Last updated on 2026-10-24 09:50:54 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.3.25 | 19.91 | 264.75 | 284.66 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.3.25 | 11.85 | 168.29 | 180.14 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.3.25 | 18.00 | 203.62 | 221.62 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.3.25 | 14.00 | 172.96 | 186.96 | OK | |
| r-devel-windows-x86_64 | 1.3.25 | 24.00 | 281.00 | 305.00 | OK | |
| r-patched-linux-x86_64 | 1.3.25 | 20.48 | 244.03 | 264.51 | OK | |
| r-release-linux-x86_64 | 1.3.25 | 18.11 | 248.74 | 266.85 | OK | |
| r-release-macos-arm64 | 1.3.25 | 5.00 | 56.00 | 61.00 | OK | |
| r-release-macos-x86_64 | 1.3.25 | 14.00 | 261.00 | 275.00 | OK | |
| r-release-windows-x86_64 | 1.3.25 | 23.00 | 267.00 | 290.00 | OK | |
| r-oldrel-macos-arm64 | 1.3.25 | 5.00 | 58.00 | 63.00 | OK | |
| r-oldrel-macos-x86_64 | 1.3.25 | 15.00 | 176.00 | 191.00 | OK | |
| r-oldrel-windows-x86_64 | 1.3.25 | 30.00 | 345.00 | 375.00 | OK |
Version: 1.3.25
Check: examples
Result: ERROR
Running examples in ‘jstable-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TableSubgroupCox
> ### Title: TableSubgroupCox: Sub-group analysis table for Cox/svycox model.
> ### Aliases: TableSubgroupCox
>
> ### ** Examples
>
> library(survival)
> library(dplyr)
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
> lung %>%
+ mutate(
+ status = as.integer(status == 1),
+ sex = factor(sex),
+ kk = factor(as.integer(pat.karno >= 70))
+ ) -> lung
> TableSubgroupCox(Surv(time, status) ~ sex, data = lung, time_eventrate = 100)
Variable Count Percent Point Estimate Lower Upper sex=1 sex=2 P value
sex2 Overall 228 100 1.91 1.14 3.2 0 1.2 0.014
P for interaction
sex2 NA
> TableSubgroupCox(Surv(time, status) ~ sex,
+ var_subgroup = "kk", data = lung,
+ time_eventrate = 100
+ )
Variable Count Percent Point Estimate Lower Upper sex=1 sex=2 P value
1 kk <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
2 0 38 16.9 2.88 0.31 26.49 0 0 0.35
3 1 187 83.1 1.84 1.08 3.14 0 1.5 0.026
P for interaction
1 0.525
2 <NA>
3 <NA>
>
> ## survey design
> library(survey)
Loading required package: grid
Loading required package: Matrix
Attaching package: ‘survey’
The following object is masked from ‘package:graphics’:
dotchart
> data.design <- svydesign(id = ~1, data = lung)
Warning in svydesign.default(id = ~1, data = lung) :
No weights or probabilities supplied, assuming equal probability
> TableSubgroupCox(Surv(time, status) ~ sex, data = data.design, time_eventrate = 100)
Independent Sampling design (with replacement)
svydesign(id = ~1, data = lung)
Variable Count Percent Point Estimate Lower Upper sex=1 sex=2 P value
sex2 Overall 228 100 1.91 1.14 3.19 0 1.2 0.013
P for interaction
sex2 NA
> TableSubgroupCox(Surv(time, status) ~ sex,
+ var_subgroup = "kk", data = data.design,
+ time_eventrate = 100
+ )
Error in a$specials[[i]] : subscript out of bounds
Calls: TableSubgroupCox ... model.matrix -> model.matrix.coxph -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.3.25
Check: tests
Result: ERROR
Running ‘testthat.R’ [40s/46s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(jstable)
>
> test_check("jstable")
Saving _problems/test-forestcox-49.R
Saving _problems/test-regtable-98.R
[ FAIL 2 | WARN 23 | SKIP 0 | PASS 119 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-forestcox.R:49:3'): Run TableSubgroupMultiCox ──────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_is(...) at test-forestcox.R:49:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─jstable::TableSubgroupMultiCox(...)
5. └─base::lapply(...)
6. └─jstable (local) FUN(X[[i]], ...)
7. └─jstable::TableSubgroupCox(...)
8. ├─car::Anova(model_int)
9. └─car:::Anova.coxme(model_int)
10. └─car:::Anova.default(...)
11. ├─stats::model.matrix(mod)
12. └─car:::model.matrix.coxme(mod)
13. ├─stats::model.matrix(object)
14. └─survival:::model.matrix.coxph(object)
15. └─stats::delete.response(object$terms)
16. └─stats (local) off(a$specials[[i]])
── Error ('test-regtable.R:98:3'): Run svycox.display ──────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survey::svycoxph(...) at test-regtable.R:98:3
2. └─survey:::svycoxph.survey.design(...)
3. ├─stats::resid(g, "dfbeta", weighted = TRUE)
4. └─survival:::residuals.coxph(g, "dfbeta", weighted = TRUE)
5. └─survival:::coxph.getdata(object, y = TRUE, x = TRUE, stratax = TRUE)
6. ├─stats::model.matrix(fit, data = mf)
7. └─survival:::model.matrix.coxph(fit, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
[ FAIL 2 | WARN 23 | SKIP 0 | PASS 119 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.3.25
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘jstable.Rmd’ using rmarkdown
Quitting from jstable.Rmd:105-119 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `a$specials[[i]]`:
! subscript out of bounds
---
Backtrace:
▆
1. ├─survey::svycoxph(...)
2. └─survey:::svycoxph.survey.design(...)
3. ├─stats::resid(g, "dfbeta", weighted = TRUE)
4. └─survival:::residuals.coxph(g, "dfbeta", weighted = TRUE)
5. └─survival:::coxph.getdata(object, y = TRUE, x = TRUE, stratax = TRUE)
6. ├─stats::model.matrix(fit, data = mf)
7. └─survival:::model.matrix.coxph(fit, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'jstable.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘jstable.Rmd’
--- re-building ‘jstable_competing_risk_analysis.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘jstable_competing_risk_analysis.Rmd’
--- re-building ‘jstable_options.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘jstable_options.Rmd’
SUMMARY: processing the following file failed:
‘jstable.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc