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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_1.5.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/CatsCradle.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* 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 Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CatsCradle/DESCRIPTION’ ... OK
* this is package ‘CatsCradle’ version ‘1.5.1’
* 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’
plotLRDotplot: no visible binding for global variable ‘sender’
plotLRDotplot: no visible binding for global variable ‘negLog10PValue’
plotLRDotplot: no visible binding for global variable ‘receiver’
Undefined global functions or variables:
  UMAP_1 UMAP_2 cellTypePair cutoff humanLRN moransI
  moransILigandReceptor mouseLRN negLog10PValue receiver sender
  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                50.155  0.602  51.011
computeNBHDVsCTObject               20.466  0.189  20.780
randomiseNodeIndices                16.484  0.420  17.023
getObjectSubsetClusteringPValue     14.216  0.768  15.096
transposeObject                     12.313  0.116  12.509
aggregateGeneExpression             11.241  0.330  11.661
computeGraphEmbedding               10.575  0.120  10.764
predictAnnotation                    9.496  0.560  10.132
predictAnnotationAllGenes            8.760  0.455   9.281
predictGeneAnnotationImpl            7.588  0.409   8.061
medianComplementPValue               6.682  0.071   6.775
getObjectSubsetClusteringStatistics  6.544  0.142   6.722
runGeometricClusteringTrials         6.545  0.126   6.724
tagRowAndColNames                    6.506  0.063   6.604
symmetriseNN                         6.366  0.168   6.578
getNearbyGenes                       6.408  0.073   6.530
geneSetsVsGeneClustersPValueMatrix   6.341  0.075   6.468
combinatorialSpheres                 6.288  0.085   6.399
symmetryCheckNN                      6.303  0.067   6.396
getAverageExpressionDF               6.230  0.112   6.391
meanGeneClusterOnCellUMAP            6.174  0.131   6.337
meanZPerClusterOnUMAP                6.244  0.054   6.322
desymmetriseNN                       6.171  0.117   6.330
getAverageExpressionMatrix           6.106  0.079   6.240
getGeneClusterAveragesPerCell        6.061  0.099   6.210
meanZPerCluster                      6.094  0.055   6.168
getGeneNeighbors                     5.905  0.076   6.025
getClusterOrder                      5.887  0.084   6.027
getNearestNeighbourLists             5.806  0.080   5.924
* 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-3.23-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/4.6-x86_64/Resources/library’
* installing *source* package ‘CatsCradle’ ...
** this is package ‘CatsCradle’ version ‘1.5.1’
** 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)