Last updated on 2023-01-17 06:00:43 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.6 | 13.31 | 328.93 | 342.24 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.2.6 | 9.72 | 235.84 | 245.56 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.2.6 | 404.07 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.2.6 | 411.36 | ERROR | |||
| r-devel-windows-x86_64 | 1.2.6 | 102.00 | 347.00 | 449.00 | ERROR | |
| r-patched-linux-x86_64 | 1.2.6 | 12.34 | 305.93 | 318.27 | ERROR | |
| r-release-linux-x86_64 | 1.2.6 | 9.61 | 301.09 | 310.70 | ERROR | |
| r-release-macos-arm64 | 1.2.6 | 152.00 | OK | |||
| r-release-macos-x86_64 | 1.2.6 | 221.00 | OK | |||
| r-release-windows-x86_64 | 1.2.6 | 69.00 | 347.00 | 416.00 | ERROR | |
| r-oldrel-macos-arm64 | 1.2.6 | 181.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.2.6 | 211.00 | OK | |||
| r-oldrel-windows-ix86+x86_64 | 1.2.6 | 25.00 | 362.00 | 387.00 | ERROR |
Version: 1.2.6
Check: package subdirectories
Result: NOTE
Problems with news in ‘NEWS.md’:
Cannot extract version info from the following section titles:
joineR <1.1
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: 1.2.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [72s/77s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(joineR)
Loading required package: survival
>
> test_check("joineR")
80% experienced event
40% experienced event
70% experienced event
100% experienced event
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-comprisk.R:17'): competing risks models ────────────────────────
Error in `model.frame.default(data = FALSE, formula = ~treat, xlev = list(
treat = c("CBZ", "LTG")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:17:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~treat, xlev = `<named list>`)
9. └─stats::model.frame.default(data = FALSE, formula = ~treat, xlev = `<named list>`)
── Error ('test-comprisk.R:54'): bootstrap SEs with competing risks ────────────
Error in `model.frame.default(data = FALSE, formula = ~treat, xlev = list(
treat = c("CBZ", "LTG")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:54:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~treat, xlev = `<named list>`)
9. └─stats::model.frame.default(data = FALSE, formula = ~treat, xlev = `<named list>`)
── Error ('test-comprisk.R:77'): ordering of subjects with competing risks ─────
Error in `model.frame.default(data = FALSE, formula = ~treat, xlev = list(
treat = c("CBZ", "LTG")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:77:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~treat, xlev = `<named list>`)
9. └─stats::model.frame.default(data = FALSE, formula = ~treat, xlev = `<named list>`)
── Error ('test-comprisk.R:116'): competing risks model with covariates ────────
Error in `model.frame.default(data = FALSE, formula = ~gender + age, xlev = list(
gender = c("F", "M")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:116:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~gender + age, xlev = `<named list>`)
9. └─stats::model.frame.default(...)
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.2.6
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘competing-risks.Rmd’ using rmarkdown
Quitting from lines 130-135 (competing-risks.Rmd)
Error: processing vignette ‘competing-risks.Rmd’ failed with diagnostics:
‘data’ must be a data.frame, environment, or list
--- failed re-building ‘competing-risks.Rmd’
--- re-building ‘joineR.Rmd’ using rmarkdown
--- finished re-building ‘joineR.Rmd’
SUMMARY: processing the following file failed:
‘competing-risks.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 1.2.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [51s/73s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(joineR)
Loading required package: survival
>
> test_check("joineR")
80% experienced event
40% experienced event
70% experienced event
100% experienced event
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-comprisk.R:17'): competing risks models ────────────────────────
Error in `model.frame.default(data = FALSE, formula = ~treat, xlev = list(
treat = c("CBZ", "LTG")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:17:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~treat, xlev = `<named list>`)
9. └─stats::model.frame.default(data = FALSE, formula = ~treat, xlev = `<named list>`)
── Error ('test-comprisk.R:54'): bootstrap SEs with competing risks ────────────
Error in `model.frame.default(data = FALSE, formula = ~treat, xlev = list(
treat = c("CBZ", "LTG")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:54:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~treat, xlev = `<named list>`)
9. └─stats::model.frame.default(data = FALSE, formula = ~treat, xlev = `<named list>`)
── Error ('test-comprisk.R:77'): ordering of subjects with competing risks ─────
Error in `model.frame.default(data = FALSE, formula = ~treat, xlev = list(
treat = c("CBZ", "LTG")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:77:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~treat, xlev = `<named list>`)
9. └─stats::model.frame.default(data = FALSE, formula = ~treat, xlev = `<named list>`)
── Error ('test-comprisk.R:116'): competing risks model with covariates ────────
Error in `model.frame.default(data = FALSE, formula = ~gender + age, xlev = list(
gender = c("F", "M")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:116:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~gender + age, xlev = `<named list>`)
9. └─stats::model.frame.default(...)
