CRAN Package Check Results for Package B2Z

Last updated on 2019-12-09 05:47:06 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.4 8.61 44.80 53.41 ERROR
r-devel-linux-x86_64-debian-gcc 1.4 7.00 37.19 44.19 NOTE
r-devel-linux-x86_64-fedora-clang 1.4 68.60 NOTE
r-devel-linux-x86_64-fedora-gcc 1.4 67.87 NOTE
r-devel-windows-ix86+x86_64 1.4 15.00 59.00 74.00 NOTE
r-devel-windows-ix86+x86_64-gcc8 1.4 20.00 58.00 78.00 NOTE
r-patched-linux-x86_64 1.4 6.87 44.81 51.68 NOTE
r-patched-solaris-x86 1.4 80.50 NOTE
r-release-linux-x86_64 1.4 6.56 43.17 49.73 NOTE
r-release-windows-ix86+x86_64 1.4 19.00 56.00 75.00 NOTE
r-release-osx-x86_64 1.4 NOTE
r-oldrel-windows-ix86+x86_64 1.4 7.00 74.00 81.00 NOTE
r-oldrel-osx-x86_64 1.4 NOTE

Check Details

Version: 1.4
Check: R code for possible problems
Result: NOTE
    BCLTB2zm: no visible global function definition for 'flush.console'
    BCLTB2zm: no visible global function definition for 'runif'
    BCLTB2zm: no visible global function definition for 'rgamma'
    BCLTB2zm: no visible global function definition for 'rexp'
    BCLTB2zm: no visible global function definition for 'rnorm'
    BCLTB2zm: no visible global function definition for 'rt'
    BCLTB2zm: no visible global function definition for 'rweibull'
    BCLTB2zm: no visible global function definition for 'rchisq'
    BCLTB2zm: no visible global function definition for 'rcauchy'
    BCLTB2zm: no visible global function definition for 'dlnorm'
    BCLTB2zm: no visible global function definition for 'nlminb'
    IMISB2zm: no visible global function definition for 'flush.console'
    IMISB2zm: no visible global function definition for 'runif'
    IMISB2zm: no visible global function definition for 'rgamma'
    IMISB2zm: no visible global function definition for 'rexp'
    IMISB2zm: no visible global function definition for 'rnorm'
    IMISB2zm: no visible global function definition for 'rt'
    IMISB2zm: no visible global function definition for 'rweibull'
    IMISB2zm: no visible global function definition for 'rchisq'
    IMISB2zm: no visible global function definition for 'rcauchy'
    IMISB2zm: no visible global function definition for 'dlnorm'
    IMISB2zm: no visible global function definition for 'plot'
    IMISB2zm: no visible global function definition for 'box'
    IMISB2zm: no visible global function definition for 'abline'
    IMISB2zm: no visible global function definition for 'axis'
    IMISB2zm: no visible global function definition for 'cov'
    IMISB2zm: no visible global function definition for 'cov.wt'
    IMISB2zm: no visible global function definition for 'segments'
    IMISB2zm: no visible global function definition for 'points'
    MCMCB2zm: no visible global function definition for 'flush.console'
    MCMCB2zm: no visible global function definition for 'runif'
    MCMCB2zm: no visible global function definition for 'rgamma'
    MCMCB2zm: no visible global function definition for 'rexp'
    MCMCB2zm: no visible global function definition for 'rnorm'
    MCMCB2zm: no visible global function definition for 'rt'
    MCMCB2zm: no visible global function definition for 'rweibull'
    MCMCB2zm: no visible global function definition for 'rchisq'
    MCMCB2zm: no visible global function definition for 'rcauchy'
    MCMCB2zm: no visible global function definition for 'dlnorm'
    MCMCB2zm: no visible global function definition for 'nlminb'
    MCMCB2zm: no visible global function definition for 'cov'
    MCMCB2zm: no visible global function definition for 'txtProgressBar'
    MCMCB2zm: no visible global function definition for 'setTxtProgressBar'
    SIRB2zm: no visible global function definition for 'flush.console'
    SIRB2zm: no visible global function definition for 'runif'
    SIRB2zm: no visible global function definition for 'rgamma'
    SIRB2zm: no visible global function definition for 'rexp'
    SIRB2zm: no visible global function definition for 'rnorm'
    SIRB2zm: no visible global function definition for 'rt'
    SIRB2zm: no visible global function definition for 'rweibull'
    SIRB2zm: no visible global function definition for 'rchisq'
    SIRB2zm: no visible global function definition for 'rcauchy'
    SIRB2zm: no visible global function definition for 'dlnorm'
    SIRB2zm: no visible global function definition for 'var'
    apply_pb: no visible global function definition for 'txtProgressBar'
    apply_pb : wrapper: no visible global function definition for
     'setTxtProgressBar'
    logpost: no visible global function definition for 'dunif'
    logpost: no visible global function definition for 'dgamma'
    logpost: no visible global function definition for 'dexp'
    logpost: no visible global function definition for 'dnorm'
    logpost: no visible global function definition for 'dt'
    logpost: no visible global function definition for 'dweibull'
    logpost: no visible global function definition for 'dchisq'
    logpost: no visible global function definition for 'dcauchy'
    logpost: no visible global function definition for 'dlnorm'
