############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pathRender.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pathRender_1.62.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/pathRender.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘pathRender/DESCRIPTION’ ... OK * this is package ‘pathRender’ version ‘1.62.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'graph', 'Rgraphviz', 'RColorBrewer', 'cMAP', 'AnnotationDbi', 'stats4' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘pathRender’ 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 graphcMAP: no visible binding for global variable ‘cMAPKEGGPATHWAY’ graphcMAP: no visible binding for global variable ‘cMAPCARTAPATHWAY’ graphcMAP: no visible binding for global variable ‘cMAPKEGGINTERACTION’ graphcMAP: no visible binding for global variable ‘cMAPKEGGMOLECULE’ graphcMAP: no visible binding for global variable ‘cMAPCARTAINTERACTION’ graphcMAP: no visible binding for global variable ‘cMAPCARTAMOLECULE’ plotExGraph: no visible global function definition for ‘colorRampPalette’ plotExGraph: no visible global function definition for ‘exprs’ quantizeByRow : : no visible global function definition for ‘quantile’ quantizeByRow: no visible global function definition for ‘featureNames’ quantizeByRow: no visible global function definition for ‘exprs<-’ quantizeByRow: no visible global function definition for ‘exprs’ quantizeByRow: no visible global function definition for ‘featureNames<-’ reduceES: no visible global function definition for ‘na.omit’ reduceES: no visible global function definition for ‘featureData<-’ reduceES: no visible global function definition for ‘exprs’ reduceES: no visible global function definition for ‘phenoData’ rendercMAPPathway: no visible binding for global variable ‘cMAPKEGGPATHWAY’ rendercMAPPathway: no visible binding for global variable ‘cMAPCARTAPATHWAY’ rendercMAPPathway: no visible binding for global variable ‘cMAPKEGGINTERACTION’ rendercMAPPathway: no visible binding for global variable ‘cMAPKEGGMOLECULE’ rendercMAPPathway: no visible binding for global variable ‘cMAPCARTAINTERACTION’ rendercMAPPathway: no visible binding for global variable ‘cMAPCARTAMOLECULE’ plot,coloredGraph-ANY: no visible global function definition for ‘palette’ Undefined global functions or variables: cMAPCARTAINTERACTION cMAPCARTAMOLECULE cMAPCARTAPATHWAY cMAPKEGGINTERACTION cMAPKEGGMOLECULE cMAPKEGGPATHWAY colorRampPalette exprs exprs<- featureData<- featureNames featureNames<- na.omit palette phenoData quantile Consider adding importFrom("grDevices", "colorRampPalette", "palette") importFrom("stats", "na.omit", "quantile") 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... 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-3.14-bioc/meat/pathRender.Rcheck/00check.log’ for details.