############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:RFLOMICS.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings RFLOMICS_1.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/RFLOMICS.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘RFLOMICS/DESCRIPTION’ ... OK * this is package ‘RFLOMICS’ version ‘1.1.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Depends: includes the non-default packages: 'SummarizedExperiment', 'MultiAssayExperiment', 'shinyBS', 'dplyr', 'ggplot2', 'htmltools', 'knitr', 'coseq' Adding so many packages to the search path is excessive and importing selectively is preferable. Imports includes 33 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 ‘RFLOMICS’ 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: ‘org.At.tair.db’ ‘reticulate’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .applyFeatureFiltering: no visible global function definition for ‘assay’ .applyFeatureFiltering: no visible global function definition for ‘assay<-’ .applyLog: no visible global function definition for ‘assay<-’ .applyLog: no visible global function definition for ‘assay’ .applyNormalization: no visible global function definition for ‘assay’ .applyNormalization: no visible global function definition for ‘assay<-’ .applyTransformation: no visible global function definition for ‘assay’ .applyTransformation: no visible global function definition for ‘assay<-’ .coseq.results.process: no visible global function definition for ‘summarise’ .coseq.results.process: no visible global function definition for ‘group_by’ .coseq.results.process: no visible binding for global variable ‘status’ .coseq.results.process: no visible binding for global variable ‘errors’ .coseq.results.process: no visible global function definition for ‘n’ .coseq.results.process: no visible global function definition for ‘filter’ .coseq.results.process: no visible binding for global variable ‘n’ .coseq.results.process: no visible global function definition for ‘mutate’ .coseq.results.process: no visible global function definition for ‘summarize’ .countSamplesPerCondition: no visible global function definition for ‘group_by_at’ .countSamplesPerCondition: no visible global function definition for ‘full_join’ .countSamplesPerCondition: no visible global function definition for ‘mutate_at’ .countSamplesPerCondition : : no visible global function definition for ‘if_else’ .defineInteractionConstrastForPairsOfFactors: no visible global function definition for ‘mutate’ .defineInteractionConstrastForPairsOfFactors: no visible global function definition for ‘group_by’ .defineInteractionConstrastForPairsOfFactors: no visible binding for global variable ‘outsideGroup’ .defineInteractionConstrastForPairsOfFactors: no visible binding for global variable ‘groupComparison’ .defineInteractionConstrastForPairsOfFactors: no visible global function definition for ‘add_tally’ .defineInteractionConstrastForPairsOfFactors: no visible binding for global variable ‘contrast’ .defineInteractionConstrastForPairsOfFactors: no visible binding for global variable ‘n’ .define_averaged_contrasts: no visible global function definition for ‘group_by’ .define_averaged_contrasts: no visible global function definition for ‘add_tally’ .define_averaged_contrasts: no visible global function definition for ‘mutate’ .define_partOfInteractionContrast_df: no visible global function definition for ‘mutate’ .define_partOfSimpleContrast_df: no visible global function definition for ‘mutate’ .edgeRAnaDiff: no visible global function definition for ‘assay’ .generateEcoseedExampleData: no visible global function definition for ‘data’ .generateEcoseedExampleData: no visible binding for global variable ‘ecoseed.df’ .getExpressionContrastF: no visible binding for global variable ‘contrast’ .getExpressionContrastF: no visible binding for global variable ‘contrastName’ .getExpressionContrastF: no visible binding for global variable ‘groupComparison’ .getExpressionContrastF: no visible binding for global variable ‘type’ .integrationMethodsParam: no visible global function definition for ‘colData’ .integrationPrepareDataUI: no visible global function definition for ‘assay’ .integrationPrepareDataUI : : no visible global function definition for ‘sd’ .limmaAnaDiff: no visible global function definition for ‘assay’ .medianNormalization: no visible global function definition for ‘assay’ .modGLMmodel : : no visible global function definition for ‘filter’ .modGLMmodel : : no visible binding for global variable ‘contrast’ .modIntegrationAnalysis: no visible global function definition for ‘mutate’ .modIntegrationAnalysis: no visible binding for global variable ‘full_join’ .modIntegrationAnalysis: no visible global function definition for ‘across’ .modIntegrationAnalysis : : no visible global function definition for ‘assay’ .modIntegrationAnalysis : : : no visible global function definition for ‘sd’ .modLoadData: no visible global function definition for ‘filter’ .modRunEnrichment: no visible global function definition for ‘rename’ .outAnnotResults : : no visible binding for global variable ‘contrastName’ .outMOFAFactorsCor: no visible global function definition for ‘cor’ .outMOFAFactorsPlot: no visible binding for global variable ‘group’ .outMOFAHeatmap: no visible binding for global variable ‘group’ .plotExperimentalDesign: no visible global function definition for ‘mutate’ .plotExperimentalDesign: no visible global function definition for ‘if_else’ .plotExperimentalDesign: no visible binding for global variable ‘Count’ .plotExperimentalDesign: no visible binding for global variable ‘status’ .plotMA: no visible binding for global variable ‘.’ .plotPValue: no visible binding for global variable ‘pvalue’ .plotVolcanoPlot: no visible global function definition for ‘last’ .plotVolcanoPlot: no visible global function definition for ‘first’ .plot_MO_1: no visible global function definition for ‘group_by’ .plot_MO_1: no visible binding for global variable ‘Dataset’ .plot_MO_1: no visible global function definition for ‘summarise’ .plot_MO_1: no visible binding for global variable ‘% of explained variance’ .plot_MO_1: no visible global function definition for ‘filter’ .plot_MO_1: no visible binding for global variable ‘Cumulative Explained Variance’ .plot_MO_2: no visible global function definition for ‘filter’ .plot_MO_2: no visible binding for global variable ‘Dataset’ .plot_MO_2: no visible binding for global variable ‘Component’ .plot_MO_2: no visible binding for global variable ‘% of explained variance’ .rbeFunction: no visible global function definition for ‘assay’ .rbeFunction: no visible global function definition for ‘assay<-’ .relationsMOFA : : no visible global function definition for ‘p.adjust’ .rnaseqRBETransform: no visible global function definition for ‘assay’ .rnaseqRBETransform: no visible global function definition for ‘assay<-’ .runMixOmicsAnalysis: no visible global function definition for ‘select_if’ .simpleContrastForOneFactor: no visible global function definition for ‘mutate’ .tmmNormalization: no visible global function definition for ‘assay’ .totalSumNormalization: no visible global function definition for ‘assay’ .updateColData: no visible global function definition for ‘colData’ .writeSessionInfo: no visible global function definition for ‘sessionInfo’ CoSeqAnalysis: no visible global function definition for ‘filter’ CoSeqAnalysis: no visible binding for global variable ‘status’ DiffExpAnalysis: no visible global function definition for ‘filter’ DiffExpAnalysis: no visible binding for global variable ‘contrastName’ RflomicsMAE: no visible global function definition for ‘ExperimentList’ RflomicsMAE: no visible global function definition for ‘packageVersion’ createRflomicsMAE: no visible global function definition for ‘assay’ createRflomicsMAE: no visible global function definition for ‘sampleMap’ createRflomicsMAE: no visible global function definition for ‘colData’ createRflomicsMAE: no visible global function definition for ‘filter’ createRflomicsMAE: no visible binding for global variable ‘factorType’ createRflomicsMAE: no visible global function definition for ‘relevel’ createRflomicsMAE: no visible global function definition for ‘mutate’ createRflomicsSE: no visible global function definition for ‘filter’ createRflomicsSE: no visible global function definition for ‘mutate’ createRflomicsSE: no visible binding for global variable ‘samples’ createRflomicsSE: no visible global function definition for ‘DataFrame’ definition: no visible global function definition for ‘mutate’ definition: no visible binding for global variable ‘n’ definition: no visible binding for global variable ‘logLike’ readExpDesign: no visible global function definition for ‘mutate’ readExpDesign: no visible global function definition for ‘across’ readExpDesign: no visible binding for global variable ‘.’ readOmicsData: no visible binding for global variable ‘.’ updateSelectedContrasts: no visible global function definition for ‘filter’ updateSelectedContrasts: no visible binding for global variable ‘contrast’ dataImputation,RflomicsSE: no visible global function definition for ‘assay’ filterDiffAnalysis,RflomicsSE: no visible binding for global variable ‘SE.name’ filterLowAbundance,RflomicsSE: no visible global function definition for ‘assay’ getCoExpAnalysesSummary,RflomicsMAE : : no visible global function definition for ‘filter’ getCoExpAnalysesSummary,RflomicsMAE : : no visible global function definition for ‘mutate’ getCoExpAnalysesSummary,RflomicsMAE : : no visible binding for global variable ‘.’ getCoExpAnalysesSummary,RflomicsMAE : : no visible binding for global variable ‘variable’ getCoExpAnalysesSummary,RflomicsMAE : : no visible global function definition for ‘full_join’ getCoExpAnalysesSummary,RflomicsMAE : : no visible global function definition for ‘group_by’ getCoExpAnalysesSummary,RflomicsMAE : : no visible binding for global variable ‘groups’ getCoExpAnalysesSummary,RflomicsMAE : : no visible global function definition for ‘summarise’ getCoExpAnalysesSummary,RflomicsMAE : : no visible binding for global variable ‘y_profiles’ getCoExpAnalysesSummary,RflomicsMAE: no visible global function definition for ‘mutate’ getCoExpAnalysesSummary,RflomicsMAE: no visible binding for global variable ‘groups’ getCoExpAnalysesSummary,RflomicsMAE: no visible binding for global variable ‘cluster’ getCoExpAnalysesSummary,RflomicsMAE: no visible binding for global variable ‘dataset’ getDEList,RflomicsSE: no visible global function definition for ‘mutate’ getDEList,RflomicsSE: no visible binding for global variable ‘.’ getDEList,RflomicsSE: no visible binding for global variable ‘DEF’ getDEList,RflomicsSE: no visible global function definition for ‘filter’ getDEList,RflomicsSE: no visible binding for global variable ‘SUMCOL’ getDEMatrix,RflomicsMAE: no visible binding for global variable ‘omicName’ getDesignMat,RflomicsMAE: no visible global function definition for ‘colData’ getDesignMat,RflomicsSE: no visible global function definition for ‘colData’ getDiffAnalysesSummary,RflomicsMAE: no visible global function definition for ‘mutate’ getDiffAnalysesSummary,RflomicsMAE: no visible binding for global variable ‘.’ getDiffAnalysesSummary,RflomicsMAE: no visible global function definition for ‘filter’ getDiffAnalysesSummary,RflomicsMAE: no visible binding for global variable ‘All’ getDiffAnalysesSummary,RflomicsMAE: no visible binding for global variable ‘Up_Down’ getDiffAnalysesSummary,RflomicsMAE : : no visible binding for global variable ‘contrastName’ getDiffAnalysesSummary,RflomicsMAE : : no visible binding for global variable ‘.’ getDiffAnalysesSummary,RflomicsMAE: no visible binding for global variable ‘tabel’ getDiffAnalysesSummary,RflomicsMAE: no visible binding for global variable ‘percent’ getDiffAnalysesSummary,RflomicsMAE: no visible binding for global variable ‘variable’ plotBoxplotDE,RflomicsSE: no visible global function definition for ‘assay’ plotBoxplotDE,RflomicsSE: no visible global function definition for ‘full_join’ plotBoxplotDE,RflomicsSE: no visible global function definition for ‘arrange’ plotBoxplotDE,RflomicsSE: no visible binding for global variable ‘groups’ plotBoxplotDE,RflomicsSE: no visible binding for global variable ‘value’ plotCoExpression,RflomicsSE: no visible global function definition for ‘mutate’ plotCoExpression,RflomicsSE: no visible binding for global variable ‘n’ plotCoExpression,RflomicsSE: no visible binding for global variable ‘logLike’ plotCoExpressionProfile,RflomicsSE: no visible global function definition for ‘mutate’ plotCoExpressionProfile,RflomicsSE: no visible binding for global variable ‘.’ plotCoExpressionProfile,RflomicsSE: no visible binding for global variable ‘variable’ plotCoExpressionProfile,RflomicsSE: no visible global function definition for ‘full_join’ plotCoExpressionProfile,RflomicsSE: no visible global function definition for ‘arrange’ plotCoExpressionProfile,RflomicsSE: no visible binding for global variable ‘groups’ plotCoExpressionProfile,RflomicsSE: no visible binding for global variable ‘y_profiles’ plotCoExpressionProfile,RflomicsSE: no visible global function definition for ‘filter’ plotCoExpressionProfile,RflomicsSE: no visible binding for global variable ‘observations’ plotCoExpressionProfile,RflomicsSE: no visible global function definition for ‘group_by’ plotCoExpressionProfile,RflomicsSE: no visible global function definition for ‘summarise’ plotCoExpressionProfile,RflomicsSE: no visible binding for global variable ‘mean.y_profiles’ plotConditionsOverview,RflomicsMAE: no visible global function definition for ‘mutate’ plotConditionsOverview,RflomicsMAE: no visible binding for global variable ‘.’ plotConditionsOverview,RflomicsMAE: no visible global function definition for ‘sampleMap’ plotConditionsOverview,RflomicsMAE: no visible global function definition for ‘left_join’ plotConditionsOverview,RflomicsMAE: no visible binding for global variable ‘assay’ plotConditionsOverview,RflomicsMAE: no visible global function definition for ‘group_by_at’ plotConditionsOverview,RflomicsMAE: no visible global function definition for ‘count’ plotConditionsOverview,RflomicsMAE: no visible global function definition for ‘right_join’ plotConditionsOverview,RflomicsMAE: no visible global function definition for ‘mutate_at’ plotConditionsOverview,RflomicsMAE : : no visible global function definition for ‘if_else’ plotConditionsOverview,RflomicsMAE: no visible global function definition for ‘if_else’ plotConditionsOverview,RflomicsMAE: no visible binding for global variable ‘Count’ plotConditionsOverview,RflomicsMAE: no visible binding for global variable ‘status’ plotCoseqContrasts,RflomicsSE: no visible global function definition for ‘filter’ plotCoseqContrasts,RflomicsSE: no visible binding for global variable ‘does.belong’ plotCoseqContrasts,RflomicsSE: no visible global function definition for ‘mutate’ plotCoseqContrasts,RflomicsSE: no visible global function definition for ‘group_by’ plotCoseqContrasts,RflomicsSE: no visible global function definition for ‘left_join’ plotCoseqContrasts,RflomicsSE: no visible binding for global variable ‘DEF’ plotCoseqContrasts,RflomicsSE: no visible binding for global variable ‘C’ plotCoseqContrasts,RflomicsSE: no visible global function definition for ‘across’ plotCoseqContrasts,RflomicsSE: no visible global function definition for ‘count’ plotCoseqContrasts,RflomicsSE: no visible binding for global variable ‘value’ plotCoseqContrasts,RflomicsSE: no visible global function definition for ‘distinct’ plotCoseqContrasts,RflomicsSE: no visible global function definition for ‘ungroup’ plotCoseqContrasts,RflomicsSE: no visible binding for global variable ‘n’ plotCoseqContrasts,RflomicsSE: no visible binding for global variable ‘prop’ plotDataDistribution,RflomicsSE: no visible global function definition for ‘assay’ plotDataDistribution,RflomicsSE: no visible global function definition for ‘full_join’ plotDataDistribution,RflomicsSE: no visible global function definition for ‘arrange’ plotDataDistribution,RflomicsSE: no visible binding for global variable ‘groups’ plotDataDistribution,RflomicsSE: no visible binding for global variable ‘value’ plotDataDistribution,RflomicsSE: no visible binding for global variable ‘samples’ plotDataOverview,RflomicsMAE: no visible global function definition for ‘full_join’ plotDataOverview,RflomicsMAE: no visible global function definition for ‘sampleMap’ plotDataOverview,RflomicsMAE: no visible global function definition for ‘mutate’ plotDataOverview,RflomicsMAE: no visible binding for global variable ‘assay’ plotDataOverview,RflomicsMAE: no visible global function definition for ‘arrange’ plotDataOverview,RflomicsMAE: no visible binding for global variable ‘primary’ plotDataOverview,RflomicsMAE: no visible binding for global variable ‘y.axis’ plotDataOverview,RflomicsMAE: no visible global function definition for ‘desc’ plotHeatmapDesign,RflomicsSE: no visible global function definition for ‘arrange’ plotHeatmapDesign,RflomicsSE: no visible binding for global variable ‘Adj.pvalue’ plotHeatmapDesign,RflomicsSE: no visible global function definition for ‘assay’ plotHeatmapDesign,RflomicsSE: no visible binding for global variable ‘samples’ plotHeatmapDesign,RflomicsSE: no visible binding for global variable ‘groups’ plotLibrarySize,RflomicsSE: no visible global function definition for ‘assay’ plotLibrarySize,RflomicsSE: no visible global function definition for ‘arrange’ plotLibrarySize,RflomicsSE: no visible global function definition for ‘full_join’ plotLibrarySize,RflomicsSE: no visible binding for global variable ‘groups’ plotLibrarySize,RflomicsSE: no visible binding for global variable ‘samples’ plotLibrarySize,RflomicsSE: no visible binding for global variable ‘value’ plotOmicsPCA,RflomicsSE: no visible global function definition for ‘right_join’ plotOmicsPCA,RflomicsSE: no visible binding for global variable ‘samples’ prepareForIntegration,RflomicsMAE: no visible global function definition for ‘experiments’ prepareForIntegration,RflomicsMAE: no visible global function definition for ‘colData’ prepareForIntegration,RflomicsMAE: no visible global function definition for ‘sampleMap’ prepareForIntegration,RflomicsMAE: no visible global function definition for ‘colData<-’ prepareForIntegration,RflomicsMAE: no visible global function definition for ‘intersectColumns’ prepareForIntegration,RflomicsMAE : : no visible global function definition for ‘assay’ rflomicsMAE2MAE,RflomicsMAE: no visible global function definition for ‘experiments’ rflomicsMAE2MAE,RflomicsMAE: no visible global function definition for ‘colData’ rflomicsMAE2MAE,RflomicsMAE: no visible global function definition for ‘sampleMap’ runAnnotationEnrichment,RflomicsSE : : no visible global function definition for ‘filter’ runAnnotationEnrichment,RflomicsSE: no visible global function definition for ‘mutate’ runAnnotationEnrichment,RflomicsSE: no visible binding for global variable ‘.’ runAnnotationEnrichment,RflomicsSE: no visible global function definition for ‘relocate’ runAnnotationEnrichment,RflomicsSE: no visible binding for global variable ‘Contrast’ runAnnotationEnrichment,RflomicsSE: no visible binding for global variable ‘Cluster’ runCoExpression,RflomicsSE: no visible global function definition for ‘assay’ runNormalization,RflomicsSE: no visible global function definition for ‘assay’ runOmicsPCA,RflomicsSE: no visible global function definition for ‘assay’ Undefined global functions or variables: % of explained variance . Adj.pvalue All C Cluster Component Contrast Count Cumulative Explained Variance DEF DataFrame Dataset ExperimentList SE.name SUMCOL Up_Down across add_tally arrange assay assay<- cluster colData colData<- contrast contrastName cor count data dataset desc distinct does.belong ecoseed.df errors experiments factorType filter first full_join group groupComparison group_by group_by_at groups if_else intersectColumns last left_join logLike mean.y_profiles mutate mutate_at n observations omicName outsideGroup p.adjust packageVersion percent primary prop pvalue relevel relocate rename right_join sampleMap samples sd select_if sessionInfo status summarise summarize tabel type ungroup value variable y.axis y_profiles Consider adding importFrom("stats", "C", "cor", "filter", "p.adjust", "relevel", "sd") importFrom("utils", "data", "packageVersion", "sessionInfo") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: RflomicsMAE-class.Rd: MultiAssayExperiment RflomicsSE-class.Rd: SummarizedExperiment createRflomicsMAE.Rd: SummarizedExperiment, MultiAssayExperiment ecoseed.mae.Rd: MultiAssayExperiment, SummarizedExperiment runCoExpression.Rd: coseq runDiffAnalysis.Rd: lmFit Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 runCoExpression 9.717 1.940 9.893 runOmicsIntegration 5.956 0.823 6.113 prepareForIntegration 6.056 0.642 6.033 * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/RFLOMICS.Rcheck/00check.log’ for details.