    logprior: no visible global function definition for 'dunif'
    logprior: no visible global function definition for 'dgamma'
    logprior: no visible global function definition for 'dexp'
    logprior: no visible global function definition for 'dnorm'
    logprior: no visible global function definition for 'dt'
    logprior: no visible global function definition for 'dweibull'
    logprior: no visible global function definition for 'dchisq'
    logprior: no visible global function definition for 'dcauchy'
    logprior: no visible global function definition for 'dlnorm'
    plot.bclt: no visible binding for global variable 'quantile'
    plot.bclt: no visible global function definition for 'plot'
    plot.bclt: no visible global function definition for 'lines'
    plot.bclt: no visible global function definition for 'legend'
    plot.bclt: no visible global function definition for 'devAskNewPage'
    plot.bclt: no visible global function definition for 'par'
    plot.bclt: no visible global function definition for 'hist'
    plot.bclt: no visible global function definition for 'density'
    plot.bclt: no visible global function definition for 'dnorm'
    plot.bclt: no visible global function definition for 'sd'
    plot.bclt: no visible global function definition for 'curve'
    plot.imis: no visible binding for global variable 'quantile'
    plot.imis: no visible global function definition for 'plot'
    plot.imis: no visible global function definition for 'lines'
    plot.imis: no visible global function definition for 'legend'
    plot.imis: no visible global function definition for 'devAskNewPage'
    plot.imis: no visible global function definition for 'par'
    plot.imis: no visible global function definition for 'hist'
    plot.imis: no visible global function definition for 'density'
    plot.imis: no visible global function definition for 'dnorm'
    plot.imis: no visible global function definition for 'sd'
    plot.imis: no visible global function definition for 'curve'
    plot.mcmc: no visible binding for global variable 'quantile'
    plot.mcmc: no visible global function definition for 'plot'
    plot.mcmc: no visible global function definition for 'lines'
    plot.mcmc: no visible global function definition for 'legend'
    plot.mcmc: no visible global function definition for 'devAskNewPage'
    plot.mcmc: no visible global function definition for 'par'
    plot.mcmc: no visible global function definition for 'hist'
    plot.mcmc: no visible global function definition for 'density'
    plot.mcmc: no visible global function definition for 'dnorm'
    plot.mcmc: no visible global function definition for 'sd'
    plot.mcmc: no visible global function definition for 'curve'
    plot.mcmc: no visible global function definition for 'ts.plot'
    plot.mcmc: no visible global function definition for 'acf'
    plot.sir: no visible binding for global variable 'quantile'
    plot.sir: no visible global function definition for 'plot'
    plot.sir: no visible global function definition for 'lines'
    plot.sir: no visible global function definition for 'legend'
    plot.sir: no visible global function definition for 'devAskNewPage'
    plot.sir: no visible global function definition for 'par'
    plot.sir: no visible global function definition for 'hist'
    plot.sir: no visible global function definition for 'density'
    plot.sir: no visible global function definition for 'dnorm'
    plot.sir: no visible global function definition for 'sd'
    plot.sir: no visible global function definition for 'curve'
    ploteps: no visible binding for global variable 'quantile'
    ploteps: no visible global function definition for 'postscript'
    ploteps: no visible global function definition for 'plot'
    ploteps: no visible global function definition for 'lines'
    ploteps: no visible global function definition for 'legend'
    ploteps: no visible global function definition for 'dev.off'
    ploteps: no visible global function definition for 'par'
    ploteps: no visible global function definition for 'hist'
    ploteps: no visible global function definition for 'density'
    ploteps: no visible global function definition for 'dnorm'
    ploteps: no visible global function definition for 'sd'
    ploteps: no visible global function definition for 'curve'
    ploteps: no visible global function definition for 'ts.plot'
    ploteps: no visible global function definition for 'acf'
    plotjpeg: no visible binding for global variable 'quantile'
    plotjpeg: no visible global function definition for 'postscript'
    plotjpeg: no visible global function definition for 'plot'
    plotjpeg: no visible global function definition for 'lines'
    plotjpeg: no visible global function definition for 'legend'
    plotjpeg: no visible global function definition for 'dev.off'
    plotjpeg: no visible global function definition for 'par'
    plotjpeg: no visible global function definition for 'hist'
    plotjpeg: no visible global function definition for 'density'
    plotjpeg: no visible global function definition for 'dnorm'
