############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HELP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HELP_1.65.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/HELP.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 ‘HELP/DESCRIPTION’ ... OK * this is package ‘HELP’ version ‘1.65.0’ * 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 ‘HELP’ 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 ... NOTE Package in Depends field not imported from: ‘methods’ 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 ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE calcTm: no visible global function definition for ‘data’ calcTm: no visible binding for global variable ‘base.stacking.thermodynamics’ readSampleKey: no visible global function definition for ‘read.table’ calcGC,ExpressionSet: no visible global function definition for ‘validObject’ calcGC,ExpressionSet: no visible global function definition for ‘callGeneric’ calcGC,ExpressionSet: no visible global function definition for ‘new’ calcPrototype,ExpressionSet: no visible global function definition for ‘validObject’ calcPrototype,ExpressionSet: no visible global function definition for ‘callGeneric’ calcPrototype,vector: no visible global function definition for ‘callGeneric’ calcTm,ExpressionSet: no visible global function definition for ‘validObject’ calcTm,ExpressionSet: no visible global function definition for ‘callGeneric’ calcTm,ExpressionSet: no visible global function definition for ‘new’ calcTm,character: no visible binding for global variable ‘base.stacking.thermodynamics’ combineData,ExpressionSet-missing-missing: no visible global function definition for ‘validObject’ combineData,ExpressionSet-missing-missing: no visible global function definition for ‘callGeneric’ combineData,ExpressionSet-vector-missing: no visible global function definition for ‘validObject’ combineData,ExpressionSet-vector-missing: no visible global function definition for ‘callGeneric’ combineData,matrix-vector-missing: no visible global function definition for ‘callGeneric’ combineData,vector-missing-missing: no visible global function definition for ‘callGeneric’ combineData,vector-missing-vector: no visible global function definition for ‘callGeneric’ combineData,vector-vector-missing: no visible global function definition for ‘callGeneric’ combineData,vector-vector-vector: no visible global function definition for ‘callGeneric’ createWiggle,ExpressionSet-matrix: no visible global function definition for ‘validObject’ createWiggle,ExpressionSet-matrix: no visible global function definition for ‘callGeneric’ createWiggle,ExpressionSet-missing: no visible global function definition for ‘validObject’ createWiggle,ExpressionSet-missing: no visible global function definition for ‘callGeneric’ createWiggle,matrix-matrix: no visible global function definition for ‘rainbow’ createWiggle,matrix-matrix: no visible global function definition for ‘col2rgb’ createWiggle,vector-matrix: no visible global function definition for ‘callGeneric’ getFeatures,AnnotatedDataFrame-NULL: no visible global function definition for ‘validObject’ getFeatures,AnnotatedDataFrame-missing: no visible global function definition for ‘validObject’ getFeatures,AnnotatedDataFrame-vector: no visible global function definition for ‘validObject’ getFeatures,AnnotatedDataFrame-vector: no visible global function definition for ‘callGeneric’ getFeatures,ExpressionSet-NULL: no visible global function definition for ‘validObject’ getFeatures,ExpressionSet-missing: no visible global function definition for ‘validObject’ getFeatures,ExpressionSet-vector: no visible global function definition for ‘validObject’ getFeatures,ExpressionSet-vector: no visible global function definition for ‘callGeneric’ getFeatures,vector-vector: no visible global function definition for ‘callGeneric’ getSamples,ExpressionSet-NULL: no visible global function definition for ‘validObject’ getSamples,ExpressionSet-missing: no visible global function definition for ‘validObject’ getSamples,ExpressionSet-vector: no visible global function definition for ‘validObject’ getSamples,ExpressionSet-vector: no visible global function definition for ‘callGeneric’ getSamples,vector-vector: no visible global function definition for ‘callGeneric’ plotBins,ExpressionSet-ExpressionSet: