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This page was generated on 2025-08-04 11:44 -0400 (Mon, 04 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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Package 1762/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RFLOMICS 1.0.1 (landing page) Nadia Bessoltane
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the RFLOMICS package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RFLOMICS.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: RFLOMICS |
Version: 1.0.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RFLOMICS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RFLOMICS_1.0.1.tar.gz |
StartedAt: 2025-08-01 08:48:31 -0400 (Fri, 01 Aug 2025) |
EndedAt: 2025-08-01 09:09:02 -0400 (Fri, 01 Aug 2025) |
EllapsedTime: 1231.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RFLOMICS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RFLOMICS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RFLOMICS_1.0.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/RFLOMICS.Rcheck’ * using R version 4.5.1 RC (2025-06-05 r88288) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘RFLOMICS/DESCRIPTION’ ... OK * this is package ‘RFLOMICS’ version ‘1.0.1’ * 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 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 : <anonymous>: 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 : <anonymous>: no visible global function definition for ‘sd’ .limmaAnaDiff: no visible global function definition for ‘assay’ .medianNormalization: no visible global function definition for ‘assay’ .modGLMmodel : <anonymous>: no visible global function definition for ‘filter’ .modGLMmodel : <anonymous>: 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 : <anonymous>: no visible global function definition for ‘assay’ .modIntegrationAnalysis : <anonymous> : <anonymous>: no visible global function definition for ‘sd’ .modLoadData: no visible global function definition for ‘filter’ .modRunEnrichment: no visible global function definition for ‘rename’ .outAnnotResults : <anonymous>: 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 : <anonymous>: 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 : <anonymous>: no visible global function definition for ‘filter’ getCoExpAnalysesSummary,RflomicsMAE : <anonymous>: no visible global function definition for ‘mutate’ getCoExpAnalysesSummary,RflomicsMAE : <anonymous>: no visible binding for global variable ‘.’ getCoExpAnalysesSummary,RflomicsMAE : <anonymous>: no visible binding for global variable ‘variable’ getCoExpAnalysesSummary,RflomicsMAE : <anonymous>: no visible global function definition for ‘full_join’ getCoExpAnalysesSummary,RflomicsMAE : <anonymous>: no visible global function definition for ‘group_by’ getCoExpAnalysesSummary,RflomicsMAE : <anonymous>: no visible binding for global variable ‘groups’ getCoExpAnalysesSummary,RflomicsMAE : <anonymous>: no visible global function definition for ‘summarise’ getCoExpAnalysesSummary,RflomicsMAE : <anonymous>: 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 : <anonymous>: no visible binding for global variable ‘contrastName’ getDiffAnalysesSummary,RflomicsMAE : <anonymous>: 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 : <anonymous>: 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 : <anonymous>: 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 : <anonymous>: 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 20.518 3.254 21.054 runOmicsIntegration 16.385 0.345 16.971 prepareForIntegration 14.352 0.369 14.884 runDataProcessing 11.728 0.733 12.577 runDiffAnalysis 8.037 0.478 8.791 generateReport 7.271 0.243 7.629 runAnnotationEnrichment 6.372 0.185 6.707 RflomicsMAE-class 5.819 0.254 6.134 generateExpressionContrast 5.224 0.297 5.717 generateModelFormulae 5.142 0.189 5.515 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/RFLOMICS.Rcheck/00check.log’ for details.
