############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AgiMicroRna.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AgiMicroRna_2.54.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/AgiMicroRna.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 ‘AgiMicroRna/DESCRIPTION’ ... OK * this is package ‘AgiMicroRna’ version ‘2.54.0’ * 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 ‘AgiMicroRna’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘Biobase’ A package should be listed in only one of these fields. * 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 ... NOTE Warning: no function found corresponding to methods exports from ‘AgiMicroRna’ for: ‘show’ A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE 'library' or 'require' calls to packages already attached by Depends: 'affy' 'affycoretools' 'preprocessCore' Please remove these calls from your code. 'library' or 'require' calls in package code: 'codelink' 'gdata' 'geneplotter' 'gplots' 'gtools' 'marray' Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Packages in Depends field not imported from: 'affy' 'affycoretools' 'limma' 'methods' 'preprocessCore' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... WARNING See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... NOTE Foreign function call to a different package: .Call("rma_c_complete_copy", ..., PACKAGE = "affy") See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE DEG.print.info: no visible global function definition for 'is' DEG.print.info: no visible global function definition for 'exprs' HeatMapMicroRna: no visible binding for global variable 'var' HeatMapMicroRna: no visible global function definition for 'rainbow' HeatMapMicroRna: no visible global function definition for 'maPalette' HeatMapMicroRna: no visible global function definition for 'heatmap.2' HeatMapMicroRna: no visible global function definition for 'title' MA.plot.miRNA: no visible global function definition for 'dev.new' MA.plot.miRNA: no visible global function definition for 'points' MA.plot.miRNA: no visible global function definition for 'fitted' MA.plot.miRNA: no visible global function definition for 'loess' MA.plot.miRNA: no visible global function definition for 'legend' MA.plot.miRNA: no visible global function definition for 'title' PCAplotMicroRna: no visible global function definition for 'is' PCAplotMicroRna: no visible global function definition for 'exprs' PCAplotMicroRna: no visible global function definition for 'na.omit' PCAplotMicroRna: no visible global function definition for 'exprs<-' PCAplotMicroRna: no visible global function definition for 'plotPCA' PCAplotMicroRna: no visible global function definition for 'dev.new' RleMicroRna: no visible binding for global variable 'median' RleMicroRna: no visible global function definition for 'par' RleMicroRna: no visible global function definition for 'boxplot' RleMicroRna: no visible global function definition for 'points' RleMicroRna: no visible global function definition for 'lines' RleMicroRna: no visible global function definition for 'title' RleMicroRna: no visible global function definition for 'abline' basicLimma: no visible global function definition for 'is' basicLimma: no visible global function definition for 'exprs' basicLimma: no visible global function definition for 'lmFit' basicLimma: no visible global function definition for 'contrasts.fit' basicLimma: no visible global function definition for 'eBayes' boxplotMicroRna: no visible global function definition for 'par' boxplotMicroRna: no visible global function definition for 'boxplot' boxplotMicroRna: no visible global function definition for 'points' boxplotMicroRna: no visible global function definition for 'lines' boxplotMicroRna: no visible global function definition for 'title' cv.array: no visible binding for global variable 'median' cvArray: no visible global function definition for 'is' esetMicroRna: no visible global function definition for 'is' esetMicroRna: no visible global function definition for 'new' esetMicroRna: no visible global function definition for 'dev.new' esetMicroRna: no visible global function definition for 'exprs' filter.IsGeneDetected: no visible global function definition for 'is' filter.control.miRNA: no visible global function definition for 'is' filter.wellaboveNEG.miRNA: no visible global function definition for 'is' filter.wellaboveNEG.miRNA: no visible binding for global variable 'sd' filterMicroRna: no visible global function definition for 'is' filterMicroRna: