Update MacOS to Catalina or Mojave for least problems with Stan-based software?

I’m getting ready to update my MacOS operating system from Sierra 10.12.6 to either Catalina or Mojave. As of right now (November 2020), which update should I expect to give me fewer problems with the Stan family of programs? I’m mainly using Stan through 1) rstanarm, 2) rethinking package, and 3) brms package. Is there even a difference now, meaning have pretty much all of the OS-related issues been seen and solved for these two OSs? I’m considering these two as my options because I’m not nearly adventurous enough to try Big Sur! Hardware is MacBook Pro (15-inch, 2017). Thanks.

I would suggest Catalina instead of Mojave. I’ve been using Catalina for a while now and all of the packages you mentioned work fine. When Catalina first came out there were issues and it was easier to get RStan (which you need for the packages you listed) to work with Mojave, but now the issues with Catalina have either been fixed or we have workarounds, and I think it’s now harder to get things working with the older Mojave (not impossible but not as straightforward).

I’m confident that if you upgrade to Catalina (and the latest version of R) either things will work easily or we’ll be able to help you get it working.

2 Likes

Both cmdstanr and rstan work well (also installation is smooth) for Catalina 10.15.7 from my experience.

4 Likes

Excellent. Thank you, I’ll upgrade to Catalina. Side note: I’ve been watching your sessions on Basics from StanCon 2018 yesterday and today. Good stuff.

2 Likes

Hmm. This page https://github.com/stan-dev/rstan/wiki/Installing-RStan-from-source-on-a-Mac says:

We recommend using the macOS R toolchain installer for pre-Catalina versions of the operating system, in which case you can then install the binary version of the RStan package. If you have Catalina , then you need to open it by pressing CTRL+right-click and then clicking Open in order to bypass the security settings that took effect on Macs with Catalina on January 1, 2020.

The way I read that paragraph is that to install on Catalina I need to CTRL+right-click on something, but what is this something? What is the ‘it’ that I need to open? The first sentence says to use the macOS R toolchain installer for pre-Catalina OSs, but doesn’t say what to use for Catalina. The way that paragraph is written specifically excludes the macOS R toolchain installer from being the thing to install, but I don’t see another option, thus my confusion. Thanks.

Hi MichiganWater,

I see the link is installing rstan from sources. Is this your aim? If you just want to install rstan on Mac, maybe you can directly follow this link https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started ? By running

remove.packages("rstan")
if (file.exists(".RData")) file.remove(".RData")
## Then, restart R. (<<---- I didn't restart R....)
install.packages("rstan", repos = "https://cloud.r-project.org/", dependencies = TRUE)

Thanks, songpeng. That’s the link I start with, but that RStan-Getting-Started page says this, before those commands you quote:

“Prior to installing RStan, you need to configure your R installation to be able to compile C++ code. Follow the link below for your respective operating system for more instructions:”

which then has a link to this page:

Mac - Configuring C++ Toolchain

And that page is the page where I’m confused about what to do. I can’t run the commands you quote until I’ve correctly followed the procedures to install the Toolchain. That’s where I’m stuck.

@bgoodri Can you clarify this and update the RStan pages as necessary? I understand @MichiganWater’s confusion here. The link on the Getting Started page for Mac - Configuring C++ Toolchain takes you to a page that says “Installing RStan from source on a Mac”, but I don’t think it’s just for installing from source, right? That title seems wrong, or am I wrong?

Then, on that page it also says the following, which seems to contradict itself:

We recommend using the macOS R toolchain installer for pre-Catalina versions of the operating system, in which case you can then install the binary version of the RStan package. If you have Catalina, then you need to open it by pressing CTRL+right-click …

This seems to say to only use the R toolchain installer for pre-Catalina but then the next sentence talks about opening it in Catalina. So I’m not sure what it’s intending to say. It also seems to imply that you can’t install the binary on Catalina, but I don’t think that’s true either. So these instructions are pretty confusing at the moment.