CRAN Package Check Results for Package MAMA

Last updated on 2014-07-30 20:48:47.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.2.1 10.18 336.15 346.33 NOTE
r-devel-linux-x86_64-debian-gcc 2.2.1 8.82 320.70 329.52 NOTE
r-devel-linux-x86_64-fedora-clang 2.2.1 743.26 NOTE
r-devel-linux-x86_64-fedora-gcc 2.2.1 707.37 NOTE
r-devel-osx-x86_64-clang 2.2.1 542.85 NOTE
r-devel-windows-ix86+x86_64 2.2.1 26.00 500.00 526.00 NOTE
r-patched-linux-x86_64 2.2.1 7.62 324.48 332.09 NOTE
r-patched-solaris-sparc 2.2.1 3777.90 NOTE
r-patched-solaris-x86 2.2.1 798.10 NOTE
r-release-linux-ix86 2.2.1 9.18 389.76 398.94 NOTE
r-release-linux-x86_64 2.2.1 7.84 312.65 320.49 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 22.00 492.00 514.00 NOTE
r-oldrel-windows-ix86+x86_64 2.2.1 33.00 562.00 595.00 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:
     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, 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: 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: 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: WARNING
    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