############################################################################## ############################################################################## ### ### 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_1.1.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/CatsCradle.Rcheck’ * using R Under development (unstable) (2025-01-22 r87618) * 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 ‘1.1.1’ * 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’ 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 ... WARNING Codoc mismatches from Rd file 'aggregateGeneExpression.Rd': aggregateGeneExpression Code: function(f, neighbourhoods, self = FALSE, verbose = TRUE, returnType = "Seurat") Docs: function(f, neighbourhoods, verbose = TRUE, returnType = "Seurat") Argument names in code not in docs: self Mismatches in argument names: Position: 3 Code: self Docs: verbose Position: 4 Code: verbose Docs: returnType Codoc mismatches from Rd file 'nbhdsAsEdgesToNbhdsAsList.Rd': nbhdsAsEdgesToNbhdsAsList Code: function(cells, neighbourhoods, self = FALSE) Docs: function(cells, neighbourhoods) Argument names in code not in docs: self * 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 19.614 0.190 19.901 randomiseNodeIndices 16.138 0.273 16.506 getObjectSubsetClusteringPValue 14.042 0.682 14.842 aggregateGeneExpression 11.593 0.312 11.985 transposeObject 10.020 0.100 10.196 computeGraphEmbedding 9.944 0.102 10.090 predictAnnotation 8.405 0.636 9.111 predictAnnotationAllGenes 7.738 0.416 8.202 predictGeneAnnotationImpl 6.687 0.257 6.985 runGeometricClusteringTrials 5.582 0.127 5.745 medianComplementPValue 5.591 0.085 5.709 combinatorialSpheres 5.547 0.108 5.690 getObjectSubsetClusteringStatistics 5.510 0.128 5.666 geneSetsVsGeneClustersPValueMatrix 5.414 0.121 5.565 getAverageExpressionMatrix 5.305 0.066 5.400 getNearbyGenes 5.274 0.071 5.387 getAverageExpressionDF 5.224 0.060 5.322 tagRowAndColNames 5.206 0.054 5.292 meanZPerClusterOnUMAP 5.129 0.053 5.200 meanGeneClusterOnCellUMAP 5.088 0.077 5.292 symmetriseNN 4.951 0.101 5.102 meanZPerCluster 4.972 0.047 5.036 * 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: 2 WARNINGs, 1 NOTE See ‘/Users/biocbuild/bbs-3.21-bioc/meat/CatsCradle.Rcheck/00check.log’ for details.