CRAN Package Check Results for Package MAMA

Last updated on 2014-09-01 21:48:53.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.2.1 8.72 317.85 326.57 NOTE
r-devel-linux-x86_64-debian-gcc 2.2.1 10.66 328.58 339.24 NOTE
r-devel-linux-x86_64-fedora-clang 2.2.1 718.95 NOTE
r-devel-linux-x86_64-fedora-gcc 2.2.1 685.97 NOTE
r-devel-osx-x86_64-clang 2.2.1 513.04 NOTE
r-devel-windows-ix86+x86_64 2.2.1 25.00 458.00 483.00 NOTE
r-patched-linux-x86_64 2.2.1 7.54 304.19 311.73 NOTE
r-patched-solaris-sparc 2.2.1 3781.60 NOTE
r-patched-solaris-x86 2.2.1 791.10 NOTE
r-release-linux-ix86 2.2.1 9.36 393.68 403.04 NOTE
r-release-linux-x86_64 2.2.1 7.76 307.04 314.80 NOTE
r-release-osx-x86_64-mavericks 2.2.1 ERROR
r-release-osx-x86_64-snowleopard 2.2.1 WARN
r-release-windows-ix86+x86_64 2.2.1 22.00 477.00 499.00 NOTE
r-oldrel-windows-ix86+x86_64 2.2.1 30.00 413.00 443.00 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-ix86, r-release-linux-x86_64, r-release-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-ix86, r-release-linux-x86_64, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+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.
    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.
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of 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-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86

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-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

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-fedora-clang, r-devel-linux-x86_64-fedora-gcc

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-fedora-clang, r-devel-linux-x86_64-fedora-gcc

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.
    Packages in Depends field not imported from:
     ‘metaMA’ ‘multtest’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of the ‘Writing R Extensions’ manual.
Flavors: r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.2.1
Check: package dependencies
Result: ERROR
    Package required but not available: ‘genefilter’
    
    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.
    
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of the ‘Writing R Extensions’ manual.
Flavor: r-release-osx-x86_64-mavericks

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-snowleopard

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’
Flavor: r-release-osx-x86_64-snowleopard

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-snowleopard

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-snowleopard