CRAN Package Check Results for Package CPHshape

Last updated on 2018-06-17 19:49:33 CEST.

Check Details

Version: 1.0.1
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     plot.CPHshape
    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: 1.0.1
Check: R code for possible problems
Result: NOTE
    find.antimodeMLE: no visible global function definition for ‘par’
    find.decreasingMLE: no visible global function definition for ‘chull’
    find.decreasingMLE: no visible global function definition for ‘points’
    find.increasingMLE: no visible global function definition for ‘chull’
    find.increasingMLE: no visible global function definition for ‘points’
    find.modeMLE: no visible global function definition for ‘par’
    plot.CPHshape: no visible global function definition for ‘plot’
    plot.CPHshape: no visible global function definition for ‘segments’
    plot.CPHshape: no visible global function definition for ‘abline’
    plot.CPHshape: no visible global function definition for ‘grey’
    plot.CPHshape: no visible global function definition for ‘points’
    Undefined global functions or variables:
     abline chull grey par plot points segments
    Consider adding
     importFrom("grDevices", "chull", "grey")
     importFrom("graphics", "abline", "par", "plot", "points", "segments")
    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: 1.0.1
Check: examples
Result: ERROR
    Running examples in ‘CPHshape-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: CPHshape-package
    > ### Title: Compute the MLE in the Cox proportional hazard model with shape
    > ### constrained baseline
    > ### Aliases: CPHshape-package CPHshape
    > ### Keywords: package
    >
    > ### ** Examples
    >
    > # random sample from the proportional hazard model
    > n <- 200
    > beta1 <- 1
    > beta2 <- 2
    > z1 <- rbinom(n,1,0.5)
    > z2 <- runif(n,-1,1)
    > w <- exp(beta1*z1+beta2*z2)
    > x <- rexp(n, rate=0.3*w)
    > delta <- 1*(x<=2.5)
    > x <- pmin(x,2.5)
    >
    > # compute MLE
    > mle <- find.shapeCPH(x, cbind(z1,z2) , delta, print=TRUE, type="decreasing")
    iter=i phi[i] |phi[i]-phi[i-1]| beta(s)
    0 147.6787 NA 1 1
    1 135.4872 12.19149 0.8794245 1.752254
    2 135.1488 0.3383608 0.8586661 1.876259
    3 135.1313 0.01756921 0.8654743 1.896823
    4 135.1263 0.004953677 0.8733547 1.89924
    5 135.1241 0.002168003 0.8786815 1.900463
    6 135.1232 0.0009537361 0.8822161 1.901261
    7 135.1228 0.0004206064 0.8845625 1.901789
    8 135.1226 0.0001857963 0.8861216 1.90214
    9 135.1225 8.216211e-05 0.8871582 1.902373
    10 135.1225 3.63597e-05 0.8878476 1.902528
    11 135.1224 1.609822e-05 0.8883064 1.902632
    12 135.1224 7.129752e-06 0.8886116 1.9027
    >
    > # estimates of the effect parameter
    > mle$beta
    [1] 0.8886116 1.9027001
    >
    > # plot resulting estimate of baseline hazard
    >
    > plot(mle)
    Error in xy.coords(x, y, xlabel, ylabel, log) :
     'x' is a list, but does not have components 'x' and 'y'
    Calls: plot -> plot.default -> xy.coords
    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