no visible global function definition for 'dev.new' getDecideTests: no visible global function definition for 'is' getDecideTests: no visible global function definition for 'decideTests' hierclusMicroRna: no visible binding for global variable 'var' hierclusMicroRna: no visible global function definition for 'dist' hierclusMicroRna: no visible global function definition for 'as.dist' hierclusMicroRna: no visible global function definition for 'cor' hierclusMicroRna: no visible global function definition for 'hclust' hierclusMicroRna: no visible global function definition for 'title' mvaBASIC: no visible binding for global variable 'median' mvaBASIC: no visible global function definition for 'title' mvaBASIC: no visible global function definition for 'abline' mvaMicroRna: no visible binding for global variable 'median' mvaMicroRna: no visible global function definition for 'points' mvaMicroRna: no visible global function definition for 'fitted' mvaMicroRna: no visible global function definition for 'loess' mvaMicroRna: no visible global function definition for 'title' mvaMicroRna: no visible global function definition for 'abline' mvaMicroRna: no visible global function definition for 'legend' plotDensityMicroRna: no visible global function definition for 'rainbow' plotDensityMicroRna: no visible global function definition for 'density' plotDensityMicroRna: no visible global function definition for 'lines' plotDensityMicroRna: no visible global function definition for 'title' plotDensityMicroRna: no visible global function definition for 'legend' pvalHistogram: no visible global function definition for 'p.adjust' pvalHistogram: no visible global function definition for 'hist' pvalHistogram: no visible global function definition for 'dev.new' qcPlots: no visible global function definition for 'is' qcPlots: no visible global function definition for 'dev.new' read.agiMicroRna: no visible global function definition for 'read.columns' read.agiMicroRna: no visible global function definition for 'new' readMicroRnaAFE: no visible global function definition for 'is' readTargets: no visible global function definition for 'read.table' rmaMicroRna: no visible global function definition for 'is' rmaMicroRna: no visible global function definition for 'rma.background.correct' rmaMicroRna: no visible global function definition for 'normalizeBetweenArrays' rmaMicroRna: no visible binding for global variable 'median' significantMicroRna: no visible global function definition for 'is' significantMicroRna: no visible global function definition for 'exprs' significantMicroRna: no visible global function definition for 'p.adjust' tgsMicroRna: no visible global function definition for 'is' tgsMicroRna: no visible global function definition for 'dev.new' tgsNormalization: no visible global function definition for 'is' tgsNormalization: no visible global function definition for 'dev.new' tgsNormalization: no visible global function definition for 'normalizeBetweenArrays' write.LIST.miRNA: no visible global function definition for 'is' write.LIST.miRNA: no visible global function definition for 'write.table' write.control.out.miRNA: no visible global function definition for 'is' write.control.out.miRNA: no visible global function definition for 'write.table' write.filt.out.miRNA: no visible global function definition for 'is' write.filt.out.miRNA: no visible global function definition for 'write.table' writeEset: no visible global function definition for 'is' writeEset: no visible global function definition for 'exprs' writeEset: no visible global function definition for 'featureNames' writeEset: no visible global function definition for 'write.table' show,uRNAList: no visible global function definition for 'slotNames' show,uRNAList: no visible global function definition for 'slot' Undefined global functions or variables: abline as.dist boxplot contrasts.fit cor decideTests density dev.new dist eBayes exprs exprs<- featureNames fitted hclust heatmap.2 hist is legend lines lmFit loess maPalette median na.omit new normalizeBetweenArrays p.adjust par plotPCA points rainbow read.columns read.table rma.background.correct sd slot slotNames title var write.table Consider adding importFrom("grDevices", "dev.new", "rainbow") importFrom("graphics", "abline", "boxplot", "hist", "legend", "lines", "par", "points", "title") importFrom("methods", "is", "new", "slot", "slotNames") importFrom("stats", "as.dist", "cor", "density", "dist", "fitted", "hclust", "loess", "median", "na.omit", "p.adjust", "sd", "var") importFrom("utils", "read.table", "write.