CRAN Package Check Results for Package lqa

Last updated on 2018-07-20 09:48:51 CEST.

Check Details

Version: 1.0-3
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     lqa.control lqa.default lqa.formula lqa.update2 plot.lqa predict.lqa
     print.cv.lqa print.penalty print.pred.lqa print.summary.lqa
     summary.lqa
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    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-patched-solaris-x86, r-release-linux-x86_64

Version: 1.0-3
Check: R code for possible problems
Result: NOTE
    ForwardBoost: no visible global function definition for ‘var’
    GBlockBoost: no visible global function definition for ‘var’
    ao : getpenmat: no visible binding for global variable ‘var’
    ao : getpenmat: no visible global function definition for ‘cor’
    cv.lqa: no visible global function definition for ‘var’
    cv.nng: no visible global function definition for ‘var’
    icb : getpenmat: no visible binding for global variable ‘var’
    icb : getpenmat: no visible global function definition for ‘cor’
    licb : a.coefs: no visible binding for global variable ‘var’
    licb : a.coefs: no visible global function definition for ‘cor’
    lqa.default: no visible global function definition for ‘gaussian’
    lqa.default: no visible global function definition for ‘var’
    lqa.default: no visible binding for global variable ‘var’
    lqa.formula: no visible global function definition for ‘model.response’
    lqa.formula: no visible global function definition for ‘is.empty.model’
    lqa.formula: no visible global function definition for ‘model.matrix’
    lqa.formula: no visible binding for global variable ‘contrasts’
    lqa.formula: no visible global function definition for ‘model.offset’
    lqa.formula: no visible global function definition for ‘model.extract’
    nng.update: no visible global function definition for ‘glm.fit’
    nng.update: no visible global function definition for ‘coef’
    nng.update: no visible global function definition for ‘optim’
    penalreg : getpenmat: no visible binding for global variable ‘var’
    penalreg : getpenmat: no visible global function definition for ‘cor’
    plot.lqa: no visible global function definition for ‘var’
    plot.lqa: no visible global function definition for ‘matplot’
    plot.lqa: no visible global function definition for ‘glm’
    plot.lqa: no visible global function definition for ‘points’
    plot.lqa: no visible global function definition for ‘axis’
    print.summary.lqa: no visible global function definition for ‘quantile’
    print.summary.lqa: no visible global function definition for
     ‘printCoefmat’
    print.summary.lqa: no visible global function definition for ‘naprint’
    summary.lqa: no visible global function definition for ‘residuals’
    weighted.fusion : getpenmat: no visible global function definition for
     ‘var’
    weighted.fusion : getpenmat: no visible global function definition for
     ‘cor’
    Undefined global functions or variables:
     axis coef contrasts cor gaussian glm glm.fit is.empty.model matplot
     model.extract model.matrix model.offset model.response naprint optim
     points printCoefmat quantile residuals var
    Consider adding
     importFrom("graphics", "axis", "matplot", "points")
     importFrom("stats", "coef", "contrasts", "cor", "gaussian", "glm",
     "glm.fit", "is.empty.model", "model.extract",
     "model.matrix", "model.offset", "model.response", "naprint",
     "optim", "printCoefmat", "quantile", "residuals", "var")
    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-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: 1.0-3
Check: Rd \usage sections
Result: NOTE
    S3 methods shown with full name in documentation object 'lqa':
     ‘lqa.update2’
    
    S3 methods shown with full name in documentation object 'lqa.control':
     ‘lqa.control’
    
    S3 methods shown with full name in documentation object 'plot.lqa':
     ‘plot.lqa’
    
    The \usage entries for S3 methods should use the \method markup and not
    their full name.
    See chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ 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-devel-windows-ix86+x86_64, 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: 1.0-3
Check: examples
Result: ERROR
    Running examples in ‘lqa-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: lqa
    > ### Title: Fitting penalized Generalized Linear Models with the LQA
    > ### algorithm
    > ### Aliases: lqa lqa.formula lqa.default lqa.update2 print.summary.lqa
    > ### summary.lqa
    > ### Keywords: methods classes
    >
    > ### ** Examples
    >
    > set.seed (1111)
    >
    > n <- 200
    > p <- 5
    > X <- matrix (rnorm (n * p), ncol = p)
    > X[,2] <- X[,1] + rnorm (n, sd = 0.1)
    > X[,3] <- X[,1] + rnorm (n, sd = 0.1)
    > true.beta <- c (1, 2, 0, 0, -1)
    > y <- drop (X %*% true.beta) + rnorm (n)
    >
    > obj1 <- lqa (y ~ X, family = gaussian (), penalty = lasso (1.5),
    + control = lqa.control ())
    Error in UseMethod("lqa") :
     no applicable method for 'lqa' applied to an object of class "formula"
    Calls: lqa
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64