Package check result: NOTE

Check: examples, Result: NOTE
  Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
  contrast 6.485   0.06   6.602

Changes to worse in reverse depends:

Package: rankCorr [Old version: 1.0.1, New version: 1.0.2]
Check: examples
New result: ERROR
  Running examples in ‘rankCorr-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: rankCorrCluster
  > ### Title: Total, between-, and within-cluster Spearman rank correlations
  > ###   for clustered data
  > ### Aliases: rankCorrCluster
  > 
  > ### ** Examples
  > 
  > library(mvtnorm)
  > k <- 50; m <- 5
  > sigma.u <- matrix(c(1, 0.6, 0.6, 4), ncol=2); sigma.e <- matrix(c(1, 0.6, 0.6, 1), ncol=2)
  > u <- rmvnorm(k, c(1, -1), sigma.u)
  > x1 <- matrix(NA, k, m)
  > y1 <- matrix(NA, k, m)
  > for (i in 1:k){
  + r <- rmvnorm(m, c(0, 0), sigma.e)
  + x1[i,] <- u[i, 1] + r[, 1]
  + y1[i,] <- u[i, 2] + r[, 2]
  + }
  > x <- as.vector(t(x1))
  > y <- as.vector(t(y1))
  > cluster <- rep(1:k, each=m)
  > rankCorrCluster(x, y, cluster, link.x = "probit", link.y = "probit",
  + methods_between_corr = "approx")
  Error in mod$trans$cumprob(g) : attempt to apply non-function
  Calls: rankCorrCluster -> scores_presid
  Execution halted

Package: riskRegression
Check: examples
New result: ERROR
  Running examples in ‘riskRegression-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: ate
  > ### Title: Average Treatment Effects Computation
  > ### Aliases: ate
  > 
  > ### ** Examples
  > 
  > library(survival)
  > library(rms)
  Loading required package: Hmisc
  
  Attaching package: ‘Hmisc’
  
  The following objects are masked from ‘package:base’:
  
      format.pval, units
  
  > library(prodlim)
  > library(data.table)
  > set.seed(10)
  > 
  > #### Survival settings  ####
  > #### ATE with Cox model ####
  > 
  > ## generate data
  > n <- 100
  > dtS <- sampleData(n, outcome="survival")
  > dtS$time <- round(dtS$time,1)
  > dtS$X1 <- factor(rbinom(n, prob = c(0.3,0.4) , size = 2), labels = paste0("T",0:2))
  > 
  > ## estimate the Cox model
  > fit <- cph(formula = Surv(time,event)~ X1+X2,data=dtS,y=TRUE,x=TRUE)
  > 
  > ## compute the ATE at times 5, 6, 7, and 8 using X1 as the treatment variable
  > ## standard error computed using the influence function
  > ## confidence intervals / p-values based on asymptotic results
  > ateFit1a <- ate(fit, data = dtS, treatment = "X1", times = 5:8)
   Input variables 
   - Treatment            : X1 (3 levels: "T0" "T1" "T2")
   - Event                : event (cause: 1, censoring: 0)
   - Time  [min;max]      : time [0.6;15.7]
   - Eval. time             :     5     6     7     8
                <char> <char> <int> <int> <int> <int>
        number at risk   T0      16    13    10     7
        number at risk   T1      26    21    18    11
        number at risk   T2       7     3     3     1
  
   Estimation procedure 
   - Estimator  : G-formula
   - Uncertainty: Gaussian approximation 
                  where the variance is estimated via the influence function 
  
   Processing
   - Prepare influence function: outcome done 
   - Point estimation:Error in `[.data.table`(newdata, , i) : 
    j (the 2nd argument inside [...]) is a single symbol but column name 'i' is not found. If you intended to select columns using a variable in calling scope, please try DT[, ..i]. The .. prefix conveys one-level-up similar to a file system path.
  Calls: ate ... [ -> [.data.table -> stopf -> raise_condition -> signal
  Execution halted