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [84s/95s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(joineR)
Loading required package: survival
>
> test_check("joineR")
80% experienced event
40% experienced event
70% experienced event
100% experienced event
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-comprisk.R:17'): competing risks models ────────────────────────
Error in `model.frame.default(data = FALSE, formula = ~treat, xlev = list(
treat = c("CBZ", "LTG")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:17:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~treat, xlev = `<named list>`)
9. └─stats::model.frame.default(data = FALSE, formula = ~treat, xlev = `<named list>`)
── Error ('test-comprisk.R:54'): bootstrap SEs with competing risks ────────────
Error in `model.frame.default(data = FALSE, formula = ~treat, xlev = list(
treat = c("CBZ", "LTG")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:54:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~treat, xlev = `<named list>`)
9. └─stats::model.frame.default(data = FALSE, formula = ~treat, xlev = `<named list>`)
── Error ('test-comprisk.R:77'): ordering of subjects with competing risks ─────
Error in `model.frame.default(data = FALSE, formula = ~treat, xlev = list(
treat = c("CBZ", "LTG")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:77:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~treat, xlev = `<named list>`)
9. └─stats::model.frame.default(data = FALSE, formula = ~treat, xlev = `<named list>`)
── Error ('test-comprisk.R:116'): competing risks model with covariates ────────
Error in `model.frame.default(data = FALSE, formula = ~gender + age, xlev = list(
gender = c("F", "M")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:116:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~gender + age, xlev = `<named list>`)
9. └─stats::model.frame.default(...)
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.2.6
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘competing-risks.Rmd’ using rmarkdown
Quitting from lines 130-135 (competing-risks.Rmd)
Error: processing vignette 'competing-risks.Rmd' failed with diagnostics:
'data' must be a data.frame, environment, or list
--- failed re-building ‘competing-risks.Rmd’
--- re-building ‘joineR.Rmd’ using rmarkdown
--- finished re-building ‘joineR.Rmd’
SUMMARY: processing the following file failed:
‘competing-risks.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64
Version: 1.2.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [80s/81s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(joineR)
Loading required package: survival
>
> test_check("joineR")
80% experienced event
40% experienced event
70% experienced event
100% experienced event
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-comprisk.R:17'): competing risks models ────────────────────────
Error in `model.frame.default(data = FALSE, formula = ~treat, xlev = list(
treat = c("CBZ", "LTG")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:17:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~treat, xlev = `<named list>`)
9. └─stats::model.frame.default(data = FALSE, formula = ~treat, xlev = `<named list>`)
── Error ('test-comprisk.R:54'): bootstrap SEs with competing risks ────────────
Error in `model.frame.default(data = FALSE, formula = ~treat, xlev = list(
treat = c("CBZ", "LTG")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:54:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~treat, xlev = `<named list>`)
9. └─stats::model.frame.default(data = FALSE, formula = ~treat, xlev = `<named list>`)
── Error ('test-comprisk.R:77'): ordering of subjects with competing risks ─────
Error in `model.frame.default(data = FALSE, formula = ~treat, xlev = list(
treat = c("CBZ", "LTG")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:77:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~treat, xlev = `<named list>`)
9. └─stats::model.frame.default(data = FALSE, formula = ~treat, xlev = `<named list>`)
── Error ('test-comprisk.R:116'): competing risks model with covariates ────────
Error in `model.frame.default(data = FALSE, formula = ~gender + age, xlev = list(
gender = c("F", "M")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:116:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~gender + age, xlev = `<named list>`)
9. └─stats::model.frame.default(...)
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.2.6
Check: tests
Result: ERROR
Running 'testthat.R' [68s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(joineR)
Loading required package: survival
>
> test_check("joineR")
80% experienced event
40% experienced event
70% experienced event
100% experienced event
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-comprisk.R:17'): competing risks models ────────────────────────
Error in `model.frame.default(data = FALSE, formula = ~treat, xlev = list(
treat = c("CBZ", "LTG")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:17:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~treat, xlev = `<named list>`)
9. └─stats::model.frame.default(data = FALSE, formula = ~treat, xlev = `<named list>`)
── Error ('test-comprisk.R:54'): bootstrap SEs with competing risks ────────────
Error in `model.frame.default(data = FALSE, formula = ~treat, xlev = list(
treat = c("CBZ", "LTG")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:54:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~treat, xlev = `<named list>`)
9. └─stats::model.frame.default(data = FALSE, formula = ~treat, xlev = `<named list>`)
── Error ('test-comprisk.R:77'): ordering of subjects with competing risks ─────
Error in `model.frame.default(data = FALSE, formula = ~treat, xlev = list(
treat = c("CBZ", "LTG")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:77:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~treat, xlev = `<named list>`)
9. └─stats::model.frame.default(data = FALSE, formula = ~treat, xlev = `<named list>`)
── Error ('test-comprisk.R:116'): competing risks model with covariates ────────
Error in `model.frame.default(data = FALSE, formula = ~gender + age, xlev = list(
gender = c("F", "M")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:116:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~gender + age, xlev = `<named list>`)
9. └─stats::model.frame.default(...)
