############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:switchBox.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings switchBox_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/switchBox.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'switchBox/DESCRIPTION' ... OK * this is package 'switchBox' version '1.28.0' * 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 'switchBox' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/RtmpYDH1IF/R.INSTALLed42bca37b6/switchBox/man/SWAP.PlotKTSP.TrainTestROC.Rd:35: missing link 'SWAP.GetkTSPTrainTestResults' See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/switchBox.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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: 'KTSP.CalculateSignedScore' 'KTSP.tiedRank' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE plotGenePairBoxplot: no visible global function definition for 'boxplot' plotGenePairBoxplot: no visible global function definition for 'stripchart' plotGenePairBoxplot: no visible global function definition for 'legend' plotGenePairBoxplot: no visible global function definition for 'grid' plotGenePairClassesBoxplot: no visible global function definition for 'boxplot' plotGenePairClassesBoxplot: no visible global function definition for 'axis' plotGenePairClassesBoxplot: no visible global function definition for 'legend' plotGenePairClassesBoxplot: no visible global function definition for 'abline' plotGenePairClassesBoxplot: no visible global function definition for 'grid' plotGenePairScatter: no visible global function definition for 'abline' plotGenePairScatter: no visible global function definition for 'grid' plotGenePairScatter: no visible global function definition for 'legend' plotGenes: no visible global function definition for 'lines' plotGenes: no visible global function definition for 'grid' plotGenes: no visible global function definition for 'abline' plotGenes: no visible global function definition for 'legend' plotkTSPTrainTestROC: no visible global function definition for 'lines' plotkTSPTrainTestROC: no visible global function definition for 'legend' plotkTSPTrainTestROC: no visible global function definition for 'grid' plotkTSPVotes: no visible global function definition for 'plot.new' Undefined global functions or variables: abline axis boxplot grid legend lines plot.new stripchart Consider adding importFrom("graphics", "abline", "axis", "boxplot", "grid", "legend", "lines", "plot.new", "stripchart") to your NAMESPACE file. * checking Rd files ... NOTE prepare_Rd: SWAP.Kby.Measurement.Rd:70-72: Dropping empty section \examples prepare_Rd: SWAP.Kby.Ttest.Rd:64-66: Dropping empty section \examples prepare_Rd: SWAP.PlotKTSP.Votes.Rd:54-56: Dropping empty section \examples * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Package unavailable to check Rd xrefs: 'mammaPrintData' Missing link or links in documentation object 'SWAP.PlotKTSP.TrainTestROC.Rd': 'SWAP.GetkTSPTrainTestResults' See section 'Cross-references' in the 'Writing R Extensions' manual. * checking for missing documentation entries ... WARNING Undocumented code objects: 'SWAP.GetKFoldIndices' 'SWAP.MakeTrainTestData' 'SWAP.ScoreMatrixToVector' 'SWAP.ScoreVectorToMatrix' All user-level objects in a package 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 Assignments in \usage in documentation object 'SWAP.Kby.Measurement': k_opts = list(disjoint = TRUE, measurement = "auc") Undocumented arguments in documentation object 'SWAP.PlotKTSP.GenePairScatter' '...' Undocumented arguments in documentation object 'SWAP.PlotKTSP.Genes' 'colors' 'legends' '...' Undocumented arguments in documentation object 'SWAP.PlotKTSP.TrainTestROC' '...' Undocumented arguments in documentation object 'SWAP.PlotKTSP.Votes' '...' Bad \usage lines found in documentation object 'SWAP.Kby.Measurement': SWAP.Kby.Measurement(inputMat, phenoGroup, scoreTable, classes, krange, 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/switchBox/libs/i386/switchBox.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/switchBox/libs/x64/switchBox.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... 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, 4 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/switchBox.Rcheck/00check.log' for details.