CRAN Package Check Results for Package casebase

Last updated on 2021-10-25 04:00:06 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.10.1 12.69 347.22 359.91 ERROR
r-devel-linux-x86_64-debian-gcc 0.10.1 10.38 246.25 256.63 OK
r-devel-linux-x86_64-fedora-clang 0.10.1 408.23 NOTE
r-devel-linux-x86_64-fedora-gcc 0.10.1 427.21 OK
r-devel-windows-x86_64 0.10.1 21.00 399.00 420.00 NOTE
r-devel-windows-x86_64-gcc10-UCRT 0.10.1 OK
r-patched-linux-x86_64 0.10.1 16.51 336.61 353.12 OK
r-patched-solaris-x86 0.10.1 302.50 NOTE
r-release-linux-x86_64 0.10.1 14.18 338.09 352.27 OK
r-release-macos-arm64 0.9.1 NOTE
r-release-macos-x86_64 0.10.1 NOTE
r-release-windows-ix86+x86_64 0.9.1 23.00 409.00 432.00 NOTE
r-oldrel-macos-x86_64 0.10.1 NOTE
r-oldrel-windows-ix86+x86_64 0.10.1 25.00 301.00 326.00 NOTE

Check Details

Version: 0.10.1
Check: tests
Result: ERROR
     Running 'testthat.R' [55s/62s]
    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: 88
     Number of base moments: 8800
     ----
    
     Call:
     fitSmoothHazard(formula = event ~ Z, data = DF, time = "ftime")
    
     Deviance Residuals:
     Min 1Q Median 3Q Max
     -0.1737 -0.1737 -0.1106 -0.1106 3.1936
    
     Coefficients:
     Estimate Std. Error z value Pr(>|z|)
     (Intercept) 0.2566 0.1801 1.425 0.154
     Z 0.9072 0.2242 4.047 5.19e-05 ***
     ---
     Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
     (Dispersion parameter for binomial family taken to be 1)
    
     Null deviance: 987.39 on 8887 degrees of freedom
     Residual deviance: 970.07 on 8886 degrees of freedom
     AIC: 974.07
    
     Number of Fisher Scoring iterations: 7
    
     Fitting smooth hazards with case-base sampling
    
     Sample size: 200
     Number of events: 88
     Number of base moments: 8800
     ----
    
     Call:
     fitSmoothHazard(formula = event ~ Z, data = DT, time = "ftime")
    
     Deviance Residuals:
     Min 1Q Median 3Q Max
     -0.1721 -0.1721 -0.1114 -0.1114 3.1892
    
     Coefficients:
     Estimate Std. Error z value Pr(>|z|)
     (Intercept) 0.2707 0.1801 1.503 0.133
     Z 0.8742 0.2242 3.900 9.62e-05 ***
     ---
     Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
     (Dispersion parameter for binomial family taken to be 1)
    
     Null deviance: 987.39 on 8887 degrees of freedom
     Residual deviance: 971.31 on 8886 degrees of freedom
     AIC: 975.31
    
     Number of Fisher Scoring iterations: 7
    
     Fitting smooth hazards with case-base sampling
    
     Sample size: 200
     Number of events: 67
     Number of base moments: 670
     ----
    
     Family: binomial
     Link function: logit
    
     Formula:
     event ~ s(ftime) + Z + offset(offset)
    
     Parametric coefficients:
     Estimate Std. Error z value Pr(>|z|)
     (Intercept) -0.07431 0.24129 -0.308 0.758
     Z 1.28800 0.30066 4.284 1.84e-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) 1 1.001 1.464 0.226
    
     R-sq.(adj) = 0.028 Deviance explained = 4.66%
     UBRE = -0.41095 Scale est. = 1 n = 737
     Fitting smooth hazards with case-base sampling
    
     Sample size: 200
     Number of events: 67
     Number of base moments: 670
     ----
    
     Family: binomial
     Link function: logit
    
     Formula:
     event ~ s(ftime) + Z + offset(offset)
    
     Parametric coefficients:
     Estimate Std. Error z value Pr(>|z|)
     (Intercept) -0.009262 0.237658 -0.039 0.968911
     Z 1.161491 0.298681 3.889 0.000101 ***
     ---
     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 1 0.305 0.581
    
     R-sq.(adj) = 0.0219 Deviance explained = 3.93%
     UBRE = -0.40652 Scale est. = 1 n = 737
     == Skipped tests ===============================================================
     * gbm cannot be loaded (2)
     * gbm not implemented (1)
    
     == Failed tests ================================================================
     -- Failure (test-absRiskComp.R:155:5): should output probabilities with data frames - two covariate profile --
     all(absRiskMC <= 1) is not TRUE
    
     `actual`: FALSE
     `expected`: TRUE
    
     [ FAIL 1 | WARN 1 | SKIP 3 | PASS 235 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.10.1
Check: installed package size
Result: NOTE
     installed size is 6.5Mb
     sub-directories of 1Mb or more:
     doc 5.2Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64, r-patched-solaris-x86, r-release-macos-x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.9.1
Check: installed package size
Result: NOTE
     installed size is 6.4Mb
     sub-directories of 1Mb or more:
     doc 5.2Mb
Flavors: r-release-macos-arm64, r-release-windows-ix86+x86_64