Updated 2018-07-16: The compatibility issues with R 3.3 and JAGS
4.2 do not affect current versions.|
've previously posted on compatibility issues encountered when
installing R and JAGS on
Ubuntu , but
Windows seemed immune to these problems ... until now!
issue arises because current R versions, 3.3.0 or later, are not
compatible with the current default installer for JAGS. Note
that the problem is with the Windows installer, not JAGS
source code, and doesn't affect other platforms. A compatible
installer is available, but it's not the default. See
Martyn Plummer's post for more details.
Download and install
R statistical software from the CRAN web site.
If you already have JAGS 4.2.0 installed, it's a good idea to
uninstall the old JAGS 4.2.0 using Control Panel > Programs and
features (Windows 7) or Settings > System > Apps & features
(Windows 8, 10) and delete the old JAGS 4.2.0 folder in Program
Files before installing the new binaries.
Download and run the new installer, " JAGS-4.2.0-Rtools33.exe ".
This is not the default on Sourceforge, so make sure you get the
right file - you may have to search a bit. The default
installer, "JAGS-4.2.0.exe", is not compatible with R
3.3.0 or later.
the JAGS page at Sourceforge and click on the Download
Latest Version button. The latest version (as at 16 July 2018)
After installing R and JAGS, install
opening R and typing
Boxes may pop up asking about personal libraries: click Yes. You
will need to select a mirror web site near you, or choose
0-cloud, which is a world-wide network.
Once installed, check that it works by running
You should see a message telling you that
has linked to JAGS 4.3.0.
Starting with R version 3.3.0, a newer compiler is used to
create the code actually used by the Windows operating system,
the "binaries", the files you get when you download and run
"R-3.3.x-win.exe". Specifically it uses the gcc 4.9.3 compiler
for C and C++ code instead of gcc 4.6.3. Some packages contain C
or C++ code, and they need to be compiled with the same compiler
that was used for R. For packages on CRAN, this is taken care of
automatically: when you run
update.packages(), you get the package binaries
that match your R version.
This applies to the
rjags package too, it has to
match the R version. But it also has to match with JAGS. JAGS
source code is also in C++, and running the "JAGS-4.2.0.exe"
installer gives you binaries from the old compiler.
Binaries created with the new compiler are in
If you are just using JAGS from the command line, not from R,
none of this matters. I have actually (inadvertently!) thoroughly tested R 3.3.0
with the old JAGS binaries on 64-bit installations and had no
problems. But when I installed R 3.3.0 on a 32-bit machine
together with the old JAGS binaries, calling
caused R to crash: "R for Windows GUI front-end has stopped