Last updated on 2026-06-06 23:52:02 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.2.2-5 | 36.81 | 205.80 | 242.61 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.2.2-5 | 22.43 | 133.04 | 155.47 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.2.2-5 | 67.00 | 339.86 | 406.86 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 2.2.2-5 | 57.00 | 433.21 | 490.21 | OK | |
| r-devel-windows-x86_64 | 2.2.2-5 | 44.00 | 91.00 | 135.00 | OK | --no-examples --no-tests --no-vignettes |
| r-patched-linux-x86_64 | 2.2.2-5 | 30.27 | 198.27 | 228.54 | OK | |
| r-release-linux-x86_64 | 2.2.2-5 | 29.27 | 201.75 | 231.02 | OK | |
| r-release-macos-arm64 | 2.2.2-5 | 12.00 | 99.00 | 111.00 | OK | |
| r-release-macos-x86_64 | 2.2.2-5 | 31.00 | 563.00 | 594.00 | OK | |
| r-release-windows-x86_64 | 2.2.2-5 | 54.00 | 93.00 | 147.00 | OK | --no-examples --no-tests --no-vignettes |
| r-oldrel-macos-arm64 | 2.2.2-5 | OK | ||||
| r-oldrel-macos-x86_64 | 2.2.2-5 | 29.00 | 462.00 | 491.00 | OK | |
| r-oldrel-windows-x86_64 | 2.2.2-5 | 59.00 | 87.00 | 146.00 | OK | --no-examples --no-tests --no-vignettes |
Version: 2.2.2-5
Check: tests
Result: ERROR
Running ‘check_huiwalter.R’ [31s/38s]
Running ‘checkinputs.R’ [10s/13s]
Running ‘checkmethods.R’ [5s/39s]
Running ‘checkmodule.R’ [4s/5s]
Running ‘checkstudy.R’ [4s/11s]
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/checkmethods.R’ failed.
Complete output:
> # test all of the runjags dispatch methods with a toy example:
>
> library(runjags)
>
> runjags.options(inits.warning=FALSE, rng.warning=FALSE, blockignore.warning=FALSE, silent.jags=TRUE)
>
> # Require for as.mcmc.list and niter:
> 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, dic, popt, pd
+ }"
>
> model_parallel <- "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)))
>
>
> # Get the JAGS path - rjags adds the JAGS path to the PATH in Windows...
> try(library(rjags))
Linked to JAGS 4.3.2
Loaded modules: basemod,bugs
> jagspath <- findjags()
>
> # Only run the JAGS methods tests if we have found JAGS and have permission to run it:
> if(jagspath!="JAGS not found" && testjags(jagspath)$JAGS.available){
+
+ testnum <- 1
+ cat('Testing the simple method\n')
+ # Try the simple method and if it doesn't work give a warning but don't fail (likely to be permissions problems)
+ success <- try({
+ results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, inits=initfunction, method='simple',temp=FALSE)
+ })
+ if(inherits(success, 'try-error')){
+ cat("JAGS was found but the simple method failed; it is possible that there were permissions issues or similar. Details as follows:\n")
+ t <- testjags(silent=FALSE)
+ cat(failed.jags('output')[[1]])
+ print(file.info(jagspath))
+ print(file.info(getwd())[,1:3])
+ cat("All test methods (except possibly rjags) were skipped\n")
+ }else{
+ cat('Running method test number', testnum, '\n'); testnum <- testnum+1
+ stopifnot(niter(as.mcmc.list(results))==1000)
+
+ cat('Running method test number', testnum, '\n'); testnum <- testnum+1
+ results <- run.jags(model_parallel, n.chains=2, sample=1000, burnin=1000, inits=initfunction, method='parallel')
+ stopifnot(niter(as.mcmc.list(results))==1000)
+
+ cat('Running method test number', testnum, '\n'); testnum <- testnum+1
+ results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, inits=initfunction, method='interruptible')
+ stopifnot(niter(as.mcmc.list(results))==1000)
+
+ # Same as in checkinputs but it's for rjags there:
+ cat('Running method 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 method 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 method 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')
+
+ # Same as in checkinputs but it's for rjags there:
+ cat('Running method test number', testnum, '\n'); testnum <- testnum+1
+ results2 <- extend.jags(results, sample=1000, add.monitor="true.y", summarise=FALSE, method='simple')
+ 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 method 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 method 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')
+
+ # Snow gives problems here ... but it does work!