Package: riskRegression
Check: tests
New result: ERROR
    Running ‘testthat.R’ [27s/27s]
  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 2023.12.21
    > 
    > 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 
    [1] "X21" "X7"  "X9" 
    [1] "X21" "X7"  "X9" 
    [1] "X21" "X7"  "X9" 
    [1] "X21" "X7"  "X9" 
    [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 
    [predictCoxPL] Check baseline hazard estimation vs survfit 
    [predictCoxPL] Check argument 'diag' + iid vs predictCox 
    [predictRisk.rfsrc]  
    [predictRisk.CauseSpecificCox] 
    [predictRisk.glm] vs. lava 
    Testing binary data with 
    Testing survival data with 
    with formula=Hist(time,event) ~ 1 and conservative = FALSE 
    with formula=Hist(time,event) ~ 1 and conservative = TRUE 
    with formula=Hist(time,event) ~ X1+X2 and conservative = FALSE 
    Testing competing.risks data with 
    with formula=Hist(time,event) ~ 1 and conservative = FALSE 
    with formula=Hist(time,event) ~ 1 and conservative = TRUE 
    with formula=Hist(time,event) ~ X1+X2 and conservative = FALSE 
    [1] "binary"
    [1] "survival"
    [1] "competing.risks"
    [ FAIL 10 | WARN 0 | SKIP 0 | PASS 445 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-AUC.R:14:5'): AUC censored data: order ─────────────────────────
    Error in ``[.data.table`(newdata, , i)`: j (the 2nd argument inside [...]) is a single symbol but column name 'i' is not found. If you intended to select columns using a variable in calling scope, please try DT[, ..i]. The .. prefix conveys one-level-up similar to a file system path.
    Backtrace:
         ▆
      1. ├─base::suppressWarnings(...) at test-AUC.R:14:5
      2. │ └─base::withCallingHandlers(...)
      3. ├─riskRegression::Score(...)
      4. └─riskRegression::Score.list(...)
      5.   └─riskRegression:::getCensoringWeights(...)
      6.     ├─base::matrix(...)
      7.     ├─rms::survest(fit, newdata = wdata, times = times, se.fit = FALSE)
      8.     └─rms:::survest.cph(fit, newdata = wdata, times = times, se.fit = FALSE)
      9.       ├─stats::predict(fit, newdata, type = "x", expand.na = FALSE)
     10.       └─rms:::predict.cph(fit, newdata, type = "x", expand.na = FALSE)
     11.         └─rms::predictrms(...)
     12.           ├─newdata[, i]
     13.           └─data.table:::`[.data.table`(newdata, , i)
     14.             └─data.table:::stopf(...)
     15.               └─data.table:::raise_condition(...)
    ── Error ('test-BrierScore.R:15:5'): Brier score censored data order ───────────
    Error in ``[.data.table`(newdata, , i)`: j (the 2nd argument inside [...]) is a single symbol but column name 'i' is not found. If you intended to select columns using a variable in calling scope, please try DT[, ..i]. The .. prefix conveys one-level-up similar to a file system path.
    Backtrace:
         ▆
      1. ├─riskRegression::Score(...) at test-BrierScore.R:15:5
      2. └─riskRegression::Score.list(...)
      3.   └─riskRegression:::getCensoringWeights(...)
      4.     ├─base::matrix(...)
      5.     ├─rms::survest(fit, newdata = wdata, times = times, se.fit = FALSE)
      6.     └─rms:::survest.cph(fit, newdata = wdata, times = times, se.fit = FALSE)
      7.       ├─stats::predict(fit, newdata, type = "x", expand.na = FALSE)
      8.       └─rms:::predict.cph(fit, newdata, type = "x", expand.na = FALSE)
      9.         └─rms::predictrms(...)
     10.           ├─newdata[, i]
     11.           └─data.table:::`[.data.table`(newdata, , i)
     12.             └─data.table:::stopf(...)
     13.               └─data.table:::raise_condition(...)
    ── Error ('test-predictCox.R:230:5'): [predictCox] compare survival and survival.se coxph/cph (1 fixed time) ──
    Error in ``[.data.table`(newdata, , i)`: j (the 2nd argument inside [...]) is a single symbol but column name 'i' is not found. If you intended to select columns using a variable in calling scope, please try DT[, ..i]. The .. prefix conveys one-level-up similar to a file system path.
    Backtrace:
         ▆
      1. └─riskRegression::predictCox(...) at test-predictCox.R:230:5
