############################################################################## ############################################################################## ### ### 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_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CatsCradle.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * 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 ‘1.0.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * 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 randomiseNodeIndices 31.615 0.369 33.225 computeNBHDVsCTObject 26.323 0.255 27.356 getObjectSubsetClusteringPValue 22.096 1.021 24.641 aggregateGeneExpression 20.552 0.578 21.709 predictAnnotation 13.848 0.844 15.076 computeGraphEmbedding 14.032 0.158 15.002 predictAnnotationAllGenes 11.966 0.655 13.050 transposeObject 12.361 0.145 13.489 predictGeneAnnotationImpl 9.591 0.566 10.391 cullEdges 9.544 0.588 10.417 edgeCutoffsByPercentile 8.680 0.693 9.628 edgeCutoffsByWatershed 8.624 0.638 9.365 edgeCutoffsByClustering 8.699 0.518 9.360 edgeLengthPlot 8.607 0.540 9.185 edgeCutoffsByZScore 8.513 0.494 9.101 edgeLengthsAndCellTypePairs 8.427 0.400 8.876 performLigandReceptorAnalysis 6.089 2.198 8.559 geneSetsVsGeneClustersPValueMatrix 7.828 0.272 8.182 collapseExtendedNBHDs 7.975 0.096 7.757 combinatorialSpheres 7.884 0.122 8.434 medianComplementPValue 7.674 0.097 8.144 runGeometricClusteringTrials 7.595 0.175 7.988 getAverageExpressionDF 7.421 0.072 7.554 getObjectSubsetClusteringStatistics 7.365 0.128 7.920 getNearbyGenes 7.257 0.072 7.438 annotateGeneAsVector 6.883 0.278 7.385 getAverageExpressionMatrix 7.026 0.070 7.132 desymmetriseNN 6.876 0.097 7.309 tagRowAndColNames 6.899 0.068 7.240 meanZPerCluster 6.535 0.078 6.786 meanZPerClusterOnUMAP 6.498 0.070 6.663 getGeneNeighbors 6.281 0.088 6.442 getClusterOrder 6.274 0.088 6.488 meanGeneClusterOnCellUMAP 6.280 0.074 6.506 getGeneClusterAveragesPerCell 6.239 0.075 6.438 getNearestNeighbourLists 6.175 0.056 6.385 symmetryCheckNN 6.062 0.085 6.563 symmetriseNN 6.006 0.071 6.256 * 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-3.20-bioc/meat/CatsCradle.Rcheck/00check.log’ for details.