+ #results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, inits=initfunction, method='snow')
+ #stopifnot(niter(as.mcmc.list(results))==1000)
+
+ cat('Running method test number', testnum, '\n'); testnum <- testnum+1
+ info <- run.jags(model, n.chains=2, sample=1000, burnin=1000, inits=initfunction, method='background')
+ t <- 0
+ repeat{
+ # Change thin, chain and variables:
+ s <- try(results <- results.jags(info, read.monitor='m', return.samples=100, recover.chains=2, summarise=FALSE))
+ if(!inherits(s, 'try-error')) break
+ if(t==30) stop("Timed out waiting for the bgparallel method")
+ Sys.sleep(1)
+ t <- t+1
+ }
+ stopifnot(niter(as.mcmc.list(results))==100)
+ stopifnot(nvar(as.mcmc.list(results))==1)
+ stopifnot(nchain(as.mcmc.list(results))==1)
+
+
+ cat('Running method test number', testnum, '\n'); testnum <- testnum+1
+ info <- run.jags(model_parallel, n.chains=2, sample=1000, burnin=1000, inits=initfunction, method='bgparallel')
+ t <- 0
+ repeat{
+ s <- try(results <- results.jags(info))
+ if(!inherits(s, 'try-error')) break
+ if(t==30) stop("Timed out waiting for the bgparallel method")
+ Sys.sleep(1)
+ t <- t+1
+ }
+ stopifnot(niter(as.mcmc.list(results))==1000)
+
+ # Check combine.mcmc does what it says on the tin:
+ stopifnot(niter(combine.mcmc(results, return.samples=1000, collapse.chains=TRUE))==1000)
+ stopifnot(niter(combine.mcmc(results, return.samples=11, collapse.chains=TRUE))==11)
+ stopifnot(niter(combine.mcmc(results, return.samples=100, collapse.chains=FALSE))==100)
+ stopifnot(niter(combine.mcmc(results, thin=1, collapse.chains=TRUE))==2000)
+ stopifnot(niter(combine.mcmc(results, thin=10, collapse.chains=TRUE))==200)
+ stopifnot((niter(combine.mcmc(results, thin=15, collapse.chains=TRUE))*15)>=2000)
+ stopifnot(niter(combine.mcmc(results, thin=10, collapse.chains=FALSE))==100)
+
+ # Check we can use the extend wrapper:
+ cat('Running method test number', testnum, '\n'); testnum <- testnum+1
+ newres <- extend.jags(results, sample=0)
+ stopifnot(newres$burnin==results$burnin)
+ stopifnot(niter(as.mcmc.list(newres))==niter(as.mcmc.list(results)))
+
+ # Check a single iteration works:
+ cat('Running method test number', testnum, '\n'); testnum <- testnum+1
+ results <- run.jags(model, n.chains=2, sample=1, burnin=1000, inits=initfunction, method='interruptible', summarise=FALSE)
+ stopifnot(niter(as.mcmc.list(results))==1)
+
+ # And that precision can be ignored:
+ cat('Running method test number', testnum, '\n'); testnum <- testnum+1
+ results <- run.jags(model, monitor=c('m','c'), n.chains=2, sample=10, burnin=100, inits=initfunction, method='interruptible', summarise=FALSE, noread.monitor='precision')
+ stopifnot(nvar(as.mcmc.list(results))==2)
+
+ # Check the version number is correct:
+ cat('Running method test number', testnum, '\n'); testnum <- testnum+1
+ stopifnot(newres$runjags.version[1]==runjags:::runjagsprivate$runjagsversion)
+
+ }
+ }else{
+ cat("JAGS could not be called externally at the path: ", jagspath, "\n")
+ cat("All test methods except possibly rjags and rjagsparallel were skipped\n")
+ }
You are using R Under development (unstable) (2026-06-05 r90111) on a
unix machine, with the X11 GUI
JAGS version 4.3.2 found successfully using the command '/usr/bin/jags'
The rjags package is installed
Testing the simple method
Running the simulation using the simple method... (output will be
displayed once the simulation has termianted)
Simulation complete. Reading coda files...
Coda files loaded successfully
Finished running the simulation
Running method test number 1
Running method test number 2
Calling 2 simulations using the parallel method...
All chains have finished
Simulation complete. Reading coda files...
Coda files loaded successfully
Finished running the simulation
Running method test number 3
Calling the simulation...
Simulation complete. Reading coda files...
Coda files loaded successfully
Finished running the simulation
Running method test number 4
Calling the simulation...
Simulation complete. Reading coda files...
Coda files loaded successfully
Finished running the simulation
Running method test number 5
Calling the simulation...
Simulation complete. Reading coda files...
Coda files loaded successfully
Finished running the simulation
Running method test number 6
Calling the simulation...
Simulation complete. Reading coda files...
Coda files loaded successfully
Finished running the simulation
Running method test number 7
Running the simulation using the simple method... (output will be
displayed once the simulation has termianted)
Simulation complete. Reading coda files...
Coda files loaded successfully
Finished running the simulation
Running method test number 8
Calling the simulation...
Waiting for the CODA index files to be created...
Error in runjags.readin(directory = startinfo$directory, silent.jags = silent.jags, :
An unexpected error occured: timed out waiting for the CODA index files to be created. The files available at time out were: data.txt, inits1.txt, inits2.txt, model.txt, out1.Rdump, out2.Rdump, scriptlauncher.sh, sim.1/deviancetable0.txt, sim.1/jagsoutput.txt, sim.1/jagspid.txt, sim.1/pdtable0.txt, sim.1/script.cmd, simchainsinfo.Rsave. Please file a bug report (including this message) to the runjags package author.
Calls: extend.jags -> runjags.readin
Note: Either one or more simulation(s) failed, or there was an error in
processing the results. You may be able to retrieve any successful
simulations using:
results.jags("/tmp/RtmpFRLcRP/runjagsfilesb4aa74b4b8a59",
recover.chains=TRUE)
See the help file for that function for possible options.
To remove failed simulation folders use cleanup.jags() - this will be
run automatically when the runjags package is unloaded
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.2.2-5
Check: PDF version of manual
Result: ERROR
Rd conversion errors:
Converting parsed Rd's to LaTeX .Warning in file(out, "wt") :
cannot open file '/tmp/RtmpkIBlja/ltxc1a735a8cc757/run.jags.tex': No space left on device
Error in file(out, "wt") : cannot open the connection
Flavor: r-devel-linux-x86_64-debian-gcc