############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:celda.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings celda_1.23.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/celda.Rcheck’ * using R Under development (unstable) (2025-01-22 r87618) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘celda/DESCRIPTION’ ... OK * this is package ‘celda’ version ‘1.23.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 32 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 ‘celda’ can be installed ... OK * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .removeZeroVariance: no visible global function definition for ‘complete.cases’ .splitMetricIGpIGd: no visible global function definition for ‘model.matrix’ .splitMetricModF1: no visible global function definition for ‘model.matrix’ findMarkersTree: no visible global function definition for ‘Idents’ findMarkersTree: no visible global function definition for ‘RunUMAP’ findMarkersTree: no visible global function definition for ‘dendrapply’ plotDendro: no visible binding for global variable ‘xend’ plotDendro: no visible binding for global variable ‘y’ plotDendro: no visible binding for global variable ‘label’ plotMarkerHeatmap: no visible global function definition for ‘head’ plotMarkerHeatmap: no visible global function definition for ‘setNames’ Undefined global functions or variables: Idents RunUMAP complete.cases dendrapply head label model.matrix setNames xend y Consider adding importFrom("stats", "complete.cases", "dendrapply", "model.matrix", "setNames") importFrom("utils", "head") to your NAMESPACE file. * 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: bestLogLikelihood.Rd: SingleCellExperiment-class, altExp celdaClusters.Rd: SingleCellExperiment-class, altExp celdaGridSearch.Rd: SingleCellExperiment-class, assay, altExp, metadata celdaHeatmap.Rd: assay, altExp celdaModel.Rd: altExp celdaModules.Rd: SingleCellExperiment-class, altExp celdaProbabilityMap.Rd: assay, altExp celdaTsne.Rd: SingleCellExperiment-class, assay, altExp, reducedDim celdaUmap.Rd: assay, altExp, reducedDim celda_C.Rd: assay, altExp, SingleCellExperiment-class, metadata, colData celda_CG.Rd: assay, altExp, SingleCellExperiment-class, metadata, colData, rowData celda_G.Rd: assay, altExp, SingleCellExperiment-class, metadata, rowData celdatosce.Rd: SingleCellExperiment-class, assay, altExp, metadata, colData, rowData clusterProbability.Rd: SingleCellExperiment-class, assay, altExp decontX.Rd: SingleCellExperiment-class, Matrix decontXcounts.Rd: SingleCellExperiment-class, assay, assay<- factorizeMatrix.Rd: SingleCellExperiment-class, assay, altExp featureModuleLookup.Rd: SingleCellExperiment-class, altExp featureModuleTable.Rd: SingleCellExperiment-class, assay, altExp geneSetEnrich.Rd: SingleCellExperiment-class, assay, altExp logLikelihood.Rd: SingleCellExperiment-class, assay, altExp logLikelihoodHistory.Rd: SingleCellExperiment-class, altExp moduleHeatmap.Rd: SingleCellExperiment-class, assay, altExp perplexity.Rd: SingleCellExperiment-class, assay, altExp plotCeldaViolin.Rd: SingleCellExperiment-class, assay, altExp plotDecontXContamination.Rd: SingleCellExperiment-class plotDecontXMarkerExpression.Rd: SingleCellExperiment-class plotDecontXMarkerPercentage.Rd: SingleCellExperiment-class plotDimReduceCluster.Rd: SingleCellExperiment-class, altExp plotDimReduceFeature.Rd: SingleCellExperiment-class, assay, altExp, scale_colour_gradient2 plotDimReduceGrid.Rd: SingleCellExperiment-class, assay, altExp, scale_colour_gradient2 plotDimReduceModule.Rd: SingleCellExperiment-class, assay, altExp, scale_colour_gradient plotGridSearchPerplexity.Rd: SingleCellExperiment-class, altExp, geom_jitter plotRPC.Rd: SingleCellExperiment-class, altExp, geom_jitter recodeClusterY.Rd: SingleCellExperiment-class, rowData, altExp recodeClusterZ.Rd: SingleCellExperiment-class, colData, altExp recursiveSplitCell.Rd: SingleCellExperiment-class, assay, altExp, metadata recursiveSplitModule.Rd: SingleCellExperiment-class, assay, altExp, metadata reorderCelda.Rd: SingleCellExperiment-class, assay, altExp reportceldaCG.Rd: SingleCellExperiment-class, altExp, assay resList.Rd: SingleCellExperiment-class, altExp resamplePerplexity.Rd: SingleCellExperiment-class, assay, altExp retrieveFeatureIndex.Rd: SummarizedExperiment-class, SingleCellExperiment-class runParams.Rd: SingleCellExperiment-class, altExp sampleLabel.Rd: SingleCellExperiment-class, altExp sceCeldaC.Rd: SingleCellExperiment-class sceCeldaCG.Rd: SingleCellExperiment-class sceCeldaCGGridSearch.Rd: SingleCellExperiment-class sceCeldaG.Rd: SingleCellExperiment-class selectBestModel.Rd: SingleCellExperiment-class, altExp, metadata selectFeatures.Rd: SingleCellExperiment-class, altExp, assay, metadata simulateCells.Rd: SingleCellExperiment-class, metadata, colData, rowData splitModule.Rd: SingleCellExperiment-class, assay, altExp, rowData subsetCeldaList.Rd: SingleCellExperiment-class, altExp, metadata 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed geneSetEnrich 32.795 0.513 49.645 findMarkersTree 17.341 0.280 17.730 plotMarkerHeatmap 16.646 0.273 16.992 plotDimReduceGrid 16.667 0.202 16.948 plotDendro 15.535 0.257 15.850 recursiveSplitCell 13.406 0.243 13.737 decontX 9.558 0.150 9.777 recursiveSplitModule 8.867 0.140 9.064 plotDimReduceModule 6.418 0.115 6.581 plotDimReduceFeature 5.291 0.087 5.398 plotDimReduceCluster 5.154 0.105 5.295 sceCeldaCGGridSearch 0.290 0.050 47.867 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... 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/celda.Rcheck/00check.log’ for details.