Running 'testthat.R' [295s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(adjustedCurves)
  > 
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > library(testthat)
  
  Attaching package: 'testthat'
  
  The following object is masked from 'package:dplyr':
  
      matches
  
  > library(vdiffr)
  > library(survival)
  > library(ggplot2)
  > library(Matching)
  Loading required package: MASS
  
  Attaching package: 'MASS'
  
  The following object is masked from 'package:dplyr':
  
      select
  
  ## 
  ##  Matching (Version 4.10-8, Build Date: 2022-11-03)
  ##  See http://sekhon.berkeley.edu/matching for additional documentation.
  ##  Please cite software as:
  ##   Jasjeet S. Sekhon. 2011. ``Multivariate and Propensity Score Matching
  ##   Software with Automated Balance Optimization: The Matching package for R.''
  ##   Journal of Statistical Software, 42(7): 1-52. 
  ##
  
  > library(WeightIt)
  > library(prodlim)
  > library(MASS)
  > library(tidyr)
  
  Attaching package: 'tidyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  > library(riskRegression)
  riskRegression version 2023.03.22
  > library(pec)
  
  Attaching package: 'pec'
  
  The following objects are masked from 'package:riskRegression':
  
      ipcw, selectCox
  
  > library(geepack)
  > library(nnet)
  > library(cmprsk)
  > library(eventglm)
  
  Attaching package: 'eventglm'
  
  The following objects are masked from 'package:prodlim':
  
      leaveOneOut.competing.risks, leaveOneOut.survival
  
  The following objects are masked from 'package:survival':
  
      colon, mgus2
  
  > library(rmarkdown)
  > library(mice)
  
  Attaching package: 'mice'
  
  The following object is masked from 'package:stats':
  
      filter
  
  The following objects are masked from 'package:base':
  
      cbind, rbind
  
  > 
  > test_check("adjustedCurves")
  Loading required namespace: pammtools
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "x1" "x2" "x3" "x4" "x5" "x6"
  [1] "group1" "x1"     "x2"    
  [1] "group1" "x1"     "x2"    
  [1] "group1" "x1"     "x2"    
  [1] "group1" "x1"     "x2"    
  Loading required namespace: doParallel
  starting worker pid=35440 on localhost:11480 at 07:51:20.776
  starting worker pid=65136 on localhost:11480 at 07:51:20.804
  Loading required package: adjustedCurves
  loaded adjustedCurves and set parent environment
  
  Attaching package: 'mice'
  
  The following object is masked from 'package:stats':
  
      filter
  
  The following objects are masked from 'package:base':
  
      cbind, rbind
  
  Loading required package: adjustedCurves
  loaded adjustedCurves and set parent environment
  
  Attaching package: 'mice'
  
  The following object is masked from 'package:stats':
  
      filter
  
  The following objects are masked from 'package:base':
  
      cbind, rbind
  
  Loading required package: survival
  
  Attaching package: 'survival'
  
  The following objects are masked from 'package:eventglm':
  
      colon, mgus2
  
  Loading required package: prodlim
  
  Attaching package: 'prodlim'
  
  The following objects are masked from 'package:eventglm':
  
      leaveOneOut.competing.risks, leaveOneOut.survival
  
  Loading required package: survival
  
  Attaching package: 'survival'
  
  The following objects are masked from 'package:eventglm':
  
      colon, mgus2
  
  Loading required package: prodlim
  
  Attaching package: 'prodlim'
  
  The following objects are masked from 'package:eventglm':
  
      leaveOneOut.competing.risks, leaveOneOut.survival
  
  riskRegression version 2023.03.22
  
  Attaching package: 'riskRegression'
  
  The following objects are masked from 'package:pec':
  
      ipcw, selectCox
  
  Loading required package: MASS
  ## 
  ##  Matching (Version 4.10-8, Build Date: 2022-11-03)
  ##  See http://sekhon.berkeley.edu/matching for additional documentation.
  ##  Please cite software as:
  ##   Jasjeet S. Sekhon. 2011. ``Multivariate and Propensity Score Matching
  ##   Software with Automated Balance Optimization: The Matching package for R.''
  ##   Journal of Statistical Software, 42(7): 1-52. 
  ##
  
  
  Attaching package: 'testthat'
  