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64
Version: 1.2.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [67s/76s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(joineR)
Loading required package: survival
>
> test_check("joineR")
80% experienced event
40% experienced event
70% experienced event
100% experienced event
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-comprisk.R:17'): competing risks models ────────────────────────
Error in `model.frame.default(data = FALSE, formula = ~treat, xlev = list(
treat = c("CBZ", "LTG")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:17:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~treat, xlev = `<named list>`)
9. └─stats::model.frame.default(data = FALSE, formula = ~treat, xlev = `<named list>`)
── Error ('test-comprisk.R:54'): bootstrap SEs with competing risks ────────────
Error in `model.frame.default(data = FALSE, formula = ~treat, xlev = list(
treat = c("CBZ", "LTG")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:54:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~treat, xlev = `<named list>`)
9. └─stats::model.frame.default(data = FALSE, formula = ~treat, xlev = `<named list>`)
── Error ('test-comprisk.R:77'): ordering of subjects with competing risks ─────
Error in `model.frame.default(data = FALSE, formula = ~treat, xlev = list(
treat = c("CBZ", "LTG")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:77:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~treat, xlev = `<named list>`)
9. └─stats::model.frame.default(data = FALSE, formula = ~treat, xlev = `<named list>`)
── Error ('test-comprisk.R:116'): competing risks model with covariates ────────
Error in `model.frame.default(data = FALSE, formula = ~gender + age, xlev = list(
gender = c("F", "M")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:116:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~gender + age, xlev = `<named list>`)
9. └─stats::model.frame.default(...)
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
Error: Test failures
Execution halted
Flavor: r-patched-linux-x86_64
Version: 1.2.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [67s/73s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(joineR)
Loading required package: survival
>
> test_check("joineR")
80% experienced event
40% experienced event
70% experienced event
100% experienced event
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-comprisk.R:17'): competing risks models ────────────────────────
Error in `model.frame.default(data = FALSE, formula = ~treat, xlev = list(
treat = c("CBZ", "LTG")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:17:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~treat, xlev = `<named list>`)
9. └─stats::model.frame.default(data = FALSE, formula = ~treat, xlev = `<named list>`)
── Error ('test-comprisk.R:54'): bootstrap SEs with competing risks ────────────
Error in `model.frame.default(data = FALSE, formula = ~treat, xlev = list(
treat = c("CBZ", "LTG")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:54:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~treat, xlev = `<named list>`)
9. └─stats::model.frame.default(data = FALSE, formula = ~treat, xlev = `<named list>`)
── Error ('test-comprisk.R:77'): ordering of subjects with competing risks ─────
Error in `model.frame.default(data = FALSE, formula = ~treat, xlev = list(
treat = c("CBZ", "LTG")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:77:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~treat, xlev = `<named list>`)
9. └─stats::model.frame.default(data = FALSE, formula = ~treat, xlev = `<named list>`)
── Error ('test-comprisk.R:116'): competing risks model with covariates ────────
Error in `model.frame.default(data = FALSE, formula = ~gender + age, xlev = list(
gender = c("F", "M")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:116:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~gender + age, xlev = `<named list>`)
9. └─stats::model.frame.default(...)
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
Error: Test failures
Execution halted
Flavor: r-release-linux-x86_64
Version: 1.2.6
Check: tests
Result: ERROR
Running 'testthat.R' [69s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(joineR)
Loading required package: survival
>
> test_check("joineR")
80% experienced event
40% experienced event
70% experienced event
100% experienced event
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-comprisk.R:17'): competing risks models ────────────────────────
Error in `model.frame.default(data = FALSE, formula = ~treat, xlev = list(
treat = c("CBZ", "LTG")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:17:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~treat, xlev = `<named list>`)
9. └─stats::model.frame.default(data = FALSE, formula = ~treat, xlev = `<named list>`)
── Error ('test-comprisk.R:54'): bootstrap SEs with competing risks ────────────
Error in `model.frame.default(data = FALSE, formula = ~treat, xlev = list(
treat = c("CBZ", "LTG")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:54:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~treat, xlev = `<named list>`)
9. └─stats::model.frame.default(data = FALSE, formula = ~treat, xlev = `<named list>`)
── Error ('test-comprisk.R:77'): ordering of subjects with competing risks ─────
Error in `model.frame.default(data = FALSE, formula = ~treat, xlev = list(
treat = c("CBZ", "LTG")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:77:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~treat, xlev = `<named list>`)
9. └─stats::model.frame.default(data = FALSE, formula = ~treat, xlev = `<named list>`)
── Error ('test-comprisk.R:116'): competing risks model with covariates ────────
Error in `model.frame.default(data = FALSE, formula = ~gender + age, xlev = list(
gender = c("F", "M")))`: 'data' must be a data.frame, environment, or list
Backtrace:
▆
1. └─joineR::joint(...) at test-comprisk.R:116:2
2. └─joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. └─survival::basehaz(surv.start, FALSE)
4. ├─survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. ├─base::eval(tcall)
7. │ └─base::eval(tcall)
8. ├─stats::model.frame(data = FALSE, formula = ~gender + age, xlev = `<named list>`)
9. └─stats::model.frame.default(...)
