- using R Under development (unstable) (2026-07-30 r90327)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-16 (Debian 16.1.0-3) 16.1.0
GNU Fortran (Debian 16.1.0-3) 16.1.0
- running under: Debian GNU/Linux forky/sid
- using session charset: UTF-8
* current time: 2026-07-31 15:40:58 UTC
- checking for file ‘jointCompRisk/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘jointCompRisk’ version ‘0.1.1’
- package encoding: UTF-8
- checking CRAN incoming feasibility ... [1s/1s] OK
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
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- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘jointCompRisk’ can be installed ... OK
See the install log for details.
- checking package directory ... OK
- checking for future file timestamps ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [2s/3s] OK
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- checking files in ‘vignettes’ ... OK
- checking examples ... [2s/3s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [4s/4s] ERROR
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(jointCompRisk)
>
> test_check("jointCompRisk")
Saving _problems/test-basic-32.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 10 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-basic.R:32:3'): do_cif_analysis returns formatted summaries ────
Error in `survfit.formula(Surv(etime, estatus) ~ 1, etype = etype2, data = data.w)`: the etype argument is no longer supported, use a factor as the status variable
Backtrace:
▆
1. └─jointCompRisk::do_cif_analysis(prepped, tau = 15) at test-basic.R:32:3
2. └─jointCompRisk:::table1_cif(Treatment, Control, tau, 0, 1, 0)
3. └─jointCompRisk:::auc.var.joint(data1, tau, a, b, c)
4. ├─survival::survfit(Surv(etime, estatus) ~ 1, etype = etype2, data = data.w)
5. └─survival::survfit.formula(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 10 ]
Error:
! Test failures.
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [5s/6s] ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Example_analysis.Rmd’ using rmarkdown
Quitting from Example_analysis.Rmd:24-42 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `survfit.formula()`:
! the etype argument is no longer supported, use a factor as the status variable
---
Backtrace:
▆
1. └─jointCompRisk::do_cif_analysis(mydata_std, tau = 15)
2. └─jointCompRisk:::table1_cif(Treatment, Control, tau, 0, 1, 0)
3. └─jointCompRisk:::auc.var.joint(data1, tau, a, b, c)
4. ├─survival::survfit(Surv(etime, estatus) ~ 1, etype = etype2, data = data.w)
5. └─survival::survfit.formula(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Example_analysis.Rmd' failed with diagnostics:
the etype argument is no longer supported, use a factor as the status variable
--- failed re-building ‘Example_analysis.Rmd’
--- re-building ‘Vignette.Rmd’ using rmarkdown
main_df package:jointCompRisk R Documentation
_ M_ a_ i_ n _ C_ o_ m_ p_ e_ t_ i_ n_ g _ R_ i_ s_ k_ s _ D_ a_ t_ a_ s_ e_ t _ S_ i_ m_ u_ l_ a_ t_ e_ d _ c_ l_ i_ n_ i_ c_ a_ l _ t_ r_ i_ a_ l _ d_ a_ t_ a _ w_ i_ t_ h
_ c_ o_ m_ p_ e_ t_ i_ n_ g _ r_ i_ s_ k_ s _ s_ u_ r_ v_ i_ v_ a_ l _ o_ u_ t_ c_ o_ m_ e_ s. _ T_ h_ i_ s _ d_ a_ t_ a_ s_ e_ t _ f_ o_ l_ l_ o_ w_ s _ t_ h_ e _ s_ t_ r_ u_ c_ t_ u_ r_ e
_ o_ f _ A_ d_ a_ p_ t_ i_ v_ e _ C_ O_ V_ I_ D-_ 1_ 9 _ T_ r_ e_ a_ t_ m_ e_ n_ t _ T_ r_ i_ a_ l_ s (_ A_ C_ T_ T) _ w_ i_ t_ h _ b_ u_ i_ l_ t-_ i_ n _ t_ r_ e_ a_ t_ m_ e_ n_ t
_ e_ f_ f_ e_ c_ t_ s _ f_ o_ r _ d_ e_ m_ o_ n_ s_ t_ r_ a_ t_ i_ o_ n _ p_ u_ r_ p_ o_ s_ e_ s.
_ D_ e_ s_ c_ r_ i_ p_ t_ i_ o_ n:
Main Competing Risks Dataset Simulated clinical trial data with
competing risks survival outcomes. This dataset follows the
structure of Adaptive COVID-19 Treatment Trials (ACTT) with
built-in treatment effects for demonstration purposes.
