Running ‘checkinputs.R’ [1m/23m]
Running the tests in ‘tests/checkinputs.R’ failed.
Complete output:
  > # First load runjags and verify that the options can be set:
  > library('runjags')
  > runjags.options(inits.warning=FALSE, rng.warning=FALSE, silent.jags=TRUE)
  > newopts <- runjags.options()
  > stopifnot(newopts$inits.warning==FALSE)
  > stopifnot(newopts$rng.warning==FALSE)
  > stopifnot(newopts$silent.jags==TRUE)
  > 
  > 
  > # Test some runjags inputs with the rjags method:
  > 
  > testnum <- 1
  > if(require("rjags")){
  + 
  + 	# Required for nvar etc:
  + 	library("coda")
  + 
  + 	model <- "model {
  + 	for(i in 1 : N){ #data# N
  + 	Y[i] ~ dnorm(true.y[i], precision); #data# Y
  + 	true.y[i] <- (m * X[i]) + c; #data# X
  + 	}
  + 	m ~ dunif(-1000,1000); #inits# m
  + 	c ~ dunif(-1000,1000);
  + 	precision ~ dexp(1);
  + 	#monitor# m, c, precision
  + 	}"
  + 
  + 	# Simulate the data
  + 	X <- 1:100
  + 	Y <- rnorm(length(X), 2*X + 10, 1)
  + 	N <- length(X)
  + 
  + 	initfunction <- function(chain) return(switch(chain, "1"=list(m=-10), "2"=list(m=10)))
  + 	initfunction2 <- function() return(switch(sample(c(1,2),1), "1"=list(m=-10), "2"=list(m=10)))
  + 
  + 	datalist <- list(X=X, Y=Y, N=N)
  + 	
  + 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
  + 	results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, inits=initfunction, method='rjags')
  + 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
  + 	results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, inits=initfunction2, method='rjags')
  + 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
  + 	results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, inits=lapply(1:2,initfunction), method='rjags')
  + 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
  + 	results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, inits=initfunction(1), method='rjags')
  + 
  + 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
  + 	results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, data=datalist, inits=initfunction, method='rjags')
  + 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
  + 	results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, data=datalist, inits=initfunction2, method='rjags')
  + 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
  + 	results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, data=datalist, inits=lapply(1:2,initfunction), method='rjags')
  + 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
  + 	results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, data=datalist, inits=initfunction(1), method='rjags')
  + 	stopifnot(nvar(as.mcmc.list(results))==(3))
  + 	stopifnot(all(varnames(as.mcmc.list(results))==c('m','c','precision')))
  + 
  + 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
  + 	results <- extend.jags(results,sample=1000)
  + 	stopifnot(niter(as.mcmc.list(results))==2000)
  + 	stopifnot(nvar(as.mcmc.list(results))==3)
  + 
  + 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
  + 	results2 <- extend.jags(results, sample=1000, drop.chain=1, summarise=FALSE)
  + 	stopifnot(nchain(as.mcmc.list(results2))==1)
  + 	stopifnot(identical(list.format(results$end.state[[2]])$.RNG.name, list.format(results2$end.state[[1]])$.RNG.name))
  +   
  + 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
  + 	results2 <- extend.jags(results, sample=1000, drop.monitor="precision", summarise=FALSE)
  + 	stopifnot(nvar(as.mcmc.list(results2))==2)
  +   
  + 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
  + 	results2 <- extend.jags(results, sample=1000, add.monitor="true.y", summarise=FALSE)
  + 	stopifnot(nvar(as.mcmc.list(results2))==(3+N))
  + 	stopifnot(varnames(as.mcmc.list(results2))[1]=='m' && varnames(as.mcmc.list(results2))[103]=='true.y[100]')
  + 
  + 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
  + 	results2 <- extend.jags(results, sample=1000, add.monitor=c("true.y", "dic"), summarise=FALSE)
  + 	stopifnot(nvar(as.mcmc.list(results2))==(3+N))
  + 	stopifnot(varnames(as.mcmc.list(results2))[1]=='m' && varnames(as.mcmc.list(results2))[103]=='true.y[100]')
  + 
  + 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
  + 	results2 <- extend.jags(results, sample=1000, add.monitor=c("true.y", "deviance"), summarise=FALSE)
  + 	stopifnot(nvar(as.mcmc.list(results2))==(4+N))
  + 	stopifnot(varnames(as.mcmc.list(results2))[1]=='m' && varnames(as.mcmc.list(results2))[104]=='deviance')
  + 	
  + 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
  + 	results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, data=datalist, inits=initfunction, method='rjparallel')
  + 	stopifnot(nvar(as.mcmc.list(results))==(3))
  + 	stopifnot(all(varnames(as.mcmc.list(results))==c('m','c','precision')))	
  + 
  + 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
  + 	results2 <- extend.jags(results, sample=1000, add.monitor="true.y", summarise=FALSE, method='rjp')
  + 	stopifnot(nvar(as.mcmc.list(results2))==(3+N))
  + 	stopifnot(varnames(as.mcmc.list(results2))[1]=='m' && varnames(as.mcmc.list(results2))[103]=='true.y[100]')
  + 	
  + 	cat('Running input test number', testnum, '\n'); testnum <- testnum+1
  + 	results2 <- extend.jags(results, sample=1000, add.monitor=c("true.y", "deviance"), summarise=FALSE, method='rjp')
  + 	stopifnot(nvar(as.mcmc.list(results2))==(4+N))
  + 	stopifnot(varnames(as.mcmc.list(results2))[1]=='m' && varnames(as.mcmc.list(results2))[104]=='deviance')
  + 	
  + 	cat("All input checks passed\n")
  + 
  + }else{
  + 	cat("The input checks were not performed as rjags is not installed\n")
  + }
  Loading required package: rjags
  Loading required package: coda
  Linked to JAGS 4.2.0
  Loaded modules: basemod,bugs
  Running input test number 1 
  Finished running the simulation
  Running input test number 2 
  Finished running the simulation
  Running input test number 3 
  Finished running the simulation
  Running input test number 4 
  Finished running the simulation
  Running input test number 5 
  Finished running the simulation
  Running input test number 6 
  Finished running the simulation
  Running input test number 7 
  Finished running the simulation
  Running input test number 8 
  Finished running the simulation
  Running input test number 9 
  Finished running the simulation
  Running input test number 10 
  Finished running the simulation
  Running input test number 11 
  Finished running the simulation
  Running input test number 12 
  Finished running the simulation
  Running input test number 13 
  module dic loaded
  Finished running the simulation
  Running input test number 14 
  Finished running the simulation
  Running input test number 15