############################################################################## ############################################################################## ### ### 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_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Statial.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘Statial/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Statial’ version ‘1.8.0’ * 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 ‘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 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 Namespaces in Imports field not imported from: ‘cluster’ ‘spatstat.explore’ ‘treekoR’ All declared Imports should be used. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.generateBPParam’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .Kontext: no visible binding for global variable ‘cellTypeI’ .Kontext: no visible binding for global variable ‘cellTypeJ’ .Kontext: no visible binding for global variable ‘weightParent’ .Kontext: no visible binding for global variable ‘edge’ .Kontext: no visible binding for global variable ‘i’ .Kontext: no visible binding for global variable ‘j’ .Lfunction: no visible binding for global variable ‘cellTypeI’ .Linhomfunction: no visible binding for global variable ‘cellTypeI’ .Linhomfunction: no visible binding for global variable ‘cellTypeJ’ .Linhomfunction: no visible binding for global variable ‘weightParent’ .Linhomfunction: no visible binding for global variable ‘edge’ .Linhomfunction: no visible binding for global variable ‘i’ .Linhomfunction: no visible binding for global variable ‘j’ Kontextual : : : no visible binding for global variable ‘d’ Kontextual: no visible binding for global variable ‘test’ Kontextual: no visible binding for global variable ‘parent_name’ KontextualCore: no visible global function definition for ‘.’ KontextualCore: no visible binding for global variable ‘i’ KontextualCore: no visible binding for global variable ‘cellTypeI’ KontextualCore: no visible binding for global variable ‘cellTypeJ’ KontextualCore: no visible binding for global variable ‘Kontext’ 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 ‘indx’ 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 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’ getParentPhylo: no visible binding for global variable ‘child’ getParentPhylo: no visible binding for global variable ‘parent’ getParentPhylo: no visible binding for global variable ‘children’ 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: . Kontext cellID cellType cellTypeI cellTypeJ child children coef d density edge fdr formula from i imageID indx j kontextual kontextualSd lm lower marker name original originalSd otherCellType parent parent_name predict primaryCellType pt pval r rfMainCellProb rfMaxCellProb rfSecondLargestCellProb test to tval type upper value weightParent x y Consider adding importFrom("stats", "coef", "density", "formula", "lm", "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 ... WARNING Undocumented arguments in Rd file 'getParentPhylo.Rd' ‘phylo_tree’ Documented arguments not in \usage in Rd file 'getParentPhylo.Rd': ‘phlyo_tree’ 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 kontextCurve 395.112 53.857 213.626 plotStateChanges 68.022 16.620 85.458 calcContamination 74.181 1.184 45.694 kontextPlot 44.145 8.668 30.273 relabelKontextual 22.157 6.718 20.651 getMarkerMeans 10.612 0.562 10.023 getAbundances 6.767 0.540 7.344 getDistances 5.715 0.534 6.294 * 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: 1 WARNING, 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/Statial.Rcheck/00check.log’ for details.