CRAN Package Check Results for Package ExactPath

Last updated on 2018-05-22 01:46:34 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0 1.08 16.83 17.91 ERROR
r-devel-linux-x86_64-debian-gcc 1.0 0.67 14.28 14.95 ERROR
r-devel-linux-x86_64-fedora-clang 1.0 24.52 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0 23.00 NOTE
r-devel-windows-ix86+x86_64 1.0 3.00 31.00 34.00 NOTE
r-patched-linux-x86_64 1.0 1.03 17.20 18.23 ERROR
r-patched-solaris-x86 1.0 37.30 NOTE
r-release-linux-x86_64 1.0 0.91 17.11 18.02 ERROR
r-release-windows-ix86+x86_64 1.0 4.00 39.00 43.00 NOTE
r-release-osx-x86_64 1.0 NOTE
r-oldrel-windows-ix86+x86_64 1.0 5.00 41.00 46.00 NOTE
r-oldrel-osx-x86_64 1.0 NOTE

Check Details

Version: 1.0
Check: dependencies in R code
Result: NOTE
    Packages in Depends field not imported from:
     ‘lars’ ‘ncvreg’
     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-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: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     plot.path print.path
    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
Check: R code for possible problems
Result: NOTE
    plot.path: no visible global function definition for ‘par’
    plot.path: no visible global function definition for ‘plot’
    plot.path: no visible global function definition for ‘axis’
    plot.path: no visible global function definition for ‘points’
    plot.path: no visible global function definition for ‘abline’
    Undefined global functions or variables:
     abline axis par plot points
    Consider adding
     importFrom("graphics", "abline", "axis", "par", "plot", "points")
    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
Check: examples
Result: ERROR
    Running examples in ‘ExactPath-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: ExactPath-package
    > ### Title: Exact Solution Paths for Regularized L_1 LASSO Regression
    > ### Aliases: ExactPath-package ExactPath
    >
    > ### ** Examples
    >
    > library(ncvreg)
    > data(prostate)
    > myfit = exact.path(as.matrix(prostate[,-9]), prostate$lpsa, verbose=TRUE)
     beta score breaks tau change
    lcavol 0 0.7344603 0.7344603 1 +
    lweight 0 0.4333194 0.4333194 0 |
    age 0 0.1695928 0.1695928 0 |
    lbph 0 0.1798094 0.1798094 0 |
    svi 0 0.5662182 0.5662182 0 |
    lcp 0 0.5488132 0.5488132 0 |
    gleason 0 0.3689868 0.3689868 0 |
    pgg45 0 0.4223159 0.4223159 0 |
    
    lambda_1 = 0.7344603
    
    
     beta score breaks tau change
    lcavol 0.3648277 0.36963266 0.734460326 1 |
    lweight 0.0000000 0.33097742 0.315905924 0 |
    age 0.0000000 0.08750666 0.005599166 0 |
    lbph 0.0000000 0.16983148 0.164213317 0 |
    svi 0.0000000 0.36963266 0.369632655 1 +
    lcp 0.0000000 0.30244122 0.162692091 0 |
    gleason 0.0000000 0.21122910 0.090548236 0 |
    pgg45 0.0000000 0.26410752 0.183306962 0 |
    
    lambda_2 = 0.3696327
    
    
     beta score breaks tau change
    lcavol 0.39987516 0.31570000 0.931045893 1 |
    lweight 0.00000000 0.31570000 0.315699999 1 +
    age 0.00000000 0.07549736 0.006689277 0 |
    lbph 0.00000000 0.17188153 0.177148069 0 |
    svi 0.03504749 0.31570000 0.369632655 1 |
    lcp 0.00000000 0.25518243 0.011433137 0 |
    gleason 0.00000000 0.18484432 0.059513515 0 |
    pgg45 0.00000000 0.23286969 0.118859665 0 |
    
    lambda_3 = 0.3157
    
    
     beta score breaks tau change
    lcavol 0.4829234 0.124387656 1.236864149 1 |
    lweight 0.1488355 0.124387656 0.315699999 1 |
    age 0.0000000 -0.009501825 0.044843100 0 |
    lbph 0.0000000 0.114381619 0.110081973 0 |
    svi 0.1584829 0.124387656 0.370020043 1 |
    lcp 0.0000000 0.091524348 0.008021252 0 |
    gleason 0.0000000 0.100916555 0.082572420 0 |
    pgg45 0.0000000 0.124387656 0.124387656 1 +
    
    lambda_4 = 0.1243877
    
    
     beta score breaks tau change
    lcavol 0.487275262 0.10869606 1.86567157 1 |
    lweight 0.161198691 0.10869606 0.31329310 1 |
    age 0.000000000 -0.01816516 0.05036808 0 |
    lbph 0.000000000 0.10869606 0.10869606 1 +
    svi 0.165712510 0.10869606 0.46836949 1 |
    lcp 0.000000000 0.07589476 0.01621793 0 |
    gleason 0.000000000 0.08912116 0.02985989 0 |
    pgg45 0.009168559 0.10869606 0.12438766 1 |
    
