Last updated on 2026-10-24 01:51:57 CEST.
| Package | OK | WARN | ERROR |
|---|---|---|---|
| ggextreme | 11 | 1 | 1 |
| krt | 13 | ||
| mlumr | 13 | ||
| respondeR | 13 | ||
| retraction | 13 | ||
| rfair | 13 | ||
| rtransparency | 13 | ||
| sysreqr | 13 |
Current CRAN status: OK: 11, WARN: 1, ERROR: 1
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘ggextreme-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggkm
> ### Title: Draw an interactive Kaplan-Meier plot
> ### Aliases: ggkm
>
> ### ** Examples
>
> if (requireNamespace("survival", quietly = TRUE)) {
+ colon <- subset(survival::colon, etype == 2)
+ colon$years <- colon$time / 365.25
+ km <- ggkm(survival::Surv(years, status) ~ rx, data = colon,
+ xlab = "Years since randomization")
+ km
+ }
Error in a$specials[[i]] : subscript out of bounds
Calls: ggkm ... model.matrix -> model.matrix.coxph -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [146s/204s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(ggextreme)
>
> test_check("ggextreme")
Saving _problems/test-km-19.R
Saving _problems/test-km-36.R
Saving _problems/test-km-46.R
Saving _problems/test-km-61.R
Saving _problems/test-km-77.R
Saving _problems/test-km-96.R
Saving _problems/test-km-105.R
Saving _problems/test-km-117.R
Saving _problems/test-km-148.R
Saving _problems/test-nomogram-70.R
[ FAIL 10 | WARN 0 | SKIP 3 | PASS 746 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-km.R:137:3', 'test-map.R:123:3', 'test-meta.R:135:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-km.R:19:3'): every time slice carries a readout with the hazard ratio ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ggextreme (local) km_fit() at test-km.R:19:3
2. └─ggextreme::ggkm(...) at test-km.R:14:3
3. └─ggextreme:::km_prepare(...)
4. └─survival::cox.zph(cox, transform = "km", terms = FALSE)
5. └─survival:::coxph.getdata(...)
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 ('test-km.R:36:3'): the risk table matches survfit ────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ggextreme (local) km_fit(breaks = c(0, 250, 500, 750)) at test-km.R:36:3
2. └─ggextreme::ggkm(...) at test-km.R:14:3
3. └─ggextreme:::km_prepare(...)
4. └─survival::cox.zph(cox, transform = "km", terms = FALSE)
5. └─survival:::coxph.getdata(...)
6. ├─stats::model.matrix(fit, data = mf)
7. └─survival:::model.matrix.coxph(fit, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-km.R:46:3'): the proportional hazards tests go in a collapsed section ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ggextreme (local) km_fit(ph_tests = TRUE) at test-km.R:46:3
2. └─ggextreme::ggkm(...) at test-km.R:14:3
3. └─ggextreme:::km_prepare(...)
4. └─survival::cox.zph(cox, transform = "km", terms = FALSE)
5. └─survival:::coxph.getdata(...)
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 ('test-km.R:61:3'): the proportional hazards table matches survival's own tests ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ggextreme (local) km_fit(ph_tests = TRUE) at test-km.R:61:3
2. └─ggextreme::ggkm(...) at test-km.R:14:3
3. └─ggextreme:::km_prepare(...)
4. └─survival::cox.zph(cox, transform = "km", terms = FALSE)
5. └─survival:::coxph.getdata(...)
6. ├─stats::model.matrix(fit, data = mf)
7. └─survival:::model.matrix.coxph(fit, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-km.R:77:3'): each method gives the hazard ratio it should ──────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ggextreme:::km_prepare(...) at test-km.R:77:3
2. └─survival::cox.zph(cox, transform = "km", terms = FALSE)
3. └─survival:::coxph.getdata(...)
4. ├─stats::model.matrix(fit, data = mf)
5. └─survival:::model.matrix.coxph(fit, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-km.R:96:3'): the cumulative incidence view starts at zero ──────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ggextreme (local) km_fit(type = "risk", ph_tests = FALSE) at test-km.R:96:3
2. └─ggextreme::ggkm(...) at test-km.R:14:3
3. └─ggextreme:::km_prepare(...)
