############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings INSPEcT_1.39.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/INSPEcT.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘INSPEcT/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘INSPEcT’ version ‘1.39.1’ * 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 ... INFO 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 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 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: INSPEcT-class.Rd: featureNames Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 72.430 0.437 72.868 modelRates 37.022 0.082 37.105 quantifyExpressionsFromBAMs 28.796 0.160 29.292 INSPEcT_diffsteady-class 28.035 0.265 28.301 rocCurve 25.159 0.142 25.301 rocThresholds 24.386 0.092 24.478 makeSimModel 24.333 0.030 24.364 plotMA 22.714 0.010 22.723 compareSteady 22.591 0.085 22.676 quantifyExpressionsFromTrCounts 15.637 0.086 15.723 newINSPEcT 14.201 0.150 14.352 processingDelay 12.698 0.031 12.728 inspectFromPCR 6.493 0.023 6.517 makeOscillatorySimModel 5.769 0.008 5.778 compareSteadyNoNascent 5.214 0.007 5.220 * 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-3.22-bioc/meat/INSPEcT.Rcheck/00check.log’ for details.