############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ClassifyR_2.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/ClassifyR.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ClassifyR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ClassifyR’ version ‘2.12.0’ * 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 ‘ClassifyR’ 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 .posterior_probs : : no visible global function definition for ‘dmvnorm’ easyHardClassifierPredict,EasyHardClassifier-MultiAssayExperiment: no visible binding for global variable ‘measurements’ kTSPclassifier,DataFrame : : no visible global function definition for ‘Pairs’ plotFeatureClasses,DataFrame : : no visible binding for global variable ‘measurement’ plotFeatureClasses,DataFrame : : no visible binding for global variable ‘..density..’ plotFeatureClasses,DataFrame : : no visible binding for global variable ‘legends grouping’ plotFeatureClasses,DataFrame : : no visible binding for global variable ‘key’ plotFeatureClasses,DataFrame : : no visible binding for global variable ‘value’ plotFeatureClasses,DataFrame : : no visible binding for global variable ‘ID’ rankingPlot,list : : : no visible global function definition for ‘first’ rankingPlot,list : : : no visible global function definition for ‘second’ rankingPlot,list : : : : no visible global function definition for ‘first’ rankingPlot,list : : : : no visible global function definition for ‘second’ runTest,DataFrame: no visible binding for global variable ‘setsNodes’ runTestEasyHard,MultiAssayExperiment: no visible binding for global variable ‘setsNodes’ runTests,DataFrame: no visible binding for global variable ‘setsNodes’ runTestsEasyHard,MultiAssayExperiment: no visible binding for global variable ‘setsNodes’ runTestsEasyHard,MultiAssayExperiment: no visible binding for global variable ‘.iteration’ samplesMetricMap,list: no visible binding for global variable ‘Class’ samplesMetricMap,list: no visible binding for global variable ‘Group’ samplesMetricMap,list: no visible binding for global variable ‘measurements’ samplesMetricMap,list: no visible binding for global variable ‘name’ samplesMetricMap,list: no visible binding for global variable ‘type’ samplesMetricMap,list: no visible binding for global variable ‘Metric’ samplesMetricMap,matrix: no visible binding for global variable ‘Class’ samplesMetricMap,matrix: no visible binding for global variable ‘Group’ samplesMetricMap,matrix: no visible binding for global variable ‘measurements’ samplesMetricMap,matrix: no visible binding for global variable ‘name’ samplesMetricMap,matrix: no visible binding for global variable ‘type’ samplesMetricMap,matrix: no visible binding for global variable ‘Metric’ selectionPlot,list : : : no visible global function definition for ‘first’ selectionPlot,list : : : no visible global function definition for ‘second’ selectionPlot,list : : : : no visible global function definition for ‘first’ selectionPlot,list : : : : no visible global function definition for ‘second’ selectionPlot,list: no visible binding for global variable ‘Freq’ Undefined global functions or variables: ..density.. .iteration Class Freq Group ID Metric Pairs dmvnorm first key legends grouping measurement measurements name second setsNodes type value Consider adding importFrom("base", "grouping") 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 ClassifyResult-class 75.098 4.337 27.858 runTests 22.790 7.941 10.854 elasticNetGLMinterface 26.663 3.373 11.027 elasticNetFeatures 16.291 2.487 11.846 distribution 10.501 3.128 5.408 samplesMetricMap 7.280 1.220 3.958 runTest 7.087 0.268 7.356 * 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 ‘/home/biocbuild/bbs-3.13-bioc/meat/ClassifyR.Rcheck/00check.log’ for details.