############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MultiBaC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MultiBaC_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/MultiBaC.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MultiBaC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MultiBaC’ version ‘1.4.0’ * package encoding: UTF-8 * 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 ‘MultiBaC’ 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 R 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE Q2_plot: no visible global function definition for ‘rgb’ explained_varPlot: no visible global function definition for ‘rgb’ Undefined global functions or variables: rgb Consider adding importFrom("grDevices", "rgb") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object 'ARSyNbac': ARSyNbac Code: function(mbac, batchEstimation = TRUE, filterNoise = TRUE, Interaction = FALSE, Variability = 0.9, beta = 2, modelName = "Model 1", showplot = TRUE) Docs: function(mbac, batchEstimation = TRUE, Interaction = FALSE, Variability = 0.9, beta = 2, modelName = "Model 1", showplot = TRUE) Argument names in code not in docs: filterNoise Mismatches in argument names (first 3): Position: 3 Code: filterNoise Docs: Interaction Position: 4 Code: Interaction Docs: Variability Position: 5 Code: Variability Docs: beta * 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 ARSyNbac 12.881 0.429 13.324 Q2_plot 11.715 0.044 11.879 MultiBaC 11.538 0.055 11.601 plot_pca 11.495 0.025 11.572 batchCorrection 11.475 0.037 11.538 explained_varPlot 11.466 0.032 11.509 inner_relPlot 11.371 0.020 11.400 plot 11.328 0.032 11.377 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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-3.14-bioc/meat/MultiBaC.Rcheck/00check.log’ for details.