Nadia Bessoltane
| Snapshot Date: 2025-09-03 13:45 -0400 (Wed, 03 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/RFLOMICS |
| git_branch: devel |
| git_last_commit: bbfebb7 |
| git_last_commit_date: 2025-04-15 13:50:31 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-04 12:08 -0400 (Thu, 04 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4822 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4617 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4564 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
| 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 1746/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RFLOMICS 1.1.0 (landing page) Nadia Bessoltane
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: RFLOMICS |
| Version: 1.1.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:RFLOMICS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RFLOMICS_1.1.0.tar.gz |
| StartedAt: 2025-09-02 10:23:08 -0000 (Tue, 02 Sep 2025) |
| EndedAt: 2025-09-02 10:37:41 -0000 (Tue, 02 Sep 2025) |
| EllapsedTime: 872.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RFLOMICS.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD check --install=check:RFLOMICS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RFLOMICS_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/RFLOMICS.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RFLOMICS/DESCRIPTION’ ... OK
* this is package ‘RFLOMICS’ version ‘1.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Depends: includes the non-default packages:
'SummarizedExperiment', 'MultiAssayExperiment', 'shinyBS', 'dplyr',
'ggplot2', 'htmltools', 'knitr', 'coseq'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Imports includes 33 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RFLOMICS’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘org.At.tair.db’ ‘reticulate’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.applyFeatureFiltering: no visible global function definition for
‘assay’
.applyFeatureFiltering: no visible global function definition for
‘assay<-’
.applyLog: no visible global function definition for ‘assay<-’
.applyLog: no visible global function definition for ‘assay’
.applyNormalization: no visible global function definition for ‘assay’
.applyNormalization: no visible global function definition for
‘assay<-’
.applyTransformation: no visible global function definition for ‘assay’
.applyTransformation: no visible global function definition for
‘assay<-’
.coseq.results.process: no visible global function definition for
‘summarise’
.coseq.results.process: no visible global function definition for
‘group_by’
.coseq.results.process: no visible binding for global variable ‘status’
.coseq.results.process: no visible binding for global variable ‘errors’
.coseq.results.process: no visible global function definition for ‘n’
.coseq.results.process: no visible global function definition for
‘filter’
.coseq.results.process: no visible binding for global variable ‘n’
.coseq.results.process: no visible global function definition for
‘mutate’
.coseq.results.process: no visible global function definition for
‘summarize’
.countSamplesPerCondition: no visible global function definition for
‘group_by_at’
.countSamplesPerCondition: no visible global function definition for
‘full_join’
.countSamplesPerCondition: no visible global function definition for
‘mutate_at’
.countSamplesPerCondition : <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 12.688 2.583 18.416
runOmicsIntegration 9.724 0.043 11.608
prepareForIntegration 8.556 0.307 9.724
runDataProcessing 7.336 0.369 9.479
runDiffAnalysis 4.927 0.287 6.909
generateReport 4.548 0.170 6.295
runAnnotationEnrichment 4.039 0.109 5.515
RflomicsMAE-class 3.676 0.178 5.539
generateExpressionContrast 3.269 0.187 5.369
* 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
‘/home/biocbuild/bbs-3.22-bioc/meat/RFLOMICS.Rcheck/00check.log’
for details.
RFLOMICS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL RFLOMICS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘RFLOMICS’ ... ** this is package ‘RFLOMICS’ version ‘1.1.0’ ** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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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: Seqinfo
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:Seqinfo':
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")
[ FAIL 0 | WARN 2 | SKIP 3 | PASS 575 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• 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'
• Tests for MOFA integration skipped. (1): 'test-7_MOFA.R:132:1'
[ FAIL 0 | WARN 2 | SKIP 3 | PASS 575 ]
>
> proc.time()
user system elapsed
259.582 8.687 331.030
RFLOMICS.Rcheck/RFLOMICS-Ex.timings
| name | user | system | elapsed | |
| RflomicsMAE-class | 3.676 | 0.178 | 5.539 | |
| createRflomicsMAE | 2.543 | 0.182 | 2.876 | |
| ecoseed.df | 0.105 | 0.000 | 0.162 | |
| ecoseed.mae | 0.128 | 0.004 | 0.265 | |
| generateExpressionContrast | 3.269 | 0.187 | 5.369 | |
| generateModelFormulae | 3.414 | 0.186 | 3.758 | |
| generateReport | 4.548 | 0.170 | 6.295 | |
| getAnalysis | 0 | 0 | 0 | |
| prepareForIntegration | 8.556 | 0.307 | 9.724 | |
| runAnnotationEnrichment | 4.039 | 0.109 | 5.515 | |
| runCoExpression | 12.688 | 2.583 | 18.416 | |
| runDataProcessing | 7.336 | 0.369 | 9.479 | |
| runDiffAnalysis | 4.927 | 0.287 | 6.909 | |
| runOmicsIntegration | 9.724 | 0.043 | 11.608 | |
| runRFLOMICS | 0 | 0 | 0 | |