############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:rnaseqcomp.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings rnaseqcomp_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/rnaseqcomp.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘rnaseqcomp/DESCRIPTION’ ... OK * this is package ‘rnaseqcomp’ version ‘1.36.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘rnaseqcomp’ 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 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 plot2TX: no visible global function definition for ‘lines’ plot2TX: no visible global function definition for ‘box’ plot2TX: no visible global function definition for ‘legend’ plot2TX : : no visible binding for global variable ‘sd’ plot2TX : : no visible global function definition for ‘sd’ plotFC: no visible global function definition for ‘loess.smooth’ plotFC: no visible global function definition for ‘lines’ plotFC: no visible global function definition for ‘legend’ plotFC : : no visible global function definition for ‘median’ plotFC : : no visible global function definition for ‘sd’ plotNE: no visible global function definition for ‘lines’ plotNE: no visible global function definition for ‘points’ plotNE: no visible global function definition for ‘box’ plotNE: no visible global function definition for ‘legend’ plotROC: no visible global function definition for ‘median’ plotROC: no visible global function definition for ‘sd’ plotROC: no visible global function definition for ‘lines’ plotROC: no visible global function definition for ‘arrows’ plotROC: no visible global function definition for ‘abline’ plotROC: no visible global function definition for ‘legend’ plotSD : : no visible binding for global variable ‘sd’ plotSD: no visible global function definition for ‘loess.smooth’ plotSD: no visible global function definition for ‘lines’ plotSD: no visible global function definition for ‘box’ plotSD: no visible global function definition for ‘legend’ plotSD : : : no visible global function definition for ‘median’ plotSD : : : no visible global function definition for ‘mad’ signalCalibrate : : no visible binding for global variable ‘median’ signalCalibrate: no visible global function definition for ‘median’ Undefined global functions or variables: abline arrows box legend lines loess.smooth mad median points sd Consider adding importFrom("graphics", "abline", "arrows", "box", "legend", "lines", "points") importFrom("stats", "loess.smooth", "mad", "median", "sd") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) plotFC.Rd:19: Lost braces; missing escapes or markup? 19 | number of matrices in \code{dat@quantData}. Only values {1, -1, 0, NA} | ^ checkRd: (-1) plotROC.Rd:19: Lost braces; missing escapes or markup? 19 | number of matrices in \code{dat@quantData}. Only values {1, -1, 0} | ^ * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotROC 6.551 0.111 6.663 * 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/rnaseqcomp.Rcheck/00check.log’ for details.