_ U_ s_ a_ g_ e:
data(main_df)
_ F_ o_ r_ m_ a_ t:
A data frame with 150 rows and 7 variables:
ID
Patient identifier (character)
TimeToRecovery
Time to recovery event in days (numeric)
TimeToDeath
Time to death event in days (numeric)
RecoveryCensoringIndicator
Recovery censoring indicator (0=event observed, 1=censored)
DeathCensoringIndicator
Death censoring indicator (0=event observed, 1=censored)
BaselineScore
Baseline severity score, range 4-7 (numeric)
Treatment
Treatment arm indicator (0=control, 1=treatment)
_ D_ e_ t_ a_ i_ l_ s:
This is a simulated dataset created for demonstration purposes
with realistic treatment effects built in: treatment group has
1.5× faster recovery times and 1.8× improved survival compared to
control. The data represents a clinical trial with competing risks
where patients can either recover or die, with administrative
censoring at 30 days.
_ S_ o_ u_ r_ c_ e:
Simulated data based on Weibull distributions with
treatment-specific parameters
_ E_ x_ a_ m_ p_ l_ e_ s:
data(main_df)
head(main_df)
summary(main_df)
# Compare outcomes by treatment
tapply(main_df$TimeToRecovery, main_df$Treatment, summary)
tapply(main_df$TimeToDeath, main_df$Treatment, summary)
long_df package:jointCompRisk R Documentation
_ L_ o_ n_ g_ i_ t_ u_ d_ i_ n_ a_ l _ S_ e_ v_ e_ r_ i_ t_ y _ S_ c_ o_ r_ e_ s _ D_ a_ t_ a_ s_ e_ t
_ D_ e_ s_ c_ r_ i_ p_ t_ i_ o_ n:
Repeated measurements of ordinal severity scores over time for the
same patients in the main_df dataset, with treatment-specific
trajectory patterns.
_ U_ s_ a_ g_ e:
data(long_df)
_ F_ o_ r_ m_ a_ t:
A data frame with variable rows per patient:
PersonID
Patient identifier matching ID in main_df (character)
OrdinalScore
Severity score on 1-8 scale (numeric)
RelativeDay
Study day (numeric) starting from day 0 (baseline)
_ D_ e_ t_ a_ i_ l_ s:
Measurements are taken at scheduled visits: days 0 (baseline), 1,
3, 5, 7, 10, 14, 18, 21, 25, 28. The trajectory follows
treatment-specific probabilities: treatment patients have 45 and
15 worsening probability, creating realistic differential clinical
progression patterns.
_ S_ o_ u_ r_ c_ e:
Simulated data using treatment-specific random walk with
boundaries
_ E_ x_ a_ m_ p_ l_ e_ s:
data(long_df)
data(main_df)
head(long_df)
# See data for first patient
subset(long_df, PersonID == "Patient_001")
# Compare average scores by treatment
long_df %>%
dplyr::left_join(main_df[,c("ID","Treatment")], by=c("PersonID"="ID")) %>%
dplyr::group_by(Treatment) %>%
dplyr::summarise(mean_score = mean(OrdinalScore))
Quitting from Vignette.Rmd:159-169 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `survfit.formula()`:
! the etype argument is no longer supported, use a factor as the status variable
---
Backtrace:
▆
1. └─jointCompRisk::do_cif_analysis(mydata_std, tau = 15)
2. └─jointCompRisk:::table1_cif(Treatment, Control, tau, 0, 1, 0)
3. └─jointCompRisk:::auc.var.joint(data1, tau, a, b, c)
4. ├─survival::survfit(Surv(etime, estatus) ~ 1, etype = etype2, data = data.w)
5. └─survival::survfit.formula(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Vignette.Rmd' failed with diagnostics:
the etype argument is no longer supported, use a factor as the status variable
--- failed re-building ‘Vignette.Rmd’
SUMMARY: processing the following files failed:
‘Example_analysis.Rmd’ ‘Vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [4s/6s] OK
- checking HTML version of manual ... [0s/0s] OK
- checking for non-standard things in the check directory ... OK
- checking for new files in some other directories ... NOTE
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‘~/tmp/scratch/xvfb-run.yzFd2J’ ‘~/.cache/quarto/sass/sass.kv-shm’
‘~/.cache/quarto/sass/sass.kv-wal’
- DONE
Status: 2 ERRORs, 1 NOTE