############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:puma.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings puma_3.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/puma.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: aarch64-apple-darwin20 (64-bit) * 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 13.6.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘puma/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘puma’ version ‘3.44.0’ * 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 ‘puma’ can be installed ... WARNING Found the following significant warnings: pumaclust_c.c:181:24: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value] See ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/puma.Rcheck/00install.out’ for details. * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘oligoClasses’ 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 R 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 'library' or 'require' calls in package code: ‘ROCR’ ‘limma’ ‘pumadata’ ‘snow’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. ':::' calls which should be '::': ‘affy:::mm’ ‘affy:::pm’ ‘affy:::probeNames’ ‘oligo:::mm’ ‘oligo:::pm’ ‘oligo:::probeNames’ ‘oligo:::rma’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE PMmmgmos: no visible binding for global variable ‘median’ PMmmgmos: no visible global function definition for ‘description’ calcAUC: no visible global function definition for ‘prediction’ calcAUC: no visible global function definition for ‘performance’ calculateLimma: no visible global function definition for ‘lmFit’ calculateLimma: no visible global function definition for ‘contrasts.fit’ calculateLimma: no visible global function definition for ‘eBayes’ calculateTtest : : no visible global function definition for ‘t.test’ clusterApplyLBDots : submit: no visible global function definition for ‘sendCall’ clusterApplyLBDots: no visible global function definition for ‘recvOneResult’ clusterNormE: no visible global function definition for ‘var’ clusterNormVar: no visible global function definition for ‘var’ compareLimmapumaDE: no visible global function definition for ‘pdf’ compareLimmapumaDE: no visible global function definition for ‘dev.off’ compareLimmapumaDE: no visible global function definition for ‘par’ compareLimmapumaDE: no visible global function definition for ‘vennDiagram’ createDesignMatrix: no visible global function definition for ‘model.matrix’ erfc: no visible global function definition for ‘pnorm’ gmhta: no visible global function definition for ‘clusterEvalQ’ gmhta: no visible global function definition for ‘data’ gmhta: no visible global function definition for ‘clusterApplyLB’ gmhta: no visible global function definition for ‘stopCluster’ gmhta: no visible binding for global variable ‘median’ gmoExon: no visible global function definition for ‘clusterEvalQ’ gmoExon: no visible global function definition for ‘data’ gmoExon: no visible global function definition for ‘clusterApplyLB’ gmoExon: no visible global function definition for ‘stopCluster’ gmoExon: no visible binding for global variable ‘median’ igmoExon: no visible global function definition for ‘clusterEvalQ’ igmoExon: no visible global function definition for ‘read.table’ igmoExon: no visible global function definition for ‘data’ igmoExon: no visible global function definition for ‘clusterApplyLB’ igmoExon: no visible global function definition for ‘stopCluster’ igmoExon: no visible binding for global variable ‘median’ just.mgmos: no visible binding for global variable ‘median’ just.mmgmos: no visible binding for global variable ‘median’ legend2: no visible global function definition for ‘par’ legend2: no visible global function definition for ‘xy.coords’ legend2 : rect2: no visible global function definition for ‘rect’ legend2 : segments2: no visible global function definition for ‘segments’ legend2 : points2: no visible global function definition for ‘points’ legend2 : text2: no visible global function definition for ‘text’ legend2: no visible global function definition for ‘strwidth’ legend2: no visible global function definition for ‘xinch’ legend2: no visible global function definition for ‘yinch’ legend2: no visible global function definition for ‘strheight’ matrixDistance: no visible global function definition for ‘dist’ mgmos: no visible binding for global variable ‘median’ mmgmos: no visible binding for global variable ‘median’ plot.pumaPCARes: no visible global function definition for ‘text’ plot.pumaPCARes: no visible global function definition for ‘legend’ plotErrorBars: no visible global function definition for ‘qnorm’ plotErrorBars: no visible global function definition for ‘par’ plotErrorBars: no visible global function definition for ‘even’ plotErrorBars: no visible global function definition for ‘odd’ plotErrorBars: no visible global function definition for ‘arrows’ plotErrorBars: no visible global function definition for ‘points’ plotErrorBars: no visible global function definition for ‘axis’ plotErrorBars: no visible global function definition for ‘title’ plotHistTwoClasses: no visible global function definition for ‘axis’ plotHistTwoClasses: no visible global