############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:flowDensity.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings flowDensity_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/flowDensity.Rcheck' * using R version 4.2.1 (2022-06-23 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'flowDensity/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'flowDensity' 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 ... OK * checking for portable file names ... OK * checking whether package 'flowDensity' can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import 'flowCore::plot' by 'graphics::plot' when loading 'flowDensity' See 'F:/biocbuild/bbs-3.15-bioc/meat/flowDensity.Rcheck/00install.out' for details. * 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 ... OK * checking Rd files ... OK * checking Rd metadata ... WARNING Rd files with duplicated alias 'flowDensity': 'flowDensity-methods.Rd' 'flowDensity.Rd' * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic 'flowDensity' and siglist 'CellPopulation,ANY,logical,missing' generic 'flowDensity' and siglist 'GatingHierarchy,ANY,logical,ANY' generic 'flowDensity' and siglist 'flowFrame,ANY,logical,missing' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Objects in \usage without \alias in documentation object 'flowDensity-methods': '\S4method{flowDensity}{CellPopulation,ANY,logical,missing}' '\S4method{flowDensity}{flowFrame,ANY,logical,missing}' '\S4method{flowDensity}{GatingHierarchy,ANY,logical,ANY}' Undocumented arguments in documentation object 'plotDens' 'dens.col' 'cex' 'dens.type' Documented arguments not in \usage in documentation object 'plotDens': 'density.type' 'density.col' 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * 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: 4 WARNINGs See 'F:/biocbuild/bbs-3.15-bioc/meat/flowDensity.Rcheck/00check.log' for details.