############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biobroom.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biobroom_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/biobroom.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘biobroom/DESCRIPTION’ ... OK * this is package ‘biobroom’ version ‘1.38.0’ * checking package namespace information ... OK * checking package dependencies ... OK * 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 ‘biobroom’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... WARNING 'library' or 'require' call to ‘DESeq2’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Missing or unexported object: ‘dplyr::tbl_dt’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE finish: no visible global function definition for ‘tbl_dt’ glance.DGEExact: no visible global function definition for ‘p.adjust’ glance.GRanges: no visible binding for global variable ‘gr’ glance.GRangesList: no visible binding for global variable ‘gr’ makeExampleDataSet: no visible global function definition for ‘estimateSizeFactors’ makeExampleDataSet: no visible global function definition for ‘counts’ makeExampleDataSet: no visible global function definition for ‘colData’ makeExampleDataSet: no visible global function definition for ‘seqnames’ makeExampleDataSet: no visible global function definition for ‘rowRanges’ makeExampleDataSet: no visible global function definition for ‘start’ makeExampleDataSet: no visible global function definition for ‘end’ makeExampleDataSet: no visible global function definition for ‘DGEList’ makeExampleDataSet: no visible global function definition for ‘calcNormFactors’ makeExampleDataSet: no visible global function definition for ‘model.matrix’ makeExampleDataSet: no visible global function definition for ‘design’ makeExampleDataSet: no visible global function definition for ‘voomWithQualityWeights’ makeExampleDataSet: no visible global function definition for ‘voom’ makeExampleDataSet: no visible global function definition for ‘pData<-’ makeExampleDataSet: no visible global function definition for ‘fData<-’ makeExampleDataSet: no visible global function definition for ‘is’ tidy.DESeqDataSet: no visible binding for global variable ‘term’ tidy.DESeqDataSet: no visible binding for global variable ‘.’ tidy.DESeqDataSet: no visible global function definition for ‘counts’ tidy.DESeqDataSet: no visible binding for global variable ‘gene’ tidy.DGEList: no visible binding for global variable ‘gene’ tidy.EList: no visible global function definition for ‘setNames’ tidy.ExpressionSet: no visible binding for global variable ‘value’ tidy.ExpressionSet: no visible binding for global variable ‘gene’ tidy.ExpressionSet: no visible global function definition for ‘pData’ tidy.MArrayLM: no visible binding for global variable ‘term’ tidy.MArrayLM: no visible binding for global variable ‘estimate’ tidy.MArrayLM: no visible binding for global variable ‘gene’ tidy.MSnSet: no visible binding for global variable ‘sample.id’ tidy.MSnSet: no visible binding for global variable ‘value’ tidy.MSnSet: no visible binding for global variable ‘protein’ tidy.MSnSet: no visible global function definition for ‘pData’ tidy.RangedSummarizedExperiment: no visible binding for global variable ‘value’ tidy.RangedSummarizedExperiment: no visible binding for global variable ‘gene’ tidy.RangedSummarizedExperiment: no visible global function definition for ‘colData’ tidy.deSet: no visible global function definition for ‘exprs<-’ tidy.deSet: no visible binding for global variable ‘value’ tidy.deSet: no visible binding for global variable ‘gene’ tidy.deSet: no visible global function definition for ‘pData’ tidy.qvalue: no visible binding for global variable ‘smoothed’ tidy.qvalue: no visible binding for global variable ‘pi0’ tidy.qvalue: no visible binding for global variable ‘lambda’ tidy_matrix: no visible binding for global variable ‘value’ tidy_matrix: no visible binding for global variable ‘gene’ Undefined global functions or variables: . DGEList calcNormFactors colData counts design end estimate estimateSizeFactors exprs<- fData<- gene gr is lambda model.matrix p.adjust pData pData<- pi0 protein rowRanges sample.id seqnames setNames smoothed start tbl_dt term value voom voomWithQualityWeights Consider adding importFrom("methods", "is") importFrom("stats", "end", "model.matrix", "p.adjust", "setNames", "start") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... OK * checking Rd metadata ... 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 ... OK * checking LazyData ... 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 DESeq2_tidiers 10.496 0.418 10.93 * 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: 1 WARNING, 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/biobroom.Rcheck/00check.log’ for details.