############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:CatsCradle.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings CatsCradle_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/CatsCradle.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * 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 loading without being on the library search path ... 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 44.585 0.886 45.475 computeNBHDVsCTObject 17.661 0.136 17.799 randomiseNodeIndices 14.739 0.004 14.744 getObjectSubsetClusteringPValue 12.680 0.174 12.856 aggregateGeneExpression 10.600 0.205 10.738 transposeObject 10.449 0.005 10.456 computeGraphEmbedding 9.392 0.003 9.423 predictAnnotation 8.000 0.094 8.096 predictAnnotationAllGenes 7.230 0.072 7.304 predictGeneAnnotationImpl 6.417 0.029 6.446 getNearbyGenes 5.845 0.074 5.922 runGeometricClusteringTrials 5.779 0.003 5.783 medianComplementPValue 5.715 0.005 5.721 geneSetsVsGeneClustersPValueMatrix 5.615 0.058 5.673 combinatorialSpheres 5.624 0.037 5.663 getGeneClusterAveragesPerCell 5.579 0.062 5.641 tagRowAndColNames 5.608 0.020 5.628 getNearestNeighbourLists 5.574 0.001 5.576 getAverageExpressionDF 5.497 0.034 5.533 getAverageExpressionMatrix 5.463 0.055 5.520 getObjectSubsetClusteringStatistics 5.427 0.067 5.495 getClusterOrder 5.379 0.051 5.431 getGeneNeighbors 5.354 0.056 5.411 meanZPerCluster 5.368 0.023 5.392 meanZPerClusterOnUMAP 5.378 0.005 5.385 symmetryCheckNN 5.056 0.069 5.126 symmetriseNN 5.039 0.057 5.097 desymmetriseNN 4.976 0.061 5.038 meanGeneClusterOnCellUMAP 4.947 0.064 5.012 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.21-bioc/meat/CatsCradle.Rcheck/00check.log’ for details.