Troubleshooting JAGS on Windows XP with Rrunjags

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In this article, we’ll explore an issue with runjags version 2.0.3-2 on Windows XP where it’s unable to locate the JAGS binary due to the lack of the 'where' system command in older versions of Windows.

Background and Context

JAGS (Just Another Gibbs Sampler) is a software package for Bayesian inference that uses Markov chain Monte Carlo methods. The runjags R package provides an interface to JAGS, allowing users to perform Bayesian analysis in R. In this article, we’ll focus on troubleshooting an issue with finding the JAGS binary on Windows XP.

The Problem

After updating to version 2.0.3-2 of runjags, users have reported encountering an error when trying to locate the JAGS binary:

Error in system("where jags", intern = TRUE) : 'where' not found

This issue arises because the 'where' system command was introduced in Windows 2003 and is no longer available in older versions like Windows XP.

Solution

To resolve this issue, we can modify the findjags() function to detect earlier versions of Windows and revert to a different method of finding JAGS. The modified code will be included below.

R Code

# runjags.R

# Modified findjags() function to support older versions of Windows
findjags <- function() {
  # Check for Windows XP
  if (Sys.version() == "MS-DOS") {
    # Use the 'where' command in a compatible way
    jags_path <- dir.path("C:/Program Files/JAGS", "JAGS-4.2.0/i386/bin")
    if (!is.null(jags_path)) {
      return(list(path = jags_path))
    }
  } else if (Sys.version() == "Windows XP") {
    # Fall back to the original method
    runjags.options <- getOption("runjags.options", list())
    if (length(runjags.options$jagspath) > 0) {
      return(list(path = runjags.options$jagspath))
    }
  } else {
    # Use the default location
    jags_path <- dir.path("C:/Program Files/JAGS", "JAGS-4.2.0/i386/bin")
    if (!is.null(jags_path)) {
      return(list(path = jags_path))
    }
  }
}

# Add the modified findjags() function to the R package
options(R_runjags_options_findjags <- findjags)

This code checks for Windows XP and falls back to a different method of finding JAGS if it’s not available. It also includes a fallback location using the runjags.options option.

Setting up the Rprofile

To use this modified function, you need to set the jagspath option in your R profile:

# runjags.Rprofile

# Set the jagspath option
.runjags.options <- list(jagspath = "C:/Program Files/JAGS/JAGS-4.2.0/i386/bin/jags-terminal.exe")

This sets the jagspath option to point to the JAGS binary.

Calling runjags

To call runjags, you can use the modified function:

# Load the runjags package
require(runjags)

# Call runjags with the modified findjags() function
runjags.getOption("findjags")

This should resolve the issue and allow you to use JAGS with runjags.

Troubleshooting Tips

Make sure that the JAGS binary is installed in the correct location (C:/Program Files/JAGS/JAGS-4.2.0/i386/bin).
Ensure that the runjags.options option is set correctly in your R profile.
If you’re using an older version of Windows, try updating to a newer version or using a different environment.

Conclusion

In this article, we’ve explored an issue with finding JAGS on Windows XP using runjags. We’ve modified the findjags() function to support older versions of Windows and provided guidance on setting up the R profile and calling runjags. By following these steps, you should be able to resolve the issue and use JAGS with runjags on Windows XP.

Last modified on 2025-04-04