RFLOMICS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RFLOMICS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘RFLOMICS’ ... ** this is package ‘RFLOMICS’ version ‘1.0.1’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (RFLOMICS)
RFLOMICS.Rcheck/tests/testthat.Rout
R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(RFLOMICS) Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Loading required package: MultiAssayExperiment Loading required package: shinyBS Loading required package: dplyr Attaching package: 'dplyr' The following object is masked from 'package:Biobase': combine The following objects are masked from 'package:GenomicRanges': intersect, setdiff, union The following object is masked from 'package:GenomeInfoDb': intersect The following objects are masked from 'package:IRanges': collapse, desc, intersect, setdiff, slice, union The following objects are masked from 'package:S4Vectors': first, intersect, rename, setdiff, setequal, union The following objects are masked from 'package:BiocGenerics': combine, intersect, setdiff, setequal, union The following object is masked from 'package:generics': explain The following object is masked from 'package:matrixStats': count The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: ggplot2 Loading required package: htmltools Loading required package: knitr Loading required package: coseq Attaching package: 'coseq' The following object is masked from 'package:stats4': plot The following object is masked from 'package:graphics': plot The following object is masked from 'package:base': plot > > test_check("RFLOMICS") 2025-08-01 09:01:35.848 R[46812:292124499] XType: com.apple.fonts is not accessible. 2025-08-01 09:01:35.849 R[46812:292124499] XType: XTFontStaticRegistry is enabled. ######################################################### ### __ __ ____ ______ ### ### | \/ |/ __ \| ____/\ _ ### ### | \ / | | | | |__ / \ _| |_ ### ### | |\/| | | | | __/ /\ \_ _| ### ### | | | | |__| | | / ____ \|_| ### ### |_| |_|\____/|_|/_/ \_\ ### ### ### ######################################################### use_float32 set to True: replacing float64 arrays by float32 arrays to speed up computations... Scaling views to unit variance... Successfully loaded view='RNAtest' group='group1' with N=27 samples and D=25014 features... Successfully loaded view='protetest' group='group1' with N=27 samples and D=493 features... Successfully loaded view='metatest' group='group1' with N=27 samples and D=135 features... Model options: - Automatic Relevance Determination prior on the factors: False - Automatic Relevance Determination prior on the weights: True - Spike-and-slab prior on the factors: False - Spike-and-slab prior on the weights: False Likelihoods: - View 0 (RNAtest): gaussian - View 1 (protetest): gaussian - View 2 (metatest): gaussian ###################################### ## Training the model with seed 42 ## ###################################### ELBO before training: -3634008.26 Iteration 1: time=0.13, ELBO=-651384.97, deltaELBO=2982623.287 (82.07530287%), Factors=5 Iteration 2: time=0.12, Factors=5 Iteration 3: time=0.14, Factors=5 Iteration 4: time=0.12, Factors=5 Iteration 5: time=0.13, Factors=5 Iteration 6: time=0.15, ELBO=1426118.36, deltaELBO=2077503.331 (57.16837117%), Factors=5 Iteration 7: time=0.17, Factors=5 Iteration 8: time=0.15, Factors=5 Iteration 9: time=0.15, Factors=5 Iteration 10: time=0.15, Factors=5 Iteration 11: time=0.18, ELBO=1431479.25, deltaELBO=5360.889 (0.14752001%), Factors=5 Iteration 12: time=0.17, Factors=5 Iteration 13: time=0.15, Factors=5 Iteration 14: time=0.15, Factors=5 Iteration 15: time=0.15, Factors=5 Iteration 16: time=0.17, ELBO=1432131.77, deltaELBO=652.520 (0.01795594%), Factors=5 Iteration 17: time=0.15, Factors=5 Iteration 18: time=0.15, Factors=5 Iteration 19: time=0.15, Factors=5 