  The following object is masked from 'package:tidyr':
  
      matches
  
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following object is masked from 'package:MASS':
  
      select
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  Loading required package: foreach
  Loading required package: rngtools
  riskRegression version 2023.03.22
  
  Attaching package: 'riskRegression'
  
  The following objects are masked from 'package:pec':
  
      ipcw, selectCox
  
  Loading required package: MASS
  ## 
  ##  Matching (Version 4.10-8, Build Date: 2022-11-03)
  ##  See http://sekhon.berkeley.edu/matching for additional documentation.
  ##  Please cite software as:
  ##   Jasjeet S. Sekhon. 2011. ``Multivariate and Propensity Score Matching
  ##   Software with Automated Balance Optimization: The Matching package for R.''
  ##   Journal of Statistical Software, 42(7): 1-52. 
  ##
  
  
  Attaching package: 'testthat'
  
  The following object is masked from 'package:tidyr':
  
      matches
  
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following object is masked from 'package:MASS':
  
      select
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  Loading required package: foreach
  Loading required package: rngtools
  starting worker pid=42968 on localhost:11480 at 07:51:29.216
  starting worker pid=1528 on localhost:11480 at 07:51:29.232
  Loading required package: adjustedCurves
  loaded adjustedCurves and set parent environment
  
  Attaching package: 'mice'
  
  The following object is masked from 'package:stats':
  
      filter
  
  The following objects are masked from 'package:base':
  
      cbind, rbind
  
  Loading required package: adjustedCurves
  loaded adjustedCurves and set parent environment
  
  Attaching package: 'mice'
  
  The following object is masked from 'package:stats':
  
      filter
  
  The following objects are masked from 'package:base':
  
      cbind, rbind
  
  Loading required package: survival
  
  Attaching package: 'survival'
  
  The following objects are masked from 'package:eventglm':
  
      colon, mgus2
  
  Loading required package: prodlim
  
  Attaching package: 'prodlim'
  
  The following objects are masked from 'package:eventglm':
  
      leaveOneOut.competing.risks, leaveOneOut.survival
  
  Loading required package: survival
  
  Attaching package: 'survival'
  
  The following objects are masked from 'package:eventglm':
  
      colon, mgus2
  
  Loading required package: prodlim
  
  Attaching package: 'prodlim'
  
  The following objects are masked from 'package:eventglm':
  
      leaveOneOut.competing.risks, leaveOneOut.survival
  
  riskRegression version 2023.03.22
  
  Attaching package: 'riskRegression'
  
  The following objects are masked from 'package:pec':
  
      ipcw, selectCox
  
  Loading required package: MASS
  ## 
  ##  Matching (Version 4.10-8, Build Date: 2022-11-03)
  ##  See http://sekhon.berkeley.edu/matching for additional documentation.
  ##  Please cite software as:
  ##   Jasjeet S. Sekhon. 2011. ``Multivariate and Propensity Score Matching
  ##   Software with Automated Balance Optimization: The Matching package for R.''
  ##   Journal of Statistical Software, 42(7): 1-52. 
  ##
  
  
  Attaching package: 'testthat'
  
  The following object is masked from 'package:tidyr':
  
      matches
  
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following object is masked from 'package:MASS':
  
      select
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  Loading required package: foreach
  Loading required package: rngtools
  riskRegression version 2023.03.22
  
  Attaching package: 'riskRegression'
  
  The following objects are masked from 'package:pec':
  
      ipcw, selectCox
  
  Loading required package: MASS
  ## 
  ##  Matching (Version 4.10-8, Build Date: 2022-11-03)
  ##  See http://sekhon.berkeley.edu/matching for additional documentation.
  ##  Please cite software as:
  ##   Jasjeet S. Sekhon. 2011. ``Multivariate and Propensity Score Matching
  ##   Software with Automated Balance Optimization: The Matching package for R.''
  ##   Journal of Statistical Software, 42(7): 1-52. 
  ##
  
  
  Attaching package: 'testthat'
  
  The following object is masked from 'package:tidyr':
  
      matches
  
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following object is masked from 'package:MASS':
  
      select
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  Loading required package: foreach
  Loading required package: rngtools
  Warning message:
  In coxph.fit(X, Y, istrat, offset, init, control, weights = weights,  :
    Loglik converged before variable  1,2 ; coefficient may be infinite. 
  starting worker pid=73716 on localhost:11480 at 07:51:38.359
  starting worker pid=44704 on localhost:11480 at 07:51:38.377
  Loading required package: adjustedCurves
  loaded adjustedCurves and set parent environment
  Loading required package: adjustedCurves
  loaded adjustedCurves and set parent environment
  
