############################################################################## ############################################################################## ### ### 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_1.4.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/CatsCradle.Rcheck’ * using R version 4.5.2 Patched (2025-11-05 r88990) * 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 ‘1.4.1’ * 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 92.130 0.913 98.155 randomiseNodeIndices 31.525 0.543 33.822 computeNBHDVsCTObject 28.287 0.215 30.055 getObjectSubsetClusteringPValue 22.355 1.010 24.704 aggregateGeneExpression 19.095 0.495 21.081 predictAnnotation 15.057 0.738 16.742 transposeObject 15.299 0.103 16.192 computeGraphEmbedding 14.618 0.228 15.613 predictAnnotationAllGenes 13.226 0.472 14.343 predictGeneAnnotationImpl 10.923 0.223 11.927 runGeometricClusteringTrials 9.211 0.174 9.490 combinatorialSpheres 9.089 0.133 9.793 getObjectSubsetClusteringStatistics 8.862 0.157 9.694 medianComplementPValue 8.756 0.072 9.406 geneSetsVsGeneClustersPValueMatrix 8.700 0.121 9.448 getNearbyGenes 8.582 0.055 9.163 getAverageExpressionDF 8.456 0.094 8.759 tagRowAndColNames 8.415 0.060 8.858 getAverageExpressionMatrix 8.390 0.079 9.240 desymmetriseNN 8.136 0.110 8.750 meanGeneClusterOnCellUMAP 7.786 0.128 8.305 getGeneClusterAveragesPerCell 7.803 0.099 8.586 meanZPerClusterOnUMAP 7.755 0.052 8.241 meanZPerCluster 7.682 0.067 8.216 symmetriseNN 7.552 0.152 8.014 symmetryCheckNN 7.624 0.075 8.122 getNearestNeighbourLists 7.589 0.077 8.108 getClusterOrder 7.562 0.072 8.713 getGeneNeighbors 7.542 0.077 8.197 collapseExtendedNBHDs 7.295 0.057 7.998 performLigandReceptorAnalysisPermutation 3.113 3.379 7.090 performLigandReceptorAnalysis 3.159 3.284 6.874 * 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.