Last updated on 2026-10-24 09:50:49 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.5 | 15.65 | 472.29 | 487.94 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.5 | 11.09 | 154.78 | 165.87 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.5 | 12.00 | 312.11 | 324.11 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.5 | 11.00 | 338.60 | 349.60 | OK | |
| r-devel-windows-x86_64 | 1.0.5 | 21.00 | 433.00 | 454.00 | OK | |
| r-patched-linux-x86_64 | 1.0.5 | 15.91 | 462.37 | 478.28 | OK | |
| r-release-linux-x86_64 | 1.0.5 | 15.21 | 458.74 | 473.95 | OK | |
| r-release-macos-arm64 | 1.0.5 | 4.00 | 97.00 | 101.00 | OK | |
| r-release-macos-x86_64 | 1.0.5 | 11.00 | 465.00 | 476.00 | OK | |
| r-release-windows-x86_64 | 1.0.5 | 20.00 | 412.00 | 432.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.5 | 4.00 | 94.00 | 98.00 | OK | |
| r-oldrel-macos-x86_64 | 1.0.5 | 11.00 | 316.00 | 327.00 | OK | |
| r-oldrel-windows-x86_64 | 1.0.5 | 25.00 | 584.00 | 609.00 | OK |
Version: 1.0.5
Check: examples
Result: ERROR
Running examples in ‘csmpv-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: XGBtraining
> ### Title: A Wrapper Function for xgboost::xgboost
> ### Aliases: XGBtraining
>
> ### ** Examples
>
> # Load in data sets:
> data("datlist", package = "csmpv")
> tdat = datlist$training
> # The function saves files locally. You can define your own temporary directory.
> # If not, tempdir() can be used to get the system's temporary directory.
> temp_dir = tempdir()
> # As an example, let's define Xvars, which will be used later:
> Xvars = c("highIPI", "B.Symptoms", "MYC.IHC", "BCL2.IHC", "CD10.IHC", "BCL6.IHC")
>
> # The function can work with three outcome types.
> # Here, we use time-to-event outcome as an example:
> txfit = XGBtraining(data = tdat, biomks = Xvars,
+ outcomeType = "time-to-event",
+ time = "FFP..Years.",event = "Code.FFP",
+ outfile = paste0(temp_dir, "/survival_XGBoost"))
Error in a$specials[[i]] : subscript out of bounds
Calls: XGBtraining ... survfit.coxph -> model.matrix.coxph -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.5
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘csmpv_vignette.rmd’ using rmarkdown
Quitting from csmpv_vignette.rmd:247-252 [unnamed-chunk-21]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `a$specials[[i]]`:
! subscript out of bounds
---
Backtrace:
▆
1. └─csmpv::LASSO2(...)
2. └─survival::basehaz(coxfit)
3. ├─survival::survfit(fit, se.fit = FALSE)
4. └─survival:::survfit.coxph(fit, se.fit = FALSE)
5. └─survival:::model.matrix.coxph(object, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'csmpv_vignette.rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘csmpv_vignette.rmd’
SUMMARY: processing the following file failed:
‘csmpv_vignette.rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc