Last updated on 2026-11-09 22:54:53 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.2.2-5 | 38.06 | 217.43 | 255.49 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.2.2-5 | 22.71 | 92.80 | 115.51 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.2.2-5 | 24.00 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.2.2-5 | 22.00 | 187.17 | 209.17 | OK | |
| r-devel-windows-x86_64 | 2.2.2-5 | 42.00 | 179.00 | 221.00 | OK | --no-examples --no-tests --no-vignettes |
| r-patched-linux-x86_64 | 2.2.2-5 | OK | ||||
| r-release-linux-x86_64 | 2.2.2-5 | 30.01 | 200.47 | 230.48 | 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 | 51.00 | 92.00 | 143.00 | 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 | 47.00 | 91.00 | 138.00 | OK | --no-examples --no-tests --no-vignettes |
Version: 2.2.2-5
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
distributions/jags/../../jagsversions.h:52:2: warning: #warning "Compiling against a later version of JAGS than has been tested for this version of runjags ... you should probably update the runjags package!" [-Wcpp]
distributions/../jagsversions.h:52:2: warning: #warning "Compiling against a later version of JAGS than has been tested for this version of runjags ... you should probably update the runjags package!" [-Wcpp]
jagsversions.h:52:2: warning: #warning "Compiling against a later version of JAGS than has been tested for this version of runjags ... you should probably update the runjags package!" [-Wcpp]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/runjags.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-16 (Debian 16.2.0-4) 16.2.0’
* used C++ compiler: ‘g++-16 (Debian 16.2.0-4) 16.2.0’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.2.2-5
Check: tests
Result: ERROR
Running ‘check_huiwalter.R’ [1s/1s]
Running ‘checkinputs.R’ [0s/0s]
Running ‘checkmethods.R’ [2s/2s]
Running ‘checkmodule.R’ [0s/1s]
Running ‘checkstudy.R’ [0s/0s]
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/check_huiwalter.R’ failed.
Complete output:
> library("runjags")
> set.seed(2022-03-09)
>
> N <- 600
> status <- rbinom(N, 1, rep(c(0.25,0.5,0.75), each=N/3))
> testdata <- data.frame(Population = rep(1:3, each=N/3), Test1 = rbinom(N, 1, status*0.75 + (1-status)*0.05), Test2 = rbinom(N, 1, status*0.75 + (1-status)*0.05), Test3=rbinom(N, 1, status*0.75 + (1-status)*0.05))
>
> template_huiwalter(testdata, outfile="huiwalter_model.txt", covariance=TRUE, cov_as_cor=TRUE)
The model and data have been written to huiwalter_model.txt in the current working directory
*** NOTE: The template provided should be examined and modified (including checking ***
*** priors, covariance terms, and verifying the code) before running the model! ***
Warning messages:
1: In template_huiwalter(testdata, outfile = "huiwalter_model.txt", :
Setting covariance=TRUE is now deprecated; please specify a data frame of desired covariance terms instead (see ?template_huiwalter)
2: In template_huiwalter(testdata, outfile = "huiwalter_model.txt", :
You have specified a lot of active conditional depdendence terms, which is not recommended; if you really need this many conditional depdendence terms then you should probably use an alternative model formulation
3: In template_huiwalter(testdata, outfile = "huiwalter_model.txt", :
The cov_as_cor option is now deprecated and ignored (i.e. always interpreted as FALSE)
> results <- run.jags("huiwalter_model.txt")
Calling the simulation...
Welcome to JAGS 5.0.1 on Mon Nov 9 20:12:08 2026
JAGS is free software and comes with ABSOLUTELY NO WARRANTY
Loading module: basemod: ok
Loading module: bugs: ok
Loading module: diag: ok
. . Reading data file data.txt
. Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Fully observed stochastic nodes: 30
Unobserved stochastic nodes: 18
Total graph size: 271
. Reading parameter file inits1.txt
. Reading parameter file inits2.txt
. Initializing model
Error in node Tally_RRR[1:8,1]
Node inconsistent with parents
Deleting model
. Adaptation skipped: model is not in adaptive mode.
. Updating 4000
-------------------------------------------------| 4000
Can't update. No model!
Deleting model
. Can't set monitor. No model!
. Can't set monitor. No model!
. Can't set monitor. No model!
. Can't set monitor. No model!
. Can't set monitor. No model!
. Can't set monitor. No model!
. Can't set monitor. No model!
. Can't set monitor. No model!
. Can't set monitor. No model!
. Can't set monitor. No model!
. Can't set monitor. No model!
. Can't set monitor. No model!
. Can't set monitor. No model!
. Can't set monitor. No model!
. Can't set monitor. No model!
. Can't set monitor. No model!
. Updating 10000
-------------------------------------------------| 10000
Can't update. No model!
Deleting model
. No model
. No model
. Can't dump CODA output. No model!
. Can't dump samplers. No model!
. Updating 0
Can't update. No model!
Deleting model
. Deleting model
. Exiting JAGS
Note: the model did not require adaptation
Error in runjags.readin(directory = startinfo$directory, silent.jags = silent.jags, :
The simulation appears to have crashed - check the model output in failed.jags() for clues
Calls: run.jags -> extend.jags -> runjags.readin
In addition: Warning messages:
1: In structure(c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, :
Replacing special names '.Dim' is deprecated; use 'dim' instead.
2: In structure(c(135, 6, 5, 8, 8, 5, 13, 20, 97, 14, 11, 13, 11, 12, :
Replacing special names '.Dim' is deprecated; use 'dim' instead.
