############################################################################## ############################################################################## ### ### 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 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.5 * 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 57.369 0.444 58.640 computeNBHDVsCTObject 27.172 0.195 27.662 randomiseNodeIndices 19.719 0.349 20.413 getObjectSubsetClusteringPValue 17.905 1.350 19.539 aggregateGeneExpression 14.169 0.363 14.786 transposeObject 14.149 0.107 14.415 computeGraphEmbedding 14.120 0.131 14.635 predictAnnotation 10.941 1.026 12.196 predictAnnotationAllGenes 9.947 0.453 10.549 predictGeneAnnotationImpl 8.861 0.313 9.240 medianComplementPValue 7.726 0.147 8.005 getObjectSubsetClusteringStatistics 7.674 0.162 7.901 geneSetsVsGeneClustersPValueMatrix 7.559 0.125 7.751 combinatorialSpheres 7.494 0.103 7.645 runGeometricClusteringTrials 7.429 0.163 7.868 getNearbyGenes 7.372 0.133 7.611 getAverageExpressionDF 7.344 0.092 7.567 tagRowAndColNames 7.349 0.060 7.581 getAverageExpressionMatrix 7.317 0.082 7.491 getGeneClusterAveragesPerCell 7.232 0.088 7.454 desymmetriseNN 7.139 0.132 7.394 symmetriseNN 7.149 0.087 7.310 getGeneNeighbors 7.136 0.074 7.354 getNearestNeighbourLists 7.137 0.057 7.234 meanZPerCluster 7.123 0.067 7.332 meanZPerClusterOnUMAP 7.109 0.074 7.322 meanGeneClusterOnCellUMAP 7.092 0.075 7.246 symmetryCheckNN 7.074 0.093 7.255 getClusterOrder 7.050 0.059 7.205 * 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.