CRAN Package Check Results for Package MAMA

Last updated on 2015-07-07 14:48:16.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.2.1 6.84 266.64 273.48 NOTE
r-devel-linux-x86_64-debian-gcc 2.2.1 7.23 262.07 269.30 NOTE
r-devel-linux-x86_64-fedora-clang 2.2.1 563.06 NOTE
r-devel-linux-x86_64-fedora-gcc 2.2.1 394.54 NOTE
r-devel-osx-x86_64-clang 2.2.1 462.50 NOTE
r-devel-windows-ix86+x86_64 2.2.1 27.00 589.00 616.00 NOTE
r-patched-linux-x86_64 2.2.1 6.94 283.14 290.08 NOTE
r-patched-solaris-sparc 2.2.1 3371.90 NOTE
r-patched-solaris-x86 2.2.1 693.40 NOTE
r-release-linux-x86_64 2.2.1 6.76 261.15 267.91 NOTE
r-release-osx-x86_64-mavericks 2.2.1 WARN
r-release-windows-ix86+x86_64 2.2.1 27.00 491.00 518.00 NOTE
r-oldrel-windows-ix86+x86_64 2.2.1 32.00 702.00 734.00 NOTE

Check Details

Version: 2.2.1
Check: package dependencies
Result: 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.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.2.1
Check: DESCRIPTION meta-information
Result: 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.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.2.1
Check: top-level files
Result: NOTE
    Non-standard file/directory found at top level:
     ‘Sweave’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 2.2.1
Check: dependencies in R code
Result: 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.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.2.1
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     plot.SOGLresult
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64

