############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Statial.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Statial_1.2.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Statial.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Statial/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Statial’ version ‘1.2.4’ * 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 ‘Statial’ 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 R 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 Kontextual: no visible binding for global variable ‘test’ Kontextual: no visible binding for global variable ‘parent_name’ calcContamination: no visible binding for global variable ‘cellType’ calcContamination: no visible global function definition for ‘predict’ calcContamination: no visible binding for global variable ‘.’ calcContamination: no visible binding for global variable ‘cellID’ calcStateChanges: no visible binding for global variable ‘cellID’ calcStateChanges: no visible binding for global variable ‘rfMaxCellProb’ calcStateChanges: no visible binding for global variable ‘rfSecondLargestCellProb’ calcStateChanges: no visible binding for global variable ‘rfMainCellProb’ calcStateChanges: no visible global function definition for ‘p.adjust’ calcStateChanges: no visible binding for global variable ‘primaryCellType’ calcStateChanges: no visible binding for global variable ‘otherCellType’ calcStateChanges: no visible binding for global variable ‘coef’ calcStateChanges: no visible binding for global variable ‘tval’ calcStateChanges: no visible binding for global variable ‘pval’ calcStateChanges: no visible binding for global variable ‘fdr’ calculateChangesMarker : : no visible global function definition for ‘pt’ distanceCalculator: no visible binding for global variable ‘cellType’ distanceCalculator: no visible binding for global variable ‘d’ getMarkerMeans: no visible binding for global variable ‘value’ inhomL: no visible binding for global variable ‘j’ inhomL: no visible binding for global variable ‘value’ inhomL: no visible binding for global variable ‘i’ inhomL: no visible binding for global variable ‘d’ inhomL: no visible binding for global variable ‘cellTypeI’ inhomL: no visible binding for global variable ‘cellTypeJ’ inhomL: no visible global function definition for ‘.’ inhomL: no visible binding for global variable ‘wt’ inhomLParent: no visible binding for global variable ‘d’ inhomLParent: no visible binding for global variable ‘i’ kontextCurve: no visible binding for global variable ‘type’ kontextCurve: no visible binding for global variable ‘r’ kontextCurve: no visible binding for global variable ‘original’ kontextCurve: no visible binding for global variable ‘kontextual’ kontextPlot: no visible binding for global variable ‘r’ kontextPlot: no visible binding for global variable ‘kontextualSd’ kontextPlot: no visible binding for global variable ‘originalSd’ kontextPlot: no visible binding for global variable ‘value’ kontextPlot: no visible binding for global variable ‘name’ kontextPlot: no visible binding for global variable ‘lower’ kontextPlot: no visible binding for global variable ‘upper’ parentCombinations: no visible binding for global variable ‘from’ parentCombinations: no visible binding for global variable ‘to’ plotStateChanges: no visible global function definition for ‘lm’ plotStateChanges: no visible global function definition for ‘formula’ plotStateChanges: no visible global function definition for ‘predict’ plotStateChanges: no visible binding for global variable ‘x’ plotStateChanges: no visible binding for global variable ‘y’ plotStateChanges: no visible binding for global variable ‘density’ plotStateChanges: no visible binding for global variable ‘lm’ prepMatrix: no visible binding for global variable ‘imageID’ prepMatrix: no visible binding for global variable ‘kontextual’ prepMatrix: no visible binding for global variable ‘primaryCellType’ prepMatrix: no visible binding for global variable ‘otherCellType’ prepMatrix: no visible binding for global variable ‘marker’ prepMatrix: no visible binding for global variable ‘type’ relabel: no visible binding for global variable ‘cellType’ Undefined global functions or variables: . cellID cellType cellTypeI cellTypeJ coef d density fdr formula from i imageID j kontextual kontextualSd lm lower marker name original originalSd otherCellType p.adjust parent_name predict primaryCellType pt pval r rfMainCellProb rfMaxCellProb rfSecondLargestCellProb test to tval type upper value wt x y Consider adding importFrom("stats", "coef", "density", "formula", "lm", "p.adjust", "predict", "pt") to your NAMESPACE file. * 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 plotStateChanges 124.766 17.339 247.840 kontextCurve 116.789 19.187 141.166 calcContamination 77.879 1.070 53.252 getMarkerMeans 12.458 0.553 23.332 relabelKontextual 10.122 2.312 16.171 getDistances 5.628 0.272 10.227 getAbundances 4.586 0.279 8.207 calcStateChanges 2.738 0.117 5.263 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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 ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Statial.Rcheck/00check.log’ for details.