Nadia Bessoltane
| Snapshot Date: 2025-08-28 13:40 -0400 (Thu, 28 Aug 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) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-09-01 11:42 -0400 (Mon, 01 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4606 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4547 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R 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 1762/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RFLOMICS 1.0.1 (landing page) Nadia Bessoltane
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | 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: 2025-08-30 09:18:31 -0400 (Sat, 30 Aug 2025) |
| EndedAt: 2025-08-30 09:30:22 -0400 (Sat, 30 Aug 2025) |
| EllapsedTime: 710.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RFLOMICS.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/RFLOMICS.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* 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 12.589 2.271 13.392
runDataProcessing 7.205 1.009 8.351
prepareForIntegration 7.770 0.291 8.235
runOmicsIntegration 7.055 0.293 7.366
* 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-arm64/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 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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> 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")
2025-08-30 09:26:09.444 R[37933:334830058] XType: Using static font registry.
#########################################################
### __ __ ____ ______ ###
### | \/ |/ __ \| ____/\ _ ###
### | \ / | | | | |__ / \ _| |_ ###
### | |\/| | | | | __/ /\ \_ _| ###
### | | | | |__| | | / ____ \|_| ###
### |_| |_|\____/|_|/_/ \_\ ###
### ###
#########################################################
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: -3634001.90
Iteration 1: time=0.13, ELBO=-651389.24, deltaELBO=2982612.660 (82.07515419%), Factors=5
Iteration 2: time=0.09, Factors=5
Iteration 3: time=0.10, Factors=5
Iteration 4: time=0.11, Factors=5
Iteration 5: time=0.11, Factors=5
Iteration 6: time=0.12, ELBO=1426118.46, deltaELBO=2077507.693 (57.16859133%), Factors=5
Iteration 7: time=0.11, Factors=5
Iteration 8: time=0.10, Factors=5
Iteration 9: time=0.11, Factors=5
Iteration 10: time=0.12, Factors=5
Iteration 11: time=0.11, ELBO=1431479.21, deltaELBO=5360.758 (0.14751666%), Factors=5
Iteration 12: time=0.11, Factors=5
Iteration 13: time=0.10, Factors=5
Iteration 14: time=0.10, Factors=5
Iteration 15: time=0.11, Factors=5
Iteration 16: time=0.12, ELBO=1432131.64, deltaELBO=652.422 (0.01795325%), Factors=5
Iteration 17: time=0.11, Factors=5
Iteration 18: time=0.10, Factors=5
Iteration 19: time=0.12, Factors=5
Iteration 20: time=0.12, Factors=5
Iteration 21: time=0.11, ELBO=1432346.45, deltaELBO=214.809 (0.00591109%), Factors=5
Iteration 22: time=0.11, Factors=5
Iteration 23: time=0.10, Factors=5
Iteration 24: time=0.11, Factors=5
Iteration 25: time=0.10, Factors=5
Iteration 26: time=0.12, ELBO=1432466.99, deltaELBO=120.548 (0.00331723%), Factors=5
Iteration 27: time=0.11, Factors=5
Iteration 28: time=0.11, Factors=5
Iteration 29: time=0.11, Factors=5
Iteration 30: time=0.10, Factors=5
Iteration 31: time=0.11, ELBO=1432532.76, deltaELBO=65.769 (0.00180983%), Factors=5
Iteration 32: time=0.12, Factors=5
Iteration 33: time=0.10, Factors=5
Iteration 34: time=0.10, Factors=5
Iteration 35: time=0.11, Factors=5
Iteration 36: time=0.13, ELBO=1432576.03, deltaELBO=43.269 (0.00119068%), Factors=5
Iteration 37: time=0.10, Factors=5
Iteration 38: time=0.10, Factors=5
Iteration 39: time=0.10, Factors=5
Iteration 40: time=0.13, Factors=5
Iteration 41: time=0.12, ELBO=1432606.21, deltaELBO=30.182 (0.00083053%), Factors=5
Iteration 42: time=0.10, Factors=5
Iteration 43: time=0.12, Factors=5
Iteration 44: time=0.12, Factors=5
Iteration 45: time=0.12, Factors=5