  Attaching package: 'mice'
  
  The following object is masked from 'package:stats':
  
      filter
  
  The following objects are masked from 'package:base':
  
      cbind, rbind
  
  
  Attaching package: 'mice'
  
  The following object is masked from 'package:stats':
  
      filter
  
  The following objects are masked from 'package:base':
  
      cbind, rbind
  
  Loading required package: survival
  
  Attaching package: 'survival'
  
  The following objects are masked from 'package:eventglm':
  
      colon, mgus2
  
  Loading required package: prodlim
  Loading required package: survival
  
  Attaching package: 'survival'
  
  The following objects are masked from 'package:eventglm':
  
      colon, mgus2
  
  Loading required package: prodlim
  
  Attaching package: 'prodlim'
  
  The following objects are masked from 'package:eventglm':
  
      leaveOneOut.competing.risks, leaveOneOut.survival
  
  
  Attaching package: 'prodlim'
  
  The following objects are masked from 'package:eventglm':
  
      leaveOneOut.competing.risks, leaveOneOut.survival
  
  riskRegression version 2023.03.22
  
  Attaching package: 'riskRegression'
  
  The following objects are masked from 'package:pec':
  
      ipcw, selectCox
  
  Loading required package: MASS
  ## 
  ##  Matching (Version 4.10-8, Build Date: 2022-11-03)
  ##  See http://sekhon.berkeley.edu/matching for additional documentation.
  ##  Please cite software as:
  ##   Jasjeet S. Sekhon. 2011. ``Multivariate and Propensity Score Matching
  ##   Software with Automated Balance Optimization: The Matching package for R.''
  ##   Journal of Statistical Software, 42(7): 1-52. 
  ##
  
  
  Attaching package: 'testthat'
  
  The following object is masked from 'package:tidyr':
  
      matches
  
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following object is masked from 'package:MASS':
  
      select
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  Loading required package: foreach
  riskRegression version 2023.03.22
  Loading required package: rngtools
  
  Attaching package: 'riskRegression'
  
  The following objects are masked from 'package:pec':
  
      ipcw, selectCox
  
  Loading required package: MASS
  ## 
  ##  Matching (Version 4.10-8, Build Date: 2022-11-03)
  ##  See http://sekhon.berkeley.edu/matching for additional documentation.
  ##  Please cite software as:
  ##   Jasjeet S. Sekhon. 2011. ``Multivariate and Propensity Score Matching
  ##   Software with Automated Balance Optimization: The Matching package for R.''
  ##   Journal of Statistical Software, 42(7): 1-52. 
  ##
  
  
  Attaching package: 'testthat'
  
  The following object is masked from 'package:tidyr':
  
      matches
  
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following object is masked from 'package:MASS':
  
      select
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  Loading required package: foreach
  Loading required package: rngtools
  starting worker pid=180836 on localhost:11480 at 07:51:46.363
  starting worker pid=38436 on localhost:11480 at 07:51:46.377
  Loading required package: adjustedCurves
  loaded adjustedCurves and set parent environment
  
  Attaching package: 'mice'
  
  The following object is masked from 'package:stats':
  
      filter
  
  The following objects are masked from 'package:base':
  
      cbind, rbind
  
  Loading required package: adjustedCurves
  loaded adjustedCurves and set parent environment
  
  Attaching package: 'mice'
  
  The following object is masked from 'package:stats':
  
      filter
  
  The following objects are masked from 'package:base':
  
      cbind, rbind
  
  Loading required package: survival
  
  Attaching package: 'survival'
  
  The following objects are masked from 'package:eventglm':
  
      colon, mgus2
  
  Loading required package: prodlim
  
  Attaching package: 'prodlim'
  
  The following objects are masked from 'package:eventglm':
  
      leaveOneOut.competing.risks, leaveOneOut.survival
  
  Loading required package: survival
  
  Attaching package: 'survival'
  
  The following objects are masked from 'package:eventglm':
  
      colon, mgus2
  
  Loading required package: prodlim
  
  Attaching package: 'prodlim'
  
