Package: riskRegression
Check: tests
New result: ERROR
    Running ‘testthat.R’ [25s/24s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > # This file is part of the standard setup for testthat.
    > # It is recommended that you do not modify it.
    > #
    > # Where should you do additional test configuration?
    > # Learn more about the roles of various files in:
    > # * https://r-pkgs.org/tests.html
    > # * https://testthat.r-lib.org/reference/test_package.html#special-files
    > 
    > library(testthat)
    > library(riskRegression)
    riskRegression version 2025.09.17
    > 
    > test_check("riskRegression")
    [iidCox] internal consistency 
    [iidCox] compare to timereg - no strata, no interaction, continuous 
    [iidCox] compare to timereg - no strata, interaction, continuous 
    [iidCox] compare to timereg - no covariate 
    [iidCox] compare to timereg - no strata, no interaction, categorical 
    [iidCox] compare to timereg - ties 
    [iidCox] compare to timereg - strata 
    [iidCox] compare to timereg - Melanoma 
    Saving _problems/test-phreg-45.R
    Saving _problems/test-phreg-60.R
    Saving _problems/test-phreg-84.R
    Saving _problems/test-phreg-113.R
    Saving _problems/test-phreg-125.R
    Saving _problems/test-phreg-136.R
    [predictCox] Estimation of the baseline hazard (no strata) 
    [predictCox] Estimation of the baseline hazard (strata) 
    [predictCox] Estimation of the baseline hazard (time varying cov, no strata) 
    [predictCox] Estimation of the baseline hazard (time varying cov, strata) 
    [predictCox] Predictions (no strata, continuous) 
    [predictCox] Predictions (no strata, categorical) 
    [predictCox] Predictions (strata) 
    [predictCox] SE/CI check against manual computation 
    [predictCox] Argument 'diag' 
    [predictCox] Confidence band vs timereg 
    [predictCox] Check same result store.iid=minimal vs. full 
    [predictCox] Does not handle weights 
    [predictCox] dealing with negative timepoints or NA 
    [predictCox] Previous bug 
    [predictRisk.rfsrc]  
    [predictRisk.CauseSpecificCox] 
    [predictRisk.glm] vs. lava 
    [1] "binary"
    [1] "survival"
    [1] "competing.risks"
    [ FAIL 6 | WARN 1 | SKIP 0 | PASS 448 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-phreg.R:45:5'): survival - no strata ───────────────────────────
    Error in `colnamesInt(x, neworder, check_dups = FALSE, skip_absent = skip_absent)`: argument specifying columns received non-existing column(s): cols[2]='stop'
    Backtrace:
        ▆
     1. ├─testthat::expect_equal(...) at test-phreg.R:45:5
     2. │ └─testthat::quasi_label(enquo(object), label)
     3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
     4. └─riskRegression::predictCox(m.phreg, center = FALSE)
     5.   ├─riskRegression::coxModelFrame(object)
     6.   └─riskRegression:::coxModelFrame.phreg(object)
     7.     └─data.table::setcolorder(dt, c(first.col, setdiff(names(dt), first.col)))
     8.       └─data.table:::colnamesInt(x, neworder, check_dups = FALSE, skip_absent = skip_absent)
    ── Error ('test-phreg.R:60:5'): survival - one strata variable ─────────────────
    Error in `colnamesInt(x, neworder, check_dups = FALSE, skip_absent = skip_absent)`: argument specifying columns received non-existing column(s): cols[2]='stop'
    Backtrace:
        ▆
     1. ├─testthat::expect_equal(...) at test-phreg.R:60:5
     2. │ └─testthat::quasi_label(enquo(object), label)
     3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
     4. └─riskRegression::predictCox(mS.phreg, center = FALSE)
     5.   ├─riskRegression::coxModelFrame(object)
     6.   └─riskRegression:::coxModelFrame.phreg(object)
     7.     └─data.table::setcolorder(dt, c(first.col, setdiff(names(dt), first.col)))
     8.       └─data.table:::colnamesInt(x, neworder, check_dups = FALSE, skip_absent = skip_absent)
    ── Error ('test-phreg.R:82:5'): survival - several strata variables ────────────
    Error in `colnamesInt(x, neworder, check_dups = FALSE, skip_absent = skip_absent)`: argument specifying columns received non-existing column(s): cols[2]='stop'
    Backtrace:
        ▆
     1. ├─testthat::expect_equal(...) at test-phreg.R:82:5
     2. │ └─testthat::quasi_label(enquo(object), label)
     3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
     4. └─riskRegression::predictCox(mS.phreg, center = FALSE)
     5.   ├─riskRegression::coxModelFrame(object)
     6.   └─riskRegression:::coxModelFrame.phreg(object)
     7.     └─data.table::setcolorder(dt, c(first.col, setdiff(names(dt), first.col)))
     8.       └─data.table:::colnamesInt(x, neworder, check_dups = FALSE, skip_absent = skip_absent)
    ── Error ('test-phreg.R:113:5'): competing risk - no strata ────────────────────
    Error in `colnamesInt(x, neworder, check_dups = FALSE, skip_absent = skip_absent)`: argument specifying columns received non-existing column(s): cols[2]='stop'
    Backtrace:
         ▆
      1. ├─stats::predict(...) at test-phreg.R:113:5
      2. └─riskRegression:::predict.CauseSpecificCox(...)
