Last updated on 2026-06-08 02:51:15 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0 | 3.28 | 67.34 | 70.62 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0 | 2.87 | 28.12 | 30.99 | FAIL | |
| r-devel-linux-x86_64-fedora-clang | 1.0 | 107.35 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0 | 117.28 | OK | |||
| r-devel-windows-x86_64 | 1.0 | 5.00 | 78.00 | 83.00 | OK | |
| r-patched-linux-x86_64 | 1.0 | 3.66 | 63.10 | 66.76 | OK | |
| r-release-linux-x86_64 | 1.0 | 3.61 | 63.59 | 67.20 | OK | |
| r-release-macos-arm64 | 1.0 | 1.00 | 23.00 | 24.00 | OK | |
| r-release-macos-x86_64 | 1.0 | 3.00 | 75.00 | 78.00 | OK | |
| r-release-windows-x86_64 | 1.0 | 5.00 | 82.00 | 87.00 | OK | |
| r-oldrel-macos-arm64 | 1.0 | OK | ||||
| r-oldrel-macos-x86_64 | 1.0 | 3.00 | 92.00 | 95.00 | OK | |
| r-oldrel-windows-x86_64 | 1.0 | 7.00 | 99.00 | 106.00 | OK |
Version: 1.0
Check: examples
Result: ERROR
Running examples in ‘jointest-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: flip2sss
> ### Title: flipscores 2-Stage Summary Statistics approach
> ### Aliases: flip2sss
>
> ### ** Examples
>
> library(jointest)
> set.seed(123)
> # Simulate data
> N=20
> n=rpois(N,20)
> reff=rep(rnorm(N),n)
>
> D=data.frame(X1=rnorm(length(reff)),
+ X2=rep(rnorm(N),n),
+ Grp=factor(rep(rep(LETTERS[1:3],length.out=N),n)),
+ Subj=rep(1:N,n))
> D$Y=rbinom(n=nrow(D),prob=plogis( 2*D$X1 * (D$Grp=="B") + 2*D$X2+reff),size=1)
>
> # model of interest formula <- Y ~ Grp * X1 + X2
> # clusters structure defined by cluster <- factor(D$Subj)
> # The 2-Stage Summary Statistics via flipscore:
> res <- flip2sss(Y ~ Grp * X1 + X2, data=D,
+ cluster=D$Subj, family="binomial")
> summary(res)
Model Coeff Estimate Score Std. Error z value
1 .Intercept. (Intercept) 4.3128538 29.0261330 24.152830 1.20176943
2 .Intercept. GrpB -0.3824975 -1.1599283 15.511347 -0.07477934
3 .Intercept. GrpC -1.7121985 -5.5300048 16.061350 -0.34430510
4 .Intercept. X2 9.5446012 151.9594953 51.196709 2.96814969
5 X1 X1 0.2882803 2.0179621 2.658795 0.75897611
6 X1 GrpB:X1 1.1367411 3.9785937 2.073856 1.91845180
7 X1 GrpC:X1 0.1228905 0.3970308 1.779620 0.22309867
Part. Cor p
1 0.29147190 0.1682
2 -0.01813665 0.9400
3 -0.08350625 0.6882
4 0.71988204 0.0062
5 0.17889239 0.1894
6 0.45218343 0.0352
7 0.05258486 0.7872
> # This is an ANOVA-like overall test:
> summary(combine(res))
Model Coeff Stat nTests S p
1 Overall many maxT 7 151.9595 0.0062
> # This is an ANOVA-like test:
> summary(combine_contrasts(res))
Model Coeff Stat nTests S p
1 .Intercept. (Intercept) Mahalanobis 1 0.02057700 0.1682
2 .Intercept. Grp Mahalanobis 2 0.19176868 0.9276
3 .Intercept. X2 Mahalanobis 1 0.03393411 0.0062
4 X1 X1 Mahalanobis 1 0.02096200 0.1894
5 X1 Grp:X1 Mahalanobis 2 3.69226237 0.1532
>
> # An alternative and more flexible definition of the model:
> # Define the summary statistics (here we propose the glm with firth correction
> # from the logistf package)
> summstats_within <- 'logistf::logistf(Y ~ X1, family = binomial(link = "logit"),
+ control=logistf::logistf.control(maxit=100))'
> # however also the classic glm function can be used:
> #summstats_within <- 'glm(Y ~ X1, family = binomial(link = "logit"))'
>
> # Then, compute the 2-Stage Summary Statistics approach
> # specifying the summary statistics (within cluster/subject)
> res <- flip2sss(Y ~ Grp * X1 + X2, data=D, cluster=D$Subj,
+ summstats_within=summstats_within)
Error in loadNamespace(x) : there is no package called ‘logistf’
Calls: flip2sss ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0
Check: for unstated dependencies in vignettes
Result: NOTE
Error: inferior call failed
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0
Check: re-building of vignette outputs
Result: FAIL
Flavor: r-devel-linux-x86_64-debian-gcc