Last updated on 2018-06-17 19:49:39 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0 | 1.07 | 18.62 | 19.69 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0 | 0.85 | 14.52 | 15.37 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0 | 24.26 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0 | 22.86 | NOTE | |||
| r-devel-windows-ix86+x86_64 | 1.0 | 3.00 | 39.00 | 42.00 | NOTE | |
| r-patched-linux-x86_64 | 1.0 | 0.94 | 17.40 | 18.34 | ERROR | |
| r-patched-solaris-x86 | 1.0 | 36.40 | NOTE | |||
| r-release-linux-x86_64 | 1.0 | 0.85 | 17.27 | 18.12 | ERROR | |
| r-release-windows-ix86+x86_64 | 1.0 | 5.00 | 32.00 | 37.00 | NOTE | |
| r-release-osx-x86_64 | 1.0 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 1.0 | 2.00 | 39.00 | 41.00 | NOTE | |
| r-oldrel-osx-x86_64 | 1.0 | NOTE |
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