############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:POMA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings POMA_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/POMA.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘POMA/DESCRIPTION’ ... OK * this is package ‘POMA’ version ‘1.10.0’ * 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 startup messages can be suppressed ... 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 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 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 ‘corr’ 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 ‘na.omit’ PomaCorr: no visible binding for global variable ‘est_corr’ PomaDESeq: no visible global function definition for ‘is’ PomaDESeq: no visible binding for global variable ‘padj’ 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 ‘predict’ PomaLasso: no visible binding for global variable ‘term’ PomaLimma: no visible global function definition for ‘is’ 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’ PomaMultivariate: no visible binding for global variable ‘value.var’ 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 ‘matches’ PomaOddsRatio: no visible binding for global variable ‘OddsRatio’ PomaOddsRatio: no visible binding for global variable ‘feature’ PomaOddsRatio: no visible binding for global variable ‘upr’ PomaOddsRatio: no visible binding for global variable ‘lwr’ PomaOutliers: no visible global function definition for ‘is’ 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’ PomaPCR: no visible global function definition for ‘is’ PomaPCR: no visible global function definition for ‘prcomp’ PomaPCR: no visible binding for global variable ‘feature’ PomaPCR: no visible binding for global variable ‘PC1’ PomaPCR: no visible global function definition for ‘lm’ 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 global function definition for ‘validObject’ PomaUMAP: no visible global function definition for ‘is’ PomaUMAP: no visible binding for global variable ‘group’ PomaUMAP: no visible binding for global variable ‘UMAP1’ PomaUMAP: no visible binding for global variable ‘UMAP2’ PomaUMAP: no visible binding for global variable ‘clust’ 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 ‘colData’ 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 ‘P.Value’ PomaVolcano: no visible binding for global variable ‘adj.P.Val’ PomaVolcano: no visible binding for global variable ‘log2FoldChange’ PomaVolcano: no visible binding for global variable ‘padj’ PomaVolcano: no visible binding for global variable ‘logFC’ PomaVolcano: no visible binding for global variable ‘pvalue’ PomaVolcano: no visible binding for global variable ‘threshold’ Undefined global functions or variables: . Dim1 Dim2 FC Group Groups ID IQR MeanDecreaseGini OOB OddsRatio P.Value P.value PC1 PC2 PCoA1 PCoA2 UMAP1 UMAP2 V1 V2 adj.P.Val aggregate anova aov as.formula chull clust colData column comp1 comp2 component conf.high conf.low cor corr diff_means est_corr estimate feature feature1 feature_sd gene.index group is kruskal.test kw_rank_sum lm log2FoldChange logFC lwr matches median na.omit name new_names out p p.adjust padj pc_var_exp prcomp predict pvalue pvalueAdj quantile real_names reorder sd t.test term threshold to_x to_y upr validObject value value.var var wilcox.test x Consider adding importFrom("grDevices", "chull") importFrom("methods", "is", "validObject") importFrom("stats", "IQR", "aggregate", "anova", "aov", "as.formula", "cor", "kruskal.test", "lm", "median", "na.omit", "p.adjust", "prcomp", "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 27.858 0.439 41.699 PomaBoxplots 18.625 0.607 29.536 PomaVolcano 7.663 0.173 12.048 PomaDESeq 6.191 0.072 9.539 PomaDensity 4.609 0.083 7.204 PomaUMAP 3.226 0.037 5.003 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: done Table1: Genes called significant under class1 < class2 Table2: Genes called significant under class1 > class2 [ FAIL 1 | WARN 692 | SKIP 0 | PASS 311 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-PomaClust.R:49:3'): PomaClust works ────────────────────────── g$optimum_cluster_num not equal to h$optimum_cluster_num. 1/1 mismatches [1] 8 - 9 == -1 [ FAIL 1 | WARN 692 | SKIP 0 | PASS 311 ] Error: Test failures Execution halted * 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 ERROR, 1 NOTE See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/POMA.Rcheck/00check.log’ for details.