    lambda_5 = 0.1086961
    
    
     beta score breaks tau change
    lcavol 0.50491055 0.05558212 1.57627146 1 |
    lweight 0.18200727 0.05558212 0.52015610 1 |
    age 0.00000000 -0.05558212 0.05558212 -1 +
    lbph 0.04431172 0.05558212 0.10869606 1 |
    svi 0.19858501 0.05558212 0.37644704 1 |
    lcp 0.00000000 0.02313882 0.01608855 0 |
    gleason 0.00000000 0.04774973 0.02015453 0 |
    pgg45 0.03388032 0.05558212 0.12840240 1 |
    
    lambda_6 = 0.05558212
    
    
     beta score breaks tau change
    lcavol 0.51741672 0.032103019 1.00350133 1 |
    lweight 0.20157703 0.032103019 0.27394789 1 |
    age -0.05185925 -0.032103019 0.05558212 -1 |
    lbph 0.07629111 0.032103019 0.08811557 1 |
    svi 0.21103160 0.032103019 0.43019063 1 |
    lcp 0.00000000 -0.003996983 0.01906527 0 |
    gleason 0.00000000 0.032103019 0.03210302 1 +
    pgg45 0.05594893 0.032103019 0.09162786 1 |
    
    lambda_7 = 0.03210302
    
    
     beta score breaks tau change
    lcavol 0.52231490 0.01913394 1.40208545 1 |
    lweight 0.21336467 0.01913394 0.25388364 1 |
    age -0.08120861 -0.01913394 0.05501892 -1 |
    lbph 0.09366845 0.01913394 0.08904069 1 |
    svi 0.21890832 0.01913394 0.37956812 1 |
    lcp 0.00000000 -0.01913394 0.01913394 -1 +
    gleason 0.01066560 0.01913394 0.03210302 1 |
    pgg45 0.06064448 0.01913394 0.18663378 1 |
    
    lambda_8 = 0.01913394
    
    
     beta score breaks tau change
    lcavol 0.57621928 1.214306e-16 0.20453520 1 |
    lweight 0.23085294 -1.752071e-16 0.25257645 1 |
    age -0.13704517 5.551115e-17 0.04696230 -1 |
    lbph 0.12155214 8.673617e-19 0.08340974 1 |
    svi 0.27317070 -8.673617e-17 0.09632513 1 |
    lcp -0.12846050 -1.075529e-16 0.01913394 -1 |
    gleason 0.03079639 1.630640e-16 0.02927139 1 |
    pgg45 0.10891159 -4.943962e-17 0.04317448 1 |
    
    lambda_9 = 0
    
    
     beta score breaks tau change
    lcavol 0.57621928 1.214306e-16 0.20453520 1 |
    lweight 0.23085294 -1.752071e-16 0.25257645 1 |
    age -0.13704517 5.551115e-17 0.04696230 -1 |
    lbph 0.12155214 8.673617e-19 0.08340974 1 |
    svi 0.27317070 -8.673617e-17 0.09632513 1 |
    lcp -0.12846050 -1.075529e-16 0.01913394 -1 |
    gleason 0.03079639 1.630640e-16 0.02927139 1 |
    pgg45 0.10891159 -4.943962e-17 0.04317448 1 |
    
    lambda_10 = 0
    
    
     beta score breaks tau change
    lcavol 0.57621928 1.214306e-16 0.20453520 1 |
    lweight 0.23085294 -1.752071e-16 0.25257645 1 |
    age -0.13704517 5.551115e-17 0.04696230 -1 |
    lbph 0.12155214 8.673617e-19 0.08340974 1 |
    svi 0.27317070 -8.673617e-17 0.09632513 1 |
    lcp -0.12846050 -1.075529e-16 0.01913394 -1 |
    gleason 0.03079639 1.630640e-16 0.02927139 1 |
    pgg45 0.10891159 -4.943962e-17 0.04317448 1 |
    
    lambda_11 = 0
    
    
     beta score breaks tau change
    lcavol 0.57621928 1.214306e-16 0.20453520 1 |
    lweight 0.23085294 -1.752071e-16 0.25257645 1 |
    age -0.13704517 5.551115e-17 0.04696230 -1 |
    lbph 0.12155214 8.673617e-19 0.08340974 1 |
    svi 0.27317070 -8.673617e-17 0.09632513 1 |
    lcp -0.12846050 -1.075529e-16 0.01913394 -1 |
    gleason 0.03079639 1.630640e-16 0.02927139 1 |
    pgg45 0.10891159 -4.943962e-17 0.04317448 1 |
    
    lambda_12 = 0
    
    
    > myfit
    $breaks
     [1] 0.73446033 0.36963266 0.31570000 0.12438766 0.10869606 0.05558212
     [7] 0.03210302 0.01913394 0.00000000 0.00000000 0.00000000 0.00000000
    
