CRAN Package Check Results for Package casebase

Last updated on 2023-06-08 04:54:46 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.10.3 14.65 386.83 401.48 OK
r-devel-linux-x86_64-debian-gcc 0.10.3 11.58 287.11 298.69 OK
r-devel-linux-x86_64-fedora-clang 0.10.3 479.83 NOTE
r-devel-linux-x86_64-fedora-gcc 0.10.3 493.59 OK
r-devel-windows-x86_64 0.10.3 16.00 283.00 299.00 NOTE
r-patched-linux-x86_64 0.10.3 21.53 356.19 377.72 OK
r-release-linux-x86_64 0.10.3 14.29 361.40 375.69 ERROR
r-release-macos-arm64 0.10.3 153.00 NOTE
r-release-macos-x86_64 0.10.3 261.00 NOTE
r-release-windows-x86_64 0.10.3 18.00 355.00 373.00 NOTE
r-oldrel-macos-arm64 0.10.3 179.00 NOTE
r-oldrel-macos-x86_64 0.10.3 202.00 NOTE
r-oldrel-windows-x86_64 0.10.3 18.00 357.00 375.00 NOTE

Check Details

Version: 0.10.3
Check: installed package size
Result: NOTE
     installed size is 5.8Mb
     sub-directories of 1Mb or more:
     doc 4.6Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Version: 0.10.3
Check: tests
Result: ERROR
     Running ‘testthat.R’ [52s/60s]
    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) -0.1058 0.2136 -0.495 0.62
     Z 1.5707 0.2503 6.275 3.49e-10 ***
     ---
     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: 874.17 on 8280 degrees of freedom
     AIC: 878.17
    
     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) -0.1011 0.2136 -0.473 0.636
     Z 1.5576 0.2503 6.223 4.88e-10 ***
     ---
     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: 874.95 on 8280 degrees of freedom
     AIC: 878.95
    
     Number of Fisher Scoring iterations: 8
    
     Fitting smooth hazards with case-base sampling
    
     Sample size: 200
     Number of events: 73
     Number of base moments: 730
     ----
    
     Family: binomial
     Link function: logit
    
     Formula:
     event ~ s(ftime) + Z + offset(offset)
    
     Parametric coefficients:
     Estimate Std. Error z value Pr(>|z|)
     (Intercept) 0.1289 0.1975 0.653 0.513959
     Z 0.9850 0.2591 3.802 0.000144 ***
     ---
     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) 1.004 1.007 0.438 0.509
    
     R-sq.(adj) = 0.0157 Deviance explained = 3.08%
     UBRE = -0.40199 Scale est. = 1 n = 803
     Fitting smooth hazards with case-base sampling
    
     Sample size: 200
     Number of events: 73
     Number of base moments: 730
     ----
    
     Family: binomial
     Link function: logit
    
     Formula:
     event ~ s(ftime) + Z + offset(offset)
    
     Parametric coefficients:
     Estimate Std. Error z value Pr(>|z|)
     (Intercept) 0.1582 0.1987 0.796 0.42604
     Z 0.8948 0.2586 3.460 0.00054 ***
     ---
     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) 1.508 1.864 1.153 0.442
    
     R-sq.(adj) = 0.0122 Deviance explained = 2.76%
     UBRE = -0.39882 Scale est. = 1 n = 803
     [ FAIL 1 | WARN 3 | SKIP 3 | PASS 235 ]
    
     ══ Skipped tests ═══════════════════════════════════════════════════════════════
     • gbm cannot be loaded (2)
     • gbm not implemented (1)
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Failure ('test-absRiskComp.R:173:5'): should output probabilities with data tables - two covariate profile ──
     all(absRiskMC <= 1 + eps) is not TRUE
    
     `actual`: FALSE
     `expected`: TRUE
    
     [ FAIL 1 | WARN 3 | SKIP 3 | PASS 235 ]
     Error: Test failures
     Execution halted
Flavor: r-release-linux-x86_64