CRAN Package Check Results for Maintainer ‘Sebastian Kaiser <Sebastian.Kaiser at stat.uni-muenchen.de>’

Last updated on 2015-02-05 23:51:05.

Package biclust

Current CRAN status: NOTE: 14

Memtest notes: valgrind

Version: 1.0.2
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to ‘flexclust’ in package code.
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
    There are ::: calls to the package's namespace in its code. A package
     almost never needs to use ::: for its own objects:
     ‘drawHeatmap’ ‘heatmapBC’
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: 1.0.2
Check: R code for possible problems
Result: NOTE
    plaid: warning in matrix(c(nr, nk, layer.df[1:layer],
     round(SS[1:layer], 2), round(SS[1:layer]/layer.df[1:layer], 2),
     status[1:layer], rows.released[1:layer], cols.released[1:layer]),
     ncol = 8, dim = list(Layer = 1:layer - background, c("Rows", "Cols",
     "Df", "SS", "MS", "Convergence", "Rows Released", "Cols Released"))):
     partial argument match of ‘dim’ to ‘dimnames’
    updatePlaid: warning in tabulate(r * row.classes, nbin =
     max(row.classes)): partial argument match of ‘nbin’ to ‘nbins’
    updatePlaid: warning in tabulate(k * col.classes, nbin =
     max(col.classes)): partial argument match of ‘nbin’ to ‘nbins’
    biclustbarchart: no visible global function definition for
     ‘grid.newpage’
    biclustbarchart: no visible global function definition for
     ‘pushViewport’
    biclustbarchart: no visible global function definition for ‘viewport’
    biclustbarchart: no visible global function definition for ‘grid.text’
    biclustbarchart: no visible global function definition for
     ‘grid.segments’
    biclustbarchart: no visible global function definition for
     ‘grid.points’
    biclustbarchart: no visible global function definition for ‘grid.rect’
    clustmember: no visible global function definition for ‘as.kcca’
    createBarchartPanel : mypanel: no visible global function definition
     for ‘grid.segments’
    createBarchartPanel : mypanel: no visible global function definition
     for ‘panel.barchart’
    createBarchartPanel : mypanel: no visible global function definition
     for ‘grid.points’
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-mavericks, r-release-windows-ix86+x86_64

Version: 1.0.2
Check: Rd line widths
Result: NOTE
    Rd file 'BCPlaid.Rd':
     \usage lines wider than 90 characters:
     background = TRUE, background.layer = NA, background.df = 1, row.release = 0.7, col.release = 0.7,
    
    Rd file 'BCQuest.rd':
     \usage lines wider than 90 characters:
     biclust(x, method=BCQuestmet(), quant=0.25, vari=1, ns=10, nd=10, sd=5, alpha=0.05, number=100)
    
    Rd file 'bubbleplot.Rd':
     \usage lines wider than 90 characters:
     bubbleplot(x, bicResult1, bicResult2=NULL, bicResult3=NULL, projection="mean", showLabels=FALSE)
    
    Rd file 'clustmember.rd':
     \usage lines wider than 90 characters:
     biclustmember(bicResult, x, mid = T, cl_label = "", which=NA, main = "BiCluster Membership Graph", xlab="Cluster", color=diverge_hcl(10 ... [TRUNCATED]
     clustmember(res, x, mid = T, cl_label = "", which=NA, main = "Cluster Membership Graph", xlab="Cluster",color=diverge_hcl(101, h = c(0, ... [TRUNCATED]
    
    Rd file 'diagnoseColRow.Rd':
     \examples lines wider than 100 characters:
     Bootstrap <- diagnoseColRow(x=xmat, bicResult = plaidmab, number = 1, nResamplings = 999, replace = TRUE)
    
    Rd file 'diagnosticPlot.Rd':
     \examples lines wider than 100 characters:
     Bootstrap <- diagnoseColRow(x=xmat, bicResult = plaidmab, number = 1, nResamplings = 999, replace = TRUE)
    
    Rd file 'ensemble.Rd':
     \usage lines wider than 90 characters:
     ensemble(x, confs, rep = 1, maxNum = 5, similar = jaccard2, thr = 0.8, simthr =0.7, subs = c(1, 1), bootstrap = FALSE, support = 0, com ... [TRUNCATED]
    
    Rd file 'jaccard.rd':
     \examples lines wider than 100 characters:
     res1<-biclust(BicatYeast, method=BCPlaid(), back.fit = 2, shuffle = 3, fit.model = ~m + a + b,iter.startup = 5, iter.layer = 30, verbo ... [TRUNCATED]
    
    Rd file 'parallelCoordinates.Rd':
     \examples lines wider than 100 characters:
     parallelCoordinates(x=s2,bicResult=bics,number=1, plotBoth=FALSE, plotcol=TRUE, compare=FALSE, info=TRUE)
    
    Rd file 'plaid.grid.Rd':
     \usage lines wider than 90 characters:
     plaid.grid(method = "BCPlaid", cluster = "b", fit.model = y ~ m + a + b, background = TRUE, background.layer = NA, background.df = 1, r ... [TRUNCATED]
    
    Rd file 'writeBiclusterResults.Rd':
     \usage lines wider than 90 characters:
     writeBiclusterResults(fileName, bicResult, bicName, geneNames, arrayNames, append=FALSE, delimiter=" ")
     \examples lines wider than 100 characters:
     writeBiclusterResults("results.txt", res,"CC with delta 1.5", dimnames(BicatYeast)[1][[1]],dimnames(BicatYeast)[2][[1]])
    
    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-ix86, r-release-linux-x86_64

Version: 1.0.2
Check: dependencies in R code
Result: NOTE
    There are ::: calls to the package's namespace in its code. A package
     almost never needs to use ::: for its own objects:
     ‘drawHeatmap’ ‘heatmapBC’
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of the ‘Writing R Extensions’ manual.
Flavors: 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-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.0.2
Check: R code for possible problems
Result: NOTE
    plaid: warning in matrix(c(nr, nk, layer.df[1:layer],
     round(SS[1:layer], 2), round(SS[1:layer]/layer.df[1:layer], 2),
     status[1:layer], rows.released[1:layer], cols.released[1:layer]),
     ncol = 8, dim = list(Layer = 1:layer - background, c("Rows", "Cols",
     "Df", "SS", "MS", "Convergence", "Rows Released", "Cols Released"))):
     partial argument match of 'dim' to 'dimnames'
    updatePlaid: warning in tabulate(r * row.classes, nbin =
     max(row.classes)): partial argument match of 'nbin' to 'nbins'
    updatePlaid: warning in tabulate(k * col.classes, nbin =
     max(col.classes)): partial argument match of 'nbin' to 'nbins'
Flavor: r-oldrel-windows-ix86+x86_64