusterOnUMAP                6.129  0.052   6.203
getGeneClusterAveragesPerCell        6.056  0.101   6.192
getGeneNeighbors                     6.041  0.064   6.132
getClusterOrder                      5.914  0.062   6.014
* 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
  ‘/Users/biocbuild/bbs-3.22-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/4.5-x86_64/Resources/library’
* installing *source* package ‘CatsCradle’ ...
** this is package ‘CatsCradle’ 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 (CatsCradle)