Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/RFLOMICS
Last Changed Rev:  / Revision: 
Last Changed Date: 

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
nebbiolo1 Linux (Ubuntu 24.04.1 LTS)/x86_64   OK     WARNINGS     skipped     OK  

nebbiolo1 Summary

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Package: RFLOMICS
Version: 0.99.4
RVersion: 4.5
BiocVersion: 3.21
BuildCommand: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RFLOMICS
BuildTime: 2 minutes 20.55 seconds
CheckCommand: BiocCheckGitClone('RFLOMICS') && /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3477/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3477/1d91ff8f330e6e507f0713cece76e887bcf32a65/RFLOMICS.install-out.txt RFLOMICS_0.99.4.tar.gz && BiocCheck('RFLOMICS_0.99.4.tar.gz', `new-package`=TRUE)
CheckTime: 10 minutes 57.73 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 5245.89 KiB
BuildID:: RFLOMICS_20250131091441
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: RFLOMICS. Starting Build package. Starting Check package.
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.WARNING: check time exceeded 10 min.

nebbiolo1 BUILD SRC output

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===============================

 R CMD BUILD

===============================

* checking for file ‘RFLOMICS/DESCRIPTION’ ... OK
* preparing ‘RFLOMICS’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘RFLOMICS_0.99.4.tar.gz’


nebbiolo1 CHECK output

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===============================

 BiocCheckGitClone('RFLOMICS')

===============================

→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3477/1d91ff8f330e6e507f0713cece76e887bcf32a65/RFLOMICS
→ BiocVersion: 3.21
→ Package: RFLOMICS
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3477/1d91ff8f330e6e507f0713cece76e887bcf32a65/RFLOMICS.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3477/1d91ff8f330e6e507f0713cece76e887bcf32a65/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/3477/1d91ff8f330e6e507f0713cece76e887bcf32a65/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 ‘0.99.4’
* 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 ... [12s/12s] 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 ... [50s/50s] 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’ [345s/352s]
 [345s/352s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
      "protetest", "metatest"), omicsTypes = c("RNAseq", "proteomics", 
      "metabolomics"), ExpDesign = ecoseed.df$design, factorInfo = factorInfo)`: The omicsData must be named.
  Backtrace:
      ▆
   1. └─RFLOMICS::createRflomicsMAE(...) at test-1_CreateRflomicsMAE.R:24:1
  ── Failure ('test-7_MOFA.R:117:5'): RunOmics is running ────────────────────────
  Expected `runOmicsIntegration(MAE, preparedObject = mofaObj, method = "MOFA")` to run without any errors.
  i Actually got a <simpleError> with text:
    mofapy2_0.7.0 is not detected in the specified python binary, see reticulate::py_config(). Consider setting use_basilisk = TRUE to create a python environment with basilisk (https://bioconductor.org/packages/release/bioc/html/basilisk.html)
  ── Error ('test-7_MOFA.R:122:1'): (code run outside of `test_that()`) ──────────
  Error in `run_mofa(MOFAObject.untrained, use_basilisk = FALSE, outfile = outfile, 
      save_data = TRUE)`: mofapy2_0.7.0 is not detected in the specified python binary, see reticulate::py_config(). Consider setting use_basilisk = TRUE to create a python environment with basilisk (https://bioconductor.org/packages/release/bioc/html/basilisk.html)
  Backtrace:
      ▆
   1. ├─RFLOMICS::runOmicsIntegration(...) at test-7_MOFA.R:122:1
   2. └─RFLOMICS::runOmicsIntegration(...)
   3.   └─RFLOMICS:::.runMOFAAnalysis(...)
   4.     └─MOFA2::run_mofa(...)
  
  [ FAIL 7 | WARN 4 | SKIP 2 | PASS 495 ]
  Error: Test failures
  Execution halted
* 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: 2 ERRORs, 2 NOTEs
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/3477/1d91ff8f330e6e507f0713cece76e887bcf32a65/RFLOMICS.Rcheck/00check.log’
for details.

 WARNING: R CMD check exceeded 10 min requirement






===============================

 BiocCheck('RFLOMICS_0.99.4.tar.gz')

===============================

── Installing RFLOMICS ─────────────────────────────────────────────────────────
✔ Package installed successfully
── RFLOMICS session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp0mUTmo/file2abe0b1212e5d9/RFLOMICS
→ BiocVersion: 3.21
→ Package: RFLOMICS
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3477/1d91ff8f330e6e507f0713cece76e887bcf32a65/RFLOMICS.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /tmp/Rtmp0mUTmo/file2abe0b1212e5d9/RFLOMICS
→ installDir: /tmp/Rtmp0mUTmo/file2abe0b713235af
→ 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)
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; 669 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#L300 #' A DataFrame or data.frame of assay n ...
• R/utils_01_load_data.R#L301 #' and colname samples ...
i NOTE: Consider multiples of 4 spaces for line indents; 6172 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 | ⚠ 0 WARNINGS | i 17 NOTES
i See the RFLOMICS.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.

nebbiolo1 BUILD BIN output

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