Running 'testthat.R' [192s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(casebase)
  See example usage at http://sahirbhatnagar.com/casebase/
  > library(data.table)
  > library(survival)
  > 
  > test_check("casebase")
  Fitting smooth hazards with case-base sampling
  
  Sample size: 200 
  Number of events: 82 
  Number of base moments: 8200 
  ----
  
  Call:
  fitSmoothHazard(formula = event ~ Z, data = DF, time = "ftime")
  
  Coefficients:
              Estimate Std. Error z value Pr(>|z|)    
  (Intercept) 0.009918   0.196634   0.050     0.96    
  Z           1.170688   0.238383   4.911 9.06e-07 ***
  ---
  Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  
  (Dispersion parameter for binomial family taken to be 1)
  
      Null deviance: 920.07  on 8281  degrees of freedom
  Residual deviance: 893.68  on 8280  degrees of freedom
  AIC: 897.68
  
  Number of Fisher Scoring iterations: 8
  
  Fitting smooth hazards with case-base sampling
  
  Sample size: 200 
  Number of events: 82 
  Number of base moments: 8200 
  ----
  
  Call:
  fitSmoothHazard(formula = event ~ Z, data = DT, time = "ftime")
  
  Coefficients:
              Estimate Std. Error z value Pr(>|z|)    
  (Intercept)  0.03296    0.19665   0.168    0.867    
  Z            1.11411    0.23837   4.674 2.96e-06 ***
  ---
  Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  
  (Dispersion parameter for binomial family taken to be 1)
  
      Null deviance: 920.07  on 8281  degrees of freedom
  Residual deviance: 896.21  on 8280  degrees of freedom
  AIC: 900.21
  
  Number of Fisher Scoring iterations: 8
  
  Fitting smooth hazards with case-base sampling
  
  Sample size: 200 
  Number of events: 78 
  Number of base moments: 780 
  ----
  
  Family: binomial 
  Link function: logit 
  
  Formula:
  event ~ s(ftime) + Z + offset(offset)
  
  Parametric coefficients:
              Estimate Std. Error z value Pr(>|z|)    
  (Intercept)   0.1027     0.1983   0.518    0.605    
  Z             0.9789     0.2467   3.967 7.26e-05 ***
  ---
  Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  
  Approximate significance of smooth terms:
             edf Ref.df Chi.sq p-value
  s(ftime) 2.629  3.327  2.304   0.528
  
  R-sq.(adj) =  0.0214   Deviance explained = 4.31%
  UBRE = -0.40618  Scale est. = 1         n = 858
  Fitting smooth hazards with case-base sampling
  
  Sample size: 200 
  Number of events: 78 
  Number of base moments: 780 
  ----
  
  Family: binomial 
  Link function: logit 
  
  Formula:
  event ~ s(ftime) + Z + offset(offset)
  
  Parametric coefficients:
              Estimate Std. Error z value Pr(>|z|)    
  (Intercept)   0.1011     0.2107   0.480 0.631444    
  Z             0.9395     0.2476   3.795 0.000148 ***
  ---
  Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  
  Approximate significance of smooth terms:
             edf Ref.df Chi.sq p-value
  s(ftime) 3.791   4.67  2.769   0.677
  
  R-sq.(adj) =  0.0207   Deviance explained = 4.23%
  UBRE = -0.40302  Scale est. = 1         n = 858
  [ FAIL 0 | WARN 2 | SKIP 3 | PASS 236 ]
  
  ══ Skipped tests (3) ═══════════════════════════════════════════════════════════
  • gbm cannot be loaded (2): 'test-plotHazard.R:3:1',
    'test-plotSingleEventCB.R:3:1'
  • gbm not implemented (1): 'test-gbm.R:2:1'
  
  [ FAIL 0 | WARN 2 | SKIP 3 | PASS 236 ]
  > 
  > proc.time()
     user  system elapsed 
    28.82    3.10   31.96