* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/CoMiRe.Rcheck’
* using R Under development (unstable) (2025-11-16 r89026)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘CoMiRe/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CoMiRe’ version ‘0.8’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CoMiRe’ can be installed ... [88s/62s] OK
* used C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [20s/20s] OK
* checking Rd files ... NOTE
checkRd: (-1) BMD.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMD.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMD.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMD.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMD.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add.risk.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add.risk.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:67-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... [11s/11s] OK
* checking examples with --run-donttest ... [30m/31m] ERROR
Running examples in ‘CoMiRe-Ex.R’ failed
The error most likely occurred in:

> ### Name: comire.gibbs
> ### Title: Gibbs sampler for CoMiRe model
> ### Aliases: comire.gibbs
> 
> ### ** Examples
> 
> {
+ 
+ data(CPP)
+ attach(CPP)
+ 
+ n <- NROW(CPP)
+ J <- H <- 10
+ 
+ premature <- as.numeric(gestage<=37)
+ 
+ mcmc <- list(nrep=5000, nb=2000, thin=5, ndisplay=4)
+ 
+ ## too few iterations to be meaningful. see below for safer and more comprehensive results
+ 
+ mcmc <- list(nrep=10, nb=2, thin=1, ndisplay=4) 
+ 
+ 
+ prior <- list(mu.theta=mean(gestage), k.theta=10, eta=rep(1, J)/J, 
+               alpha=rep(1,H)/H, a=2, b=2, J=J, H=H)
+               
+ fit.dummy <- comire.gibbs(gestage, dde, family="continuous", 
+                      mcmc=mcmc, prior=prior, seed=1, max.x=180)
+                      
+ summary(fit.dummy)
+  
+ 
+ ## No test: 
+ ## safer procedure with more iterations (it may take some time)
+ 
+ mcmc <- list(nrep=5000, nb=2000, thin=5, ndisplay=4) 
+ 
+ ## 1. binary case ##
+ 
+ prior <- list(pi0=mean(gestage), eta=rep(1, J)/J, 
+              a.pi0=27, b.pi0=360, J=J)
+              
+ fit_binary<- comire.gibbs(premature, dde, family="binary", 
+                           mcmc=mcmc, prior=prior, seed=5, max.x=180)
+                           
+                           
+ ## 2. continuous case ##
+ 
+ prior <- list(mu.theta=mean(gestage), k.theta=10, eta=rep(1, J)/J, 
+               alpha=rep(1,H)/H, a=2, b=2, J=J, H=H)
+               
+ fit1 <- comire.gibbs(gestage, dde, family="continuous", 
+                      mcmc=mcmc, prior=prior, seed=5, max.x=180)
+ 
+ 
+ ## 2.2 One confunder ##
+ 
+ mage_std <- scale(mage, center = TRUE, scale = TRUE) 
+ 
+ prior <- list(mu.theta=mean(gestage), k.theta=10, mu.gamma=0, k.gamma=10, 
+               eta=rep(1, J)/J, alpha=1/H, a=2, b=2, H=H, J=J)
+               
+ fit2 <- comire.gibbs(gestage, dde, mage_std, family="continuous", 
+               mcmc=mcmc, prior=prior, seed=5, max.x=180)
+ 
+ 
+ ## 2.3 More confunders ##
+ 
+ Z <- cbind(mage, mbmi, sei)
+ Z <- scale(Z, center = TRUE, scale = TRUE)
+ Z <- as.matrix(cbind(Z, CPP$smoke))
+ colnames(Z) <- c("age", "BMI", "sei", "smoke")
+ 
+ mod <- lm(gestage ~ dde + Z)
+ prior <- list(mu.theta = mod$coefficients[1], k.theta = 10,
+               mu.gamma = mod$coefficients[-c(1, 2)], sigma.gamma = diag(rep(10, 4)),
+               eta = rep(1, J)/J, alpha = 1/H, a = 2, b = 2, H = H, J = J)
+               
+ fit3 <- comire.gibbs(y = gestage, x = dde, z = Z, family = "continuous", mcmc = mcmc, 
+                      prior = prior, seed = 5)
+ 
+ ## End(No test)
+  
+ }
CoMiRe model fit via Gibbs Sampler
Family: continuous
Burn in done
7 iterations over 12 
12 iterations over 12 
CoMiRe model fit via Gibbs Sampler
Family: Continuous
Formula: gestage ~ . | beta(dde)
Posterior approximation based on 10 iterationsCoMiRe model fit via Gibbs Sampler
Family: binary
Burn in done
3250 iterations over 7000 
4500 iterations over 7000 
5750 iterations over 7000 
7000 iterations over 7000 
CoMiRe model fit via Gibbs Sampler
Family: continuous
Burn in done
3250 iterations over 7000 
4500 iterations over 7000 
5750 iterations over 7000 
7000 iterations over 7000 
CoMiRe model fit via Gibbs Sampler
Family: continuous 
Burn in done
3250 iterations over 7000 
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/CoMiRe.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 33:16.09, 1947.48 + 25.97