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) basicLimma.Rd:46: Escaped LaTeX specials: \_ \_ checkRd: (-1) basicLimma.Rd:47: Escaped LaTeX specials: \_ \_ checkRd: (-1) basicLimma.Rd:53: Escaped LaTeX specials: \$ \$ checkRd: (-1) basicLimma.Rd:54: Escaped LaTeX specials: \$ checkRd: (-1) basicLimma.Rd:58: Escaped LaTeX specials: \_ \_ \_ \_ checkRd: (-1) dd.micro.Rd:22: Escaped LaTeX specials: \$ checkRd: (-1) dd.micro.Rd:23: Escaped LaTeX specials: \$ checkRd: (-1) dd.micro.Rd:24: Escaped LaTeX specials: \$ checkRd: (-1) dd.micro.Rd:25: Escaped LaTeX specials: \$ checkRd: (-1) dd.micro.Rd:26: Escaped LaTeX specials: \$ checkRd: (-1) dd.micro.Rd:27: Escaped LaTeX specials: \$ \$ checkRd: (-1) dd.micro.Rd:28: Escaped LaTeX specials: \$ \$ checkRd: (-1) dd.micro.Rd:29: Escaped LaTeX specials: \$ \$ checkRd: (-1) dd.micro.Rd:30: Escaped LaTeX specials: \$ \$ checkRd: (-1) dd.micro.Rd:31: Escaped LaTeX specials: \$ \$ checkRd: (-1) dd.micro.Rd:32: Escaped LaTeX specials: \$ \$ checkRd: (-1) dd.micro.Rd:33: Escaped LaTeX specials: \$ \$ checkRd: (-1) dd.micro.Rd:34: Escaped LaTeX specials: \$ \$ checkRd: (-1) dd.micro.Rd:35: Escaped LaTeX specials: \$ \$ checkRd: (-1) filterMicroRna.Rd:56: Escaped LaTeX specials: \_ checkRd: (-1) filterMicroRna.Rd:57: Escaped LaTeX specials: \_ checkRd: (-1) readMicroRnaAFE.Rd:27: Escaped LaTeX specials: \$ checkRd: (-1) readMicroRnaAFE.Rd:28: Escaped LaTeX specials: \$ checkRd: (-1) readMicroRnaAFE.Rd:29: Escaped LaTeX specials: \$ checkRd: (-1) readMicroRnaAFE.Rd:30: Escaped LaTeX specials: \$ checkRd: (-1) readMicroRnaAFE.Rd:31: Escaped LaTeX specials: \$ checkRd: (-1) readMicroRnaAFE.Rd:32: Escaped LaTeX specials: \$ \$ checkRd: (-1) readMicroRnaAFE.Rd:33: Escaped LaTeX specials: \$ \$ checkRd: (-1) readMicroRnaAFE.Rd:34: Escaped LaTeX specials: \$ \$ checkRd: (-1) readMicroRnaAFE.Rd:35: Escaped LaTeX specials: \$ \$ checkRd: (-1) readMicroRnaAFE.Rd:36: Escaped LaTeX specials: \$ \$ checkRd: (-1) readMicroRnaAFE.Rd:37: Escaped LaTeX specials: \$ \$ checkRd: (-1) readMicroRnaAFE.Rd:38: Escaped LaTeX specials: \$ \$ checkRd: (-1) readMicroRnaAFE.Rd:39: Escaped LaTeX specials: \$ \$ checkRd: (-1) readMicroRnaAFE.Rd:40: Escaped LaTeX specials: \$ \$ checkRd: (-1) readMicroRnaAFE.Rd:44: Escaped LaTeX specials: \$ checkRd: (-1) readMicroRnaAFE.Rd:45: Escaped LaTeX specials: \$ checkRd: (-1) readMicroRnaAFE.Rd:46: Escaped LaTeX specials: \$ checkRd: (-1) readMicroRnaAFE.Rd:47: Escaped LaTeX specials: \$ checkRd: (-1) readMicroRnaAFE.Rd:48: Escaped LaTeX specials: \$ checkRd: (-1) readMicroRnaAFE.Rd:49: Escaped LaTeX specials: \$ \$ checkRd: (-1) readMicroRnaAFE.Rd:50: Escaped LaTeX specials: \$ \$ checkRd: (-1) readMicroRnaAFE.Rd:51: Escaped LaTeX specials: \$ \$ checkRd: (-1) readMicroRnaAFE.Rd:52: Escaped LaTeX specials: \$ \$ checkRd: (-1) readMicroRnaAFE.Rd:53: Escaped LaTeX specials: \$ \$ checkRd: (-1) readMicroRnaAFE.Rd:54: Escaped LaTeX specials: \$ \$ checkRd: (-1) readMicroRnaAFE.Rd:55: Escaped LaTeX specials: \$ \$ checkRd: (-1) readMicroRnaAFE.Rd:56: Escaped LaTeX specials: \$ \$ checkRd: (-1) readMicroRnaAFE.Rd:57: Escaped LaTeX specials: \$ \$ checkRd: (-1) significantMicroRna.Rd:41: Escaped LaTeX specials: \_ checkRd: (-1) significantMicroRna.Rd:59: Escaped LaTeX specials: \_ checkRd: (-1) uRNAList.Rd:18: Escaped LaTeX specials: \$ checkRd: (-1) uRNAList.Rd:19: Escaped LaTeX specials: \$ checkRd: (-1) uRNAList.Rd:20: Escaped LaTeX specials: \$ checkRd: (-1) uRNAList.Rd:21: Escaped LaTeX specials: \$ checkRd: (-1) uRNAList.Rd:22: Escaped LaTeX specials: \$ checkRd: (-1) uRNAList.Rd:23: Escaped LaTeX specials: \$ \$ checkRd: (-1) uRNAList.Rd:24: Escaped LaTeX specials: \$ \$ checkRd: (-1) uRNAList.Rd:25: Escaped LaTeX specials: \$ \$ checkRd: (-1) uRNAList.Rd:26: Escaped LaTeX specials: \$ \$ checkRd: (-1) uRNAList.Rd:27: Escaped LaTeX specials: \$ \$ checkRd: (-1) uRNAList.Rd:28: Escaped LaTeX specials: \$ \$ checkRd: (-1) uRNAList.Rd:29: Escaped LaTeX specials: \$ \$ checkRd: (-1) uRNAList.Rd:30: Escaped LaTeX specials: \$ \$ checkRd: (-1) uRNAList.Rd:31: Escaped LaTeX specials: \$ \$ * 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 The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed mvaMicroRna 25.382 0.822 29.163 rmaMicroRna 7.836 0.178 8.874 mvaBASIC 5.262 0.277 6.216 * 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: 1 WARNING, 7 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/AgiMicroRna.Rcheck/00check.log’ for details.