############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RRHO.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RRHO_1.46.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/RRHO.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 ‘RRHO/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RRHO’ version ‘1.46.0’ * 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 ‘RRHO’ 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: Version 1.6.0 (currently 1.5.xx) () Major documentation cleanup. () Added two sided hypotheses to RRHO() with signed pvalue plotting. () Added comparison of three lists using RRHOCOmparison(). () Added an option for log10 pvalues in RRHO. () Added error handling to RRHO so that failed plotting does not crash the computation. * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE RRHO: no visible global function definition for ‘p.adjust’ RRHO : color.bar: no visible global function definition for ‘mtext’ RRHO : color.bar: no visible global function definition for ‘axis’ RRHO : color.bar: no visible global function definition for ‘rect’ RRHO: no visible global function definition for ‘jpeg’ RRHO: no visible global function definition for ‘colorRampPalette’ RRHO: no visible global function definition for ‘layout’ RRHO: no visible global function definition for ‘image’ RRHO: no visible global function definition for ‘mtext’ RRHO: no visible global function definition for ‘dev.off’ RRHO: no visible global function definition for ‘cor’ RRHO: no visible global function definition for ‘lm’ RRHO: no visible global function definition for ‘lines’ RRHO: no visible global function definition for ‘predict’ RRHO: no visible global function definition for ‘write.table’ RRHOComparison: no visible global function definition for ‘phyper’ RRHOComparison: no visible global function definition for ‘pnorm’ RRHOComparison: no visible global function definition for ‘p.adjust’ RRHOComparison : color.bar: no visible global function definition for ‘mtext’ RRHOComparison : color.bar: no visible global function definition for ‘axis’ RRHOComparison : color.bar: no visible global function definition for ‘rect’ RRHOComparison: no visible global function definition for ‘pdf’ RRHOComparison: no visible global function definition for ‘colorRampPalette’ RRHOComparison: no visible global function definition for ‘layout’ RRHOComparison: no visible global function definition for ‘image’ RRHOComparison: no visible global function definition for ‘mtext’ RRHOComparison: no visible global function definition for ‘dev.off’ numericListOverlap : overlap: no visible global function definition for ‘phyper’ pvalRRHO: no visible global function definition for ‘txtProgressBar’ pvalRRHO: no visible global function definition for ‘na.omit’ pvalRRHO: no visible global function definition for ‘setTxtProgressBar’ pvalRRHO : FUN.ecdf: no visible global function definition for ‘ecdf’ Undefined global functions or variables: axis colorRampPalette cor dev.off ecdf image jpeg layout lines lm mtext na.omit p.adjust pdf phyper pnorm predict rect setTxtProgressBar txtProgressBar write.table Consider adding importFrom("grDevices", "colorRampPalette", "dev.off", "jpeg", "pdf") importFrom("graphics", "axis", "image", "layout", "lines", "mtext", "rect") importFrom("stats", "cor", "ecdf", "lm", "na.omit", "p.adjust", "phyper", "pnorm", "predict") importFrom("utils", "setTxtProgressBar", "txtProgressBar", "write.table") 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 ... OK * 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 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/RRHO.Rcheck/00check.log’ for details.