Last updated on 2026-10-24 09:50:53 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.3 | 19.89 | 210.66 | 230.55 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 2.0.3 | 15.07 | 150.32 | 165.39 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.0.3 | 15.00 | 144.92 | 159.92 | NOTE | |
| r-devel-linux-x86_64-fedora-gcc | 2.0.3 | 14.00 | 144.65 | 158.65 | NOTE | |
| r-devel-windows-x86_64 | 2.0.3 | 25.00 | 219.00 | 244.00 | NOTE | |
| r-patched-linux-x86_64 | 2.0.3 | 19.71 | 203.29 | 223.00 | OK | |
| r-release-linux-x86_64 | 2.0.3 | 18.98 | 204.06 | 223.04 | OK | |
| r-release-macos-arm64 | 2.0.3 | 5.00 | 53.00 | 58.00 | OK | |
| r-release-macos-x86_64 | 2.0.3 | 14.00 | 214.00 | 228.00 | OK | |
| r-release-windows-x86_64 | 2.0.3 | 22.00 | 205.00 | 227.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.3 | OK | ||||
| r-oldrel-macos-x86_64 | 2.0.3 | 13.00 | 179.00 | 192.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.3 | 29.00 | 265.00 | 294.00 | OK |
Version: 2.0.3
Check: dependencies in R code
Result: NOTE
Base package in Suggests/Enhances imported in NAMESPACE:
‘parallel’
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-x86_64
Version: 2.0.3
Check: R code for possible problems
Result: NOTE
Found calls to structure() using deprecated special names:
Greg/tests/testthat/test-private_functions.R (.Label: 3, .Names: 1)
'.Label' should be changed to 'levels'.
'.Names' should be changed to 'names'.
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-x86_64
Version: 2.0.3
Check: examples
Result: ERROR
Running examples in ‘Greg-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotHR
> ### Title: Plot a spline in a Cox regression model
> ### Aliases: plotHR print.plotHR plot.plotHR
>
> ### ** Examples
>
> org_par <- par(xaxs = "i", ask = TRUE)
> library(survival)
> library(rms)
Loading required package: Hmisc
Attaching package: ‘Hmisc’
The following objects are masked from ‘package:base’:
format.pval, units
> library(dplyr)
Attaching package: ‘dplyr’
The following objects are masked from ‘package:Hmisc’:
src, summarize
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
> library(Gmisc)
>
> # Get data for example
> n <- 1000
> set.seed(731)
>
> ds <- tibble(age = round(50 + 12 * rnorm(n), 1),
+ smoking = sample(c("Yes", "No"), n, rep = TRUE, prob = c(.2, .75)),
+ sex = sample(c("Male", "Female"), n, rep = TRUE, prob = c(.6, .4))) |>
+ # Build outcome
+ mutate(h = .02 * exp(.02 * (age - 50) + .1 *
+ ((age - 50) / 10)^3 + .8 *
+ (sex == "Female") + 2 *
+ (smoking == "Yes")),
+ cens = 15 * runif(n),
+ dt = -log(runif(n)) / h,
+ e = if_else(dt <= cens, 1, 0),
+ dt = pmin(dt, cens),
+ # Add missing data to smoking
+ smoking = case_when(runif(n) < 0.05 ~ NA_character_,
+ TRUE ~ smoking)) |>
+ set_column_labels(age = "Age",
+ dt = "Follow-up time") |>
+ set_column_units(dt = "Year")
>
>
> library(splines)
> fit.coxph <- coxph(Surv(dt, e) ~ bs(age, 3) + sex + smoking, data = ds)
>
> plotHR(fit.coxph, term = "age", plot.bty = "o", xlim = c(30, 70), xlab = "Age")
Error in a$specials[[i]] : subscript out of bounds
Calls: plotHR ... <Anonymous> -> predict -> predict.coxph -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.0.3
Check: tests
Result: ERROR
Running ‘test-interval-timeSplitter.R’ [4s/6s]
Running ‘test-nonlin_4_coxph.R’ [4s/6s]
Running ‘testthat.R’ [14s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
>
> test_check("Greg")
Loading required package: Greg
Loading required package: Gmisc
Loading required package: htmlTable
Attaching package: 'Gmisc'
The following object is masked from 'package:base':
append
Loading required package: forestplot
Loading required package: grid
Loading required package: checkmate
Loading required package: abind
Saving _problems/test-plotHR-157.R
Saving _problems/test-plotHR-256.R
[ FAIL 2 | WARN 4 | SKIP 0 | PASS 283 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-plotHR.R:152:3'): Check the prPhEstimate function ──────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─Greg:::prPhEstimate(...) at test-plotHR.R:152:3
2. ├─stats::predict(...)
3. └─survival:::predict.coxph(...)
4. └─stats::delete.response(Terms)
5. └─stats (local) off(a$specials[[i]])
── Error ('test-plotHR.R:256:3'): General plotting funcitonality of plotHR ─────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─Greg::plotHR(...) at test-plotHR.R:256:3
2. ├─base::do.call(prPhEstimate, est_list)
3. └─Greg (local) `<fn>`(...)
4. ├─stats::predict(...)
5. └─survival:::predict.coxph(...)
6. └─stats::delete.response(Terms)
7. └─stats (local) off(a$specials[[i]])
[ FAIL 2 | WARN 4 | SKIP 0 | PASS 283 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.0.3
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘printCrudeAndAdjustedModel.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘printCrudeAndAdjustedModel.Rmd’
--- re-building ‘timeSplitter.Rmd’ using rmarkdown
Quitting from timeSplitter.Rmd:425-481 [unnamed-chunk-12]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `a$specials[[i]]`:
! subscript out of bounds
---
Backtrace:
▆
1. ├─stats::predict(...)
2. ├─survival:::predict.coxph.penal(...)
3. ├─base::NextMethod("predict", object, ...)
4. └─survival:::predict.coxph(...)
5. └─stats::delete.response(Terms)
6. └─stats (local) off(a$specials[[i]])
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'timeSplitter.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘timeSplitter.Rmd’
SUMMARY: processing the following file failed:
‘timeSplitter.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc