############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:esetVis.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings esetVis_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/esetVis.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘esetVis/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘esetVis’ version ‘1.32.0’ * 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 ‘esetVis’ 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 ggvisPlotEset: no visible global function definition for ‘:=’ ggvisPlotEset: no visible binding for global variable ‘fill’ ggvisPlotEset: no visible binding for global variable ‘shape’ ggvisPlotEset: no visible binding for global variable ‘size’ ggvisPlotEset: no visible binding for global variable ‘opacity’ Undefined global functions or variables: := fill opacity shape size * checking Rd files ... NOTE checkRd: (-1) esetLda.Rd:122: Lost braces in \itemize; meant \describe ? checkRd: (-1) esetLda.Rd:123: Lost braces in \itemize; meant \describe ? checkRd: (-1) esetLda.Rd:124: Lost braces in \itemize; meant \describe ? checkRd: (-1) esetLda.Rd:242: Lost braces in \itemize; meant \describe ? checkRd: (-1) esetLda.Rd:243: Lost braces in \itemize; meant \describe ? checkRd: (-1) esetLda.Rd:264-265: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) esetLda.Rd:267: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) esetLda.Rd:268: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) esetLda.Rd:269: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) esetLda.Rd:271: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) esetLda.Rd:272: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) esetPlot-class.Rd:79: Lost braces in \itemize; meant \describe ? checkRd: (-1) esetPlot-class.Rd:80: Lost braces in \itemize; meant \describe ? checkRd: (-1) esetPlot-class.Rd:81: Lost braces in \itemize; meant \describe ? checkRd: (-1) esetPlotWrapper.Rd:127: Lost braces in \itemize; meant \describe ? checkRd: (-1) esetPlotWrapper.Rd:128: Lost braces in \itemize; meant \describe ? checkRd: (-1) esetPlotWrapper.Rd:129: Lost braces in \itemize; meant \describe ? checkRd: (-1) esetPlotWrapper.Rd:243: Lost braces in \itemize; meant \describe ? checkRd: (-1) esetPlotWrapper.Rd:244: Lost braces in \itemize; meant \describe ? checkRd: (-1) esetPlotWrapper.Rd:272: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) esetPlotWrapper.Rd:273: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) esetPlotWrapper.Rd:277-278: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) esetSpectralMap.Rd:131: Lost braces in \itemize; meant \describe ? checkRd: (-1) esetSpectralMap.Rd:132: Lost braces in \itemize; meant \describe ? checkRd: (-1) esetSpectralMap.Rd:133: Lost braces in \itemize; meant \describe ? checkRd: (-1) esetSpectralMap.Rd:251: Lost braces in \itemize; meant \describe ? checkRd: (-1) esetSpectralMap.Rd:252: Lost braces in \itemize; meant \describe ? checkRd: (-1) esetSpectralMap.Rd:273: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) esetSpectralMap.Rd:275: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) esetSpectralMap.Rd:276: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) esetSpectralMap.Rd:277: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) esetSpectralMap.Rd:278: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) esetSpectralMap.Rd:281: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) esetSpectralMap.Rd:282: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) esetTsne.Rd:111: Lost braces in \itemize; meant \describe ? checkRd: (-1) esetTsne.Rd:112: Lost braces in \itemize; meant \describe ? checkRd: (-1) esetTsne.Rd:113: Lost braces in \itemize; meant \describe ? checkRd: (-1) esetTsne.Rd:157: Lost braces in \itemize; meant \describe ? checkRd: (-1) esetTsne.Rd:158: Lost braces in \itemize; meant \describe ? checkRd: (-1) esetTsne.Rd:179-180: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) esetTsne.Rd:182: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) esetTsne.Rd:183: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) esetTsne.Rd:185: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) esetTsne.Rd:186: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) getGeneSetsForPlot.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) getGeneSetsForPlot.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) getMethodsInputObjectEsetVis.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) getMethodsInputObjectEsetVis.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) getMethodsInputObjectEsetVis.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) getMethodsInputObjectEsetVis.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) getMethodsInputObjectEsetVis.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) getMethodsInputObjectEsetVis.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) getMethodsInputObjectEsetVis.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plotTopElements.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plotTopElements.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plotTopElements.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plotTopElements.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly * 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 ... NOTE Documented arguments not in \usage in Rd file 'getCoordGeneSets.Rd': ‘...’ Documented arguments not in \usage in Rd file 'getTopElements.Rd': ‘returnTopElements’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed getGeneSetsForPlot 88.605 6.868 102.722 esetLda 10.143 0.449 14.470 esetPlotWrapper 7.967 0.345 9.243 esetSpectralMap 6.429 0.281 7.327 esetTsne 5.570 0.129 6.210 * 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-3.20-bioc/meat/esetVis.Rcheck/00check.log’ for details.