function definition for ‘box’ plotROC: no visible global function definition for ‘prediction’ plotROC: no visible global function definition for ‘performance’ plotWhiskers: no visible global function definition for ‘segments’ plotWhiskers: no visible global function definition for ‘qnorm’ plotWhiskers: no visible global function definition for ‘points’ plotWhiskers: no visible global function definition for ‘abline’ pumaClust: no visible global function definition for ‘read.csv’ pumaClust: no visible global function definition for ‘kmeans’ pumaClust: no visible global function definition for ‘cov’ pumaClustii: no visible global function definition for ‘read.csv’ pumaClustii: no visible global function definition for ‘cov’ pumaComb: no visible global function definition for ‘getMPIcluster’ pumaComb: no visible global function definition for ‘makeCluster’ pumaComb: no visible global function definition for ‘clusterEvalQ’ pumaComb: no visible global function definition for ‘clusterApplyLB’ pumaCombImproved: no visible global function definition for ‘getMPIcluster’ pumaCombImproved: no visible global function definition for ‘makeCluster’ pumaCombImproved: no visible global function definition for ‘clusterEvalQ’ pumaCombImproved: no visible global function definition for ‘clusterApplyLB’ pumaFull: no visible global function definition for ‘pdf’ pumaFull: no visible global function definition for ‘par’ pumaFull: no visible global function definition for ‘prcomp’ pumaFull: no visible global function definition for ‘dev.off’ pumaNormalize: no visible binding for global variable ‘median’ pumaPCA: no visible global function definition for ‘prcomp’ pumaPCA: no visible global function definition for ‘rnorm’ pumaPCA: no visible global function definition for ‘optimise’ pumaPCA: no visible global function definition for ‘optim’ pumaPCA: no visible global function definition for ‘par’ pumaPCARemoveRedundancy: no visible global function definition for ‘dist’ write.reslts,DEResult: no visible global function definition for ‘write.table’ write.reslts,ExpressionSet: no visible global function definition for ‘write.table’ write.reslts,exprReslt: no visible global function definition for ‘write.table’ write.reslts,pumaPCARes: no visible global function definition for ‘write.table’ Undefined global functions or variables: abline arrows axis box clusterApplyLB clusterEvalQ contrasts.fit cov data description dev.off dist eBayes even getMPIcluster kmeans legend lmFit makeCluster median model.matrix odd optim optimise par pdf performance pnorm points prcomp prediction qnorm read.csv read.table rect recvOneResult rnorm segments sendCall stopCluster strheight strwidth t.test text title var vennDiagram write.table xinch xy.coords yinch Consider adding importFrom("grDevices", "dev.off", "pdf", "xy.coords") importFrom("graphics", "abline", "arrows", "axis", "box", "legend", "par", "points", "rect", "segments", "strheight", "strwidth", "text", "title", "xinch", "yinch") importFrom("stats", "cov", "dist", "kmeans", "median", "model.matrix", "optim", "optimise", "pnorm", "prcomp", "qnorm", "rnorm", "t.test", "var") importFrom("utils", "data", "read.csv", "read.table", "write.table") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) DEResult-class.Rd:92: Escaped LaTeX specials: \_ checkRd: (-1) DEResult-class.Rd:93: Escaped LaTeX specials: \_ checkRd: (-1) PMmmgmos.Rd:26: Escaped LaTeX specials: \_ checkRd: (-1) PMmmgmos.Rd:37: Escaped LaTeX specials: \_ checkRd: (-1) createContrastMatrix.Rd:20: Escaped LaTeX specials: \& checkRd: (-1) exprReslt-class.Rd:100: Escaped LaTeX specials: \_ checkRd: (-1) exprReslt-class.Rd:101: Escaped LaTeX specials: \_ \_ \_ checkRd: (-1) exprReslt-class.Rd:102: Escaped LaTeX specials: \_ \_ \_ checkRd: (-1) gmhta.Rd:26: Escaped LaTeX specials: \_ checkRd: (-1) gmoExon.Rd:28: Escaped LaTeX specials: \_ checkRd: (-1) hcomb.Rd:22: Escaped LaTeX specials: \_ checkRd: (-1) hcomb.Rd:23: Escaped LaTeX specials: \_ checkRd: (-1) igmoExon.Rd:28: Escaped LaTeX specials: \_ checkRd: (-1) justmgMOS.Rd:41: Escaped LaTeX specials: \_ \_ checkRd: (-1) justmmgMOS.Rd:41: Escaped LaTeX specials: \_ \_ checkRd: (-1) legend2.Rd:134: Escaped LaTeX specials: \& checkRd: (-1) mgmos.Rd:25: Escaped LaTeX specials: \_ \_ checkRd: (-1) mgmos.Rd:35: Escaped LaTeX specials: \_ checkRd: (-1) mmgmos.Rd:26: Escaped LaTeX specials: \_ \_ checkRd: (-1) mmgmos.Rd:37: Escaped LaTeX specials: \_ checkRd: (-1) mmgmos.Rd:38: Escaped LaTeX specials: \_ checkRd: (-1) pumaFull.Rd:23: Escaped LaTeX specials: \_ \_ checkRd: (-1) pumaFull.Rd:24: Escaped LaTeX specials: \_ checkRd: (-1) pumaFull.Rd:25: 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 ... 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 line endings in C/C++/Fortran sources/headers ... 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed puma-package 39.032 1.021 40.150 pumaDE 26.556 0.074 26.649 pumaCombImproved 14.829 0.133 14.966 pumaComb 12.174 0.060 12.240 plot-methods 5.662 0.263 5.929 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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, 5 NOTEs See ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/puma.Rcheck/00check.log’ for details.