Version: 2.2.1
Check: R code for possible problems
Result: NOTE
    MAP.Matches: no visible global function definition for ‘quantile’
    MAP.genes: no visible global function definition for ‘write.table’
    RandomScore: no visible binding for global variable ‘quantile’
    RankProduct: no visible global function definition for ‘RPadvance’
    RankProduct: no visible global function definition for ‘topGene’
    T.select: no visible global function definition for ‘quantile’
    T.select: no visible global function definition for ‘lm’
    T.select: no visible global function definition for ‘abline’
    T.select: no visible global function definition for ‘points’
    cv.filter : <anonymous>: no visible global function definition for ‘sd’
    cv.filter: no visible global function definition for ‘abline’
    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’
    meta.test: no visible global function definition for ‘pt’
    metaMA: no visible global function definition for ‘pvalcombination’
    metaMA: no visible global function definition for ‘EScombination’
    metaheat: no visible binding for global variable ‘dist’
    metaheat: no visible binding for global variable ‘hclust’
    metaheat: no visible global function definition for ‘heat.colors’
    metaheat: no visible global function definition for ‘as.dendrogram’
    metaheat: no visible global function definition for ‘reorder’
    metaheat: no visible global function definition for ‘order.dendrogram’
    metaheat: no visible global function definition for ‘par’
    metaheat: no visible global function definition for ‘layout’
    metaheat: no visible global function definition for ‘image’
    metaheat: no visible global function definition for ‘axis’
    metaheat: no visible global function definition for ‘barplot’
    metaheat2: no visible binding for global variable ‘dist’
    metaheat2: no visible binding for global variable ‘hclust’
    metaheat2: no visible global function definition for ‘par’
    metaheat2: no visible global function definition for ‘median’
    metaheat2: no visible global function definition for ‘order.dendrogram’
    metaheat2: no visible global function definition for ‘as.dendrogram’
    metaheat2: no visible global function definition for ‘reorder’
    metaheat2: no visible binding for global variable ‘sd’
    metaheat2: no visible global function definition for ‘layout’
    metaheat2: no visible global function definition for ‘image’
    metaheat2: no visible global function definition for ‘axis’
    metaheat2: no visible global function definition for ‘mtext’
    metaheat2: no visible global function definition for ‘rect’
    metaheat2: no visible global function definition for ‘abline’
    metaheat2: no visible global function definition for ‘lines’
    metaheat2: no visible global function definition for ‘text’
    metaheat2: no visible global function definition for ‘plot.new’
    metaheat2: no visible global function definition for ‘title’
    metaheat2: no visible global function definition for ‘density’
    metaheat2: no visible global function definition for ‘hist’
    metaheat2: no visible global function definition for ‘legend’
    plot.SOGLresult: no visible global function definition for ‘abline’
    plot.SOGLresult: no visible global function definition for ‘mtext’
    plot.SOGLresult: no visible global function definition for ‘density’
    plot.SOGLresult: no visible global function definition for ‘lines’
    plot.SOGLresult: no visible global function definition for ‘text’
    plot.SOGLresult: no visible global function definition for ‘rug’
    plot.SOGLresult: no visible global function definition for ‘legend’
    plot.SOGLresult: no visible global function definition for ‘matplot’
    plot.SOGLresult: no visible global function definition for ‘axis’
    plotES: no visible global function definition for ‘par’
    plotES: no visible global function definition for ‘points’
    plotES: no visible global function definition for ‘legend’
    plotQvsChi: no visible global function definition for ‘qchisq’
    plotQvsChi: no visible global function definition for ‘quantile’
    plotQvsChi: no visible global function definition for ‘qqplot’
    plotQvsChi: no visible global function definition for ‘lines’
    plotclinical: no visible global function definition for ‘layout’
    plotclinical: no visible global function definition for ‘par’
    plotclinical: no visible global function definition for ‘text’
    plotclinical: no visible global function definition for ‘barplot’
    plotclinical: no visible global function definition for ‘boxplot’
    plotclinical: no visible global function definition for ‘legend’
    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’
    plotgene2: no visible global function definition for ‘layout’
    plotgene2: no visible global function definition for ‘par’
    plotgene2: no visible global function definition for ‘image’
    plotgene2: no visible global function definition for ‘axis’
    plotgene2: no visible global function definition for ‘abline’
    plotgene2: no visible global function definition for ‘lines’
    plotpattern: no visible global function definition for ‘matplot’
    plotpattern: no visible global function definition for ‘legend’
    plotpattern: no visible global function definition for ‘abline’
    plotpattern: no visible global function definition for ‘lines’
    plotpattern: no visible global function definition for ‘points’
    plotpattern: no visible global function definition for ‘axis’
    sd.filter: no visible global function definition for ‘abline’
    selectAlpha: no visible global function definition for ‘integrate’
    zScores: no visible global function definition for ‘pchisq’
    plot,MetaArray-ANY: no visible global function definition for
     ‘grid.newpage’
    plot,MetaArray-ANY: no visible global function definition for
     ‘grid.layout’
    plot,MetaArray-ANY: no visible global function definition for ‘unit’
    plot,MetaArray-ANY: no visible global function definition for
     ‘viewport’
    plot,MetaArray-ANY: no visible global function definition for
     ‘pushViewport’
    plot,MetaArray-ANY: no visible global function definition for
     ‘plotViewport’
    plot,MetaArray-ANY: no visible global function definition for
     ‘grid.text’
    plot,MetaArray-ANY: no visible global function definition for
     ‘popViewport’
    plot,MetaArray-ANY: no visible global function definition for
     ‘grid.rect’
    plot,MetaArray-ANY: no visible global function definition for ‘gpar’
    plot,MetaArray-ANY: no visible global function definition for
     ‘grid.lines’
    plot,MetaArray-ANY: no visible global function definition for
     ‘grid.xaxis’
    Undefined global functions or variables:
     EScombination RPadvance abline as.dendrogram assayData assayData<-
     axis barplot boxplot convertHeight convertX dataViewport density dist
     featureNames featureNames<- gpar grid.layout grid.lines grid.newpage
     grid.points grid.rect grid.text grid.xaxis grobHeight hclust
     heat.colors hist image integrate layout legend lines lm matplot
     median mt.teststat mtext order.dendrogram par pchisq plot.new
     plotViewport points popViewport pt pushViewport pvalcombination
     qchisq qqplot quantile rect reorder rug sd text textGrob title
     topGene unit unit.c viewport write.table
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64

Version: 2.2.1
Check: Rd line widths
Result: NOTE
    Rd file 'MAP.Matches.Rd':
     \usage lines wider than 90 characters:
     MAP.Matches(data, varname, t.cutoff = "98.00%", multiple = TRUE, perm = c("both", "columns", "labels")[1], nperm = 1000, test = c("t", ... [TRUNCATED]
    
