############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:POMA.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings POMA_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/POMA.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘POMA/DESCRIPTION’ ... OK * this is package ‘POMA’ version ‘1.6.0’ * 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 ‘POMA’ 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 ... NOTE 'library' or 'require' calls in package code: ‘ggraph’ ‘plotly’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE PomaBoxplots: no visible global function definition for ‘is’ PomaBoxplots: no visible binding for global variable ‘ID’ PomaBoxplots: no visible binding for global variable ‘Group’ PomaBoxplots: no visible binding for global variable ‘value’ PomaBoxplots: no visible binding for global variable ‘name’ PomaClust: no visible global function definition for ‘is’ PomaClust : : no visible global function definition for ‘kmeans’ PomaClust: no visible global function definition for ‘kmeans’ PomaClust: no visible global function definition for ‘dist’ PomaClust: no visible global function definition for ‘cmdscale’ PomaClust: no visible binding for global variable ‘group’ PomaClust: no visible binding for global variable ‘clust’ PomaClust: no visible binding for global variable ‘V1’ PomaClust: no visible binding for global variable ‘V2’ PomaClust: no visible binding for global variable ‘Dim1’ PomaClust: no visible binding for global variable ‘Dim2’ PomaCorr: no visible global function definition for ‘is’ PomaCorr: no visible global function definition for ‘cor’ PomaCorr: no visible binding for global variable ‘column’ PomaCorr: no visible binding for global variable ‘cor’ PomaCorr: no visible binding for global variable ‘p’ PomaCorr: no visible global function definition for ‘p.adjust’ PomaCorr: no visible binding for global variable ‘pvalue’ PomaCorr: no visible binding for global variable ‘R’ PomaCorr: no visible binding for global variable ‘feature1’ PomaCorr: no visible binding for global variable ‘name’ PomaCorr: no visible binding for global variable ‘value’ PomaCorr: no visible global function definition for ‘ggraph’ PomaCorr: no visible global function definition for ‘geom_edge_link’ PomaCorr: no visible global function definition for ‘scale_edge_colour_gradientn’ PomaCorr: no visible global function definition for ‘geom_node_point’ PomaCorr: no visible global function definition for ‘geom_node_label’ PomaCorr: no visible global function definition for ‘theme_graph’ PomaCorr: no visible global function definition for ‘na.omit’ PomaCorr: no visible binding for global variable ‘EstimatedCorr’ PomaDensity: no visible global function definition for ‘is’ PomaDensity: no visible binding for global variable ‘ID’ PomaDensity: no visible binding for global variable ‘Group’ PomaDensity: no visible binding for global variable ‘value’ PomaDensity: no visible binding for global variable ‘name’ PomaEDA: no visible global function definition for ‘is’ PomaHeatmap: no visible global function definition for ‘is’ PomaImpute: no visible global function definition for ‘is’ PomaImpute: no visible global function definition for ‘aggregate’ PomaImpute: no visible binding for global variable ‘Group’ PomaImpute : : no visible global function definition for ‘median’ PomaImpute: no visible binding for global variable ‘group’ PomaImpute: no visible global function definition for ‘validObject’ PomaLasso: no visible global function definition for ‘is’ PomaLasso: no visible binding for global variable ‘estimate’ PomaLasso: no visible binding for global variable ‘conf.low’ PomaLasso: no visible binding for global variable ‘conf.high’ PomaLasso: no visible global function definition for ‘coef’ PomaLasso: no visible global function definition for ‘predict’ PomaLasso: no visible binding for global variable ‘term’ PomaLimma: no visible global function definition for ‘is’ PomaLimma: no visible global function definition for ‘model.matrix’ PomaLimma: no visible binding for global variable ‘adj.P.Val’ PomaLimma: no visible global function definition for ‘as.formula’ PomaMultivariate: no visible global function definition for ‘is’ PomaMultivariate: no visible binding for global variable ‘PC1’ PomaMultivariate: no visible binding for global variable ‘PC2’ PomaMultivariate: no visible binding for global variable ‘Groups’ PomaMultivariate: no visible binding for global variable ‘ID’ PomaMultivariate: no visible global function definition for ‘reorder’ PomaMultivariate: no visible binding for global variable ‘component’ PomaMultivariate: no visible binding for global variable ‘pc_var_exp’ PomaMultivariate: no visible binding for global variable ‘feature’ PomaMultivariate: no visible binding for global variable ‘value’ PomaMultivariate: no visible binding for global variable ‘name’ PomaMultivariate: no visible binding for global variable ‘to_x’ PomaMultivariate: no visible binding for global variable ‘to_y’ PomaMultivariate: no visible binding for global variable ‘comp1’ PomaMultivariate: no visible binding for global variable ‘comp2’ PomaMultivariate: no visible binding for global variable ‘feature_sd’ PomaMultivariate: no visible binding for global variable ‘sd’ PomaNorm: no visible global function definition for ‘is’ PomaNorm: no visible binding for global variable ‘var’ PomaNorm : : no visible global function definition for ‘sd’ PomaNorm: no visible global function definition for ‘validObject’ PomaOddsRatio: no visible global function definition for ‘is’ PomaOddsRatio: no visible binding for global variable ‘Group’ PomaOddsRatio: no visible global function definition for ‘glm’ PomaOddsRatio: no visible global function definition for ‘binomial’ PomaOddsRatio: no visible global function definition for ‘coef’ PomaOddsRatio: no visible global function definition for ‘confint.default’ PomaOddsRatio: no visible binding for global variable ‘X2.5..’ PomaOddsRatio: no visible binding for global variable ‘X97.5..’ PomaOddsRatio: no visible binding for global variable ‘OddsRatio’ PomaOddsRatio: no visible binding for global variable ‘feature’ PomaOddsRatio: no visible binding for global variable ‘CIHigh’ PomaOddsRatio: no visible binding for global variable ‘CILow’ PomaOutliers: no visible global function definition for ‘is’ PomaOutliers: no visible global function definition for ‘dist’ PomaOutliers: no visible global function definition for ‘aggregate’ PomaOutliers : : no visible global function definition for ‘quantile’ PomaOutliers : : no visible global function definition for ‘IQR’ PomaOutliers: no visible binding for global variable ‘x’ PomaOutliers: no visible binding for global variable ‘out’ PomaOutliers: no visible binding for global variable ‘Groups’ PomaOutliers : find_hull: no visible global function definition for ‘chull’ PomaOutliers: no visible binding for global variable ‘Group’ PomaOutliers: no visible binding for global variable ‘.’ PomaOutliers: no visible binding for global variable ‘PCoA1’ PomaOutliers: no visible binding for global variable ‘PCoA2’ PomaOutliers: no visible global function definition for ‘validObject’ PomaRandForest: no visible global function definition for ‘is’ PomaRandForest: no visible binding for global variable ‘.’ PomaRandForest: no visible binding for global variable ‘Group’ PomaRandForest: no visible binding for global variable ‘OOB’ PomaRandForest: no visible binding for global variable ‘MeanDecreaseGini’ PomaRandForest: no visible binding for global variable ‘real_names’ PomaRandForest: no visible global function definition for ‘reorder’ PomaRandForest: no visible binding for global variable ‘feature’ PomaRandForest: no visible binding for global variable ‘new_names’ PomaRankProd: no visible global function definition for ‘is’ PomaRankProd: no visible binding for global variable ‘P.value’ PomaRankProd: no visible binding for global variable ‘gene.index’ PomaSummarizedExperiment: no visible binding for global variable ‘group’ PomaSummarizedExperiment: no visible global function definition for ‘validObject’ PomaUnivariate: no visible global function definition for ‘is’ PomaUnivariate: no visible binding for global variable ‘group’ PomaUnivariate : stat_ttest: no visible global function definition for ‘t.test’ PomaUnivariate: no visible global function definition for ‘p.adjust’ PomaUnivariate: no visible binding for global variable ‘pvalue’ PomaUnivariate: no visible binding for global variable ‘feature’ PomaUnivariate: no visible binding for global variable ‘FC’ PomaUnivariate: no visible binding for global variable ‘diff_means’ PomaUnivariate: no visible binding for global variable ‘pvalueAdj’ PomaUnivariate : stat_aov: no visible global function definition for ‘anova’ PomaUnivariate : stat_aov: no visible global function definition for ‘aov’ PomaUnivariate: no visible global function definition for ‘anova’ PomaUnivariate: no visible global function definition for ‘aov’ PomaUnivariate: no visible global function definition for ‘as.formula’ PomaUnivariate : : no visible global function definition for ‘wilcox.test’ PomaUnivariate : : no visible global function definition for ‘kruskal.test’ PomaUnivariate: no visible binding for global variable ‘kw_rank_sum’ PomaVolcano: no visible global function definition for ‘is’ PomaVolcano: no visible binding for global variable ‘FC’ PomaVolcano: no visible binding for global variable ‘pvalue’ PomaVolcano: no visible binding for global variable ‘threshold’ Undefined global functions or variables: . CIHigh CILow Dim1 Dim2 EstimatedCorr FC Group Groups ID IQR MeanDecreaseGini OOB OddsRatio P.value PC1 PC2 PCoA1 PCoA2 R V1 V2 X2.5.. X97.5.. adj.P.Val aggregate anova aov as.formula binomial chull clust cmdscale coef column comp1 comp2 component conf.high conf.low confint.default cor diff_means dist estimate feature feature1 feature_sd gene.index geom_edge_link geom_node_label geom_node_point ggraph glm group is kmeans kruskal.test kw_rank_sum median model.matrix na.omit name new_names out p p.adjust pc_var_exp predict pvalue pvalueAdj quantile real_names reorder scale_edge_colour_gradientn sd t.test term theme_graph threshold to_x to_y validObject value var wilcox.test x Consider adding importFrom("grDevices", "chull") importFrom("methods", "is", "validObject") importFrom("stats", "IQR", "aggregate", "anova", "aov", "as.formula", "binomial", "cmdscale", "coef", "confint.default", "cor", "dist", "glm", "kmeans", "kruskal.test", "median", "model.matrix", "na.omit", "p.adjust", "predict", "quantile", "reorder", "sd", "t.test", "var", "wilcox.test") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 LazyData ... 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 PomaMultivariate 19.516 0.229 19.778 PomaBoxplots 6.479 0.167 6.647 * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.15-bioc/meat/POMA.Rcheck/00check.log’ for details.