############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:categoryCompare.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings categoryCompare_1.51.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/categoryCompare.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘categoryCompare/DESCRIPTION’ ... OK * this is package ‘categoryCompare’ version ‘1.51.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘categoryCompare’ 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 code 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 .ccCompareGO: no visible binding for global variable ‘GOBPPARENTS’ .ccCompareGO: no visible binding for global variable ‘GOMFPARENTS’ .ccCompareGO: no visible binding for global variable ‘GOCCPARENTS’ .ccCompareGO: no visible binding for global variable ‘GOTERM’ .ccCompareGO: no visible binding for global variable ‘Term’ .cytOutNodes: ... may be used in an incorrect context: exportImage(filename = fileName, type = "png", network = cwObj, ...) .getDesc : : no visible global function definition for ‘Term’ show,HyperGResultCC: no visible global function definition for ‘description’ Undefined global functions or variables: GOBPPARENTS GOCCPARENTS GOMFPARENTS GOTERM Term description * checking Rd files ... NOTE checkRd: (-1) ccData.Rd:21: Lost braces 21 | \code{table10}{: Log-ratio output from \pkg{limma} for the comparison of presence-absence of estrogen at 10 hours} | ^ checkRd: (-1) ccData.Rd:23: Lost braces 23 | \code{table48}{: Log-ratio output from \pkg{limma} for the comparison of presence-absence of estrogen at 48 hours} | ^ checkRd: (-1) ccData.Rd:25: Lost braces 25 | \code{gUniverse}{: All of the genes measured on the chip} | ^ checkRd: (-1) ccData.Rd:27: Lost braces 27 | \code{gseaRes}{: Toy results of GSEA analysis of 3 different tissues} | ^ checkRd: (-1) ccData.Rd:29: Lost braces 29 | \code{enrichLists}{: Apply \code{\link{ccEnrich}} to a ccGeneList from \code{table10} and \code{table48}} | ^ checkRd: (-1) ccData.Rd:31: Lost braces 31 | \code{ccResults}{: Apply \code{\link{ccCompare}} to \code{enrichLists}} | ^ checkRd: (-1) ccData.Rd:33: Lost braces 33 | \code{ccResultsBPHier}{: Modify \code{enrichLists$BP} to use a "hierarchical" layout} | ^ checkRd: (-1) ccData.Rd:35: Lost braces 35 | \code{geneLists}{: a \code{ccGeneList} generated from genes in table10 and table48} | ^ checkRd: (-1) ccData.Rd:37: Lost braces 37 | \code{ccOpts}{: a \code{ccOptions} object describing what we are going to do as far as feature list comparisons} | ^ * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: GENccEnrichResult-class.Rd: AssayData-class HyperGResultCC-class.Rd: HyperGParams-class, HyperGResult-class, HyperGResultBase-class ccCompareCollection-class.Rd: AssayData-class ccEnrichCollection-class.Rd: AssayData-class ccEnrichResult-class.Rd: AssayData-class mergedData-class.Rd: data.frameOrNULL-class resetColors-methods.Rd: setNodeColorMapping Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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-3.21-bioc/meat/categoryCompare.Rcheck/00check.log’ for details.