CRAN Package Check Results for Package MAMA

Last updated on 2014-04-16 15:49:30.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.2.1 8.10 329.62 337.72 NOTE
r-devel-linux-x86_64-debian-gcc 2.2.1 8.22 313.51 321.74 NOTE
r-devel-linux-x86_64-fedora-clang 2.2.1 698.53 NOTE
r-devel-linux-x86_64-fedora-gcc 2.2.1 678.45 NOTE
r-devel-macosx-x86_64-clang 2.2.1 522.58 NOTE
r-devel-macosx-x86_64-gcc 2.2.1 ERROR
r-devel-windows-ix86+x86_64 2.2.1 21.00 477.00 498.00 NOTE
r-patched-linux-x86_64 2.2.1 8.74 316.42 325.16 NOTE
r-patched-solaris-sparc 2.2.1 3711.60 NOTE
r-patched-solaris-x86 2.2.1 793.50 NOTE
r-release-linux-ix86 2.2.1 16.00 489.00 505.00 NOTE
r-release-linux-x86_64 2.2.1 8.24 324.82 333.05 NOTE
r-release-macosx-x86_64 2.2.1 ERROR
r-release-windows-ix86+x86_64 2.2.1 23.00 464.00 487.00 NOTE
r-oldrel-windows-ix86+x86_64 2.2.1 21.00 423.00 444.00 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-macosx-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-macosx-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, 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-macosx-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, 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
    Packages required but not available:
     ‘genefilter’ ‘metaMA’ ‘multtest’ ‘GeneMeta’ ‘MergeMaid’ ‘metaArray’
    
    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.
Flavors: r-devel-macosx-x86_64-gcc, r-release-macosx-x86_64