no visible global function definition for ‘validObject’ plotBins,ExpressionSet-ExpressionSet: no visible global function definition for ‘callGeneric’ plotBins,ExpressionSet-missing: no visible global function definition for ‘validObject’ plotBins,ExpressionSet-missing: no visible global function definition for ‘callGeneric’ plotBins,ExpressionSet-vector: no visible global function definition for ‘validObject’ plotBins,ExpressionSet-vector: no visible global function definition for ‘callGeneric’ plotBins,matrix-missing: no visible global function definition for ‘callGeneric’ plotBins,vector-ExpressionSet: no visible global function definition for ‘validObject’ plotBins,vector-ExpressionSet: no visible global function definition for ‘callGeneric’ plotBins,vector-vector: no visible global function definition for ‘rainbow’ plotBins,vector-vector: no visible global function definition for ‘quantile’ plotBins,vector-vector: no visible global function definition for ‘layout’ plotBins,vector-vector: no visible global function definition for ‘axis’ plotBins,vector-vector: no visible global function definition for ‘rect’ plotBins,vector-vector: no visible global function definition for ‘density’ plotBins,vector-vector: no visible global function definition for ‘lines’ plotChip,ExpressionSet-ExpressionSet-missing: no visible global function definition for ‘validObject’ plotChip,ExpressionSet-ExpressionSet-missing: no visible global function definition for ‘callGeneric’ plotChip,ExpressionSet-missing-missing: no visible global function definition for ‘validObject’ plotChip,ExpressionSet-missing-missing: no visible global function definition for ‘callGeneric’ plotChip,ExpressionSet-vector-missing: no visible global function definition for ‘validObject’ plotChip,ExpressionSet-vector-missing: no visible global function definition for ‘callGeneric’ plotChip,matrix-missing-missing: no visible global function definition for ‘callGeneric’ plotChip,vector-vector-ExpressionSet: no visible global function definition for ‘validObject’ plotChip,vector-vector-ExpressionSet: no visible global function definition for ‘callGeneric’ plotChip,vector-vector-vector: no visible global function definition for ‘rainbow’ plotChip,vector-vector-vector: no visible global function definition for ‘quantile’ plotChip,vector-vector-vector: no visible global function definition for ‘rect’ plotFeature,ExpressionSet-missing: no visible global function definition for ‘callGeneric’ plotFeature,ExpressionSet-vector: no visible global function definition for ‘validObject’ plotFeature,ExpressionSet-vector: no visible global function definition for ‘callGeneric’ plotFeature,matrix-vector: no visible global function definition for ‘par’ plotFeature,matrix-vector: no visible global function definition for ‘median’ plotFeature,matrix-vector: no visible global function definition for ‘mad’ plotFeature,matrix-vector: no visible global function definition for ‘layout’ plotFeature,matrix-vector: no visible global function definition for ‘density’ plotFeature,matrix-vector: no visible global function definition for ‘points’ plotFeature,matrix-vector: no visible global function definition for ‘abline’ plotPairs,ExpressionSet: no visible global function definition for ‘validObject’ plotPairs,ExpressionSet: no visible global function definition for ‘callGeneric’ plotPairs,matrix: no visible global function definition for ‘par’ plotPairs,matrix: no visible global function definition for ‘hclust’ plotPairs,matrix: no visible global function definition for ‘dist’ plotPairs,matrix: no visible global function definition for ‘cutree’ plotPairs,matrix: no visible global function definition for ‘rainbow’ plotPairs,matrix : plot.pairs.upper: no visible global function definition for ‘par’ plotPairs,matrix : plot.pairs.upper: no visible global function definition for ‘points’ plotPairs,matrix : plot.pairs.upper: no visible global function definition for ‘cor’ plotPairs,matrix : plot.pairs.upper: no visible global function definition for ‘lowess’ plotPairs,matrix : plot.pairs.upper: no visible global function definition for ‘lines’ plotPairs,matrix : plot.pairs.upper: no visible global function definition for ‘text’ plotPairs,matrix: no visible global function definition for ‘layout’ plotPairs,matrix: no visible global