Last updated on 2025-06-02 21:48:35 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 6.0.4 | 18.28 | 185.65 | 203.93 | OK | |
| r-devel-linux-x86_64-debian-gcc | 6.0.4 | 12.50 | 125.32 | 137.82 | OK | |
| r-devel-linux-x86_64-fedora-clang | 6.0.4 | 260.04 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 6.0.4 | 263.97 | ERROR | |||
| r-devel-windows-x86_64 | 6.0.4 | 24.00 | 187.00 | 211.00 | OK | |
| r-patched-linux-x86_64 | 6.0.4 | 19.67 | 171.20 | 190.87 | OK | |
| r-release-linux-x86_64 | 6.0.4 | 16.51 | 170.81 | 187.32 | OK | |
| r-release-macos-arm64 | 6.0.4 | 111.00 | OK | |||
| r-release-macos-x86_64 | 6.0.4 | 167.00 | OK | |||
| r-release-windows-x86_64 | 6.0.4 | 24.00 | 183.00 | 207.00 | OK | |
| r-oldrel-macos-arm64 | 6.0.4 | 94.00 | OK | |||
| r-oldrel-macos-x86_64 | 6.0.4 | 203.00 | OK | |||
| r-oldrel-windows-x86_64 | 6.0.4 | 32.00 | 235.00 | 267.00 | OK |
Version: 6.0.4
Check: examples
Result: ERROR
Running examples in ‘hdnom-Ex.R’ failed
The error most likely occurred in:
> ### Name: as_nomogram
> ### Title: Construct nomogram ojects for high-dimensional Cox models
> ### Aliases: as_nomogram
>
> ### ** Examples
>
> data(smart)
> x <- as.matrix(smart[, -c(1, 2)])
> time <- smart$TEVENT
> event <- smart$EVENT
> y <- survival::Surv(time, event)
>
> fit <- fit_lasso(x, y, nfolds = 5, rule = "lambda.1se", seed = 11)
>
> nom <- as_nomogram(
+ fit, x, time, event, pred.at = 365 * 2,
+ funlabel = "2-Year Overall Survival Probability"
+ )
>
> print(nom)
Points per unit of linear predictor: 4.987753e+16
Linear predictor units per point : 2.004911e-17
AGE Points
15 0
20 7
25 14
30 21
35 29
40 36
45 43
50 50
55 57
60 64
65 71
70 79
75 86
80 93
85 100
Total Points 2-Year Overall Survival Probability
> plot(nom)
Error in axis(sides[jj], at = scaled[jj], labels = fat[jj], pos = y, cex.axis = cex.axis, :
no locations are finite
Calls: plot ... plot.hdnom.nomogram -> plot -> plot.nomogram.raw -> axis
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 6.0.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘hdnom.Rmd’ using rmarkdown
Quitting from hdnom.Rmd:377-390 [unnamed-chunk-16]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `fit_alasso()`:
! Null model produced by the full fit (all coefficients are zero). Please try to tune rule, seed, nfolds, or increase sample size.
---
Backtrace:
▆
1. └─hdnom::compare_by_validate(...)
2. └─hdnom::fit_alasso(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'hdnom.Rmd' failed with diagnostics:
Null model produced by the full fit (all coefficients are zero). Please try to tune rule, seed, nfolds, or increase sample size.
--- failed re-building ‘hdnom.Rmd’
SUMMARY: processing the following file failed:
‘hdnom.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc