CRAN Package Check Results for Package seqCBS

Last updated on 2014-09-17 21:46:45.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.2 1.43 16.51 17.94 NOTE
r-devel-linux-x86_64-debian-gcc 1.2 1.56 16.63 18.19 NOTE
r-devel-linux-x86_64-fedora-clang 1.2 35.05 NOTE
r-devel-linux-x86_64-fedora-gcc 1.2 31.73 NOTE
r-devel-osx-x86_64-clang 1.2 35.16 NOTE
r-devel-windows-ix86+x86_64 1.2 7.00 29.00 36.00 NOTE
r-patched-linux-x86_64 1.2 1.59 16.50 18.09 NOTE
r-patched-solaris-sparc 1.2 219.60 NOTE
r-patched-solaris-x86 1.2 47.10 NOTE
r-release-linux-ix86 1.2 2.34 25.31 27.65 NOTE
r-release-linux-x86_64 1.2 1.77 17.27 19.04 NOTE
r-release-osx-x86_64-mavericks 1.2 NOTE
r-release-osx-x86_64-snowleopard 1.2 NOTE
r-release-windows-ix86+x86_64 1.2 6.00 31.00 37.00 NOTE
r-oldrel-windows-ix86+x86_64 1.2 8.00 33.00 41.00 NOTE

Check Details

Version: 1.2
Check: R code for possible problems
Result: NOTE
    NB: .First.lib is obsolete and will not be used in R >= 3.0.0
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-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.2
Check: Rd line widths
Result: NOTE
    Rd file 'BayesCptCI.Rd':
     \usage lines wider than 90 characters:
     BayesCptCI(cases, controls, CBSRes, stepSize="adaptive", adaptMaxMix=80, alpha=0.05, epsilon=10^-4, epsCDF=10^-4, verbose=FALSE)
    
    Rd file 'CombineReadsAcrossRuns.Rd':
     \examples lines wider than 100 characters:
     write.table(JSSim_NormalSim1, file="JSSim_NormalSim1.txt", sep="\t", quote=FALSE, row.names=FALSE, col.names=FALSE)
     write.table(JSSim_NormalSim2, file="JSSim_NormalSim2.txt", sep="\t", quote=FALSE, row.names=FALSE, col.names=FALSE)
    
    Rd file 'ScanCBS.Rd':
     \usage lines wider than 90 characters:
     ScanCBS(cases, controls, statistic = "binomial", grid.size = "auto", takeN = 5, maxNCut = 100, minStat = 0, alpha=0.05, verbose = FALSE ... [TRUNCATED]
    
    Rd file 'ScanCBSPlot.Rd':
     \usage lines wider than 90 characters:
     ScanCBSPlot(cases, controls, CBSObj, filename, mainTitle, CIObj=NULL, length.out=10000, localWindow=0.5*10^5, localSeparatePlot=TRUE, s ... [TRUNCATED]
    
    Rd file 'ScanCBSSimPlot.Rd':
     \usage lines wider than 90 characters:
     ScanCBSSimPlot(cases, controls, CBSObj, trueTau, SpikeMat, filename, mainTitle, CIObj=NULL, length.out=10000, localWindow=0.5*10^5, loc ... [TRUNCATED]
    
    Rd file 'ScanIterateGrid.Rd':
     \usage lines wider than 90 characters:
     ScanIterateGrid(combX, combZ, combL, statistic, grid.size, nGridSize, timeIGSBreakDown, takeN, verbose, timing)
    
    Rd file 'ScanStatNewComp.Rd':
     \usage lines wider than 90 characters:
     ScanStatNewComp(combZCumSum, combXCumSum, combZPoint, combXPoint, p, nTotal, grid.cur, max.win, statistic)
    
    Rd file 'ScanStatRefineComp.Rd':
     \usage lines wider than 90 characters:
     ScanStatRefineComp(combZCumSum, combXCumSum, combZPoint, combXPoint, p, nTotal, grid.cur, grid.LR, max.win, statistic)
    
    Rd file 'nhppSimConstWindowAnalysis.Rd':
     \usage lines wider than 90 characters:
     nhppSimConstWindowAnalysis(filePrefix, chromosomeN, distMetric=c(20,50,100,150,200,300,500,1000), cptLen=c(3,5,8,12,15,20,30,50,100), n ... [TRUNCATED]
    
    Rd file 'nhppSimConstWindowGen.Rd':
     \usage lines wider than 90 characters:
     nhppSimConstWindowGen(controlRates, filename, chromosomeN, nSpike=25, cptLen=c(3,5,8,12,20,30,50,75,100), nPair=2, nRepeat=10, minGain= ... [TRUNCATED]
    
    Rd file 'nhppSpike.Rd':
     \usage lines wider than 90 characters:
     nhppSpike(smoothRates, nSpike = 25, cptLenR = 4, cptLenMean = 10, minGain = 1.5, maxGain = 10, minLoss = 0.01, maxLoss = 0.5, pGain = 0 ... [TRUNCATED]
    
    Rd file 'nhppSpikeConstWindow.Rd':
     \usage lines wider than 90 characters:
     nhppSpikeConstWindow(smoothRates, nSpike = 25, cptLen = 5, minGain = 1.5, maxGain = 10, minLoss = 0.01, maxLoss = 0.5, pGain = 0.6)
    
    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-release-linux-x86_64