3: In structure(c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, :
Replacing special names '.Dim' is deprecated; use 'dim' instead.
4: In structure(c(135, 6, 5, 8, 8, 5, 13, 20, 97, 14, 11, 13, 11, 12, :
Replacing special names '.Dim' is deprecated; use 'dim' instead.
Note: Either one or more simulation(s) failed, or there was an error in
processing the results. You may be able to retrieve any successful
simulations using:
results.jags("/home/hornik/tmp/scratch/RtmpAZWXtc/runjagsfilesafb05614c29c1",
recover.chains=TRUE)
See the help file for that function for possible options.
To remove failed simulation folders use cleanup.jags() - this will be
run automatically when the runjags package is unloaded
Execution halted
Running the tests in ‘tests/checkmodule.R’ failed.
Complete output:
> library("runjags")
> runjags.options(nodata.warning=FALSE)
>
> # Checks that the runjags module distributions are correct.
>
> # Loading the dynlib requires rjags for Windows:
> if(.Platform$OS.type != 'windows' || requireNamespace('rjags')){
+
+ loaded <- runjags:::dynloadmodule()
+ if(!loaded)
+ stop("The internal JAGS dynlib could not be loaded - if you installed this package from CRAN, please file a bug report to the package author")
+
+ cat('Running module tests\n')
+
+ # Required for nchain etc:
+ library("coda")
+
+ load("moduletargets.Rsave")
+
+ checksok <- rep(TRUE, N)
+ for(i in 1:N){
+ success <- try({
+ obs <- runjags:::userunjagsmodule(tests[[i]]$distribution, tests[[i]]$funtype, tests[[i]]$parameters, tests[[i]]$x, tests[[i]]$uselog, tests[[i]]$lower)
+ expect <- results[[i]]
+
+ # Allow a bit of a larger tolerance than usual as we have saved the results from a different machine:
+ problem <- abs(expect-obs) > max(10^-5, .Machine$double.eps^0.5)
+
+ # Or obs is NA:
+ problem[is.na(problem)] <- TRUE
+ if(any(problem)){
+ cat("Error with check number ", i, " (which expected observed): ", paste(paste(which(problem), " ", expect[problem], " ", obs[problem], "; ", sep=""), collapse=""), "\n", sep="")
+ checksok[i] <- FALSE
+ }
+ })
+ if(inherits(success, 'try-error')){
+ checksok[i] <- FALSE
+ cat("Uncaught crash error with check number", i, "\n")
+ }
+ }
+
+ if(!all(checksok)) stop(paste("The runjags module checks failed for test number(s) ", paste(which(!checksok),collapse=","), sep=""))
+
+ # From: Gelman, A. (2006). Prior distributions for variance parameters in hierarchical models. Bayesian Analysis, (3), 515–533.
+ # ... the half cauchy should be the same as a ratio of two gammas:
+ scale <- seq(1,100,length.out=10)
+ quantiles <- seq(0.05,0.95,length.out=10)
+ checksok <- rep(TRUE, 10)
+ set.seed(1)
+
+ for(i in 1:10){
+ success <- try({
+
+ xi <- rnorm(10^6, 0, sd=scale[i])
+ tau <- rgamma(10^6, shape=0.5, rate=0.5) # Chi-squared with 1 df - i.e.= rchisq(10^6, 1)
+ gelman <- abs(xi)/sqrt(tau)
+ expect <- quantile(gelman,quantiles)
+ obs <- runjags:::userunjagsmodule('halfcauchy', 'q', scale[i], quantiles, FALSE, TRUE)
+ # Allow a fairly large 5% tolerance as this is a numerical approximation:
+ problem <- (abs(expect-obs)/expect) > 0.05
+
+ # Or obs is NA:
+ problem[is.na(problem)] <- TRUE
+ if(any(problem)){
+ cat("Error with Half Cauchy check number ", i, " - scale=", scale[i], " - (which expected observed): ", paste(paste(which(problem), " ", expect[problem], " ", obs[problem], "; ", sep=""), collapse=""), "\n", sep="")
+ checksok[i] <- FALSE
+ }
+ })
+ if(inherits(success, 'try-error')){
+ checksok[i] <- FALSE
+ cat("Uncaught crash error with Half Cauchy check number", i, "\n")
+ }
+ }
+ if(!all(checksok)) stop(paste("The runjags module Half Cauchy checks failed for test number(s) ", paste(which(!checksok),collapse=","), sep=""))
+
+ cat("The internal module tests were passed\n")
+ }else{
+ cat("The internal module tests were skipped (not available on Windows)\n")
+ }
Error in !loaded : invalid argument type
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.2.2-5
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘quickjags.Rmd’ using knitr
Warning: The chunk 'unnamed-chunk-8' opened new graphics device(s) (e.g., via dev.new()), from which knitr cannot capture plots. Please remove the code that opens new devices such as dev.new().
Quitting from quickjags.Rmd:167-170 [unnamed-chunk-14]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error: JAGS reported syntax errors in the command script: please send the above error message to the package mainainter
---
Backtrace:
▆
1. └─runjags::run.jags(model)
2. └─runjags::extend.jags(...)
3. └─runjags:::runjags.readin(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'quickjags.Rmd' failed with diagnostics:
Error: JAGS reported syntax errors in the command script: please send the above error message to the package mainainter
--- failed re-building ‘quickjags.Rmd’
--- re-building ‘UserGuide.Rtex’ using Sweave
--- finished re-building ‘UserGuide.Rtex’
SUMMARY: processing the following file failed:
‘quickjags.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc