############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:puma.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings puma_3.37.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/puma.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'puma/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'puma' version '3.37.0' * 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 whether package 'puma' can be installed ... OK * 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 ... OK * 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 for x64 is not available File 'D:/biocbuild/bbs-3.15-bioc/R/library/puma/libs/x64/puma.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * 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 36.09 0.17 36.26 pumaDE 20.71 0.03 20.75 pumaComb 12.78 0.00 12.78 pumaCombImproved 9.63 0.00 9.63 pumaclust 5.70 0.02 5.72 * 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: 4 NOTEs See 'D:/biocbuild/bbs-3.15-bioc/meat/puma.Rcheck/00check.log' for details.