############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:switchBox.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings switchBox_1.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/switchBox.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘switchBox/DESCRIPTION’ ... OK * this is package ‘switchBox’ version ‘1.42.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘switchBox’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ * used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ * 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 loading without being on the library search path ... 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 checkRd: (-1) matTesting.Rd:24: Lost braces 24 | Group information (emph{``bad'' versus ``good'' }prognosis) | ^ checkRd: (-1) matTraining.Rd:24: Lost braces 24 | Group information (emph{``bad'' versus ``good'' }prognosis) | ^ checkRd: (-1) switchBox-package.Rd:27-28: Lost braces 27 | {B) Compute the scores for all available feature pairs | ^ checkRd: (-1) switchBox-package.Rd:30-31: Lost braces 30 | {C) Compute the scores for selected feature pairs | ^ checkRd: (-1) switchBox-package.Rd:33: Lost braces; missing escapes or markup? 33 | {D) Identify the number of $K$ TSP to be used in the final classifier using the analysis of variance;} | ^ checkRd: (-1) switchBox-package.Rd:35-36: Lost braces 35 | {E) Compute individual TSP votes for one class or the other | ^ checkRd: (-1) switchBox-package.Rd:38-39: Lost braces 38 | {F) Classify new samples based on the top KTSP | ^ * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link or links in Rd file '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 Rd file 'SWAP.Kby.Measurement.Rd': k_opts = list(disjoint = TRUE, measurement = "auc") Undocumented arguments in Rd file 'SWAP.PlotKTSP.GenePairScatter.Rd' ‘...’ Undocumented arguments in Rd file 'SWAP.PlotKTSP.Genes.Rd' ‘colors’ ‘legends’ ‘...’ Undocumented arguments in Rd file 'SWAP.PlotKTSP.TrainTestROC.Rd' ‘...’ Undocumented arguments in Rd file 'SWAP.PlotKTSP.Votes.Rd' ‘...’ Bad \usage lines found in Rd file 'SWAP.Kby.Measurement.Rd': 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 is not available * 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 ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 WARNINGs, 4 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/switchBox.Rcheck/00check.log’ for details.