############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:qusage.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings qusage_2.41.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/qusage.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * 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 ‘qusage/DESCRIPTION’ ... OK * this is package ‘qusage’ version ‘2.41.0’ * 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 ‘qusage’ can be installed ... OK * checking installed package size ... INFO installed size is 8.8Mb sub-directories of 1Mb or more: data 8.5Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 absoluteTest : : no visible global function definition for ‘pchisq’ absoluteTest.genePvals: no visible global function definition for ‘qt’ absoluteTest.genePvals: no visible global function definition for ‘approx’ absoluteTest.genePvals: no visible global function definition for ‘dt’ absoluteTest.genePvals: no visible global function definition for ‘pnorm’ absoluteTest.genePvals: no visible global function definition for ‘pt’ absoluteTest.genePvalsFAST : : no visible global function definition for ‘pt’ aggregateGeneSet: no visible global function definition for ‘qt’ aggregateGeneSet : : no visible global function definition for ‘dt’ calcPCor: no visible global function definition for ‘model.matrix’ calcPCor: no visible global function definition for ‘formula’ calcPCor : : no visible global function definition for ‘cov’ calcVIF: no visible global function definition for ‘model.matrix’ calcVIF: no visible global function definition for ‘formula’ calcVIF : : no visible global function definition for ‘cov’ combinePDFs : : : no visible global function definition for ‘approx’ combinePDFs : : no visible global function definition for ‘approx’ compareTwoDistsFaster: no visible global function definition for ‘runif’ getExAbs: no visible global function definition for ‘approx’ homogeneityScore : : no visible global function definition for ‘pchisq’ makeComparison: no visible global function definition for ‘model.matrix’ makeComparison: no visible global function definition for ‘formula’ multi_conv : : no visible global function definition for ‘fft’ multi_conv: no visible global function definition for ‘fft’ plotCIs: no visible global function definition for ‘p.adjust’ plotCIs: no visible global function definition for ‘par’ plotCIs: no visible global function definition for ‘rgb’ plotCIs: no visible global function definition for ‘abline’ plotCIs: no visible global function definition for ‘gray’ plotCIs: no visible global function definition for ‘axis’ plotCIs: no visible global function definition for ‘text’ plotCIs: no visible global function definition for ‘arrows’ plotCIs: no visible global function definition for ‘points’ plotCIs: no visible global function definition for ‘strwidth’ plotCIs: no visible global function definition for ‘strheight’ plotCIs: no visible global function definition for ‘polygon’ plotCIs: no visible global function definition for ‘box’ plotCIsGenes : : no visible global function definition for ‘qt’ plotCIsGenes: no visible global function definition for ‘dt’ plotCIsGenes: no visible global function definition for ‘par’ plotCIsGenes: no visible global function definition for ‘abline’ plotCIsGenes: no visible global function definition for ‘gray’ plotCIsGenes: no visible global function definition for ‘polygon’ plotCIsGenes: no visible global function definition for ‘grey’ plotCIsGenes: no visible global function definition for ‘points’ plotCIsGenes: no visible global function definition for ‘arrows’ plotCIsGenes: no visible global function definition for ‘axis’ plotCIsGenes: no visible global function definition for ‘text’ plotCIsGenes: no visible global function definition for ‘box’ plotCombinedPDF: no visible global function definition for ‘par’ plotCombinedPDF: no visible global function definition for ‘abline’ plotCombinedPDF: no visible global function definition for ‘lines’ plotDensityCurves: no visible global function definition for ‘par’ plotDensityCurves: no visible global function definition for ‘abline’ plotDensityCurves: no visible global function definition for ‘lines’ plotGeneSetDistributions: no visible global function definition for ‘layout’ plotGeneSetDistributions: no visible global function definition for ‘par’ plotGeneSetDistributions: no visible global function definition for ‘frame’ plotGeneSetDistributions: no visible global function definition for ‘text’ plotGeneSetDistributions: no visible global function definition for ‘axis’ plotGeneSetDistributions: no visible global function definition for ‘dt’ plotGeneSetDistributions: no visible global function definition for ‘quantile’ plotGeneSetDistributions: no visible global function definition for ‘rect’ plotGeneSetDistributions: no visible global function definition for ‘col2rgb’ plotGeneSetDistributions: no visible global function definition for ‘rainbow’ plotGeneSetDistributions: no visible global function definition for ‘colorRamp’ plotGeneSetDistributions: no visible global function definition for ‘rgb’ plotGeneSetDistributions: no visible global function definition for ‘approx’ plotGeneSetDistributions: no visible global function definition for ‘lines’ plotGeneSetDistributions: no visible global function definition for ‘abline’ qgen: no visible global function definition for ‘median’ qgen: no visible global function definition for ‘model.matrix’ qgen: no visible global function definition for ‘formula’ qgen: no visible global function definition for ‘residuals’ qgen: no visible global function definition for ‘lm’ qgen: no visible global function definition for ‘setNames’ qsTable: no visible global function definition for ‘p.adjust’ twoCurve.pVal : : no visible global function definition for ‘approx’ weighted_conv: no visible global function definition for ‘approx’ weighted_conv: no visible global function definition for ‘convolve’ Undefined global functions or variables: abline approx arrows axis box col2rgb colorRamp convolve cov dt fft formula frame gray grey layout lines lm median model.matrix p.adjust par pchisq pnorm points polygon pt qt quantile rainbow rect residuals rgb runif setNames strheight strwidth text Consider adding importFrom("grDevices", "col2rgb", "colorRamp", "gray", "grey", "rainbow", "rgb") importFrom("graphics", "abline", "arrows", "axis", "box", "frame", "layout", "lines", "par", "points", "polygon", "rect", "strheight", "strwidth", "text") importFrom("stats", "approx", "convolve", "cov", "dt", "fft", "formula", "lm", "median", "model.matrix", "p.adjust", "pchisq", "pnorm", "pt", "qt", "quantile", "residuals", "runif", "setNames") to your NAMESPACE file. * checking Rd files ... NOTE prepare_Rd: GeneSets.Rd:20: Dropping empty section \format * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: qgen.Rd: nlme Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 qgen 14.16 0.438 14.651 * 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/qusage.Rcheck/00check.log’ for details.