############################################################################## ############################################################################## ### ### 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_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/CatsCradle.Rcheck’ * using R version 4.5.0 RC (2025-04-04 r88126) * 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 ‘1.2.0’ * 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 89.153 1.056 93.060 randomiseNodeIndices 31.548 0.463 32.177 computeNBHDVsCTObject 28.066 0.201 28.663 getObjectSubsetClusteringPValue 22.198 1.162 23.960 aggregateGeneExpression 19.323 0.491 20.871 predictAnnotation 14.935 1.297 16.553 computeGraphEmbedding 15.289 0.202 16.596 transposeObject 15.181 0.119 15.371 predictAnnotationAllGenes 13.040 0.707 14.051 predictGeneAnnotationImpl 10.802 0.329 11.305 runGeometricClusteringTrials 9.118 0.228 9.410 getObjectSubsetClusteringStatistics 8.765 0.139 9.043 combinatorialSpheres 8.667 0.189 9.809 medianComplementPValue 8.650 0.103 9.088 geneSetsVsGeneClustersPValueMatrix 8.626 0.086 9.160 getNearbyGenes 8.591 0.061 8.713 getAverageExpressionDF 8.231 0.098 8.683 getAverageExpressionMatrix 8.256 0.069 8.406 tagRowAndColNames 8.246 0.064 8.354 collapseExtendedNBHDs 8.028 0.208 9.353 desymmetriseNN 7.910 0.210 8.260 performLigandReceptorAnalysis 5.533 2.321 7.918 getGeneClusterAveragesPerCell 7.721 0.104 8.125 symmetriseNN 7.661 0.123 7.879 meanZPerClusterOnUMAP 7.598 0.058 7.822 meanZPerCluster 7.591 0.055 7.893 meanGeneClusterOnCellUMAP 7.521 0.073 7.670 getNearestNeighbourLists 7.472 0.083 7.616 symmetryCheckNN 7.466 0.089 7.613 getClusterOrder 7.418 0.057 7.762 getGeneNeighbors 7.269 0.061 7.353 * 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-3.21-bioc/meat/CatsCradle.Rcheck/00check.log’ for details.