CRAN Package Check Results for Package MetStaT

Last updated on 2019-12-14 16:46:37 CET.

Check Details

Version: 1.0
Check: dependencies in R code
Result: NOTE
    Packages in Depends field not imported from:
     'MASS' 'abind' 'pls'
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
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, r-devel-windows-ix86+x86_64-gcc8, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 1.0
Check: R code for possible problems
Result: NOTE
    ASCA.PlotLoadings: no visible global function definition for 'par'
    ASCA.PlotLoadings: no visible global function definition for 'plot'
    ASCA.PlotLoadings: no visible global function definition for 'axis'
    ASCA.PlotScores: no visible global function definition for 'plot'
    ASCA.PlotScoresPerLevel: no visible global function definition for
     'plot'
    ASCA.PlotScoresPerLevel: no visible global function definition for
     'colors'
    ASCA.PlotScoresPerLevel: no visible global function definition for
     'legend'
    ASCA.PlotScoresPerLevel: no visible global function definition for
     'points'
    FoM.FitBinnedSampleRepeatErrors : local.fit.function: no visible global
     function definition for 'lm'
    FoM.FitBinnedSampleRepeatErrors : local.fit.function: no visible global
     function definition for 'rlm'
    FoM.FitBinnedSampleRepeatErrors: no visible global function definition
     for 'plot'
    FoM.FitBinnedSampleRepeatErrors: no visible global function definition
     for 'lines'
    MetStaT.CreateFileFromHeaderMatrix: no visible global function
     definition for 'write.table'
    MetStaT.CreateFileFromHeaderRowMatrix: no visible global function
     definition for 'write.table'
    MetStaT.KillAllDevices: no visible global function definition for
     'dev.list'
    MetStaT.KillAllDevices: no visible global function definition for
     'dev.off'
    MetStaT.PlotToFile: no visible global function definition for 'pdf'
    MetStaT.PlotToFile: no visible global function definition for 'bmp'
    MetStaT.PlotToFile: no visible global function definition for 'jpeg'
    MetStaT.PlotToFile: no visible global function definition for 'png'
    MetStaT.PlotToFile: no visible global function definition for 'tiff'
    MetStaT.PlotToFile: no visible global function definition for 'dev.off'
    MetStaT.PlotToFile: no visible global function definition for 'dev.cur'
    MetStaT.ReadFileToHeaderMatrix: no visible global function definition
     for 'read.delim'
    PCA.PlotLoadings: no visible global function definition for 'par'
    PCA.PlotLoadings: no visible global function definition for 'plot'
    PCA.PlotLoadings: no visible global function definition for 'axis'
    PCA.PlotScores: no visible global function definition for 'par'
    PCA.PlotScores: no visible global function definition for 'plot'
    PCA.PlotScores: no visible global function definition for 'text'
    PCA.PlotScores: no visible global function definition for 'legend'
    RevNet.JacobianMethod : RevNet.FirstEstimate: no visible global
     function definition for 'coef'
    RevNet.JacobianMethod : RevNet.FirstEstimate: no visible global
     function definition for 'lm.ridge'
    RevNet.TimeLaggedMethod : RevNet.CcfMax: no visible global function
     definition for 'ccf'
    RevNet.TimeLaggedMethod : RevNet.Connection: no visible global function
     definition for 'quantile'
    Undefined global functions or variables:
     axis bmp ccf coef colors dev.cur dev.list dev.off jpeg legend lines
     lm lm.ridge par pdf plot png points quantile read.delim rlm text tiff
     write.table
    Consider adding
     importFrom("grDevices", "bmp", "colors", "dev.cur", "dev.list",
     "dev.off", "jpeg", "pdf", "png", "tiff")
     importFrom("graphics", "axis", "legend", "lines", "par", "plot",
     "points", "text")
     importFrom("stats", "ccf", "coef", "lm", "quantile")
     importFrom("utils", "read.delim", "write.table")
    to your NAMESPACE file.
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, r-devel-windows-ix86+x86_64-gcc8, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 1.0
Check: examples
Result: ERROR
    Running examples in 'MetStaT-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: QStat.Calculate
    > ### Title: Global test for metabolic pathway differences between conditions
    > ### Aliases: QStat.Calculate
    > ### Keywords: Goeman's test Metabolomic network
    >
    > ### ** Examples
    >
    > data(QStat)
    > QStat.Calculate(QStatX, QStatY, 1000)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    MetStaT
     --- call from context ---
    QStat.Calculate(QStatX, QStatY, 1000)
     --- call from argument ---
    if (class(y.boolean) != "logical") {
     y.boolean <- MetStaT.ConvertToNumericClasses(y.boolean, new.classes = c(1,
     0)) == 1
    }
     --- R stacktrace ---
    where 1: QStat.Calculate(QStatX, QStatY, 1000)
    
     --- value of length: 2 type: logical ---
    [1] TRUE TRUE
     --- function from context ---
    function (X, y.boolean, permutations = "all")
    {
     QStat.GetQValue <- function(X, y.boolean) {
     q <- sum(y.boolean)
     t <- length(y.boolean)
     mu <- q/t
     m <- dim(X)[2]
     Z <- y.boolean - mu
     R <- X %*% t(X)/m
     Q <- t(Z) %*% R %*% Z/(mu * (1 - mu))
     Q
     }
     result <- list()
     if (class(y.boolean) != "logical") {
     y.boolean <- MetStaT.ConvertToNumericClasses(y.boolean,
     new.classes = c(1, 0)) == 1
     }
     result$y.boolean <- y.boolean
     result$X <- X
     Q <- QStat.GetQValue(X, y.boolean)
     result$Q <- Q
     if (permutations != 0) {
     result$p <- QStat.PermutationTest(result, no.permutations = permutations)
     }
     else {
     result$p <- NA
     }
     result
    }
    <bytecode: 0x2a9f7b0>
    <environment: namespace:MetStaT>
     --- function search by body ---
    Function QStat.Calculate in namespace MetStaT has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(y.boolean) != "logical") { :
     the condition has length > 1
    Calls: QStat.Calculate
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0
Check: for non-standard things in the check directory
Result: NOTE
    Found the following files/directories:
     'ASCA_Results.pdf'
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