4. └─survival::cox.zph(cox, transform = "km", terms = FALSE)
5. └─survival:::coxph.getdata(...)
6. ├─stats::model.matrix(fit, data = mf)
7. └─survival:::model.matrix.coxph(fit, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-km.R:105:3'): the reference group and the hazard ratio method can be chosen ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ggextreme (local) km_fit(reference = "Female", hr_time = "none", ph_tests = FALSE) at test-km.R:105:3
2. └─ggextreme::ggkm(...) at test-km.R:14:3
3. └─ggextreme:::km_prepare(...)
4. └─survival::cox.zph(cox, transform = "km", terms = FALSE)
5. └─survival:::coxph.getdata(...)
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 ('test-km.R:117:3'): more than two groups compare each with the reference ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ggextreme::ggkm(...) at test-km.R:117:3
2. └─ggextreme:::km_prepare(...)
3. └─survival::cox.zph(cox, transform = "km", terms = FALSE)
4. └─survival:::coxph.getdata(...)
5. ├─stats::model.matrix(fit, data = mf)
6. └─survival:::model.matrix.coxph(fit, data = mf)
7. └─stats::delete.response(object$terms)
8. └─stats (local) off(a$specials[[i]])
── Error ('test-km.R:148:3'): restricted mean survival matches survfit and stays within follow-up ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ggextreme (local) km_fit(rmst = 365) at test-km.R:148:3
2. └─ggextreme::ggkm(...) at test-km.R:14:3
3. └─ggextreme:::km_prepare(...)
4. └─survival::cox.zph(cox, transform = "km", terms = FALSE)
5. └─survival:::coxph.getdata(...)
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 ('test-nomogram.R:70:3'): survival models match survfit() and predict() ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ggextreme::ggnomogram(m, times = c(`1 year` = 365)) at test-nomogram.R:70:3
2. └─ggextreme:::nomo_model(fit, data, times)
3. └─ggextreme:::nomo_cox(fit)
4. └─ggextreme:::nomo_terms(...)
5. └─stats::delete.response(tt)
6. └─stats (local) off(a$specials[[i]])
[ FAIL 10 | WARN 0 | SKIP 3 | PASS 746 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.0
Check: whether startup messages can be suppressed
Result: NOTE
2026-10-07 09:30:22.380 R[16038:328833] XType: Using static font registry.
It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
Flavor: r-oldrel-macos-arm64
Version: 0.1.0
Check: dependencies in R code
Result: NOTE
2026-10-07 09:30:23.019 R[16298:329218] XType: Using static font registry.
Flavor: r-oldrel-macos-arm64
Version: 0.1.0
Check: S3 generic/method consistency
Result: WARN
2026-10-07 09:30:28.224 R[19141:333329] XType: Using static font registry.
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Flavor: r-oldrel-macos-arm64
Version: 0.1.0
Check: replacement functions
Result: WARN
2026-10-07 09:30:29.081 R[19763:334207] XType: Using static font registry.
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
Flavor: r-oldrel-macos-arm64
Version: 0.1.0
Check: foreign function calls
Result: NOTE
2026-10-07 09:30:29.773 R[20073:334722] XType: Using static font registry.
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Flavor: r-oldrel-macos-arm64
Version: 0.1.0
Check: R code for possible problems
Result: NOTE
2026-10-07 09:30:31.991 R[20493:335455] XType: Using static font registry.
Flavor: r-oldrel-macos-arm64
Version: 0.1.0
Check: for missing documentation entries
Result: WARN
2026-10-07 09:30:40.715 R[23898:340478] XType: Using static font registry.
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Flavor: r-oldrel-macos-arm64
Version: 0.1.0
Check: for code/documentation mismatches
Result: WARN
2026-10-07 09:30:41.605 R[24370:341167] XType: Using static font registry.
2026-10-07 09:30:42.628 R[24913:341924] XType: Using static font registry.
2026-10-07 09:30:43.457 R[25608:342865] XType: Using static font registry.
Flavor: r-oldrel-macos-arm64
Version: 0.1.0
Check: Rd \usage sections
Result: NOTE
2026-10-07 09:30:44.488 R[26413:343996] XType: Using static font registry.
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Flavor: r-oldrel-macos-arm64
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13