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This page was generated on 2025-08-04 11:44 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1762/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RFLOMICS 1.0.1  (landing page)
Nadia Bessoltane
Snapshot Date: 2025-07-31 13:40 -0400 (Thu, 31 Jul 2025)
git_url: https://git.bioconductor.org/packages/RFLOMICS
git_branch: RELEASE_3_21
git_last_commit: bf9f004
git_last_commit_date: 2025-05-08 12:29:53 -0400 (Thu, 08 May 2025)
nebbiolo1Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for RFLOMICS on merida1

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.

raw results


Summary

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

Command output

##############################################################################
##############################################################################
###
### 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.


Installation output

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)

Tests output

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.

        #########################################################
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        ###          | |\/| | |  | |  __/ /\ \_   _|          ###
        ###          | |  | | |__| | | / ____ \|_|            ###
        ###          |_|  |_|\____/|_|/_/    \_\              ###
        ###                                                   ### 
        ######################################################### 
       
 
        
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 

Example timings

RFLOMICS.Rcheck/RFLOMICS-Ex.timings

nameusersystemelapsed
RflomicsMAE-class5.8190.2546.134
createRflomicsMAE3.8550.2014.101
ecoseed.df0.1620.0100.173
ecoseed.mae0.190.010.20
generateExpressionContrast5.2240.2975.717
generateModelFormulae5.1420.1895.515
generateReport7.2710.2437.629
getAnalysis0.0000.0000.001
prepareForIntegration14.352 0.36914.884
runAnnotationEnrichment6.3720.1856.707
runCoExpression20.518 3.25421.054
runDataProcessing11.728 0.73312.577
runDiffAnalysis8.0370.4788.791
runOmicsIntegration16.385 0.34516.971
runRFLOMICS0.0010.0010.002