############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:epiNEM.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings epiNEM_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/epiNEM.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘epiNEM/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘epiNEM’ version ‘1.18.0’ * package encoding: UTF-8 * 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 ‘epiNEM’ 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 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 ... NOTE Foreign function call to a different package: .Call("getTruthTable_R", ..., PACKAGE = "BoolNet") See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE SimEpiNEM: no visible global function definition for ‘epiNEM2Bg’ SimEpiNEM: no visible global function definition for ‘dummyCNOlist’ SimEpiNEM: no visible global function definition for ‘readSIF’ SimEpiNEM: no visible global function definition for ‘preprocessing’ SimEpiNEM: no visible global function definition for ‘absorption’ SimEpiNEM: no visible global function definition for ‘bnem’ SimEpiNEM: no visible binding for global variable ‘popSize’ SimEpiNEM: no visible global function definition for ‘computeFc’ SimEpiNEM: no visible global function definition for ‘simulateStatesRecursive’ SimEpiNEM: no visible global function definition for ‘dnf2adj’ epiNEM: no visible binding for global variable ‘inference’ plot.epiSim: no visible binding for global variable ‘sim’ plot.epiSim: no visible global function definition for ‘layout’ plot.epiSim: no visible global function definition for ‘boxplot’ plot.epiSim: no visible global function definition for ‘abline’ plot.epiSim: no visible global function definition for ‘axis’ Undefined global functions or variables: abline absorption axis bnem boxplot computeFc dnf2adj dummyCNOlist epiNEM2Bg inference layout popSize preprocessing readSIF sim simulateStatesRecursive Consider adding importFrom("graphics", "abline", "axis", "boxplot", "layout") 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 LazyData ... 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 epiScreen 9.092 0.160 9.251 plot.epiScreen 8.808 0.056 8.864 SimEpiNEM 6.066 0.144 6.210 plot.epiSim 5.847 0.072 5.920 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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 ‘/home/biocbuild/bbs-3.14-bioc/meat/epiNEM.Rcheck/00check.log’ for details.