############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:POMA.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings POMA_1.17.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/POMA.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 ‘POMA/DESCRIPTION’ ... OK * this is package ‘POMA’ version ‘1.17.6’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 31 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 ‘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 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE ':::' call which should be '::': ‘purrr:::map_chr’ See the note in ?`:::` about the use of this operator. Unexported object imported by a ':::' call: ‘utils:::.getHelpFile’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE PomaBatch: no visible global function definition for ‘is’ PomaBatch: no visible global function definition for ‘validObject’ PomaBoxplots: no visible global function definition for ‘is’ PomaBoxplots: no visible binding for global variable ‘sample_id’ PomaBoxplots: no visible binding for global variable ‘group_factor’ 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 ‘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’ PomaCreateObject: no visible global function definition for ‘validObject’ PomaDESeq: no visible global function definition for ‘is’ PomaDESeq: no visible global function definition for ‘formula’ PomaDESeq: no visible binding for global variable ‘log2FoldChange’ PomaDESeq: no visible binding for global variable ‘padj’ PomaDESeq: no visible binding for global variable ‘adj_pvalue’ PomaDensity: no visible global function definition for ‘is’ PomaDensity: no visible binding for global variable ‘sample_id’ PomaDensity: no visible binding for global variable ‘group_factor’ PomaDensity: no visible binding for global variable ‘name’ PomaDensity: no visible binding for global variable ‘value’ PomaEnrichment: no visible binding for global variable ‘leadingEdge’ PomaEnrichment: no visible binding for global variable ‘NES’ PomaEnrichment: no visible binding for global variable ‘pathway’ PomaEnrichment: no visible binding for global variable ‘pval’ PomaEnrichment: no visible binding for global variable ‘padj’ PomaEnrichment: no visible binding for global variable ‘direction’ PomaEnrichment: no visible binding for global variable ‘size’ PomaEnrichment: no visible binding for global variable ‘leading_edge’ PomaEnrichment: no visible binding for global variable ‘adjPval’ PomaEnrichment: no visible binding for global variable ‘overlapGenes’ PomaEnrichment: no visible binding for global variable ‘overlap’ PomaEnrichment: no visible binding for global variable ‘overlap_genes’ 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_factor’ PomaImpute: no visible global function definition for ‘validObject’ PomaLM: no visible global function definition for ‘is’ PomaLM: no visible global function definition for ‘lm’ PomaLM: no visible global function definition for ‘p.adjust’ PomaLM: no visible binding for global variable ‘p.value’ PomaLM: no visible binding for global variable ‘term’ PomaLM: no visible binding for global variable ‘estimate’ PomaLM: no visible binding for global variable ‘std.error’ PomaLM: no visible binding for global variable ‘statistic’ PomaLM: no visible binding for global variable ‘adj_pvalue’ PomaLM: no visible binding for global variable ‘pvalue’ PomaLM: no visible global function definition for ‘reorder’ PomaLM: no visible binding for global variable ‘feature’ PomaLM: no visible binding for global variable ‘std_err’ PomaLMM: no visible global function definition for ‘is’ PomaLMM : lmm_fun: no visible global function definition for ‘vcov’ PomaLMM : lmm_fun: no visible binding for global variable ‘vcov’ PomaLMM : lmm_fun: no visible binding for global variable ‘grp’ PomaLMM : lmm_fun: no visible binding for global variable ‘variance_percent’ PomaLMM: no visible binding for global variable ‘feature’ PomaLMM: no visible binding for global variable ‘name’ PomaLMM: no visible binding for global variable ‘value’ 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 global function definition for ‘as.formula’ PomaLimma: no visible binding for global variable ‘logFC’ PomaLimma: no visible binding for global variable ‘P.Value’ PomaLimma: no visible binding for global variable ‘adj.P.Val’ 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 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 binding for global variable ‘groups’ PomaOutliers: no visible global function definition for ‘quantile’ PomaOutliers: no visible global function definition for ‘IQR’ PomaOutliers: no visible binding for global variable ‘limit’ PomaOutliers: no visible binding for global variable ‘out’ 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’ PomaPCA: no visible global function definition for ‘is’ PomaPCA: no visible global function definition for ‘prcomp’ PomaPCA: no visible binding for global variable ‘PC1’ PomaPCA: no visible binding for global variable ‘PC2’ PomaPCA: no visible binding for global variable ‘group’ PomaPCA: no visible binding for global variable ‘sample_id’ PomaPCA: no visible global function definition for ‘reorder’ PomaPCA: no visible binding for global variable ‘comp’ PomaPCA: no visible binding for global variable ‘var_exp’ PomaPCA: no visible binding for global variable ‘feature’ PomaPCA: no visible binding for global variable ‘value’ PomaPCA: no visible binding for global variable ‘name’ PomaPCA: no visible binding for global