Last updated on 2014-11-24 23:47:08.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.2.1 | 9.24 | 319.16 | 328.39 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 2.2.1 | 8.87 | 310.22 | 319.09 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 2.2.1 | 677.31 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 2.2.1 | 659.24 | NOTE | |||
| r-devel-osx-x86_64-clang | 2.2.1 | 544.60 | NOTE | |||
| r-devel-windows-ix86+x86_64 | 2.2.1 | 26.00 | 464.00 | 490.00 | NOTE | |
| r-patched-linux-x86_64 | 2.2.1 | 8.96 | 337.30 | 346.26 | NOTE | |
| r-patched-solaris-sparc | 2.2.1 | 3949.10 | NOTE | |||
| r-patched-solaris-x86 | 2.2.1 | 862.80 | NOTE | |||
| r-release-linux-ix86 | 2.2.1 | 10.96 | 400.71 | 411.67 | NOTE | |
| r-release-linux-x86_64 | 2.2.1 | 9.28 | 331.42 | 340.70 | 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 | 30.00 | 505.00 | 535.00 | NOTE | |
| r-oldrel-windows-ix86+x86_64 | 2.2.1 | 23.00 | 423.00 | 446.00 | NOTE |
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: 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.
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, r-release-linux-ix86, r-release-linux-x86_64, r-release-windows-ix86+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’
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: 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: 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: 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-osx-x86_64-snowleopard, r-oldrel-windows-ix86+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’
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