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
Error: Test failures
Execution halted
Flavor: r-release-windows-x86_64
Version: 1.2.6
Check: tests
Result: ERROR
Running 'testthat.R' [74s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(joineR)
Loading required package: survival
>
> test_check("joineR")
80% experienced event
40% experienced event
70% experienced event
100% experienced event
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
== Failed tests ================================================================
-- Error ('test-comprisk.R:17'): competing risks models ------------------------
Error in `model.frame.default(data = FALSE, formula = ~treat, xlev = list(
treat = c("CBZ", "LTG")))`: 'data' must be a data.frame, environment, or list
Backtrace:
x
1. \-joineR::joint(...) at test-comprisk.R:17:2
2. \-joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. \-survival::basehaz(surv.start, FALSE)
4. +-survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. \-survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. +-base::eval(tcall)
7. | \-base::eval(tcall)
8. +-stats::model.frame(data = FALSE, formula = ~treat, xlev = `<named list>`)
9. \-stats::model.frame.default(data = FALSE, formula = ~treat, xlev = `<named list>`)
-- Error ('test-comprisk.R:54'): bootstrap SEs with competing risks ------------
Error in `model.frame.default(data = FALSE, formula = ~treat, xlev = list(
treat = c("CBZ", "LTG")))`: 'data' must be a data.frame, environment, or list
Backtrace:
x
1. \-joineR::joint(...) at test-comprisk.R:54:2
2. \-joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. \-survival::basehaz(surv.start, FALSE)
4. +-survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. \-survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. +-base::eval(tcall)
7. | \-base::eval(tcall)
8. +-stats::model.frame(data = FALSE, formula = ~treat, xlev = `<named list>`)
9. \-stats::model.frame.default(data = FALSE, formula = ~treat, xlev = `<named list>`)
-- Error ('test-comprisk.R:77'): ordering of subjects with competing risks -----
Error in `model.frame.default(data = FALSE, formula = ~treat, xlev = list(
treat = c("CBZ", "LTG")))`: 'data' must be a data.frame, environment, or list
Backtrace:
x
1. \-joineR::joint(...) at test-comprisk.R:77:2
2. \-joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. \-survival::basehaz(surv.start, FALSE)
4. +-survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. \-survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. +-base::eval(tcall)
7. | \-base::eval(tcall)
8. +-stats::model.frame(data = FALSE, formula = ~treat, xlev = `<named list>`)
9. \-stats::model.frame.default(data = FALSE, formula = ~treat, xlev = `<named list>`)
-- Error ('test-comprisk.R:116'): competing risks model with covariates --------
Error in `model.frame.default(data = FALSE, formula = ~gender + age, xlev = list(
gender = c("F", "M")))`: 'data' must be a data.frame, environment, or list
Backtrace:
x
1. \-joineR::joint(...) at test-comprisk.R:116:2
2. \-joineR:::survstCR(survdat, surv.formula, survdat2, event = 1)
3. \-survival::basehaz(surv.start, FALSE)
4. +-survival::survfit(fit, newdata = newdata, se.fit = FALSE)
5. \-survival:::survfit.coxph(fit, newdata = newdata, se.fit = FALSE)
6. +-base::eval(tcall)
7. | \-base::eval(tcall)
8. +-stats::model.frame(data = FALSE, formula = ~gender + age, xlev = `<named list>`)
9. \-stats::model.frame.default(...)
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64
Version: 1.2.6
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building 'competing-risks.Rmd' using rmarkdown
Quitting from lines 130-135 (competing-risks.Rmd)
Error: processing vignette 'competing-risks.Rmd' failed with diagnostics:
'data' must be a data.frame, environment, or list
--- failed re-building 'competing-risks.Rmd'
--- re-building 'joineR.Rmd' using rmarkdown
--- finished re-building 'joineR.Rmd'
SUMMARY: processing the following file failed:
'competing-risks.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64