############################################################################## ############################################################################## ### ### 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_1.10.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Statial.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Statial/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Statial’ version ‘1.10.3’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 23 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 ‘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’ ‘.quiet’ * 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 ‘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 ‘var’ calculateChangesMarker : : no visible global function definition for ‘pt’ calculateChangesMarker : : no visible global function definition for ‘qnorm’ 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 qnorm r test to tval type upper value var weightParent x y Consider adding importFrom("stats", "coef", "density", "formula", "lm", "predict", "pt", "qnorm", "var") 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 kontextCurve 421.204 77.446 247.384 plotStateChanges 72.658 20.419 93.585 calcContamination 75.951 1.626 48.052 kontextPlot 48.845 11.483 35.420 relabelKontextual 30.345 9.522 30.437 getMarkerMeans 22.296 1.099 23.154 getDistances 9.044 0.892 9.999 getAbundances 8.445 0.610 9.084 calcStateChanges 6.565 0.225 6.877 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/Statial.Rcheck/00check.log’ for details.