############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MetaVolcanoR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MetaVolcanoR_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/MetaVolcanoR.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MetaVolcanoR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MetaVolcanoR’ version ‘1.6.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt 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 ‘MetaVolcanoR’ 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 ... OK * checking R code for possible problems ... NOTE combining_mv: no visible binding for global variable ‘study’ combining_mv: no visible binding for global variable ‘value’ combining_mv: no visible binding for global variable ‘metap’ combining_mv: no visible binding for global variable ‘idx’ draw_cum_freq: no visible binding for global variable ‘ndatasets’ draw_cum_freq: no visible binding for global variable ‘DEGs’ draw_degbar: no visible binding for global variable ‘dataset’ draw_degbar: no visible binding for global variable ‘Regulation’ draw_forest: no visible binding for global variable ‘group’ plot_mv: no visible binding for global variable ‘metap’ plot_mv: no visible binding for global variable ‘degcomb’ plot_mv: no visible binding for global variable ‘ddeg’ plot_mv: no visible binding for global variable ‘ndeg’ plot_mv: no visible binding for global variable ‘degvcount’ plot_rem: no visible binding for global variable ‘signcon’ plot_rem: no visible binding for global variable ‘randomCi.ub’ plot_rem: no visible binding for global variable ‘randomCi.lb’ plot_rem: no visible binding for global variable ‘randomSummary’ plot_rem: no visible binding for global variable ‘randomP’ plot_rem: no visible binding for global variable ‘signcon2’ plot_rem: no visible binding for global variable ‘Ci.ub’ plot_rem: no visible binding for global variable ‘Ci.lb’ rem_mv: no visible binding for global variable ‘error’ rem_mv: no visible binding for global variable ‘randomCi.ub’ rem_mv: no visible binding for global variable ‘randomCi.lb’ rem_mv: no visible binding for global variable ‘index’ rem_mv: no visible global function definition for ‘head’ votecount_mv: no visible binding for global variable ‘ddeg’ votecount_mv: no visible binding for global variable ‘ndeg’ votecount_mv: no visible binding for global variable ‘idx’ Undefined global functions or variables: Ci.lb Ci.ub DEGs Regulation dataset ddeg degcomb degvcount error group head idx index metap ndatasets ndeg randomCi.lb randomCi.ub randomP randomSummary signcon signcon2 study value Consider adding importFrom("utils", "head") 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 combining_mv 7.922 0.671 8.751 votecount_mv 5.482 0.617 6.158 plot_mv 5.197 0.590 5.913 plot_rem 5.397 0.161 5.620 draw_forest 5.330 0.191 5.552 rem_mv 5.187 0.225 5.427 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/MetaVolcanoR.Rcheck/00check.log’ for details.