      2.   ├─stats::model.matrix(object, data = newdata)
      3.   └─riskRegression:::model.matrix.cph(object, data = newdata)
      4.     ├─stats::predict(object, newdata = data, type = "x")
      5.     └─rms:::predict.cph(object, newdata = data, type = "x")
      6.       └─rms::predictrms(...)
      7.         ├─newdata[, i]
      8.         └─data.table:::`[.data.table`(newdata, , i)
      9.           └─data.table:::stopf(...)
     10.             └─data.table:::raise_condition(...)
    ── Error ('test-predictCox.R:303:5'): [predictCox] compare survival and survival.se coxph/cph (eventtimes) ──
    Error in ``[.data.table`(newdata, , i)`: j (the 2nd argument inside [...]) is a single symbol but column name 'i' is not found. If you intended to select columns using a variable in calling scope, please try DT[, ..i]. The .. prefix conveys one-level-up similar to a file system path.
    Backtrace:
         ▆
      1. └─riskRegression::predictCox(...) at test-predictCox.R:303:5
      2.   ├─stats::model.matrix(object, data = newdata)
      3.   └─riskRegression:::model.matrix.cph(object, data = newdata)
      4.     ├─stats::predict(object, newdata = data, type = "x")
      5.     └─rms:::predict.cph(object, newdata = data, type = "x")
      6.       └─rms::predictrms(...)
      7.         ├─newdata[, i]
      8.         └─data.table:::`[.data.table`(newdata, , i)
      9.           └─data.table:::stopf(...)
     10.             └─data.table:::raise_condition(...)
    ── Error ('test-predictCox.R:531:5'): [predictCox] compare survival and survival.se to timereg/cph (categorical variable) ──
    Error in ``[.data.table`(newdata, , i)`: j (the 2nd argument inside [...]) is a single symbol but column name 'i' is not found. If you intended to select columns using a variable in calling scope, please try DT[, ..i]. The .. prefix conveys one-level-up similar to a file system path.
    Backtrace:
         ▆
      1. └─riskRegression::predictCox(e.cph, newdata = dt, times = 10, se = TRUE) at test-predictCox.R:531:5
      2.   ├─stats::model.matrix(object, data = newdata)
      3.   └─riskRegression:::model.matrix.cph(object, data = newdata)
      4.     ├─stats::predict(object, newdata = data, type = "x")
      5.     └─rms:::predict.cph(object, newdata = data, type = "x")
      6.       └─rms::predictrms(...)
      7.         ├─newdata[, i]
      8.         └─data.table:::`[.data.table`(newdata, , i)
      9.           └─data.table:::stopf(...)
     10.             └─data.table:::raise_condition(...)
    ── Error ('test-predictCox.R:591:5'): [predictCox] compare survival and survival.se coxph/cph (1 fixed time, strata) ──
    Error in ``[.data.table`(newdata, , i)`: j (the 2nd argument inside [...]) is a single symbol but column name 'i' is not found. If you intended to select columns using a variable in calling scope, please try DT[, ..i]. The .. prefix conveys one-level-up similar to a file system path.
    Backtrace:
         ▆
      1. └─riskRegression::predictCox(...) at test-predictCox.R:591:5
      2.   ├─stats::model.matrix(object, data = newdata)
      3.   └─riskRegression:::model.matrix.cph(object, data = newdata)
      4.     ├─stats::predict(object, newdata = data, type = "x")
      5.     └─rms:::predict.cph(object, newdata = data, type = "x")
      6.       └─rms::predictrms(...)
      7.         ├─newdata[, i]
      8.         └─data.table:::`[.data.table`(newdata, , i)
      9.           └─data.table:::stopf(...)
     10.             └─data.table:::raise_condition(...)
    ── Error ('test-predictCox.R:661:5'): [predictCox] compare survival and survival.se coxph/cph (eventtime, strata) ──
    Error in ``[.data.table`(newdata, , i)`: j (the 2nd argument inside [...]) is a single symbol but column name 'i' is not found. If you intended to select columns using a variable in calling scope, please try DT[, ..i]. The .. prefix conveys one-level-up similar to a file system path.
    Backtrace:
         ▆
      1. └─riskRegression::predictCox(...) at test-predictCox.R:661:5
