############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rnaseqcomp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rnaseqcomp_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 鈥�/Users/biocbuild/bbs-3.14-bioc/meat/rnaseqcomp.Rcheck鈥� * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option 鈥�--no-vignettes鈥� * checking for file 鈥榬naseqcomp/DESCRIPTION鈥� ... OK * this is package 鈥榬naseqcomp鈥� version 鈥�1.24.0鈥� * 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 鈥榬naseqcomp鈥� can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 鈥榖uild鈥� 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 ... NOTE plot2TX: no visible global function definition for 鈥榣ines鈥� plot2TX: no visible global function definition for 鈥榖ox鈥� plot2TX: no visible global function definition for 鈥榣egend鈥� plot2TX : <anonymous>: no visible binding for global variable 鈥榮d鈥� plot2TX : <anonymous>: no visible global function definition for 鈥榮d鈥� plotFC: no visible global function definition for 鈥榣oess.smooth鈥� plotFC: no visible global function definition for 鈥榣ines鈥� plotFC: no visible global function definition for 鈥榣egend鈥� plotFC : <anonymous>: no visible global function definition for 鈥榤edian鈥� plotFC : <anonymous>: no visible global function definition for 鈥榮d鈥� plotNE: no visible global function definition for 鈥榣ines鈥� plotNE: no visible global function definition for 鈥榩oints鈥� plotNE: no visible global function definition for 鈥榖ox鈥� plotNE: no visible global function definition for 鈥榣egend鈥� plotROC: no visible global function definition for 鈥榤edian鈥� plotROC: no visible global function definition for 鈥榮d鈥� plotROC: no visible global function definition for 鈥榣ines鈥� plotROC: no visible global function definition for 鈥榓rrows鈥� plotROC: no visible global function definition for 鈥榓bline鈥� plotROC: no visible global function definition for 鈥榣egend鈥� plotSD : <anonymous>: no visible binding for global variable 鈥榮d鈥� plotSD: no visible global function definition for 鈥榣oess.smooth鈥� plotSD: no visible global function definition for 鈥榣ines鈥� plotSD: no visible global function definition for 鈥榖ox鈥� plotSD: no visible global function definition for 鈥榣egend鈥� plotSD : <anonymous> : <anonymous>: no visible global function definition for 鈥榤edian鈥� plotSD : <anonymous> : <anonymous>: no visible global function definition for 鈥榤ad鈥� signalCalibrate : <anonymous>: no visible binding for global variable 鈥榤edian鈥� signalCalibrate: no visible global function definition for 鈥榤edian鈥� 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 ... 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 鈥榙ata鈥� directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in 鈥榲ignettes鈥� ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotROC 9.051 2.743 11.798 plotNE 4.077 1.149 5.228 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 鈥榠nst/doc鈥� ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See 鈥�/Users/biocbuild/bbs-3.14-bioc/meat/rnaseqcomp.Rcheck/00check.log鈥� for details.