############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-data-experiment/R/bin/R CMD check --install=check:IHWpaper.install-out.txt --library=/home/biocbuild/bbs-3.15-data-experiment/R/library --no-vignettes --timings IHWpaper_1.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.15-data-experiment/meat/IHWpaper.Rcheck’ * using R Under development (unstable) (2022-01-05 r81451) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘IHWpaper/DESCRIPTION’ ... OK * this is package ‘IHWpaper’ version ‘1.23.0’ * 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 ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘IHWpaper’ can be installed ... OK * checking installed package size ... NOTE installed size is 72.8Mb sub-directories of 1Mb or more: extdata 70.6Mb libs 1.3Mb * 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 ... OK * checking R code for possible problems ... NOTE scott_fdrreg: no visible global function definition for ‘FDRreg’ scott_fdrreg: no visible global function definition for ‘getFDR’ sim_fun_eval: no visible binding for global variable ‘fdr_method’ sim_fun_eval: no visible binding for global variable ‘fdr_pars’ sim_fun_eval: no visible binding for global variable ‘FDP’ sim_fun_eval: no visible binding for global variable ‘power’ sim_fun_eval: no visible binding for global variable ‘rj_ratio’ sim_fun_eval: no visible binding for global variable ‘FPR’ sim_fun_eval: no visible global function definition for ‘sd’ sim_fun_eval: no visible binding for global variable ‘FWER’ Undefined global functions or variables: FDP FDRreg FPR FWER fdr_method fdr_pars getFDR power rj_ratio sd Consider adding importFrom("stats", "power", "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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed analyze_dataset 17.145 0.684 17.846 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: 4 NOTEs See ‘/home/biocbuild/bbs-3.15-data-experiment/meat/IHWpaper.Rcheck/00check.log’ for details.