  The following objects are masked from 'package:eventglm':
  
      leaveOneOut.competing.risks, leaveOneOut.survival
  
  riskRegression version 2023.03.22
  
  Attaching package: 'riskRegression'
  
  The following objects are masked from 'package:pec':
  
      ipcw, selectCox
  
  Loading required package: MASS
  ## 
  ##  Matching (Version 4.10-8, Build Date: 2022-11-03)
  ##  See http://sekhon.berkeley.edu/matching for additional documentation.
  ##  Please cite software as:
  ##   Jasjeet S. Sekhon. 2011. ``Multivariate and Propensity Score Matching
  ##   Software with Automated Balance Optimization: The Matching package for R.''
  ##   Journal of Statistical Software, 42(7): 1-52. 
  ##
  
  
  Attaching package: 'testthat'
  
  The following object is masked from 'package:tidyr':
  
      matches
  
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following object is masked from 'package:MASS':
  
      select
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  Loading required package: foreach
  Loading required package: rngtools
  riskRegression version 2023.03.22
  
  Attaching package: 'riskRegression'
  
  The following objects are masked from 'package:pec':
  
      ipcw, selectCox
  
  Loading required package: MASS
  ## 
  ##  Matching (Version 4.10-8, Build Date: 2022-11-03)
  ##  See http://sekhon.berkeley.edu/matching for additional documentation.
  ##  Please cite software as:
  ##   Jasjeet S. Sekhon. 2011. ``Multivariate and Propensity Score Matching
  ##   Software with Automated Balance Optimization: The Matching package for R.''
  ##   Journal of Statistical Software, 42(7): 1-52. 
  ##
  
  
  Attaching package: 'testthat'
  
  The following object is masked from 'package:tidyr':
  
      matches
  
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following object is masked from 'package:MASS':
  
      select
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  Loading required package: foreach
  Loading required package: rngtools
  Warning messages:
  1: In coxph.fit(X, Y, istrat, offset, init, control, weights = weights,  :
    Loglik converged before variable  1 ; coefficient may be infinite. 
  Warning messages:
  1: In coxph.fit(X, Y, istrat, offset, init, control, weights = weights,  :
   2:  Ran out of iterations and did not converge
  In ate_checkArgs(call = call, object.event = object.event, object.censor = object.censor,  :2: 
    Rare event 
  
  In coxph.fit(X, Y, istrat, offset, init, control, weights = weights,  :
    Loglik converged before variable  1 ; coefficient may be infinite. 
  3: In predictCoxPL(object = object, newdata = newdata, times = times,  :
    Estimated survival outside the range [0,1]. 
  Consider using predictCox instead of predictCoxPL. 
  
  3: In ate_checkArgs(call = call, object.event = object.event, object.censor = object.censor,  :
    Rare event 
  
  4: In predict.CauseSpecificCox(object = object, newdata = newdata,  :
    Estimated risk outside the range [0,1].
  Consider setting the argument 'product.limit' to FALSE. 
  
  5: In predict.CauseSpecificCox(object = object, newdata = newdata,  :
    Estimated risk outside the range [0,1].
  Consider setting the argument 'product.limit' to FALSE. 
  
  6: In predict.CauseSpecificCox(object = object, newdata = newdata,  :
    Estimated risk outside the range [0,1].
  Consider setting the argument 'product.limit' to FALSE. 
  
  Loading required namespace: ggpp
  [ FAIL 2 | WARN 13 | SKIP 122 | PASS 1505 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (122)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_cif_iptw_pseudo.r:168:3'): 3 ways of iptw calculation are equal ──
  all.equal(out$w_se, out$weightit_se, tolerance = tol) is not TRUE
  
  `actual` is a character vector ('\'is.NA\' value mismatch: 0 in current 2 in target')
  `expected` is a logical vector (TRUE)
  ── Failure ('test_cif_iptw_pseudo.r:169:3'): 3 ways of iptw calculation are equal ──
  all.equal(out$glm_se, out$weightit_se, tolerance = tol) is not TRUE
  
  `actual` is a character vector ('\'is.NA\' value mismatch: 0 in current 2 in target')
  `expected` is a logical vector (TRUE)
  
  [ FAIL 2 | WARN 13 | SKIP 122 | PASS 1505 ]
  Error: Test failures
  Execution halted