############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowClean.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowClean_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/flowClean.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘flowClean/DESCRIPTION’ ... OK * this is package ‘flowClean’ version ‘1.30.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘flowClean’ 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 clean: no visible global function definition for ‘runif’ clean: no visible global function definition for ‘png’ clean: no visible global function definition for ‘dev.off’ diagnosticPlot: no visible global function definition for ‘points’ diagnosticPlot: no visible global function definition for ‘abline’ makeFCS: no visible global function definition for ‘new’ make_pops : : no visible global function definition for ‘quantile’ make_pops : : no visible global function definition for ‘median’ Undefined global functions or variables: abline dev.off median new png points quantile runif Consider adding importFrom("grDevices", "dev.off", "png") importFrom("graphics", "abline", "points") importFrom("methods", "new") importFrom("stats", "median", "quantile", "runif") 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 ... WARNING Codoc mismatches from documentation object 'clean': clean Code: function(fF, vectMarkers, filePrefixWithDir, ext, binSize = 0.01, nCellCutoff = 500, announce = TRUE, cutoff = "median", diagnostic = FALSE, fcMax = 1.3, returnVector = FALSE, nstable = 5) Docs: function(fF, vectMarkers, filePrefixWithDir, ext, binSize = 0.01, nCellCutoff = 500, announce = TRUE, cutoff = "median", diagnostic = FALSE, fcMax = 1.3) Argument names in code not in docs: returnVector nstable * checking Rd \usage sections ... WARNING Duplicated \argument entries in documentation object 'clean': ‘announce’ Documented arguments not in \usage in documentation object 'clean': ‘returnVector’ ‘nstable’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... WARNING Found the following significant warnings: Warning: '.local' is deprecated. Warning: '.local' is deprecated. Warning: '.local' is deprecated. Warning: '.local' is deprecated. Warning: '.local' is deprecated. Warning: 'description<-' is deprecated. Warning: '.local' is deprecated. Warning: '.local' is deprecated. Warning: 'description<-' is deprecated. Warning: '.local' is deprecated. Warning: '.local' is deprecated. Warning: 'description<-' is deprecated. Warning: '.local' is deprecated. Warning: 'description<-' is deprecated. Warning: '.local' is deprecated. Warning: 'description<-' is deprecated. Warning: '.local' is deprecated. Warning: 'description<-' is deprecated. Warning: '.local' is deprecated. Warning: 'description<-' is deprecated. Warning: '.local' is deprecated. Warning: 'description<-' is deprecated. Warning: '.local' is deprecated. Warning: 'description<-' is deprecated. Warning: '.local' is deprecated. Warning: 'description<-' is deprecated. Warning: '.local' is deprecated. Warning: '.local' is deprecated. Warning: 'description<-' is deprecated. Warning: '.local' is deprecated. Warning: 'description<-' is deprecated. Warning: '.local' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. Examples with CPU (user + system) or elapsed time > 5s user system elapsed clean 17.077 1.428 18.517 * 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: 3 WARNINGs, 2 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/flowClean.Rcheck/00check.log’ for details.