Last updated on 2023-06-05 16:54:50 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.10.3 | 15.64 | 394.03 | 409.67 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.10.3 | 13.30 | 284.93 | 298.23 | 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 | 281.00 | 297.00 | NOTE | |
| r-patched-linux-x86_64 | 0.10.3 | 18.50 | 358.83 | 377.33 | 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 | 365.00 | 383.00 | 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 | 19.00 | 349.00 | 368.00 | NOTE |
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