CRAN Package Check Results for Package seqCBS

Last updated on 2015-08-05 08:48:46.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.2 1.37 15.74 17.11 NOTE
r-devel-linux-x86_64-debian-gcc 1.2 1.75 15.09 16.84 NOTE
r-devel-linux-x86_64-fedora-clang 1.2 31.51 NOTE
r-devel-linux-x86_64-fedora-gcc 1.2 29.07 NOTE
r-devel-osx-x86_64-clang 1.2 30.34 NOTE
r-devel-windows-ix86+x86_64 1.2 11.00 45.00 56.00 NOTE
r-patched-linux-x86_64 1.2 1.48 14.57 16.05 NOTE
r-patched-solaris-sparc 1.2 210.70 NOTE
r-patched-solaris-x86 1.2 43.80 NOTE
r-release-linux-x86_64 1.2 1.47 16.10 17.58 NOTE
r-release-osx-x86_64-mavericks 1.2 NOTE
r-release-windows-ix86+x86_64 1.2 13.00 35.00 48.00 NOTE
r-oldrel-windows-ix86+x86_64 1.2 14.00 39.00 53.00 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    NB: .First.lib is obsolete and will not be used in R 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
    
    BayesCptCI: no visible global function definition for ‘qbeta’
    BayesCptCI: no visible global function definition for ‘quantile’
    ScanCBSPlot: no visible global function definition for ‘lowess’
    ScanCBSPlot: no visible global function definition for ‘pdf’
    ScanCBSPlot: no visible global function definition for ‘par’
    ScanCBSPlot: no visible global function definition for ‘plot’
    ScanCBSPlot: no visible global function definition for ‘lines’
    ScanCBSPlot: no visible global function definition for ‘abline’
    ScanCBSPlot: no visible global function definition for ‘matplot’
    ScanCBSPlot: no visible global function definition for ‘points’
    ScanCBSPlot: no visible global function definition for ‘legend’
    ScanCBSPlot: no visible global function definition for ‘dev.off’
    ScanCBSPlot: no visible global function definition for ‘axis’
    ScanCBSSimPlot: no visible global function definition for ‘lowess’
    ScanCBSSimPlot: no visible global function definition for ‘pdf’
    ScanCBSSimPlot: no visible global function definition for ‘par’
    ScanCBSSimPlot: no visible global function definition for ‘plot’
    ScanCBSSimPlot: no visible global function definition for ‘lines’
    ScanCBSSimPlot: no visible global function definition for ‘abline’
    ScanCBSSimPlot: no visible global function definition for ‘matplot’
    ScanCBSSimPlot: no visible global function definition for ‘points’
    ScanCBSSimPlot: no visible global function definition for ‘legend’
    ScanCBSSimPlot: no visible global function definition for ‘dev.off’
    ScanCBSSimPlot: no visible global function definition for ‘axis’
    ScanIterateGrid: no visible binding for global variable ‘grid’
    SegSeqResProcess: no visible global function definition for
     ‘read.delim’
    getCountsInWindow: no visible global function definition for ‘tail’
    getCountsInWindow: no visible global function definition for ‘hist’
    hppSimulate: no visible global function definition for ‘rpois’
    hppSimulate: no visible global function definition for ‘runif’
    nhppRateEstimate: no visible global function definition for ‘lowess’
    nhppSimConstWindowAnalysis: no visible global function definition for
     ‘read.delim’
    nhppSimConstWindowAnalysis: no visible global function definition for
     ‘pdf’
    nhppSimConstWindowAnalysis: no visible global function definition for
     ‘par’
    nhppSimConstWindowAnalysis: no visible global function definition for
     ‘plot’
    nhppSimConstWindowAnalysis: no visible global function definition for
     ‘matplot’
    nhppSimConstWindowAnalysis: no visible global function definition for
     ‘legend’
    nhppSimConstWindowAnalysis: no visible global function definition for
     ‘dev.off’
    nhppSimConstWindowAnalysis: no visible global function definition for
     ‘abline’
    nhppSimConstWindowGen: no visible global function definition for
     ‘write.table’
    nhppSimulate: no visible global function definition for ‘runif’
    nhppSpike: no visible global function definition for ‘rnbinom’
    nhppSpike: no visible global function definition for ‘runif’
    nhppSpikeConstWindow: no visible global function definition for ‘runif’
    readListInputFile: no visible global function definition for
     ‘read.table’
    readSeqChiang: no visible global function definition for ‘read.table’
    readSeqELANDPaired: no visible global function definition for
     ‘read.table’
    relCNComp: no visible global function definition for ‘binom.test’
    Undefined global functions or variables:
     abline axis binom.test dev.off grid hist legend lines lowess matplot
     par pdf plot points qbeta quantile read.delim read.table rnbinom
     rpois runif tail write.table
    Consider adding
     importFrom("grDevices", "dev.off", "pdf")
     importFrom("graphics", "abline", "axis", "grid", "hist", "legend",
     "lines", "matplot", "par", "plot", "points")
     importFrom("stats", "binom.test", "lowess", "qbeta", "quantile",
     "rnbinom", "rpois", "runif")
     importFrom("utils", "read.delim", "read.table", "tail", "write.table")
    to your NAMESPACE.
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-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-patched-linux-x86_64, r-release-linux-x86_64

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-osx-x86_64-clang, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64