      2.   ├─stats::model.matrix(object, data = newdata)
      3.   └─riskRegression:::model.matrix.cph(object, data = newdata)
      4.     ├─stats::predict(object, newdata = data, type = "x")
      5.     └─rms:::predict.cph(object, newdata = data, type = "x")
      6.       └─rms::predictrms(...)
      7.         ├─newdata[, i]
      8.         └─data.table:::`[.data.table`(newdata, , i)
      9.           └─data.table:::stopf(...)
     10.             └─data.table:::raise_condition(...)
    ── Error ('test-score-train-test.R:42:9'): Testing survival data with  ─────────
    Error in ``[.data.table`(newdata, , i)`: j (the 2nd argument inside [...]) is a single symbol but column name 'i' is not found. If you intended to select columns using a variable in calling scope, please try DT[, ..i]. The .. prefix conveys one-level-up similar to a file system path.
    Backtrace:
         ▆
      1. ├─base::do.call(Score, input.score) at test-score-train-test.R:42:9
      2. ├─riskRegression (local) `<fn>`(...)
      3. └─riskRegression::Score.list(...)
      4.   └─riskRegression:::getCensoringWeights(...)
      5.     ├─rms::survest(fit, newdata = wdata, times = times, se.fit = FALSE)
      6.     └─rms:::survest.cph(fit, newdata = wdata, times = times, se.fit = FALSE)
      7.       ├─stats::predict(fit, newdata, type = "x", expand.na = FALSE)
      8.       └─rms:::predict.cph(fit, newdata, type = "x", expand.na = FALSE)
      9.         └─rms::predictrms(...)
     10.           ├─newdata[, i]
     11.           └─data.table:::`[.data.table`(newdata, , i)
     12.             └─data.table:::stopf(...)
     13.               └─data.table:::raise_condition(...)
    ── Error ('test-score-train-test.R:42:9'): Testing competing.risks data with  ──
    Error in ``[.data.table`(newdata, , i)`: j (the 2nd argument inside [...]) is a single symbol but column name 'i' is not found. If you intended to select columns using a variable in calling scope, please try DT[, ..i]. The .. prefix conveys one-level-up similar to a file system path.
    Backtrace:
         ▆
      1. ├─base::do.call(Score, input.score) at test-score-train-test.R:42:9
      2. ├─riskRegression (local) `<fn>`(...)
      3. └─riskRegression::Score.list(...)
      4.   └─riskRegression:::getCensoringWeights(...)
      5.     ├─rms::survest(fit, newdata = wdata, times = times, se.fit = FALSE)
      6.     └─rms:::survest.cph(fit, newdata = wdata, times = times, se.fit = FALSE)
      7.       ├─stats::predict(fit, newdata, type = "x", expand.na = FALSE)
      8.       └─rms:::predict.cph(fit, newdata, type = "x", expand.na = FALSE)
      9.         └─rms::predictrms(...)
     10.           ├─newdata[, i]
     11.           └─data.table:::`[.data.table`(newdata, , i)
     12.             └─data.table:::stopf(...)
     13.               └─data.table:::raise_condition(...)
    ── Error ('test-score.R:92:9'): survival outcome,Brier Score, external prediction ──
    Error in ``[.data.table`(newdata, , i)`: j (the 2nd argument inside [...]) is a single symbol but column name 'i' is not found. If you intended to select columns using a variable in calling scope, please try DT[, ..i]. The .. prefix conveys one-level-up similar to a file system path.
    Backtrace:
         ▆
      1. ├─riskRegression::Score(...) at test-score.R:92:9
      2. └─riskRegression::Score.list(...)
      3.   └─riskRegression:::getCensoringWeights(...)
      4.     ├─base::matrix(...)
      5.     ├─rms::survest(fit, newdata = wdata, times = times, se.fit = FALSE)
      6.     └─rms:::survest.cph(fit, newdata = wdata, times = times, se.fit = FALSE)
      7.       ├─stats::predict(fit, newdata, type = "x", expand.na = FALSE)
      8.       └─rms:::predict.cph(fit, newdata, type = "x", expand.na = FALSE)
      9.         └─rms::predictrms(...)
     10.           ├─newdata[, i]
     11.           └─data.table:::`[.data.table`(newdata, , i)
     12.             └─data.table:::stopf(...)
     13.               └─data.table:::raise_condition(...)
    
    [ FAIL 10 | WARN 0 | SKIP 0 | PASS 445 ]
    Error: Test failures
    Execution halted