CRAN Package Check Results for Package MAMA

Last updated on 2016-12-05 08:48:49.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.2.1 8.79 290.69 299.48 WARN
r-devel-linux-x86_64-debian-gcc 2.2.1 8.38 273.23 281.61 WARN
r-devel-linux-x86_64-fedora-clang 2.2.1 634.01 WARN --no-stop-on-test-error
r-devel-linux-x86_64-fedora-gcc 2.2.1 611.40 WARN --no-stop-on-test-error
r-devel-macos-x86_64-clang 2.2.1 438.93 WARN
r-devel-windows-ix86+x86_64 2.2.1 22.00 241.00 263.00 ERROR --no-vignettes
r-patched-linux-x86_64 2.2.1 9.14 258.98 268.13 WARN
r-patched-solaris-sparc 2.2.1 3440.90 WARN
r-patched-solaris-x86 2.2.1 649.90 WARN
r-release-linux-x86_64 2.2.1 8.37 252.35 260.73 WARN
r-release-osx-x86_64-mavericks 2.2.1 NOTE
r-release-windows-ix86+x86_64 2.2.1 30.00 178.00 208.00 NOTE --no-vignettes
r-oldrel-windows-ix86+x86_64 2.2.1 23.00 187.00 210.00 NOTE --no-vignettes

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-macos-x86_64-clang, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks

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-macos-x86_64-clang, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks

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-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-macos-x86_64-clang, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks

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-macos-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
    Consider adding
     importFrom("grDevices", "heat.colors")
     importFrom("graphics", "abline", "axis", "barplot", "boxplot", "hist",
     "image", "layout", "legend", "lines", "matplot", "mtext",
     "par", "plot.new", "points", "rect", "rug", "text", "title")
     importFrom("stats", "as.dendrogram", "density", "dist", "hclust",
     "integrate", "lm", "median", "order.dendrogram", "pchisq",
     "pt", "qchisq", "qqplot", "quantile", "reorder", "sd")
     importFrom("utils", "write.table")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-macos-x86_64-clang, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks

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-patched-linux-x86_64, r-release-linux-x86_64

Version: 2.2.1
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
     %*%, apply, crossprod, matrix, tcrossprod
    
    C code of R package 'Rmpfr': GMP using 64 bits per limb
    
    
    Attaching package: ‘Rmpfr’
    
    The following objects are masked from ‘package:BiocGenerics’:
    
     cbind, pmax, pmin, rbind
    
    The following objects are masked from ‘package:stats’:
    
     dbinom, dnorm, dpois, pnorm
    
    The following objects are masked from ‘package:base’:
    
     cbind, pmax, pmin, rbind
    
    
    Error: processing vignette ‘MAMA.rnw’ failed with diagnostics:
     chunk 9
    Error in inputmatrix[badrows.ori, ] <- NA :
     object ‘inputmatrix’ not found
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-macos-x86_64-clang, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 2.2.1
Flags: --no-stop-on-test-error
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-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 2.2.1
Flags: --no-stop-on-test-error
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-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 2.2.1
Flags: --no-stop-on-test-error
Check: top-level files
Result: NOTE
    Non-standard file/directory found at top level:
     ‘Sweave’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 2.2.1
Flags: --no-stop-on-test-error
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-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 2.2.1
Flags: --no-stop-on-test-error
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-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 2.2.1
Flags: --no-stop-on-test-error
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
    Consider adding
     importFrom("grDevices", "heat.colors")
     importFrom("graphics", "abline", "axis", "barplot", "boxplot", "hist",
     "image", "layout", "legend", "lines", "matplot", "mtext",
     "par", "plot.new", "points", "rect", "rug", "text", "title")
     importFrom("stats", "as.dendrogram", "density", "dist", "hclust",
     "integrate", "lm", "median", "order.dendrogram", "pchisq",
     "pt", "qchisq", "qqplot", "quantile", "reorder", "sd")
     importFrom("utils", "write.table")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 2.2.1
Flags: --no-stop-on-test-error
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-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 2.2.1
Flags: --no-stop-on-test-error
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Loading required package: genefilter
    Loading required package: metaMA
    
    Attaching package: ‘metaMA’
    
    The following object is masked from ‘package:genefilter’:
    
     rowVars
    
    Loading required package: xtable
    Loading required package: multtest
    Loading required package: BiocGenerics
    Loading required package: parallel
    
    Attaching package: ‘BiocGenerics’
    
    The following objects are masked from ‘package:parallel’:
    
     clusterApply, clusterApplyLB, clusterCall,
     clusterEvalQ, clusterExport, clusterMap,
     parApply, parCapply, parLapply, parLapplyLB,
     parRapply, parSapply, parSapplyLB
    
    The following objects are masked from ‘package:stats’:
    
     IQR, mad, sd, var, xtabs
    
    The following objects are masked from ‘package:base’:
    