    Rd file 'RandomScore.Rd':
     \usage lines wider than 90 characters:
     RandomScore(data, varname, B, alpha, test, which = c("random", "empirical", "subsample"), two.sided = TRUE)
    
    Rd file 'RankProduct.Rd':
     \usage lines wider than 90 characters:
     RankProduct(data, varname, num.perm = 100, logged = TRUE, na.rm = FALSE, gene.names = NULL, plot = FALSE, rand = NULL, cutoff = 0.05)
    
    Rd file 'Z.Rd':
     \examples lines wider than 100 characters:
     lists<-list(Method1=c("Gene_A", "Gene_V","Gene_S","Gene_C","Gene_U","Gene_D","Gene_E","Gene_G","Gene_W"),
    
    Rd file 'conting.tab.Rd':
     \examples lines wider than 100 characters:
     lists<-list(Method1=c("Gene_A", "Gene_V","Gene_S","Gene_C","Gene_U","Gene_D","Gene_E","Gene_G","Gene_W"),
    
    Rd file 'entitybuild2.Rd':
     \usage lines wider than 90 characters:
     entitybuild2(expr.mat, ALLtype = NULL, type, dataset = NULL, minSampleNum = 3, method = "t", random = FALSE)
    
    Rd file 'fold.change.Rd':
     \examples lines wider than 100 characters:
     dataset<-new("MetaArray", GEDM=list(Singhdata$esets[[1]], Singhdata$esets[[2]], Singhdata$esets[[3]]),
    
    Rd file 'gene.list.Rd':
     \examples lines wider than 100 characters:
     lists<-list(Method1=c("Gene_A", "Gene_V","Gene_S","Gene_C","Gene_U","Gene_D","Gene_E","Gene_G","Gene_W"),
    
    Rd file 'gene.select.FC.Rd':
     \examples lines wider than 100 characters:
     dataset<-new("MetaArray", GEDM=list(Singhdata$esets[[1]], Singhdata$esets[[2]], Singhdata$esets[[3]]),
    
    Rd file 'make.matrix.Rd':
     \examples lines wider than 100 characters:
     lists<-list(Method1=c("Gene_A", "Gene_V","Gene_S","Gene_C","Gene_U","Gene_D","Gene_E","Gene_G","Gene_W"),
    
    Rd file 'metaMA.Rd':
     \usage lines wider than 90 characters:
     metaMA(data, varname, moderated = c("limma", "SMVar", "t")[1], BHth = 0.05, which = c("pval", "ES")[1])
    
    Rd file 'metaheat.Rd':
     \usage lines wider than 90 characters:
     metaheat(x, Rowv = NA, Colv = NA, distfun = dist, hclustfun = hclust, na.rm = TRUE, do.dendro = c(TRUE, TRUE), legend = 0, legfrac = 8, ... [TRUNCATED]
     \examples lines wider than 100 characters:
     lists<-list(Method1=c("Gene_A", "Gene_V","Gene_S","Gene_C","Gene_U","Gene_D","Gene_E","Gene_G","Gene_W"),
    
    Rd file 'metaheat2.Rd':
     \usage lines wider than 90 characters:
     metaheat2(x, Rowv = TRUE, Colv = if (symm) "Rowv" else TRUE, distfun = dist, hclustfun = hclust, dendrogram = c("both", "row", "column" ... [TRUNCATED]
    
    Rd file 'performSOGL.Rd':
     \usage lines wider than 90 characters:
     performSOGL(data, varname, test, B, which = c("score", "empirical"), min.weight = 1e-05, two.sided = TRUE, percent = 0.95)
    
    Rd file 'probs.to.matrix.Rd':
     \examples lines wider than 100 characters:
     lists<-list(Method1=c("Gene_A", "Gene_V","Gene_S","Gene_C","Gene_U","Gene_D","Gene_E","Gene_G","Gene_W"),
    
