* using log directory ‘/data/localhost/ripley/R/packages/tests-donttest/bml.Rcheck’
* using R Under development (unstable) (2026-08-24 r90445)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)
    GNU Fortran (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)
* running under: Fedora Linux 44 (Server Edition)
* using session charset: UTF-8
* current time: 2026-08-24 22:42:19 UTC
* checking for file ‘bml/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bml’ version ‘0.9.0’
* 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 ‘bml’ can be installed ... OK
* checking package directory ... OK
* checking ‘build’ 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 use of S3 registration ... 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 ... [9s/17s] OK
* checking Rd files ... OK
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking examples with --run-donttest ... [7m/12m] ERROR
Running examples in ‘bml-Ex.R’ failed
The error most likely occurred in:

> ### Name: bml
> ### Title: Bayesian Multiple-Membership Multilevel Models with
> ###   Parameterizable Weight Functions Using JAGS
> ### Aliases: bml
> 
> ### ** Examples
> 
> ## No test: 
> data(coalgov)
> 
> # Basic multiple-membership model
> # Parties (pid) within governments (gid), nested in countries (cid)
> m1 <- bml(
+   Surv(dur_wkb, event_wkb) ~ 1 + majority +
+     mm(
+       id   = id(pid, gid),
+       vars = vars(cohesion),
+       fn   = fn(w ~ 1/n, c = TRUE),
+       RE   = TRUE
+     ) +
+     hm(id = id(cid), type = "RE"),
+   family = "Weibull",
+   data   = coalgov
+ )
module glm loaded
Compiling model graph
   Resolving undeclared variables
   Allocating nodes
Graph information:
   Observed stochastic nodes: 873
   Unobserved stochastic nodes: 1358
   Total graph size: 19185

Initializing model

> 
> # View results
> summary(m1)
Outcome family: Weibull survival (duration: dur_wkb, event: event_wkb) 
Estimates: Posterior mean (MCMC) 
Uncertainty: 95% equal-tailed credible intervals [2.5%, 97.5%] 

Level specification:
  hm.1: cid (RE, indep)
  mm.1: pid, gid (RE, indep) 

                   Parameter   mean    sd     lb     ub
b[1]               Intercept  7.012 0.187  6.713  7.458
b[2]                majority  0.350 0.154  0.070  0.664
b.mm.1       cohesion (mm.1) -0.339 0.136 -0.607 -0.069
shape                  shape  1.207 0.069  1.077  1.342
sigma                  sigma  0.831 0.048  0.745  0.929
sigma.hm.1   sigma.hm (hm.1)  0.323 0.202  0.030  0.723
sigma.mm.1 sigma.mm.1 (mm.1)  0.966 0.198  0.586  1.355

Model fit: DIC = 3864.093 
> monetPlot(m1, "b[2]")  # Plot for majority coefficient
Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
ℹ The deprecated feature was likely used in the ggmcmc package.
  Please report the issue at <https://github.com/xfim/ggmcmc/issues/>.
> 
> # Multiple mm() blocks with different weight functions
> m2 <- bml(
+   Surv(dur_wkb, event_wkb) ~ 1 + majority +
+     mm(id = id(pid, gid), vars = vars(cohesion),
+        fn = fn(w ~ cohesion == max(cohesion)), RE = FALSE) +
+     mm(id = id(pid, gid), vars = NULL, fn = fn(w ~ 1/n), RE = TRUE),
+   family = "Weibull",
+   data   = coalgov
+ )
Compiling model graph
   Resolving undeclared variables
   Allocating nodes
Graph information:
   Observed stochastic nodes: 873
   Unobserved stochastic nodes: 1328
   Total graph size: 21229

Initializing model

> 
> # Cox model with piecewise baseline hazard (faster for large datasets)
> m3 <- bml(
+   Surv(dur_wkb, event_wkb) ~ 1 + majority +
+     mm(id = id(pid, gid), vars = vars(cohesion), fn = fn(w ~ 1/n), RE = TRUE),
+   family = "Cox",
+   cox_intervals = 10,  # Use 10 intervals instead of all unique times
+   data   = coalgov
+ )
Compiling model graph
   Resolving undeclared variables
   Allocating nodes
Graph information:
   Observed stochastic nodes: 6280
   Unobserved stochastic nodes: 326
   Total graph size: 33603

Initializing model

Warning in FUN(X[[i]], ...) : Failed to set trace monitor for pred
Variable pred not found

> 
> # Parameterized weight function
> # ilogit() bounds raw weights between 0 and 1; c = TRUE normalizes to sum to 1
> m4 <- bml(
+   Surv(dur_wkb, event_wkb) ~ 1 + majority +
+     mm(
+       id   = id(pid, gid),
+       vars = vars(cohesion),
+       fn   = fn(w ~ ilogit(b0 + b1 * pseat), c = TRUE),
+       RE   = FALSE
+     ),
+   family = "Weibull",
+   data   = coalgov
+ )
Compiling model graph
   Resolving undeclared variables
   Allocating nodes
Graph information:
   Observed stochastic nodes: 873
   Unobserved stochastic nodes: 1017
   Total graph size: 28221

Initializing model

> 
> # Fixed coefficients (offsets)
> m5 <- bml(
+   Surv(dur_wkb, event_wkb) ~ 1 + fix(majority, 1) + # Fix majority coefficient to 1.0
+     mm(
+       id   = id(pid, gid),
+       vars = vars(rile),
+       fn   = fn(w ~ 1/n, c = TRUE),
+       RE   = FALSE
+     ),
+   family = "Weibull",
+   data   = coalgov
+ )
Compiling model graph
   Resolving undeclared variables
   Allocating nodes
Graph information:
   Observed stochastic nodes: 873
   Unobserved stochastic nodes: 1014
   Total graph size: 14526

Initializing model

> 
> # Custom priors
> m6 <- bml(
+   Surv(dur_wkb, event_wkb) ~ 1 + majority +
+     mm(id = id(pid, gid), vars = vars(cohesion), fn = fn(w ~ 1/n), RE = TRUE),
+   family = "Weibull",
+   priors = list(
+     "b[1] ~ dnorm(0, 0.01)",       # Intercept prior
+     "b.mm.1 ~ dnorm(0, 0.1)",      # MM coefficient prior
+     "tau.mm.1 ~ dgamma(2, 0.5)"    # MM precision prior
+   ),
+   data   = coalgov
+ )
Compiling model graph
   Resolving undeclared variables
   Allocating nodes
Graph information:
   Observed stochastic nodes: 873
   Unobserved stochastic nodes: 1328
   Total graph size: 18525

Initializing model

> 
> # Cross-classified model (multiple hm blocks)
> # Governments are cross-classified by country and election year
> m7 <- bml(
+   Surv(dur_wkb, event_wkb) ~ 1 + majority +
+     mm(id = id(pid, gid), vars = vars(cohesion), fn = fn(w ~ 1/n), RE = TRUE) +
+     hm(id = id(cid), type = "RE") +
+     hm(id = id(year), type = "RE"),
+   family = "Weibull",
+   data   = coalgov |> mutate(year = format(election, "%Y") |> as.integer())
+ )
Error in mutate(coalgov, year = as.integer(format(election, "%Y"))) : 
  could not find function "mutate"
Calls: bml
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [28s/53s]
 [28s/53s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [12s/24s] OK
* checking PDF version of manual ... OK
* checking HTML 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
See
  ‘/data/localhost/ripley/R/packages/tests-donttest/bml.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 16:00.51, 478.46 + 26.54