     Filter, Find, Map, Position, Reduce,
     anyDuplicated, append, as.data.frame, cbind,
     colMeans, colSums, colnames, do.call, duplicated,
     eval, evalq, get, grep, grepl, intersect,
     is.unsorted, lapply, lengths, mapply, match,
     mget, order, paste, pmax, pmax.int, pmin,
     pmin.int, rank, rbind, rowMeans, rowSums,
     rownames, sapply, setdiff, sort, table, tapply,
     union, unique, unsplit, which, which.max,
     which.min
    
    Loading required package: Biobase
    Welcome to Bioconductor
    
     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
    Loading required package: Rmpfr
    Loading required package: gmp
    
    Attaching package: ‘gmp’
    
    The following objects are masked from ‘package:base’:
    
     %*%, apply, crossprod, matrix, tcrossprod
    
    C code of R package 'Rmpfr': GMP using 64 bits per limb
    
    
    Attaching package: ‘Rmpfr’
    
    The following objects are masked from ‘package:BiocGenerics’:
    
     cbind, pmax, pmin, rbind
    
    The following objects are masked from ‘package:stats’:
    
     dbinom, dnorm, dpois, pnorm
    
    The following objects are masked from ‘package:base’:
    
     cbind, pmax, pmin, rbind
    
    
    Error: processing vignette 'MAMA.rnw' failed with diagnostics:
     chunk 9
    Error in inputmatrix[badrows.ori, ] <- NA :
     object 'inputmatrix' not found
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 2.2.1
Flags: --no-vignettes
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-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.2.1
Flags: --no-vignettes
Check: whether package can be installed
Result: ERROR
    Installation failed.
Flavor: r-devel-windows-ix86+x86_64

Version: 2.2.1
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Loading required package: genefilter
    Loading required package: metaMA
    
    Attaching package: ‘metaMA’
    
    The following object is masked from ‘package:genefilter’:
    
     rowVars
    
    Loading required package: xtable
    Loading required package: multtest
    Loading required package: BiocGenerics
    Loading required package: parallel
    
    Attaching package: ‘BiocGenerics’
    
    The following objects are masked from ‘package:parallel’:
    
     clusterApply, clusterApplyLB, clusterCall,
     clusterEvalQ, clusterExport, clusterMap,
     parApply, parCapply, parLapply, parLapplyLB,
     parRapply, parSapply, parSapplyLB
    
    The following objects are masked from ‘package:stats’:
    
     IQR, mad, xtabs
    
    The following objects are masked from ‘package:base’:
    
     Filter, Find, Map, Position, Reduce,
     anyDuplicated, append, as.data.frame, cbind,
     colnames, do.call, duplicated, eval, evalq, get,
     grep, grepl, intersect, is.unsorted, lapply,
     lengths, mapply, match, mget, order, paste, pmax,
     pmax.int, pmin, pmin.int, rank, rbind, rownames,
     sapply, setdiff, sort, table, tapply, union,
     unique, unsplit, which, which.max, which.min
    
    Loading required package: Biobase
    Welcome to Bioconductor
    
     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
    Loading required package: Rmpfr
    Loading required package: gmp
    
    Attaching package: ‘gmp’
    
    The following objects are masked from ‘package:base’:
    
     %*%, apply, crossprod, matrix, tcrossprod
    
    C code of R package 'Rmpfr': GMP using 32 bits per limb
    
    
    Attaching package: ‘Rmpfr’
    
    The following objects are masked from ‘package:BiocGenerics’:
    
     cbind, pmax, pmin, rbind
    
    The following objects are masked from ‘package:stats’:
    
     dbinom, dnorm, dpois, pnorm
    
    The following objects are masked from ‘package:base’:
    
     cbind, pmax, pmin, rbind
    
    
    Error: processing vignette 'MAMA.rnw' failed with diagnostics:
     chunk 9
    Error in inputmatrix[badrows.ori, ] <- NA :
     object 'inputmatrix' not found
    Execution halted
Flavors: r-patched-solaris-sparc, r-patched-solaris-x86

Version: 2.2.1
Flags: --no-vignettes
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-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.2.1
Flags: --no-vignettes
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-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.2.1
Flags: --no-vignettes
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
    Consider adding
     importFrom("grDevices", "heat.colors")
     importFrom("graphics", "abline", "axis", "barplot", "boxplot", "hist",
     "image", "layout", "legend", "lines", "matplot", "mtext",
     "par", "plot.new", "points", "rect", "rug", "text", "title")
     importFrom("stats", "as.dendrogram", "density", "dist", "hclust",
     "integrate", "lm", "median", "order.dendrogram", "pchisq",
     "pt", "qchisq", "qqplot", "quantile", "reorder", "sd")
     importFrom("utils", "write.table")
    to your NAMESPACE file.
Flavor: r-release-windows-ix86+x86_64

Version: 2.2.1
Flags: --no-vignettes
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 : .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'
Flavor: r-oldrel-windows-ix86+x86_64