############################################################################## ############################################################################## ### ### 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_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/CatsCradle.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * 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 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 22.192 0.104 22.340 randomiseNodeIndices 20.759 0.123 20.764 getObjectSubsetClusteringPValue 18.511 0.095 18.483 aggregateGeneExpression 14.776 0.324 15.032 transposeObject 12.190 0.040 12.074 computeGraphEmbedding 11.754 0.088 11.864 predictAnnotation 10.511 0.076 10.519 predictAnnotationAllGenes 9.621 0.052 9.652 predictGeneAnnotationImpl 8.129 0.040 8.094 runGeometricClusteringTrials 7.192 0.056 7.172 medianComplementPValue 7.131 0.072 7.128 geneSetsVsGeneClustersPValueMatrix 6.976 0.204 7.105 combinatorialSpheres 7.077 0.052 7.052 getObjectSubsetClusteringStatistics 7.003 0.124 7.052 getNearbyGenes 7.031 0.048 7.001 desymmetriseNN 6.335 0.555 6.814 getAverageExpressionDF 6.583 0.059 6.565 getAverageExpressionMatrix 6.511 0.080 6.584 tagRowAndColNames 6.481 0.044 6.447 getGeneClusterAveragesPerCell 6.206 0.104 6.231 getGeneNeighbors 6.254 0.040 6.218 meanZPerClusterOnUMAP 6.228 0.048 6.199 meanGeneClusterOnCellUMAP 6.201 0.044 6.171 symmetriseNN 6.145 0.060 6.127 meanZPerCluster 6.149 0.012 6.083 getClusterOrder 6.066 0.044 6.031 symmetryCheckNN 6.093 0.008 6.022 getNearestNeighbourLists 5.948 0.096 6.013 edgeCutoffsByWatershed 5.520 0.203 5.735 cullEdges 5.559 0.008 5.580 edgeCutoffsByPercentile 5.298 0.140 5.451 edgeLengthPlot 5.202 0.195 5.410 annotateGeneAsVector 5.213 0.147 5.404 edgeCutoffsByClustering 5.015 0.323 5.351 edgeCutoffsByZScore 5.069 0.252 5.332 edgeLengthsAndCellTypePairs 5.144 0.100 5.255 * 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-3.20-bioc/meat/CatsCradle.Rcheck/00check.log’ for details.