    plotjpeg: no visible global function definition for 'sd'
    plotjpeg: no visible global function definition for 'curve'
    plotjpeg: no visible global function definition for 'ts.plot'
    plotjpeg: no visible global function definition for 'acf'
    plotpdf: no visible binding for global variable 'quantile'
    plotpdf: no visible global function definition for 'pdf'
    plotpdf: no visible global function definition for 'plot'
    plotpdf: no visible global function definition for 'lines'
    plotpdf: no visible global function definition for 'legend'
    plotpdf: no visible global function definition for 'dev.off'
    plotpdf: no visible global function definition for 'par'
    plotpdf: no visible global function definition for 'hist'
    plotpdf: no visible global function definition for 'density'
    plotpdf: no visible global function definition for 'dnorm'
    plotpdf: no visible global function definition for 'sd'
    plotpdf: no visible global function definition for 'curve'
    plotpdf: no visible global function definition for 'ts.plot'
    plotpdf: no visible global function definition for 'acf'
    plotpng: no visible binding for global variable 'quantile'
    plotpng: no visible global function definition for 'png'
    plotpng: no visible global function definition for 'plot'
    plotpng: no visible global function definition for 'lines'
    plotpng: no visible global function definition for 'legend'
    plotpng: no visible global function definition for 'dev.off'
    plotpng: no visible global function definition for 'par'
    plotpng: no visible global function definition for 'hist'
    plotpng: no visible global function definition for 'density'
    plotpng: no visible global function definition for 'dnorm'
    plotpng: no visible global function definition for 'sd'
    plotpng: no visible global function definition for 'curve'
    plotpng: no visible global function definition for 'ts.plot'
    plotpng: no visible global function definition for 'acf'
    plotps: no visible binding for global variable 'quantile'
    plotps: no visible global function definition for 'postscript'
    plotps: no visible global function definition for 'plot'
    plotps: no visible global function definition for 'lines'
    plotps: no visible global function definition for 'legend'
    plotps: no visible global function definition for 'dev.off'
    plotps: no visible global function definition for 'par'
    plotps: no visible global function definition for 'hist'
    plotps: no visible global function definition for 'density'
    plotps: no visible global function definition for 'dnorm'
    plotps: no visible global function definition for 'sd'
    plotps: no visible global function definition for 'curve'
    plotps: no visible global function definition for 'ts.plot'
    plotps: no visible global function definition for 'acf'
    predY: no visible global function definition for 'rnorm'
    rwish: no visible global function definition for 'rchisq'
    rwish: no visible global function definition for 'rnorm'
    summary.bclt: no visible global function definition for 'cov'
    summary.imis: no visible global function definition for 'cov'
    summary.mcmc: no visible global function definition for 'cov'
    summary.out: no visible global function definition for 'quantile'
    summary.out: no visible global function definition for 'sd'
    summary.sir: no visible global function definition for 'cov'
    Undefined global functions or variables:
     abline acf axis box cov cov.wt curve dcauchy dchisq density dev.off
     devAskNewPage dexp dgamma dlnorm dnorm dt dunif dweibull
     flush.console hist legend lines nlminb par pdf plot png points
     postscript quantile rcauchy rchisq rexp rgamma rnorm rt runif
     rweibull sd segments setTxtProgressBar ts.plot txtProgressBar var
    Consider adding
     importFrom("grDevices", "dev.off", "devAskNewPage", "pdf", "png",
     "postscript")
     importFrom("graphics", "abline", "axis", "box", "curve", "hist",
     "legend", "lines", "par", "plot", "points", "segments")
     importFrom("stats", "acf", "cov", "cov.wt", "dcauchy", "dchisq",
     "density", "dexp", "dgamma", "dlnorm", "dnorm", "dt",
     "dunif", "dweibull", "nlminb", "quantile", "rcauchy",
     "rchisq", "rexp", "rgamma", "rnorm", "rt", "runif",
     "rweibull", "sd", "ts.plot", "var")
     importFrom("utils", "flush.console", "setTxtProgressBar",
     "txtProgressBar")
    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: 1.4
Check: examples
Result: ERROR
    Running examples in 'B2Z-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: B2ZM_IMIS
    > ### Title: Bayesian Two-Zone Models: using IMIS sampler
    > ### Aliases: B2ZM_IMIS
    > ### Keywords: models
    >
    > ### ** Examples
    >
    > ##################
    > #Dependent Model#
    > ################
    >
    > #Data 1: 100 simulated concentrations during the times
    > #between 0 and 4, using the parameters Beta = 5, Q = 13.8,
    > #G = 351.5, VN = pi*10^-3, VF = 3.8, Tau_N = 1,
    > #Tau_NF = 0.5 and Tau_F = 0.64.
