===============================
BiocCheckGitClone('RFLOMICS')
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→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3477/6c78cf71dc18d5c5b9dd52cd03eb3296758ecd11/RFLOMICS
→ BiocVersion: 3.21
→ Package: RFLOMICS
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3477/6c78cf71dc18d5c5b9dd52cd03eb3296758ecd11/RFLOMICS.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3477/6c78cf71dc18d5c5b9dd52cd03eb3296758ecd11/RFLOMICS
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
── BiocCheck v1.43.2 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3477/6c78cf71dc18d5c5b9dd52cd03eb3296758ecd11/RFLOMICS.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RFLOMICS/DESCRIPTION’ ... OK
* this is package ‘RFLOMICS’ version ‘0.99.5’
* 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 for future file timestamps ... 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 ... [12s/12s] OK
* checking whether the package can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the namespace can be unloaded cleanly ... [12s/12s] OK
* checking loading without being on the library search path ... [12s/12s] OK
* checking use of S3 registration ... 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 ... [49s/49s] 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
‘count’
.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’
.edgeRAnaDiff: no visible global function definition for ‘rename’
.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’
.limmaAnaDiff: no visible global function definition for ‘rename’
.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 global function definition for ‘rename’
.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 global
function definition for ‘rename’
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 global function
definition for ‘rename’
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 ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* 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 ... [6s/6s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [27s/27s] ERROR
Running examples in ‘RFLOMICS-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: generateReport
> ### Title: Generate RFLOMICS html report or archive
> ### Aliases: generateReport generateReport,RflomicsMAE-method
>
> ### ** Examples
>
> library(RFLOMICS)
> # load ecoseed data
> data(ecoseed.mae)
>
> factorInfo <- data.frame(
+ "factorName" = c("Repeat", "temperature", "imbibition"),
+ "factorType" = c("batch", "Bio", "Bio")
+ )
>
> # create rflomicsMAE object with ecoseed data
> MAE <- RFLOMICS::createRflomicsMAE(
+ projectName = "Tests",
+ omicsData = ecoseed.mae,
+ omicsTypes = c("RNAseq","proteomics","metabolomics"),
+ factorInfo = factorInfo)
>
> formulae <- generateModelFormulae(MAE)
> MAE <- setModelFormula(MAE, modelFormula = formulae[[1]])
>
> selectedContrasts <-
+ generateExpressionContrast(MAE, contrastType="simple")
>
> MAE <- setSelectedContrasts(MAE, contrastList = selectedContrasts)
>
> ## data processing
> MAE <- runDataProcessing(
+ object = MAE,
+ SE.name = "protetest",
+ samples=NULL,
+ normMethod="none",
+ transformMethod="none")
[RFLOMICS] # => select samples... protetest
[RFLOMICS] # The experimental design is complete and balanced.
[RFLOMICS] # => feature filtering... protetest
[RFLOMICS] # Data Imputation...
[RFLOMICS] # method: MVI
[RFLOMICS] # => Data transformation... protetest
[RFLOMICS] # method: already transformed (unknown)
[RFLOMICS] # => Data normalization... protetest
[RFLOMICS] # method: already normalized (unknown)
[RFLOMICS] # => Computing PCA... protetest
>
> ## diff analysis
> MAE <- runDiffAnalysis(
+ object = MAE,
+ SE.name = "protetest",
+ contrastList =
+ selectedContrasts,
+ p.adj.method="BH",
+ method = "limmalmFit",
+ p.adj.cutoff = 0.05,
+ logFC.cutoff = 0)
Error in `rownames<-`(`*tmp*`, value = colnamesGLMdesign) :
attempt to set 'rownames' on an object with no dimensions
Calls: runDiffAnalysis ... generateContrastMatrix -> .local -> .getContrastMatrixF -> rownames<-
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [350s/361s]
[351s/361s] 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 ... [4s/4s] OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3477/6c78cf71dc18d5c5b9dd52cd03eb3296758ecd11/RFLOMICS.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('RFLOMICS_0.99.5.tar.gz')
===============================
── Installing RFLOMICS ─────────────────────────────────────────────────────────
✔ Package installed successfully
── RFLOMICS session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpMbNpBI/file2468ff79d709ea/RFLOMICS
→ BiocVersion: 3.21
→ Package: RFLOMICS
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3477/6c78cf71dc18d5c5b9dd52cd03eb3296758ecd11/RFLOMICS.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /tmp/RtmpMbNpBI/file2468ff79d709ea/RFLOMICS
→ installDir: /tmp/RtmpMbNpBI/file2468ff4886e56
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on RFLOMICS ───────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
i NOTE: Update R version dependency from 4.4.0 to 4.5.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
i NOTE: Consider adding these automatically suggested biocViews: Sequencing,
Coverage, ExperimentalDesign, GeneExpression, RNASeq, ImmunoOncology
i Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (29%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/RFLOMICS-input-data.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of RFLOMICS...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/module_04_diff_analysis.R (line 590, column 22)
• ...
• R/utils_02_set_stat_model.R (line 599, column 25)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• server.R (line 159, column 38)
• ...
• utils_03_data_explor.R (line 421, column 28)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• cat() in R/module_06_annot_enrichment.R (line 1664, column 18)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/RFLOMICS-Methods_03_data_explor.R (line 1028, column 22)
• ...
• R/utils_04_diff_analysis.R (line 140, column 19)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/RFLOMICS-Methods_03_data_explor.R (line 668, column 29)
• R/RFLOMICS-Methods_03_data_explor.R (line 803, column 29)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/utils_00_common.R (line 226, column 13)
• R/utils_00_common.R (line 229, column 13)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
Found in files:
• utils_01_load_data.R (line 96, column 34)
i NOTE: Avoid system() ; use system2()
Found in files:
• system() in R/RFLOMICS-Methods_00_Common.R (line 211, column 7)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid '<<-' if possible (found 3 times)
• <<- in R/utils_00_common.R (line 88, column 23)
• <<- in R/utils_00_common.R (line 91, column 23)
• <<- in R/utils_07_integration.R (line 303, column 52)
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
• suppressWarnings() in R/RFLOMICS-Methods_06_annot_enrichment.R (line 805,
column 9)
• suppressWarnings() in R/RFLOMICS-Methods_06_annot_enrichment.R (line 1200,
column 46)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 87
functions greater than 50 lines.
The longest 5 functions are:
• QCNormalizationTab() (R/module_03_data_explor.R): 611 lines
• ...
• .modLoadData() (R/module_01_load_data.R): 399 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• getAnalysis.Rd
• rflomicsMAE2MAE.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 670 lines (3%) are > 80 characters long.
First few lines:
• R/coverPage.R#L12 h1(tags$span("An int ...
• ...
• vignettes/RFLOMICS.Rmd#L495 All methods from the MultiAssayExperimen ...
i NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs.
First few lines:
• R/utils_01_load_data.R#L302 #' A DataFrame or data.frame of assay n ...
• R/utils_01_load_data.R#L303 #' and colname samples ...
i NOTE: Consider multiples of 4 spaces for line indents; 6176 lines (30%) are
not.
First few lines:
• R/coverPage.R#L8 fluidPage( ...
• ...
• vignettes/RFLOMICS.Rmd#L483 factorInfo = factorInfo ...
i See https://contributions.bioconductor.org/r-code.html
i See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.43.2 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 17 NOTES
i See the RFLOMICS.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.