function definition for ‘pairs’ plotPairs,matrix: no visible global function definition for ‘points’ plotPairs,matrix: no visible global function definition for ‘abline’ plotPairs,matrix: no visible global function definition for ‘text’ plotPairs,matrix : draw.tree: no visible global function definition for ‘points’ plotPairs,matrix: no visible global function definition for ‘as.dendrogram’ quantileNormalize,ExpressionSet-ExpressionSet: no visible global function definition for ‘validObject’ quantileNormalize,ExpressionSet-ExpressionSet: no visible global function definition for ‘callGeneric’ quantileNormalize,ExpressionSet-missing: no visible global function definition for ‘validObject’ quantileNormalize,ExpressionSet-missing: no visible global function definition for ‘callGeneric’ quantileNormalize,ExpressionSet-vector: no visible global function definition for ‘validObject’ quantileNormalize,ExpressionSet-vector: no visible global function definition for ‘callGeneric’ quantileNormalize,matrix-missing: no visible global function definition for ‘callGeneric’ quantileNormalize,vector-ExpressionSet: no visible global function definition for ‘validObject’ quantileNormalize,vector-ExpressionSet: no visible global function definition for ‘callGeneric’ quantileNormalize,vector-vector: no visible global function definition for ‘quantile’ readDesign,character-character-ExpressionSet: no visible global function definition for ‘validObject’ readDesign,character-character-ExpressionSet: no visible global function definition for ‘read.table’ readDesign,character-character-ExpressionSet: no visible global function definition for ‘new’ readDesign,vector-missing-missing: no visible global function definition for ‘callGeneric’ readDesign,vector-missing-missing: no visible global function definition for ‘new’ readDesign,vector-vector-missing: no visible global function definition for ‘callGeneric’ readDesign,vector-vector-missing: no visible global function definition for ‘new’ readPairs,character-character-ExpressionSet: no visible global function definition for ‘validObject’ readPairs,character-character-ExpressionSet: no visible global function definition for ‘read.table’ readPairs,character-character-ExpressionSet: no visible global function definition for ‘new’ readPairs,vector-missing-missing: no visible global function definition for ‘callGeneric’ readPairs,vector-missing-missing: no visible global function definition for ‘new’ readPairs,vector-vector-missing: no visible global function definition for ‘callGeneric’ readPairs,vector-vector-missing: no visible global function definition for ‘new’ Undefined global functions or variables: abline as.dendrogram axis base.stacking.thermodynamics callGeneric col2rgb cor cutree data density dist hclust layout lines lowess mad median new pairs par points quantile rainbow read.table rect text validObject Consider adding importFrom("grDevices", "col2rgb", "rainbow") importFrom("graphics", "abline", "axis", "layout", "lines", "pairs", "par", "points", "rect", "text") importFrom("methods", "callGeneric", "new", "validObject") importFrom("stats", "as.dendrogram", "cor", "cutree", "density", "dist", "hclust", "lowess", "mad", "median", "quantile") importFrom("utils", "data", "read.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) combineData-methods.Rd:36: Lost braces 36 | \item{x = "ExpressionSet", y = "vector", w = "missing"}{ Handle input of an object of class \code{ExpressionSet} and a vector specifying grouping information. Derive weighting data from code{AssayDataElement}. } | ^ checkRd: (-1) fuzzyMatches.Rd:22: Lost braces 22 | \item{\option{nomatch}}{ numerical, specifying a value for non-matching values in code{x} when \code{strict = FALSE}, \code{keep = TRUE}, and \code{alias = FALSE}.} | ^ checkRd: (-1) fuzzyMatches.Rd:23: Lost braces 23 | \item{\option{na.rm}}{ a logical value indicating whether NA values should be stripped before the computation proceeds (default is \option{TRUE}). If \option{FALSE} any missing values in \code{x} will cause an error and missing values in code{y} may cause unexpected behavior. } | ^ * 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 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 * 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/HELP.Rcheck/00check.log’ for details.