############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings INSPEcT_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/INSPEcT.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘INSPEcT/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘INSPEcT’ 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 ‘INSPEcT’ can be installed ... OK * checking installed package size ... NOTE installed size is 7.1Mb sub-directories of 1Mb or more: R 1.8Mb data 2.8Mb * 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 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 output_pars: no visible global function definition for ‘plot.new’ plotSingleRNADynamic: no visible global function definition for ‘lines’ Undefined global functions or variables: lines plot.new Consider adding importFrom("graphics", "lines", "plot.new") 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed makeSimDataset 226.269 0.960 247.521 modelRates 101.087 0.489 110.618 rocCurve 77.820 0.533 87.842 makeSimModel 77.714 0.358 82.816 rocThresholds 76.772 0.384 84.469 quantifyExpressionsFromBAMs 70.346 6.334 84.627 INSPEcT_diffsteady-class 71.096 0.584 77.624 plotMA 64.791 0.332 73.430 compareSteady 64.280 0.272 69.408 newINSPEcT 42.297 0.243 49.800 quantifyExpressionsFromTrCounts 35.248 0.203 38.499 processingDelay 34.139 0.170 37.638 makeOscillatorySimModel 18.916 0.152 20.370 inspectFromPCR 18.107 0.074 18.726 compareSteadyNoNascent 13.735 0.060 14.343 modelRatesNF 11.706 0.206 12.843 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/INSPEcT.Rcheck/00check.log’ for details.