Matt Denwood

A small change in compilation speed between JAGS 4.2.0 and 4.3.2 could be expected due to the changes to the way in which JAGS reads the model definition, as described at https://martynplummer.wordpress.com/2016/09/14/you-can-always-make-it-faster/#more-822 However, you say "much faster", which implies a more dramatic difference. Can you provide a minimal reproducible example of a model that compiles much more quickly using JAGS 4.2.0 (preferably also including details of the timings under both versions,...

Yes, we have JAGS installed on our (red hat enterprise) cluster, and I know of several others that have also done this, so it is very possible. Although obviously it depends on which precise distribution (and version) of Linux you are using (there are dozens, each of which would need a different binary) - so we would need further details to help. But in any case, linux software is usually managed via the package management environment for the relevant distribution (yum, apt-get and friends), so I...

Hi Thomas The good news is that your JAGS/Matlab/matjags installation seems to be working perfectly: up to the RUNTIME ERROR the output shown is completely normal. The runtime error given by JAGS ("Index out of range taking subset of counts") indicates that there is something wrong with the model specified (or perhaps data specified). I guess these are generated automatically by the HMeta-d toolbox (?), in which case that would be something you would have to bring up with the toolbox authors. Hope...

JAGS is a standalone application that is designed to interface with R - so we can help with standalone installation of JAGS and installation of the R packages rjags and runjags. On macOS, the easiest way to install JAGS is via the provided .pkg (signed) binary installers, which you can find from this page: https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Mac%20OS%20X/ After downloading the most recent version (JAGS-4.3.2.pkg at the time of writing), you should just double click it and follow...

The load.module function (in rjags) uses .Platform$dynlib.ext to determine the extension for the basemod file - using the official macOS binaries of R this is .so but if you have a version of R compiled a different way (perhaps with -DBUILD_SHARED_LIBS=ON or similar) then you could end up with .dylib instead, which would not match what is assumed by the official macOS binaries of JAGS (which assume you are using the official macOS binaries of R). You might be able to get away with simply renaming...

For future readers: please use https://sourceforge.net/p/mcmc-jags/discussion/610037/thread/115edca29d/ for installation problems of JAGS on macOS, rather than this (rather old and cross-platform) thread on rjags.

Hi Javier Unless you really want to compile from source (e.g. because you have also compiled R from source), then I would recommend using the official JAGS 4.3.1 installer from https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Mac%20OS%20X/ (this is binary compatible with the official version of R 4.2.2). Otherwise you can have a look at the R42_compile_script.sh file at https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Mac%20OS%20X/extras/ which gives full details of how to compile...

I can confirm that T(,) behaves (in general) as expected on Apple silicon (and the official binary passed the test suite before being released). But if you can share a reproducible example I can run it on the same hardware to double check your use case.