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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: aarch64-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 Ventura 13.7.1
* 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
computeNBHDVsCTObject 26.923 0.203 27.166
randomiseNodeIndices 19.985 0.340 20.566
getObjectSubsetClusteringPValue 18.784 1.032 19.973
aggregateGeneExpression 15.540 0.439 15.482
computeGraphEmbedding 14.211 0.123 14.343
transposeObject 12.721 0.093 12.894
predictAnnotation 9.957 0.710 10.783
predictAnnotationAllGenes 9.231 0.380 9.699
predictGeneAnnotationImpl 8.351 0.409 8.857
runGeometricClusteringTrials 7.089 0.147 7.295
geneSetsVsGeneClustersPValueMatrix 6.797 0.209 7.010
getObjectSubsetClusteringStatistics 6.889 0.104 7.036
getNearbyGenes 6.900 0.088 7.033
combinatorialSpheres 6.831 0.122 6.975
medianComplementPValue 6.679 0.083 6.805
getAverageExpressionMatrix 6.618 0.090 6.716
tagRowAndColNames 6.592 0.061 6.708
annotateGeneAsVector 6.404 0.173 6.591
meanGeneClusterOnCellUMAP 6.487 0.073 6.608
meanZPerClusterOnUMAP 6.493 0.063 6.632
symmetriseNN 6.438 0.090 6.577
meanZPerCluster 6.432 0.076 6.555
getClusterOrder 6.363 0.104 6.473
getGeneNeighbors 6.376 0.071 6.548
getNearestNeighbourLists 6.371 0.058 6.461
desymmetriseNN 6.324 0.091 6.424
symmetryCheckNN 6.330 0.066 6.428
getGeneClusterAveragesPerCell 6.219 0.071 6.335
getAverageExpressionDF 6.066 0.063 6.135
* 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.