Iteration 46: time=0.12, ELBO=1432632.55, deltaELBO=26.332 (0.00072460%), Factors=5
Iteration 47: time=0.12, Factors=5
Iteration 48: time=0.12, Factors=5
Iteration 49: time=0.13, Factors=5
Iteration 50: time=0.11, Factors=5
Iteration 51: time=0.12, ELBO=1432666.67, deltaELBO=34.121 (0.00093893%), Factors=5
Iteration 52: time=0.12, Factors=5
Iteration 53: time=0.12, Factors=5
Iteration 54: time=0.11, Factors=5
Iteration 55: time=0.12, Factors=5
Iteration 56: time=0.13, ELBO=1432750.99, deltaELBO=84.321 (0.00232034%), Factors=5
Iteration 57: time=0.10, Factors=5
Iteration 58: time=0.11, Factors=5
Iteration 59: time=0.12, Factors=5
Iteration 60: time=0.11, Factors=5
Iteration 61: time=0.11, ELBO=1432933.36, deltaELBO=182.371 (0.00501846%), Factors=5
Iteration 62: time=0.10, Factors=5
Iteration 63: time=0.11, Factors=5
Iteration 64: time=0.13, Factors=5
Iteration 65: time=0.11, Factors=5
Iteration 66: time=0.12, ELBO=1432958.45, deltaELBO=25.087 (0.00069035%), Factors=5
Iteration 67: time=0.11, Factors=5
Iteration 68: time=0.12, Factors=5
Iteration 69: time=0.13, Factors=5
Iteration 70: time=0.11, Factors=5
Iteration 71: time=0.12, ELBO=1432967.58, deltaELBO=9.137 (0.00025143%), Factors=5
Iteration 72: time=0.12, Factors=5
Iteration 73: time=0.11, Factors=5
Iteration 74: time=0.10, Factors=5
Iteration 75: time=0.12, Factors=5
Iteration 76: time=0.11, ELBO=1432977.68, deltaELBO=10.098 (0.00027788%), Factors=5
Converged!
#######################
## Training finished ##
#######################
Saving model in /tmp/RtmpHhd7xO/mofa_20250830-092942.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: -5346346256462.20
Iteration 1: time=0.21, ELBO=-4732268.68, deltaELBO=5346341524193.521 (99.99991149%), Factors=10
Iteration 2: time=0.18, Factors=10
Iteration 3: time=0.17, Factors=10
Iteration 4: time=0.17, Factors=10
Iteration 5: time=0.16, Factors=10
Iteration 6: time=0.17, ELBO=-3514065.02, deltaELBO=1218203.662 (0.00002279%), Factors=10
Iteration 7: time=0.16, Factors=10
Iteration 8: time=0.17, Factors=10
Iteration 9: time=0.17, Factors=10
Iteration 10: time=0.18, Factors=10
Iteration 11: time=0.19, ELBO=-3433704.38, deltaELBO=80360.633 (0.00000150%), Factors=10
Converged!
#######################
## Training finished ##
#######################
Saving model in /tmp/RtmpHhd7xO/mofa_20250830-093001.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: -5346346256462.20
Iteration 1: time=0.21, ELBO=-4732268.68, deltaELBO=5346341524193.521 (99.99991149%), Factors=10
Iteration 2: time=0.22, Factors=10
Iteration 3: time=0.16, Factors=10
Iteration 4: time=0.18, Factors=10
Iteration 5: time=0.18, Factors=10
Iteration 6: time=0.18, ELBO=-3514065.02, deltaELBO=1218203.662 (0.00002279%), Factors=10
Iteration 7: time=0.16, Factors=10
Iteration 8: time=0.16, Factors=10
Iteration 9: time=0.17, Factors=10
Iteration 10: time=0.17, Factors=10
Iteration 11: time=0.19, ELBO=-3433704.38, deltaELBO=80360.633 (0.00000150%), Factors=10
Converged!
#######################
## Training finished ##
#######################
Saving model in /tmp/RtmpHhd7xO/mofa_20250830-093005.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
260.617 18.267 274.191
RFLOMICS.Rcheck/RFLOMICS-Ex.timings
| name | user | system | elapsed | |
| RflomicsMAE-class | 4.577 | 0.140 | 4.813 | |
| createRflomicsMAE | 2.731 | 0.123 | 2.930 | |
| ecoseed.df | 0.176 | 0.008 | 0.186 | |
| ecoseed.mae | 0.194 | 0.007 | 0.202 | |
| generateExpressionContrast | 2.723 | 0.166 | 2.965 | |
| generateModelFormulae | 2.762 | 0.148 | 2.962 | |
| generateReport | 3.681 | 0.172 | 3.899 | |
| getAnalysis | 0 | 0 | 0 | |
| prepareForIntegration | 7.770 | 0.291 | 8.235 | |
| runAnnotationEnrichment | 3.259 | 0.166 | 3.461 | |
| runCoExpression | 12.589 | 2.271 | 13.392 | |
| runDataProcessing | 7.205 | 1.009 | 8.351 | |
| runDiffAnalysis | 3.301 | 0.155 | 3.480 | |
| runOmicsIntegration | 7.055 | 0.293 | 7.366 | |
| runRFLOMICS | 0 | 0 | 0 | |