############################################################################## ############################################################################## ### ### 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_1.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/CatsCradle.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * 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) * 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 ...Warning: program compiled against libxml 212 using older 211 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 ... 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 22.663 0.168 22.879 randomiseNodeIndices 21.708 0.012 21.774 getObjectSubsetClusteringPValue 18.215 0.084 18.347 aggregateGeneExpression 14.734 0.247 15.010 computeGraphEmbedding 11.864 0.040 11.932 transposeObject 11.799 0.044 11.875 predictAnnotation 10.130 0.044 10.199 predictAnnotationAllGenes 9.276 0.016 9.315 predictGeneAnnotationImpl 7.852 0.016 7.888 combinatorialSpheres 6.767 0.151 6.939 runGeometricClusteringTrials 6.757 0.019 6.797 geneSetsVsGeneClustersPValueMatrix 6.713 0.056 6.789 medianComplementPValue 6.741 0.023 6.780 getNearbyGenes 6.536 0.063 6.619 getObjectSubsetClusteringStatistics 6.565 0.024 6.607 getAverageExpressionMatrix 6.300 0.000 6.316 tagRowAndColNames 6.282 0.000 6.298 getAverageExpressionDF 6.268 0.003 6.288 meanZPerClusterOnUMAP 5.971 0.044 6.032 symmetryCheckNN 5.928 0.044 5.989 desymmetriseNN 5.919 0.028 5.965 getGeneClusterAveragesPerCell 5.895 0.028 5.937 meanZPerCluster 5.913 0.000 5.929 symmetriseNN 5.901 0.000 5.917 getGeneNeighbors 5.864 0.000 5.881 getClusterOrder 5.804 0.040 5.859 meanGeneClusterOnCellUMAP 5.803 0.008 5.830 getNearestNeighbourLists 5.801 0.000 5.817 annotateGeneAsVector 5.145 0.152 5.340 cullEdges 5.220 0.028 5.259 * 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 ‘/home/biocbuild/bbs-3.21-bioc/meat/CatsCradle.Rcheck/00check.log’ for details.