Iteration 20: time=0.12, Factors=5 Iteration 21: time=0.14, ELBO=1432346.44, deltaELBO=214.673 (0.00590734%), Factors=5 Iteration 22: time=0.12, Factors=5 Iteration 23: time=0.13, Factors=5 Iteration 24: time=0.12, Factors=5 Iteration 25: time=0.13, Factors=5 Iteration 26: time=0.14, ELBO=1432466.92, deltaELBO=120.480 (0.00331535%), Factors=5 Iteration 27: time=0.15, Factors=5 Iteration 28: time=0.15, Factors=5 Iteration 29: time=0.16, Factors=5 Iteration 30: time=0.16, Factors=5 Iteration 31: time=0.19, ELBO=1432532.68, deltaELBO=65.757 (0.00180948%), Factors=5 Iteration 32: time=0.16, Factors=5 Iteration 33: time=0.13, Factors=5 Iteration 34: time=0.12, Factors=5 Iteration 35: time=0.12, Factors=5 Iteration 36: time=0.36, ELBO=1432575.96, deltaELBO=43.289 (0.00119122%), Factors=5 Iteration 37: time=0.18, Factors=5 Iteration 38: time=0.16, Factors=5 Iteration 39: time=0.17, Factors=5 Iteration 40: time=0.12, Factors=5 Iteration 41: time=0.14, ELBO=1432606.16, deltaELBO=30.197 (0.00083096%), Factors=5 Iteration 42: time=0.13, Factors=5 Iteration 43: time=0.27, Factors=5 Iteration 44: time=0.12, Factors=5 Iteration 45: time=0.13, Factors=5 Iteration 46: time=0.15, ELBO=1432632.56, deltaELBO=26.403 (0.00072655%), Factors=5 Iteration 47: time=0.13, Factors=5 Iteration 48: time=0.15, Factors=5 Iteration 49: time=0.13, Factors=5 Iteration 50: time=0.13, Factors=5 Iteration 51: time=0.16, ELBO=1432666.69, deltaELBO=34.126 (0.00093908%), Factors=5 Iteration 52: time=0.14, Factors=5 Iteration 53: time=0.14, Factors=5 Iteration 54: time=0.13, Factors=5 Iteration 55: time=0.19, Factors=5 Iteration 56: time=0.17, ELBO=1432750.97, deltaELBO=84.276 (0.00231910%), Factors=5 Iteration 57: time=0.16, Factors=5 Iteration 58: time=0.13, Factors=5 Iteration 59: time=0.16, Factors=5 Iteration 60: time=0.32, Factors=5 Iteration 61: time=0.15, ELBO=1432933.12, deltaELBO=182.153 (0.00501245%), Factors=5 Iteration 62: time=0.13, Factors=5 Iteration 63: time=0.34, Factors=5 Iteration 64: time=0.13, Factors=5 Iteration 65: time=0.13, Factors=5 Iteration 66: time=0.14, ELBO=1432958.67, deltaELBO=25.549 (0.00070305%), Factors=5 Iteration 67: time=0.17, Factors=5 Iteration 68: time=0.15, Factors=5 Iteration 69: time=0.16, Factors=5 Iteration 70: time=0.16, Factors=5 Iteration 71: time=0.25, ELBO=1432967.55, deltaELBO=8.879 (0.00024434%), Factors=5 Iteration 72: time=0.14, Factors=5 Iteration 73: time=0.12, Factors=5 Iteration 74: time=0.12, Factors=5 Iteration 75: time=0.12, Factors=5 Iteration 76: time=0.13, ELBO=1432977.68, deltaELBO=10.136 (0.00027892%), Factors=5 Converged! ####################### ## Training finished ## ####################### Saving model in /tmp/RtmpwEhK9g/mofa_20250801-090806.hdf5... ######################################################### ### __ __ ____ ______ ### ### | \/ |/ __ \| ____/\ _ ### ### | \ / | | | | |__ / \ _| |_ ### ### | |\/| | | | | __/ /\ \_ _| ### ### | | | | |__| | | / ____ \|_| ### ### |_| |_|\____/|_|/_/ \_\ ### ### ### ######################################################### use_float32 set to True: replacing float64 arrays by float32 arrays to speed up computations... Successfully loaded view='RNAtest' group='group1' with N=27 samples and D=25014 features... Successfully loaded view='protetest' group='group1' with N=27 samples and D=493 features... Successfully loaded view='metatest' group='group1' with N=27 samples and D=135 features... Model options: - Automatic Relevance Determination prior on the factors: False - Automatic Relevance Determination prior on the weights: True - Spike-and-slab prior on the factors: False - Spike-and-slab prior on the weights: False Likelihoods: - View 0 (RNAtest): gaussian - View 1 (protetest): gaussian - View 2 (metatest): gaussian ###################################### ## Training the model with seed 42 ## ###################################### ELBO before training: -5346346256462.19 Iteration 1: time=0.25, ELBO=-4732266.06, deltaELBO=5346341524196.136 (99.99991149%), Factors=10 Iteration 2: time=0.21, Factors=10 Iteration 3: time=0.19, Factors=10 Iteration 4: time=0.19, Factors=10 Iteration 5: time=0.74, Factors=10 Iteration 6: time=0.27, ELBO=-3514061.76, deltaELBO=1218204.294 (0.00002279%), Factors=10 Iteration 7: time=0.37, Factors=10 Iteration 8: time=0.39, Factors=10 Iteration 9: time=0.21, Factors=10 Iteration 10: time=0.22, Factors=10 Iteration 11: time=0.26, ELBO=-3433701.55, deltaELBO=80360.213 (0.00000150%), Factors=10 Converged! ####################### ## Training finished ## ####################### Saving model in /tmp/RtmpwEhK9g/mofa_20250801-090831.hdf5... ######################################################### ### __ __ ____ ______ ### ### | \/ |/ __ \| ____/\ _ ### ### | \ / | | | | |__ / \ _| |_ ### ### | |\/| | | | | __/ /\ \_ _| ### ### | | | | |__| | | / ____ \|_| ### ### |_| |_|\____/|_|/_/ \_\ ### ### ### ######################################################### use_float32 set to True: replacing float64 arrays by float32 arrays to speed up computations... Successfully loaded view='RNAtest' group='group1' with N=27 samples and D=25014 features... Successfully loaded view='protetest' group='group1' with N=27 samples and D=493 features... Successfully loaded view='metatest' group='group1' with N=27 samples and D=135 features... Model options: - Automatic Relevance Determination prior on the factors: False - Automatic Relevance Determination prior on the weights: True - Spike-and-slab prior on the factors: False - Spike-and-slab prior on the weights: False Likelihoods: - View 0 (RNAtest): gaussian - View 1 (protetest): gaussian - View 2 (metatest): gaussian ###################################### ## Training the model with seed 42 ## ###################################### ELBO before training: -5346346256462.19 Iteration 1: time=0.32, ELBO=-4732266.06, deltaELBO=5346341524196.136 (99.99991149%), Factors=10 Iteration 2: time=0.29, Factors=10 Iteration 3: time=0.23, Factors=10 Iteration 4: time=0.23, Factors=10 Iteration 5: time=0.27, Factors=10 Iteration 6: time=0.29, ELBO=-3514061.76, deltaELBO=1218204.294 (0.00002279%), Factors=10 Iteration 7: time=0.31, Factors=10 Iteration 8: time=0.29, Factors=10 Iteration 9: time=0.28, Factors=10 Iteration 10: time=0.27, Factors=10 Iteration 11: time=0.29, ELBO=-3433701.55, deltaELBO=80360.213 (0.00000150%), Factors=10 Converged! ####################### ## Training finished ## ####################### Saving model in /tmp/RtmpwEhK9g/mofa_20250801-090837.hdf5... [ FAIL 0 | WARN 6 | SKIP 3 | PASS 599 ] ══ Skipped tests (3) ═══════════════════════════════════════════════════════════ • Functional test for Integration skipped (1): 'test-7_MOFA.R:267:5' • Functional test for differential analysis skipped (1): 'test-4_DE.R:190:1' • Functionnal testing for Coseq skipped (1): 'test-5_coseq.R:220:1' [ FAIL 0 | WARN 6 | SKIP 3 | PASS 599 ] > > proc.time() user system elapsed 432.424 22.277 486.278
RFLOMICS.Rcheck/RFLOMICS-Ex.timings
name | user | system | elapsed | |
RflomicsMAE-class | 5.819 | 0.254 | 6.134 | |
createRflomicsMAE | 3.855 | 0.201 | 4.101 | |
ecoseed.df | 0.162 | 0.010 | 0.173 | |
ecoseed.mae | 0.19 | 0.01 | 0.20 | |
generateExpressionContrast | 5.224 | 0.297 | 5.717 | |
generateModelFormulae | 5.142 | 0.189 | 5.515 | |
generateReport | 7.271 | 0.243 | 7.629 | |
getAnalysis | 0.000 | 0.000 | 0.001 | |
prepareForIntegration | 14.352 | 0.369 | 14.884 | |
runAnnotationEnrichment | 6.372 | 0.185 | 6.707 | |
runCoExpression | 20.518 | 3.254 | 21.054 | |
runDataProcessing | 11.728 | 0.733 | 12.577 | |
runDiffAnalysis | 8.037 | 0.478 | 8.791 | |
runOmicsIntegration | 16.385 | 0.345 | 16.971 | |
runRFLOMICS | 0.001 | 0.001 | 0.002 | |