############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:statTarget.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings statTarget_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/statTarget.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 ‘statTarget/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘statTarget’ version ‘1.22.0’ * 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: .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 ‘statTarget’ 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 ... NOTE 'library' or 'require' calls in package code: ‘gWidgets2’ ‘gWidgets2RGtk2’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE ComBat_qcFree: no visible global function definition for ‘model.matrix’ ComBat_qcFree: no visible binding for global variable ‘Beta.NA’ ComBat_qcFree: no visible global function definition for ‘dnorm’ ComBat_qcFree: no visible global function definition for ‘qqnorm’ ComBat_qcFree: no visible global function definition for ‘qqline’ oddRatio : logit_or: no visible global function definition for ‘relevel’ pvimPlot: no visible binding for global variable ‘GiniImportance’ pvimPlot: no visible binding for global variable ‘p.value’ shiftCor_dQC: no visible global function definition for ‘model.matrix’ statTargetGUI: no visible global function definition for ‘svalue<-’ statTargetGUI: no visible global function definition for ‘gexpandgroup’ statTargetGUI : : no visible global function definition for ‘galert’ statTargetGUI: no visible global function definition for ‘ggroup’ statTargetGUI: no visible global function definition for ‘gformlayout’ statTargetGUI: no visible global function definition for ‘glayout’ statTargetGUI: no visible global function definition for ‘glabel’ statTargetGUI : : no visible global function definition for ‘svalue’ statTargetGUI : : no visible global function definition for ‘size<-’ statTargetGUI : : : no visible global function definition for ‘dispose’ statTargetGUI : : : no visible global function definition for ‘gwindow’ statTargetGUI : : : no visible global function definition for ‘gvbox’ statTargetGUI : : : no visible global function definition for ‘glabel’ statTargetGUI : : : no visible global function definition for ‘gseparator’ statTargetGUI : : : no visible global function definition for ‘ggroup’ statTargetGUI : : : no visible global function definition for ‘addSpring’ statTargetGUI : : : no visible global function definition for ‘gbutton’ statTargetGUI : : : : no visible global function definition for ‘dispose’ statTargetGUI : : no visible global function definition for ‘gtext’ statTargetGUI : : no visible global function definition for ‘gseparator’ statTargetGUI : : no visible global function definition for ‘ggroup’ statTargetGUI : : no visible global function definition for ‘addSpring’ statTargetGUI : : no visible global function definition for ‘gbutton’ transCode : skyline: no visible binding for global variable ‘Replicate.Name’ Undefined global functions or variables: Beta.NA GiniImportance Replicate.Name addSpring dispose dnorm galert gbutton gexpandgroup gformlayout ggroup glabel glayout gseparator gtext gvbox gwindow model.matrix p.value qqline qqnorm relevel size<- svalue svalue<- Consider adding importFrom("stats", "dnorm", "model.matrix", "qqline", "qqnorm", "relevel") 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 files in ‘vignettes’ ... OK * checking examples ... OK * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/statTarget.Rcheck/00check.log’ for details.