    Rd file 'rank.genes.Rd':
     \examples lines wider than 100 characters:
     p1<-apply(Singhdata$esets[[1]],1,function(x) {t=t.test(x~Singhdata$classes[[1]], alternative="two.sided"); return(t$p.value) })
     p2<-apply(Singhdata$esets[[2]],1,function(x) {t=t.test(x~Singhdata$classes[[2]], alternative="two.sided"); return(t$p.value) })
     p3<-apply(Singhdata$esets[[3]],1,function(x) {t=t.test(x~Singhdata$classes[[3]], alternative="two.sided"); return(t$p.value) })
     T1<-apply(Singhdata$esets[[1]],1,function(x) {t=t.test(x~Singhdata$classes[[1]], alternative="two.sided"); return(t$statistic) })
     T2<-apply(Singhdata$esets[[2]],1,function(x) {t=t.test(x~Singhdata$classes[[2]], alternative="two.sided"); return(t$statistic) })
     T3<-apply(Singhdata$esets[[3]],1,function(x) {t=t.test(x~Singhdata$classes[[3]], alternative="two.sided"); return(t$statistic) })
    
    Rd file 'selectClass.Rd':
     \examples lines wider than 100 characters:
     dataset<-new("MetaArray", GEDM=list(Singhdata$esets[[1]], Singhdata$esets[[2]], Singhdata$esets[[3]]),
    
    These lines will be truncated in the PDF manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 2.2.1
Check: R code for possible problems
Result: 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: no visible global function definition for
     ‘grid.newpage’
    plot,MetaArray-ANY: no visible global function definition for
     ‘grid.layout’
    plot,MetaArray-ANY: no visible global function definition for ‘unit’
    plot,MetaArray-ANY: no visible global function definition for
     ‘viewport’
    plot,MetaArray-ANY: no visible global function definition for
     ‘pushViewport’
    plot,MetaArray-ANY: no visible global function definition for
     ‘plotViewport’
    plot,MetaArray-ANY: no visible global function definition for
     ‘grid.text’
    plot,MetaArray-ANY: no visible global function definition for
     ‘popViewport’
    plot,MetaArray-ANY: no visible global function definition for
     ‘grid.rect’
    plot,MetaArray-ANY: no visible global function definition for ‘gpar’
    plot,MetaArray-ANY: no visible global function definition for
     ‘grid.lines’
    plot,MetaArray-ANY: no visible global function definition for
     ‘grid.xaxis’
    Undefined global functions or variables:
     EScombination RPadvance assayData assayData<- convertHeight convertX
     dataViewport featureNames featureNames<- gpar grid.layout grid.lines
     grid.newpage grid.points grid.rect grid.text grid.xaxis grobHeight
     mt.teststat plotViewport popViewport pushViewport pvalcombination
     textGrob topGene unit unit.c viewport
Flavor: r-devel-osx-x86_64-clang

Version: 2.2.1
Check: R code for possible problems
Result: 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’
Flavors: r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.2.1
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘RankProd’
    
    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.
Flavor: r-release-osx-x86_64-mavericks

Version: 2.2.1
Check: running R code from vignettes
Result: WARN
    Errors in running code in vignettes:
    when running code in ‘MAMA.rnw’
     ...
    
    > rp <- RankProduct(ColonData, "MSIstatus", num.perm = 50,
    + gene.names = rownames(GEDM(ColonData)[[1]]))
    Loading required package: RankProd
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called ‘RankProd’
    
     When sourcing ‘MAMA.R’:
    Error: library RankProd is missing
    Execution halted
Flavor: r-release-osx-x86_64-mavericks

Version: 2.2.1
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    
     Vignettes contain introductory material; view
     with 'browseVignettes()'. To cite Bioconductor,
     see 'citation("Biobase")', and for packages
     'citation("pkgname")'.
    
    Loading required package: gtools
    Loading required package: grid
    Loading required package: GeneMeta
    
    Attaching package: ‘MAMA’
    
    The following objects are masked from ‘package:GeneMeta’:
    
     multExpFDR, zScoreFDR, zScorePermuted, zScores
    
    Loading required package: RankProd
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called ‘RankProd’
    
    Error: processing vignette 'MAMA.rnw' failed with diagnostics:
     chunk 9
    Error in RankProduct(ColonData, "MSIstatus", num.perm = 50, gene.names = rownames(GEDM(ColonData)[[1]])) :
     library RankProd is missing
    Execution halted
Flavor: r-release-osx-x86_64-mavericks