variable ‘to_x’ PomaPCA: no visible binding for global variable ‘to_y’ PomaPCR: no visible global function definition for ‘is’ PomaPCR: no visible binding for global variable ‘PC1’ PomaPCR: no visible global function definition for ‘lm’ PomaPCR: no visible global function definition for ‘p.adjust’ PomaPCR: no visible binding for global variable ‘p.value’ PomaPCR: no visible binding for global variable ‘term’ PomaPCR: no visible binding for global variable ‘estimate’ PomaPCR: no visible binding for global variable ‘std.error’ PomaPCR: no visible binding for global variable ‘statistic’ PomaPCR: no visible binding for global variable ‘adj_pvalue’ PomaPCR: no visible binding for global variable ‘pvalue’ PomaPLS: no visible global function definition for ‘is’ PomaPLS: no visible binding for global variable ‘comp1’ PomaPLS: no visible binding for global variable ‘comp2’ PomaPLS: no visible binding for global variable ‘sample_id’ PomaPLS: no visible binding for global variable ‘feature’ PomaPLS: no visible global function definition for ‘reorder’ PomaPLS: no visible binding for global variable ‘value’ PomaPLS: no visible binding for global variable ‘name’ PomaPLS: no visible binding for global variable ‘component’ PomaPLS: no visible binding for global variable ‘error’ PomaPLS: no visible binding for global variable ‘feature_sd’ PomaPLS: no visible binding for global variable ‘sd’ PomaRandForest: no visible global function definition for ‘is’ PomaRandForest: no visible binding for global variable ‘OOB’ PomaRandForest: no visible binding for global variable ‘MeanDecreaseGini’ PomaRandForest: no visible global function definition for ‘reorder’ PomaRandForest: no visible binding for global variable ‘feature’ PomaRankProd: no visible global function definition for ‘is’ PomaRankProd: no visible global function definition for ‘capture.output’ PomaRankProd: no visible binding for global variable ‘P.value’ PomaRankProd: no visible binding for global variable ‘gene.index’ PomaUMAP: no visible global function definition for ‘is’ PomaUMAP: no visible binding for global variable ‘clust’ PomaUMAP: no visible binding for global variable ‘UMAP1’ PomaUMAP: no visible binding for global variable ‘UMAP2’ PomaUnivariate: no visible global function definition for ‘is’ PomaUnivariate: no visible binding for global variable ‘group’ PomaUnivariate : : 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 ‘fold_change’ PomaUnivariate: no visible binding for global variable ‘diff_means’ PomaUnivariate: no visible binding for global variable ‘adj_pvalue’ PomaUnivariate : : no visible global function definition for ‘anova’ PomaUnivariate : : no visible global function definition for ‘aov’ PomaUnivariate: no visible global function definition for ‘TukeyHSD’ PomaUnivariate: no visible global function definition for ‘aov’ PomaUnivariate: no visible binding for global variable ‘adj.p.value’ PomaUnivariate: no visible global function definition for ‘as.formula’ PomaUnivariate: no visible binding for global variable ‘term’ PomaUnivariate: no visible binding for global variable ‘p.value’ 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’ PomaUnivariate: no visible binding for global variable ‘Comparison’ PomaUnivariate: no visible binding for global variable ‘P.adj’ PomaUnivariate: no visible binding for global variable ‘contrast’ PomaVolcano: no visible global function definition for ‘quantile’ PomaVolcano: no visible binding for global variable ‘logFC’ PomaVolcano: no visible binding for global variable ‘pvalue’ PomaVolcano: no visible binding for global variable ‘feature’ create_mock_data: no visible global function definition for ‘runif’ create_mock_summarized_experiment: no visible global function definition for ‘runif’ help_extract: no visible global function definition for ‘capture.output’ make_legend: no visible binding for global variable ‘POMA’ title_extract: no visible global function definition for ‘capture.output’ Undefined global functions or variables: . Comparison Dim1 Dim2 IQR MeanDecreaseGini NES OOB OddsRatio P.Value P.adj P.value PC1 PC2 PCoA1 PCoA2 POMA TukeyHSD UMAP1 UMAP2 V1 V2 adj.P.Val adj.p.value adjPval adj_pvalue aggregate anova aov as.formula capture.output chull clust column comp comp1 comp2 component conf.high conf.low contrast cor corr diff_means direction error estimate feature feature_sd fold_change formula gene.index group group_factor groups grp is kruskal.test kw_rank_sum leadingEdge leading_edge limit lm log2FoldChange logFC lwr name out overlap overlapGenes overlap_genes p p.adjust p.value padj pathway prcomp predict pval pvalue quantile reorder runif sample_id sd size statistic std.error std_err t.test term to_x to_y upr validObject value var var_exp variance_percent vcov wilcox.test Consider adding importFrom("grDevices", "chull") importFrom("methods", "is", "validObject") importFrom("stats", "IQR", "TukeyHSD", "aggregate", "anova", "aov", "as.formula", "cor", "formula", "kruskal.test", "lm", "p.adjust", "prcomp", "predict", "quantile", "reorder", "runif", "sd", "t.test", "var", "vcov", "wilcox.test") importFrom("utils", "capture.output") 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 PomaPLS 31.332 0.989 32.342 PomaUnivariate 26.087 0.241 26.330 PomaBoxplots 19.518 0.419 19.937 PomaBatch 11.597 0.353 11.950 PomaEnrichment 10.894 0.657 11.544 PomaLimma 8.825 0.034 8.862 PomaHeatmap 6.627 0.085 6.714 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/POMA.Rcheck/00check.log’ for details.