      3.   └─riskRegression:::compressData(...)
      4.     └─base::lapply(...)
      5.       └─riskRegression (local) FUN(X[[i]], ...)
      6.         ├─riskRegression::coxVariableName(iO, model.frame = coxModelFrame(iO))
      7.         │ ├─stats::delete.response(...)
      8.         │ ├─stats::terms(ff, special = unlist(special.object), data = model.frame)
      9.         │ └─stats::terms.formula(ff, special = unlist(special.object), data = model.frame)
     10.         ├─riskRegression::coxModelFrame(iO)
     11.         └─riskRegression:::coxModelFrame.phreg(iO)
     12.           └─data.table::setcolorder(dt, c(first.col, setdiff(names(dt), first.col)))
     13.             └─data.table:::colnamesInt(x, neworder, check_dups = FALSE, skip_absent = skip_absent)
    ── Error ('test-phreg.R:125:5'): competing risk - one strata variable ──────────
    Error in `colnamesInt(x, neworder, check_dups = FALSE, skip_absent = skip_absent)`: argument specifying columns received non-existing column(s): cols[2]='stop'
    Backtrace:
         ▆
      1. ├─stats::predict(...) at test-phreg.R:125:5
      2. └─riskRegression:::predict.CauseSpecificCox(...)
      3.   └─riskRegression:::compressData(...)
      4.     └─base::lapply(...)
      5.       └─riskRegression (local) FUN(X[[i]], ...)
      6.         ├─riskRegression::coxVariableName(iO, model.frame = coxModelFrame(iO))
      7.         │ ├─stats::delete.response(...)
      8.         │ ├─stats::terms(ff, special = unlist(special.object), data = model.frame)
      9.         │ └─stats::terms.formula(ff, special = unlist(special.object), data = model.frame)
     10.         ├─riskRegression::coxModelFrame(iO)
     11.         └─riskRegression:::coxModelFrame.phreg(iO)
     12.           └─data.table::setcolorder(dt, c(first.col, setdiff(names(dt), first.col)))
     13.             └─data.table:::colnamesInt(x, neworder, check_dups = FALSE, skip_absent = skip_absent)
    ── Error ('test-phreg.R:136:5'): competing risk - several strata variables ─────
    Error in `colnamesInt(x, neworder, check_dups = FALSE, skip_absent = skip_absent)`: argument specifying columns received non-existing column(s): cols[2]='stop'
    Backtrace:
         ▆
      1. ├─stats::predict(...) at test-phreg.R:136:5
      2. └─riskRegression:::predict.CauseSpecificCox(...)
      3.   └─riskRegression:::compressData(...)
      4.     └─base::lapply(...)
      5.       └─riskRegression (local) FUN(X[[i]], ...)
      6.         ├─riskRegression::coxVariableName(iO, model.frame = coxModelFrame(iO))
      7.         │ ├─stats::delete.response(...)
      8.         │ ├─stats::terms(ff, special = unlist(special.object), data = model.frame)
      9.         │ └─stats::terms.formula(ff, special = unlist(special.object), data = model.frame)
     10.         ├─riskRegression::coxModelFrame(iO)
     11.         └─riskRegression:::coxModelFrame.phreg(iO)
     12.           └─data.table::setcolorder(dt, c(first.col, setdiff(names(dt), first.col)))
     13.             └─data.table:::colnamesInt(x, neworder, check_dups = FALSE, skip_absent = skip_absent)
    
    [ FAIL 6 | WARN 1 | SKIP 0 | PASS 448 ]
    Error:
    ! Test failures.
    Execution halted