############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiSeq_1.46.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BiSeq.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 ‘BiSeq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BiSeq’ version ‘1.46.0’ * 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 ‘BiSeq’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘methods’ ‘S4Vectors’ ‘IRanges’ ‘GenomicRanges’ ‘SummarizedExperiment’ ‘Formula’ 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 ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘Formula’ All declared Imports should be used. Package in Depends field not imported from: ‘Formula’ 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 .betaRegression : inv.link: no visible global function definition for ‘pnorm’ .betaRegression : beta.regr: no visible global function definition for ‘as.formula’ .categorialColors: no visible global function definition for ‘colors’ .estLocCor: no visible global function definition for ‘combn’ .logisticRegression : inv.link: no visible global function definition for ‘pnorm’ .logisticRegression : logistic.regr: no visible global function definition for ‘lm’ .logisticRegression : logistic.regr: no visible global function definition for ‘as.formula’ .makeVariogram: no visible global function definition for ‘qnorm’ .plotBindingSites: no visible global function definition for ‘txtProgressBar’ .plotBindingSites: no visible global function definition for ‘setTxtProgressBar’ .plotBindingSites : : no visible global function definition for ‘ksmooth’ .plotBindingSites: no visible global function definition for ‘rainbow’ .plotBindingSites: no visible global function definition for ‘lines’ .plotBindingSites: no visible global function definition for ‘rgb’ .plotBindingSites: no visible global function definition for ‘col2rgb’ .plotMeth: no visible global function definition for ‘col2rgb’ .plotMeth: no visible global function definition for ‘rgb’ .plotMeth: no visible global function definition for ‘lines’ .plotMeth: no visible global function definition for ‘legend’ .plotMethMap: no visible global function definition for ‘colorRampPalette’ .plotMethMap: no visible binding for global variable ‘heatmap’ .plotSmoothMeth: no visible global function definition for ‘rainbow’ .plotSmoothMeth: no visible global function definition for ‘lines’ .predictMeth: no visible global function definition for ‘txtProgressBar’ .predictMeth: no visible global function definition for ‘setTxtProgressBar’ .testClusters: no visible global function definition for ‘pnorm’ .trimClusters : integrand: no visible global function definition for ‘pnorm’ .trimClusters : integrand: no visible global function definition for ‘qnorm’ .trimClusters : integrand: no visible global function definition for ‘dnorm’ .trimClusters: no visible global function definition for ‘integrate’ .trimClusters: no visible global function definition for ‘pnorm’ .trimClusters: no visible global function definition for ‘qnorm’ .variogram: no visible global function definition for ‘dist’ .variogram: no visible global function definition for ‘txtProgressBar’ .variogram: no visible global function definition for ‘setTxtProgressBar’ .writeBED_BSraw: no visible global function definition for ‘colorRamp’ .writeBED_BSraw: no visible global function definition for ‘rgb’ .writeBED_BSrel: no visible global function definition for ‘colorRamp’ .writeBED_BSrel: no visible global function definition for ‘rgb’ betaRegression,formula-character-BSrel-numeric : inv.link: no visible global function definition for ‘pnorm’ betaRegression,formula-character-BSrel-numeric : beta.regr: no visible global function definition for ‘as.formula’ estLocCor,list: no visible global function definition for ‘combn’ logisticRegression,formula-character-BSrel-numeric : inv.link: no visible global function definition for ‘pnorm’ logisticRegression,formula-character-BSrel-numeric : logistic.regr: no visible global function definition for ‘lm’ logisticRegression,formula-character-BSrel-numeric : logistic.regr: no visible global function definition for ‘as.formula’ makeVariogram,data.frame-logical-numeric-numeric: no visible global function definition for ‘qnorm’ plotMethMap,BSrel-GRanges-factor-logical: no visible global function definition for ‘colorRampPalette’ plotMethMap,BSrel-GRanges-factor-logical: no visible binding for global variable ‘heatmap’ plotMethMap,BSrel-GRanges-factor-missing: no visible global function definition for ‘colorRampPalette’ plotMethMap,BSrel-GRanges-factor-missing: no visible binding for global variable ‘heatmap’ plotMethMap,BSrel-GRanges-missing-logical: no visible global function definition for ‘colorRampPalette’ plotMethMap,BSrel-GRanges-missing-logical: no visible binding for global variable ‘heatmap’ plotMethMap,BSrel-GRanges-missing-missing: no visible global function definition for ‘colorRampPalette’ plotMethMap,BSrel-GRanges-missing-missing: no visible binding for global variable ‘heatmap’ predictMeth,BSraw-numeric-numeric-numeric: no visible global function definition for ‘txtProgressBar’ predictMeth,BSraw-numeric-numeric-numeric: no visible global function definition for ‘setTxtProgressBar’ testClusters,list-numeric: no visible global function definition for ‘pnorm’ trimClusters,list-numeric : integrand: no visible global function definition for ‘pnorm’ trimClusters,list-numeric : integrand: no visible global function definition for ‘qnorm’ trimClusters,list-numeric : integrand: no visible global function definition for ‘dnorm’ trimClusters,list-numeric: no visible global function definition for ‘integrate’ trimClusters,list-numeric: no visible global function definition for ‘pnorm’ trimClusters,list-numeric: no visible global function definition for ‘qnorm’ writeBED,BSraw-character-character: no visible global function definition for ‘colorRamp’ writeBED,BSraw-character-character: no visible global function definition for ‘rgb’ writeBED,BSrel-character-character: no visible global function definition for ‘colorRamp’ writeBED,BSrel-character-character: no visible global function definition for ‘rgb’ Undefined global functions or variables: as.formula col2rgb colorRamp colorRampPalette colors combn dist dnorm heatmap integrate ksmooth legend lines lm pnorm qnorm rainbow rgb setTxtProgressBar txtProgressBar Consider adding importFrom("grDevices", "col2rgb", "colorRamp", "colorRampPalette", "colors", "rainbow", "rgb") importFrom("graphics", "legend", "lines") importFrom("stats", "as.formula", "dist", "dnorm", "heatmap", "integrate", "ksmooth", "lm", "pnorm", "qnorm") importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) DMRs.Rd:16: Lost braces 16 | DMRs: \code{median.p}, code{median.meth.group1}, | ^ checkRd: (-1) DMRs.Rd:17: Lost braces 17 | code{median.meth.group2}, \code{median.meth.diff}. | ^ * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed betaRegression 13.672 0.305 14.051 globalTest 11.143 0.059 11.252 * 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-3.20-bioc/meat/BiSeq.Rcheck/00check.log’ for details.