* using log directory 'd:/Rcompile/CRANpkg/local/3.1/MAMA.Rcheck' * using R version 3.1.3 (2015-03-09) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'MAMA/DESCRIPTION' ... OK * this is package 'MAMA' version '2.2.1' * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'genefilter' 'metaMA' 'xtable' 'multtest' 'gtools' 'grid' 'GeneMeta' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 'MAMA' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: 'GeneMeta' 'xtable' 'methods' 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE 'library' or 'require' calls to packages already attached by Depends: 'gtools' 'xtable' Please remove these calls from your code. 'library' or 'require' calls in package code: 'RankProd' 'gplots' Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Packages in Depends field not imported from: 'grid' 'metaMA' 'multtest' 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 RankProduct: no visible global function definition for 'RPadvance' RankProduct: no visible global function definition for 'topGene' entitybuild2: no visible global function definition for 'mt.teststat' mergeExprs2: no visible global function definition for 'featureNames' mergeExprs2: no visible global function definition for 'assayData' mergeExprs2: no visible global function definition for 'assayData<-' mergeExprs2: no visible global function definition for 'featureNames<-' meta.test: no visible global function definition for 'mt.teststat' metaMA: no visible global function definition for 'pvalcombination' metaMA: no visible global function definition for 'EScombination' plotgene: no visible global function definition for 'grid.newpage' plotgene: no visible global function definition for 'grid.layout' plotgene: no visible global function definition for 'unit' plotgene: no visible global function definition for 'viewport' plotgene: no visible global function definition for 'pushViewport' plotgene: no visible global function definition for 'convertHeight' plotgene: no visible global function definition for 'grobHeight' plotgene: no visible global function definition for 'textGrob' plotgene: no visible global function definition for 'grid.rect' plotgene: no visible global function definition for 'gpar' plotgene: no visible global function definition for 'grid.text' plotgene: no visible global function definition for 'popViewport' plotgene: no visible global function definition for 'grid.points' plotgene: no visible global function definition for 'grid.lines' plotgene: no visible global function definition for 'dataViewport' plotgene: no visible global function definition for 'grid.xaxis' plotgene: no visible global function definition for 'unit.c' plotgene: no visible global function definition for 'convertX' plot,MetaArray-ANY : .local: no visible global function definition for 'grid.newpage' plot,MetaArray-ANY : .local: no visible global function definition for 'grid.layout' plot,MetaArray-ANY : .local: no visible global function definition for 'unit' plot,MetaArray-ANY : .local: no visible global function definition for 'viewport' plot,MetaArray-ANY : .local: no visible global function definition for 'pushViewport' plot,MetaArray-ANY : .local: no visible global function definition for 'plotViewport' plot,MetaArray-ANY : .local: no visible global function definition for 'grid.text' plot,MetaArray-ANY : .local: no visible global function definition for 'popViewport' plot,MetaArray-ANY : .local: no visible global function definition for 'grid.rect' plot,MetaArray-ANY : .local: no visible global function definition for 'gpar' plot,MetaArray-ANY : .local: no visible global function definition for 'grid.lines' plot,MetaArray-ANY : .local: no visible global function definition for 'grid.xaxis' * 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 sizes of PDF files under 'inst/doc' ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [31s] OK * 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 NOTE: There were 4 notes.