############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:COTAN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings COTAN_2.7.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/COTAN.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘COTAN/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘COTAN’ version ‘2.7.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' INFO Imports includes 28 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 ‘COTAN’ 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 ... NOTE 'library' or 'require' call to ‘torch’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Unexported object imported by a ':::' call: ‘ggplot2:::ggname’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE mergeUniformCellsClusters : fromMergedName: warning in vapply(currentClNames, function(clName, mergedName) {: partial argument match of 'FUN.VAL' to 'FUN.VALUE' mergeUniformCellsClusters : fromMergedName: warning in return(str_detect(mergedName, clName)): partial argument match of 'FUN.VAL' to 'FUN.VALUE' mergeUniformCellsClusters : fromMergedName: warning in }, FUN.VAL = logical(1L), mergedClName): partial argument match of 'FUN.VAL' to 'FUN.VALUE' ECDPlot: no visible binding for global variable ‘.’ GDIPlot: no visible binding for global variable ‘sum.raw.norm’ GDIPlot: no visible binding for global variable ‘GDI’ UMAPPlot: no visible binding for global variable ‘x’ UMAPPlot: no visible binding for global variable ‘y’ UMAPPlot: no visible binding for global variable ‘types’ calculateCoex_Legacy: no visible binding for global variable ‘expectedNN’ calculateCoex_Legacy: no visible binding for global variable ‘expectedNY’ calculateCoex_Legacy: no visible binding for global variable ‘expectedYN’ calculateCoex_Legacy: no visible binding for global variable ‘expectedYY’ calculateCoex_Legacy: no visible binding for global variable ‘observedYY’ calculateCoex_Legacy: no visible binding for global variable ‘.’ calculateG: no visible binding for global variable ‘observedNN’ calculateG: no visible binding for global variable ‘observedNY’ calculateG: no visible binding for global variable ‘observedYN’ calculateG: no visible binding for global variable ‘observedYY’ calculateG: no visible binding for global variable ‘expectedNN’ calculateG: no visible binding for global variable ‘expectedNY’ calculateG: no visible binding for global variable ‘expectedYN’ calculateG: no visible binding for global variable ‘expectedYY’ calculatePartialCoex: no visible binding for global variable ‘expectedNN’ calculatePartialCoex: no visible binding for global variable ‘expectedNY’ calculatePartialCoex: no visible binding for global variable ‘expectedYN’ calculatePartialCoex: no visible binding for global variable ‘expectedYY’ calculatePartialCoex: no visible binding for global variable ‘observedYY’ calculatePartialCoex: no visible binding for global variable ‘.’ cellSizePlot: no visible binding for global variable ‘.’ cellsUniformClustering: no visible binding for global variable ‘objSeurat’ cellsUniformClustering: no visible binding for global variable ‘usedMaxResolution’ cellsUniformClustering: no visible binding for global variable ‘permMap’ checkClusterUniformity: no visible binding for global variable ‘pcaCellsPlot’ checkClusterUniformity: no visible binding for global variable ‘.’ checkClusterUniformity: no visible binding for global variable ‘bGroupGenesPlot’ checkClusterUniformity: no visible binding for global variable ‘UDEPLot’ checkClusterUniformity: no visible binding for global variable ‘nuPlot’ checkClusterUniformity: no visible binding for global variable ‘zoomedNuPlot’ cleanPlots: no visible binding for global variable ‘PC1’ cleanPlots: no visible binding for global variable ‘PC2’ cleanPlots: no visible binding for global variable ‘n’ cleanPlots: no visible binding for global variable ‘means’ cleanPlots: no visible binding for global variable ‘nu’ clustersMarkersHeatmapPlot: no visible binding for global variable ‘condName’ clustersMarkersHeatmapPlot: no visible binding for global variable ‘conditions’ clustersSummaryPlot: no visible binding for global variable ‘keys’ clustersSummaryPlot: no visible binding for global variable ‘values’ clustersSummaryPlot: no visible binding for global variable ‘CellNumber’ clustersSummaryPlot: no visible binding for global variable ‘ExpGenes’ clustersSummaryPlot: no visible binding for global variable ‘Cluster’ clustersSummaryPlot: no visible binding for global variable ‘Condition’ establishGenesClusters: no visible binding for global variable ‘secondaryMarkers’ establishGenesClusters: no visible binding for global variable ‘GCS’ establishGenesClusters: no visible binding for global variable ‘rankGenes’ expectedContingencyTables: no visible binding for global variable ‘expectedN’ expectedPartialContingencyTables: no visible binding for global variable ‘expectedNN’ expectedPartialContingencyTables: no visible binding for global variable ‘expectedN’ genesSizePlot: no visible binding for global variable ‘.’ geom_flat_violin : : no visible binding for global variable ‘group’ geom_flat_violin : : no visible binding for global variable ‘y’ geom_flat_violin : : no visible binding for global variable ‘x’ geom_flat_violin : : no visible binding for global variable ‘width’ geom_flat_violin : : no visible binding for global variable ‘violinwidth’ geom_flat_violin : : no visible binding for global variable ‘xmax’ geom_flat_violin : : no visible binding for global variable ‘xminv’ geom_flat_violin : : no visible binding for global variable ‘xmaxv’ heatmapPlot: no visible binding for global variable ‘obj’ heatmapPlot: no visible binding for global variable ‘type’ heatmapPlot: no visible binding for global variable ‘g2’ heatmapPlot: no visible binding for global variable ‘coex’ mergeUniformCellsClusters : fromMergedName: no visible binding for global variable ‘clName1’ mergeUniformCellsClusters : fromMergedName: no visible binding for global variable ‘clName2’ mergeUniformCellsClusters : testPairListMerge: no visible binding for global variable ‘cl1’ mergeUniformCellsClusters : testPairListMerge: no visible binding for global variable ‘cl2’ mergeUniformCellsClusters : mergeAllClusters : : no visible binding for global variable ‘clName1’ mergeUniformCellsClusters : mergeAllClusters : : no visible binding for global variable ‘clName2’ mergeUniformCellsClusters : mergeAllClusters: no visible binding for global variable ‘clName1’ mergeUniformCellsClusters : mergeAllClusters: no visible binding for global variable ‘clName2’ mergeUniformCellsClusters: no visible binding for global variable ‘permMap’ mitochondrialPercentagePlot: no visible binding for global variable ‘.’ mitochondrialPercentagePlot: no visible binding for global variable ‘mit.percentage’ observedContingencyTables: no visible binding for global variable ‘observedY’ observedPartialContingencyTables: no visible binding for global variable ‘observedYY’ observedPartialContingencyTables: no visible binding for global variable ‘observedY’ scatterPlot: no visible binding for global variable ‘.’ scatterPlot: no visible binding for global variable ‘.x’ calculateCoex,COTAN: no visible binding for global variable ‘useTorch’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘rawNorm’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘nu’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘lambda’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘a’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘hk’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘clusters’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘clusterData’ Undefined global functions or variables: . .x CellNumber Cluster Condition ExpGenes GCS GDI PC1 PC2 UDEPLot a bGroupGenesPlot cl1 cl2 clName1 clName2 clusterData clusters coex condName conditions expectedN expectedNN expectedNY expectedYN expectedYY g2 group hk keys lambda means mit.percentage n nu nuPlot obj objSeurat observedNN observedNY observedY observedYN observedYY pcaCellsPlot permMap rankGenes rawNorm secondaryMarkers sum.raw.norm type types useTorch usedMaxResolution values violinwidth width x xmax xmaxv xminv y zoomedNuPlot * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: Conversions.Rd: SingleCellExperiment-class, Assays-class, SingleCellExperiment HandlingClusterizations.Rd: umap.defaults getColorsVector.Rd: brewer.pal, brewer.pal.info Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 UniformClusters 89.590 0.531 90.042 CalculatingCOEX 22.563 0.287 22.851 HeatmapPlots 14.363 0.323 14.687 HandlingClusterizations 11.373 0.254 11.558 ParametersEstimations 10.298 0.257 10.555 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘outputTestDatasetCreation.R’ Running ‘spelling.R’ Running ‘testthat.R’ OK * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/COTAN.Rcheck/00check.log’ for details.