############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:CatsCradle.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CatsCradle_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/CatsCradle.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * 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 computeNBHDVsCTObject 22.482 0.020 22.554 randomiseNodeIndices 21.291 0.020 21.358 getObjectSubsetClusteringPValue 19.590 0.119 19.759 aggregateGeneExpression 14.863 0.195 15.080 computeGraphEmbedding 11.666 0.012 11.697 transposeObject 11.356 0.000 11.387 predictAnnotation 9.993 0.004 10.023 predictAnnotationAllGenes 9.108 0.064 9.196 predictGeneAnnotationImpl 7.607 0.008 7.635 medianComplementPValue 6.506 0.080 6.604 getNearbyGenes 6.413 0.068 6.499 getObjectSubsetClusteringStatistics 6.408 0.008 6.431 runGeometricClusteringTrials 6.404 0.003 6.425 getAverageExpressionMatrix 6.225 0.012 6.254 combinatorialSpheres 6.219 0.000 6.237 geneSetsVsGeneClustersPValueMatrix 6.153 0.048 6.216 getAverageExpressionDF 6.188 0.004 6.205 tagRowAndColNames 6.135 0.000 6.152 meanZPerCluster 5.969 0.000 5.985 symmetryCheckNN 5.895 0.000 5.913 desymmetriseNN 5.885 0.008 5.909 meanGeneClusterOnCellUMAP 5.872 0.004 5.894 meanZPerClusterOnUMAP 5.861 0.000 5.878 getClusterOrder 5.838 0.000 5.853 getNearestNeighbourLists 5.810 0.000 5.826 getGeneNeighbors 5.795 0.004 5.815 symmetriseNN 5.723 0.000 5.738 getGeneClusterAveragesPerCell 5.684 0.015 5.717 * 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 ‘/home/biocbuild/bbs-3.21-bioc/meat/CatsCradle.Rcheck/00check.log’ for details.