############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Statial.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Statial_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Statial.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘Statial/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Statial’ version ‘1.9.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' INFO Imports includes 22 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 loading without being on the library search path ... 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 304.713 64.860 225.801 plotStateChanges 65.453 23.056 88.619 calcContamination 62.392 0.701 36.495 kontextPlot 36.145 12.135 32.263 relabelKontextual 18.726 9.042 20.868 getMarkerMeans 14.019 0.526 14.184 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/Statial.Rcheck/00check.log’ for details.