############################################################################## ############################################################################## ### ### 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_1.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/CatsCradle.Rcheck’ * using R Under development (unstable) (2025-01-20 r87609) * 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 ‘1.1.0’ * 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 ... 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 20.260 0.249 20.693 randomiseNodeIndices 16.462 0.278 16.840 getObjectSubsetClusteringPValue 14.891 0.771 15.824 aggregateGeneExpression 12.522 0.380 13.000 computeGraphEmbedding 10.063 0.137 10.298 transposeObject 9.920 0.114 10.122 predictAnnotation 8.722 0.623 9.426 predictAnnotationAllGenes 7.779 0.475 8.319 predictGeneAnnotationImpl 6.715 0.290 7.038 getNearbyGenes 5.688 0.099 5.848 medianComplementPValue 5.660 0.077 5.790 runGeometricClusteringTrials 5.584 0.123 5.740 combinatorialSpheres 5.579 0.094 5.706 getObjectSubsetClusteringStatistics 5.554 0.093 5.695 geneSetsVsGeneClustersPValueMatrix 5.379 0.125 5.555 getGeneClusterAveragesPerCell 5.378 0.076 5.511 getAverageExpressionMatrix 5.288 0.078 5.417 getGeneNeighbors 5.229 0.066 5.342 tagRowAndColNames 5.186 0.077 5.304 getAverageExpressionDF 5.119 0.069 5.229 getClusterOrder 5.068 0.065 5.191 meanZPerClusterOnUMAP 5.046 0.074 5.176 meanGeneClusterOnCellUMAP 5.045 0.073 5.157 getNearestNeighbourLists 5.060 0.058 5.166 symmetryCheckNN 4.978 0.061 5.073 meanZPerCluster 4.945 0.043 5.023 symmetriseNN 4.913 0.072 5.012 * 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 WARNING, 1 NOTE See ‘/Users/biocbuild/bbs-3.21-bioc/meat/CatsCradle.Rcheck/00check.log’ for details.