############################################################################## ############################################################################## ### ### 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 (2025-11-04 r88984) * 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 13.7.8 * 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 58.222 0.696 82.149 computeNBHDVsCTObject 28.781 0.267 40.267 randomiseNodeIndices 21.168 0.437 28.889 getObjectSubsetClusteringPValue 18.875 0.840 27.306 transposeObject 15.429 0.136 21.129 aggregateGeneExpression 14.698 0.329 20.889 computeGraphEmbedding 14.828 0.176 20.556 predictAnnotation 11.967 0.644 17.323 predictAnnotationAllGenes 10.675 0.431 15.328 predictGeneAnnotationImpl 9.373 0.273 13.321 runGeometricClusteringTrials 8.370 0.142 11.365 combinatorialSpheres 8.325 0.121 11.776 medianComplementPValue 8.235 0.103 11.830 getObjectSubsetClusteringStatistics 8.122 0.139 11.704 getNearbyGenes 8.131 0.092 10.499 geneSetsVsGeneClustersPValueMatrix 8.055 0.139 10.587 tagRowAndColNames 8.096 0.084 11.442 getAverageExpressionMatrix 7.980 0.101 10.713 getAverageExpressionDF 7.934 0.099 10.685 getGeneClusterAveragesPerCell 7.803 0.109 10.570 symmetriseNN 7.781 0.126 11.066 symmetryCheckNN 7.780 0.078 10.869 getGeneNeighbors 7.753 0.086 10.178 meanZPerClusterOnUMAP 7.692 0.079 11.099 desymmetriseNN 7.620 0.100 10.734 getClusterOrder 7.615 0.098 10.544 getNearestNeighbourLists 7.605 0.086 10.315 meanGeneClusterOnCellUMAP 7.518 0.092 10.411 meanZPerCluster 7.470 0.067 10.713 * 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.