    $tau
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
    [1,] 1 1 1 1 1 1 1 1 1 1 1 1
    [2,] 0 0 1 1 1 1 1 1 1 1 1 1
    [3,] 0 0 0 0 0 -1 -1 -1 -1 -1 -1 -1
    [4,] 0 0 0 0 1 1 1 1 1 1 1 1
    [5,] 0 1 1 1 1 1 1 1 1 1 1 1
    [6,] 0 0 0 0 0 0 0 -1 -1 -1 -1 -1
    [7,] 0 0 0 0 0 0 1 1 1 1 1 1
    [8,] 0 0 0 1 1 1 1 1 1 1 1 1
    
    $beta
     [,1] [,2] [,3] [,4] [,5] [,6] [,7]
    [1,] 0 0.3648277 0.39987516 0.4829234 0.487275262 0.50491055 0.51741672
    [2,] 0 0.0000000 0.00000000 0.1488355 0.161198691 0.18200727 0.20157703
    [3,] 0 0.0000000 0.00000000 0.0000000 0.000000000 0.00000000 -0.05185925
    [4,] 0 0.0000000 0.00000000 0.0000000 0.000000000 0.04431172 0.07629111
    [5,] 0 0.0000000 0.03504749 0.1584829 0.165712510 0.19858501 0.21103160
    [6,] 0 0.0000000 0.00000000 0.0000000 0.000000000 0.00000000 0.00000000
    [7,] 0 0.0000000 0.00000000 0.0000000 0.000000000 0.00000000 0.00000000
    [8,] 0 0.0000000 0.00000000 0.0000000 0.009168559 0.03388032 0.05594893
     [,8] [,9] [,10] [,11] [,12]
    [1,] 0.52231490 0.57621928 0.57621928 0.57621928 0.57621928
    [2,] 0.21336467 0.23085294 0.23085294 0.23085294 0.23085294
    [3,] -0.08120861 -0.13704517 -0.13704517 -0.13704517 -0.13704517
    [4,] 0.09366845 0.12155214 0.12155214 0.12155214 0.12155214
    [5,] 0.21890832 0.27317070 0.27317070 0.27317070 0.27317070
    [6,] 0.00000000 -0.12846050 -0.12846050 -0.12846050 -0.12846050
    [7,] 0.01066560 0.03079639 0.03079639 0.03079639 0.03079639
    [8,] 0.06064448 0.10891159 0.10891159 0.10891159 0.10891159
    
    $score
     [,1] [,2] [,3] [,4] [,5] [,6]
    [1,] 0.7344603 0.36963266 0.31570000 0.124387656 0.10869606 0.05558212
    [2,] 0.4333194 0.33097742 0.31570000 0.124387656 0.10869606 0.05558212
    [3,] 0.1695928 0.08750666 0.07549736 -0.009501825 -0.01816516 -0.05558212
    [4,] 0.1798094 0.16983148 0.17188153 0.114381619 0.10869606 0.05558212
    [5,] 0.5662182 0.36963266 0.31570000 0.124387656 0.10869606 0.05558212
    [6,] 0.5488132 0.30244122 0.25518243 0.091524348 0.07589476 0.02313882
    [7,] 0.3689868 0.21122910 0.18484432 0.100916555 0.08912116 0.04774973
    [8,] 0.4223159 0.26410752 0.23286969 0.124387656 0.10869606 0.05558212
     [,7] [,8] [,9] [,10] [,11]
    [1,] 0.032103019 0.01913394 1.214306e-16 1.214306e-16 1.214306e-16
    [2,] 0.032103019 0.01913394 -1.752071e-16 -1.752071e-16 -1.752071e-16
    [3,] -0.032103019 -0.01913394 5.551115e-17 5.551115e-17 5.551115e-17
    [4,] 0.032103019 0.01913394 8.673617e-19 8.673617e-19 8.673617e-19
    [5,] 0.032103019 0.01913394 -8.673617e-17 -8.673617e-17 -8.673617e-17
    [6,] -0.003996983 -0.01913394 -1.075529e-16 -1.075529e-16 -1.075529e-16
    [7,] 0.032103019 0.01913394 1.630640e-16 1.630640e-16 1.630640e-16
    [8,] 0.032103019 0.01913394 -4.943962e-17 -4.943962e-17 -4.943962e-17
     [,12]
    [1,] 1.214306e-16
    [2,] -1.752071e-16
    [3,] 5.551115e-17
    [4,] 8.673617e-19
    [5,] -8.673617e-17
    [6,] -1.075529e-16
    [7,] 1.630640e-16
    [8,] -4.943962e-17
    
    attr(,"class")
    [1] "path"
    > plot(myfit)
    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