    >
    > data(ex1)
    >
    > r <- B2ZM_IMIS(data = ex1, priorBeta = "unif(0,10)",
    + priorQ="unif(11,17)", priorG = "unif(281,482)", S = diag(10,2),
    + v = 4, VN = pi*10^-3, VF = 3.8, N0 = 500, B = 50, M = 250,
    + it.max = 4)
    1 - Initial Stage...
    
    
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     |
     | | 0% ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    B2Z
     --- call from context ---
    is.pos.def(W)
     --- call from argument ---
    if (class(val) == "try-error") return(FALSE) else return(TRUE)
     --- R stacktrace ---
    where 1: is.pos.def(W)
    where 2: logdiwish(W, v, S)
    where 3: logprior(parms, indep, Y, times, VN, VF, n, indBeta, aBeta, bBeta,
     indQ, aQ, bQ, indG, aG, bG, S, v, tauN_sh, tauN_sc, tauF_sh,
     tauF_sc)
    where 4: FUN(...)
    where 5: FUN(newX[, i], ...)
    where 6: apply(X, MARGIN, wrapper, ...)
    where 7: apply_pb(params_transf, 1, logprior_transf, indep = indep, Y = Y,
     times = times, VN = VN, VF = VF, n = n, indBeta = indBeta,
     aBeta = aBeta, bBeta = bBeta, rangeBeta = rangeBeta, indQ = indQ,
     aQ = aQ, bQ = bQ, rangeQ = rangeQ, indG = indG, aG = aG,
     bG = bG, rangeG = rangeG, S = S, v = v, tauN_sh = tauN_sh,
     tauN_sc = tauN_sc, tauF_sh = tauF_sh, tauF_sc = tauF_sc)
    where 8: IMISB2zm(N0, B, M, it.max, S, v, tauN.sh, tauN.sc, tauF.sh, tauF.sc,
     VN, VF, times, Y, indep, cred, indBeta, aBeta, bBeta, indQ,
     aQ, bQ, indG, aG, bG)
    where 9: B2ZM(data = data, priorBeta = priorBeta, priorQ = priorQ, priorG = priorG,
     v = v, S = S, tauN.sh = tauN.sh, tauN.sc = tauN.sc, tauF.sh = tauF.sh,
     tauF.sc = tauF.sc, VN = VN, VF = VF, indep.model = indep.model,
     cred = 95, sampler = "IMIS", imis.control = list(N0 = N0,
     B = B, M = M, it.max = it.max), figures = figures)
    where 10: B2ZM_IMIS(data = ex1, priorBeta = "unif(0,10)", priorQ = "unif(11,17)",
     priorG = "unif(281,482)", S = diag(10, 2), v = 4, VN = pi *
     10^-3, VF = 3.8, N0 = 500, B = 50, M = 250, it.max = 4)
    
     --- value of length: 2 type: logical ---
    [1] FALSE FALSE
     --- function from context ---
    function (mat)
    {
     val = try(chol(mat), silent = TRUE)
     if (class(val) == "try-error")
     return(FALSE)
     else return(TRUE)
    }
    <bytecode: 0x2b9ad58>
    <environment: namespace:B2Z>
     --- function search by body ---
    Function is.pos.def in namespace B2Z has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(val) == "try-error") return(FALSE) else return(TRUE) :
     the condition has length > 1
    Calls: B2ZM_IMIS ... apply -> FUN -> FUN -> logprior -> logdiwish -> is.pos.def
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang