############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PAA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PAA_1.41.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/PAA.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: aarch64-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 Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘PAA/DESCRIPTION’ ... OK * this is package ‘PAA’ version ‘1.41.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘PAA’ can be installed ... OK * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Authors@R field gives more than one person with maintainer role: Michael Turewicz [aut, cre] Martin Eisenacher [ctb, cre] * 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 batchFilter: no visible global function definition for ‘t.test’ batchFilter: no visible global function definition for ‘points’ batchFilter: no visible global function definition for ‘abline’ batchFilter: no visible global function definition for ‘write.table’ batchFilter: no visible global function definition for ‘tiff’ batchFilter: no visible global function definition for ‘dev.off’ batchFilter.anova: no visible global function definition for ‘combn’ batchFilter.anova: no visible global function definition for ‘oneway.test’ batchFilter.anova: no visible global function definition for ‘points’ batchFilter.anova: no visible global function definition for ‘abline’ batchFilter.anova: no visible global function definition for ‘write.table’ batchFilter.anova: no visible global function definition for ‘tiff’ batchFilter.anova: no visible global function definition for ‘dev.off’ classify.svm.ensemble: no visible global function definition for ‘predict’ classify.svm.ensemble: no visible global function definition for ‘tiff’ classify.svm.ensemble: no visible global function definition for ‘dev.off’ diffAnalysis: no visible global function definition for ‘t.test’ diffAnalysis: no visible global function definition for ‘median’ diffAnalysis: no visible global function definition for ‘sd’ diffAnalysis: no visible global function definition for ‘p.adjust’ diffAnalysis: no visible global function definition for ‘write.table’ final.classify.rf: no visible global function definition for ‘predict’ final.classify.rf: no visible global function definition for ‘tiff’ final.classify.rf: no visible global function definition for ‘dev.off’ final.classify.svm: no visible global function definition for ‘predict’ final.classify.svm: no visible global function definition for ‘tiff’ final.classify.svm: no visible global function definition for ‘dev.off’ normalizeRLM: no visible global function definition for ‘rnorm’ normalizeRLM: no visible global function definition for ‘tiff’ normalizeRLM: no visible global function definition for ‘boxplot’ normalizeRLM: no visible global function definition for ‘dev.off’ plotArray: no visible global function definition for ‘par’ plotArrayPng: no visible global function definition for ‘png’ plotArrayPng: no visible global function definition for ‘dev.off’ plotArrayTiff: no visible global function definition for ‘tiff’ plotArrayTiff: no visible global function definition for ‘dev.off’ plotFeatures: no visible global function definition for ‘tiff’ plotFeatures: no visible global function definition for ‘par’ plotFeatures: no visible global function definition for ‘axis’ plotFeatures: no visible global function definition for ‘box’ plotFeatures: no visible global function definition for ‘points’ plotFeatures: no visible global function definition for ‘legend’ plotFeatures: no visible global function definition for ‘dev.off’ plotFeaturesHeatmap: no visible global function definition for ‘na.exclude’ plotFeaturesHeatmap : my.dist: no visible global function definition for ‘as.dist’ plotFeaturesHeatmap : my.dist: no visible global function definition for ‘cor’ plotFeaturesHeatmap : my.hclust: no visible global function definition for ‘hclust’ plotFeaturesHeatmap: no visible global function definition for ‘tiff’ plotFeaturesHeatmap: no visible global function definition for ‘heatmap’ plotFeaturesHeatmap: no visible global function definition for ‘dev.off’ plotFeaturesHeatmap.2: no visible global function definition for ‘na.exclude’ plotFeaturesHeatmap.2 : my.dist: no visible global function definition for ‘as.dist’ plotFeaturesHeatmap.2 : my.dist: no visible global function definition for ‘cor’ plotFeaturesHeatmap.2: no visible global function definition for ‘png’ plotFeaturesHeatmap.2 : : no visible global function definition for ‘as.dist’ plotFeaturesHeatmap.2 : : no visible global function definition for ‘cor’ plotFeaturesHeatmap.2: no visible global function definition for ‘par’ plotFeaturesHeatmap.2: no visible global function definition for ‘legend’ plotFeaturesHeatmap.2: no visible global function definition for ‘dev.off’ plotMAPlots: no visible binding for global variable ‘median’ plotMAPlots: no visible global function definition for ‘tiff’ plotMAPlots: no visible global function definition for ‘par’ plotMAPlots: no visible global function definition for ‘abline’ plotMAPlots: no visible global function definition for ‘lines’ plotMAPlots: no visible global function definition for ‘lowess’ plotMAPlots: no visible global function definition for ‘dev.off’ plotNormMethods: no visible global function definition for ‘par’ plotNormMethods: no visible global function definition for ‘boxplot’ plotNormMethods: no visible global function definition for ‘dev.off’ plotNormMethods: no visible global function definition for ‘tiff’ printFeatures: no visible global function definition for ‘write.table’ pvaluePlot: no visible global function definition for ‘t.test’ pvaluePlot: no visible global function definition for ‘p.adjust’ pvaluePlot: no visible global function definition for ‘abline’ pvaluePlot: no visible global function definition for ‘legend’ pvaluePlot: no visible global function definition for ‘tiff’ pvaluePlot: no visible global function definition for ‘dev.off’ rj.rfe: no visible global function definition for ‘write.table’ rj.rfe: no visible global function definition for ‘read.table’ selectFeatures.ensemble: no visible global function definition for ‘write.table’ selectFeatures.frequency.cv: no visible global function definition for ‘write.table’ selectFeatures.frequency.cv: no visible global function definition for ‘read.table’ selectFeatures.frequency.cv: no visible global function definition for ‘tiff’ selectFeatures.frequency.cv: no visible global function definition for ‘title’ selectFeatures.frequency.cv: no visible global function definition for ‘dev.off’ selectFeatures.frequency.cv: no visible global function definition for ‘na.omit’ svm.rfe: no visible global function definition for ‘predict’ tTest: no visible global function definition for ‘t.test’ tTestFS: no visible global function definition for ‘t.test’ volcanoPlot: no visible global function definition for ‘t.test’ volcanoPlot: no visible global function definition for ‘tiff’ volcanoPlot: no visible global function definition for ‘dev.off’ volcanoPlot: no visible global function definition for ‘points’ volcanoPlot: no visible global function definition for ‘abline’ Undefined global functions or variables: abline as.dist axis box boxplot combn cor dev.off hclust heatmap legend lines lowess median na.exclude na.omit oneway.test p.adjust par png points predict read.table rnorm sd t.test tiff title write.table Consider adding importFrom("grDevices", "dev.off", "png", "tiff") importFrom("graphics", "abline", "axis", "box", "boxplot", "legend", "lines", "par", "points", "title") importFrom("stats", "as.dist", "cor", "hclust", "heatmap", "lowess", "median", "na.exclude", "na.omit", "oneway.test", "p.adjust", "predict", "rnorm", "sd", "t.test") importFrom("utils", "combn", "read.table", "write.table") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) normalizeArrays.Rd:63-65: Lost braces in \itemize; meant \describe ? checkRd: (-1) normalizeArrays.Rd:66-67: Lost braces in \itemize; meant \describe ? checkRd: (-1) normalizeArrays.Rd:68-70: Lost braces in \itemize; meant \describe ? checkRd: (-1) normalizeArrays.Rd:79-80: Lost braces in \itemize; meant \describe ? checkRd: (-1) normalizeArrays.Rd:81-82: Lost braces 81 | \item{\code{"Anti-HumanIgA"} {Only anti-human-IgAs are selected (esp., | ^ checkRd: (-1) normalizeArrays.Rd:83-84: Lost braces 83 | \item{\code{"(Anti-HumanIg|^V5control|BSA|ERa)"} {Only anti-human IgGs and | ^ checkRd: (-1) normalizeArrays.Rd:85: Lost braces; missing escapes or markup? 85 | \item{\code{"HumanIgG"} {Only human IgGs and anti-human IgGs are selected}.} | ^ checkRd: (-1) normalizeArrays.Rd:86: Lost braces; missing escapes or markup? 86 | \item{\code{"V5control"} {Only the V5-CMK1 series is selected.}} | ^ * 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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/PAA.Rcheck/00check.log’ for details.