CRAN Package Check Results for Package QuantumClone

Last updated on 2015-09-06 23:47:36.

Check Details

Version: 0.6.15
Check: R code for possible problems
Result: NOTE
    BIC_criterion: no visible global function definition for ‘na.omit’
    CellularitiesFromFreq: no visible global function definition for ‘tail’
    CellularitiesFromFreq: no visible binding for global variable
     ‘frequency’
    EM.algo: no visible global function definition for ‘runif’
    Multitest: no visible global function definition for ‘aggregate’
    QuantumCat: no visible global function definition for ‘rpois’
    QuantumCat: no visible global function definition for ‘tail’
    QuantumCat: no visible global function definition for ‘rnbinom’
    QuantumCat: no visible global function definition for ‘rbinom’
    ThreeD_plot: no visible global function definition for
     ‘colorRampPalette’
    create_priors: no visible global function definition for ‘runif’
    eval.fik: no visible global function definition for ‘dbinom’
    m.step: no visible global function definition for ‘optim’
    manual_plot_trees: no visible global function definition for ‘plot’
    manual_plot_trees: no visible global function definition for ‘segments’
    manual_plot_trees: no visible global function definition for ‘text’
    multiplot_trees: no visible global function definition for ‘par’
    statistics_on_Multitest: no visible global function definition for
     ‘write.table’
    statistics_on_Multitest: no visible global function definition for ‘sd’
    strcount : <anonymous>: no visible global function definition for
     ‘na.omit’
    Undefined global functions or variables:
     aggregate colorRampPalette dbinom frequency na.omit optim par plot
     rbinom rnbinom rpois runif sd segments tail text write.table
    Consider adding
     importFrom("grDevices", "colorRampPalette")
     importFrom("graphics", "par", "plot", "segments", "text")
     importFrom("stats", "aggregate", "dbinom", "frequency", "na.omit",
     "optim", "rbinom", "rnbinom", "rpois", "runif", "sd")
     importFrom("utils", "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: 0.6.15
Check: examples
Result: ERROR
    Running examples in ‘QuantumClone-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: ThreeD_plot
    > ### Title: 3D Plot
    > ### Aliases: ThreeD_plot
    > ### Keywords: Clonal inference phylogeny
    >
    > ### ** Examples
    >
    > print("Generating data...")
    [1] "Generating data..."
    > QC<-QuantumCat(number_of_clones = 4,number_of_mutations = 200,
    + depth= 100, ploidy = "AB")
    > print("Formating data so it can be used as input")
    [1] "Formating data so it can be used as input"
    > alpha<-rep(1,time=200)
    > for(i in 1:2){
    + print(head(2*QC[[i]]$Alt/QC[[i]]$Depth))
    + QC[[i]][,4]<-2*QC[[i]]$Alt/QC[[i]]$Depth
    + QC[[i]]<-cbind(QC[[i]],alpha)
    + }
    [1] 0.6030151 0.9896907 1.4054054 1.0681818 0.7166667 0.2739726
    [1] 0.13333333 0.66666667 0.97014925 1.07368421 0.06896552 0.31746032
    > print("Creating 3D plot")
    [1] "Creating 3D plot"
    > ThreeD_plot(QC,c(0,0))
    Warning in rgl.init(initValue, onlyNULL) :
     RGL: unable to open X11 display
    Warning in fun(libname, pkgname) : error in rgl_init
    Error in rgl.open(useNULL) : rgl.open failed
    Calls: ThreeD_plot -> <Anonymous> -> rgl.open
    Execution halted
Flavor: r-release-osx-x86_64-mavericks