############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:Statial.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings Statial_1.4.5.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/Statial.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘Statial/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Statial’ version ‘1.4.5’ * 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘data.table’ ‘spatstat.explore’ 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 Kontextual: no visible binding for global variable ‘test’ Kontextual: no visible binding for global variable ‘parent_name’ calcContamination: no visible global function definition for ‘predict’ calcContamination: no visible binding for global variable ‘.’ calcContamination: no visible binding for global variable ‘cellID’ calcKontextual: no visible binding for global variable ‘d’ calcKontextual: no visible binding for global variable ‘i’ calcKontextual: no visible binding for global variable ‘cellTypeI’ calcKontextual: no visible binding for global variable ‘cellTypeJ’ calcKontextual: no visible binding for global variable ‘Kontext’ 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’ 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 coef d density fdr formula from i imageID kontextual kontextualSd lm lower marker name original originalSd otherCellType parent_name predict primaryCellType pt pval r rfMainCellProb rfMaxCellProb rfSecondLargestCellProb test to tval type upper value 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 ... 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 calcContamination 541.960 7.211 24.043 kontextPlot 175.580 7.683 5.202 plotStateChanges 84.291 25.508 109.809 kontextCurve 63.200 8.495 192.527 relabelKontextual 29.045 5.312 21.892 getMarkerMeans 9.299 0.512 9.493 getDistances 4.914 0.296 5.210 getAbundances 4.775 0.427 5.202 * 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 ... ‘Statial.Rmd’ using ‘UTF-8’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/Statial.Rcheck/00check.log’ for details.