pymer4 since version 0.6.0 is only compatible with Python 3. Versions 0.5.0 and lower will work with Python 2, but will not contain any new features.

Using pip


It’s strongly advised to use the conda install method above because of how notoriously finicky it can be to install rpy2 on various platforms. I recommend only following the directions below if you’re comfortable with pip and the command line or prefer not to use Anaconda.


pymer4 requires a working R installation along with three R packages: lme4, lmerTest, and emmeans. Follow either option below to make sure these are installed.

1. If you already have R/RStudio installed

Make sure you also have the 3 required R packages which can be installed from within R/RStudio using:


2. If you don’t have R/RStudio installed

The Anaconda Python distribution can also install and maintain R and R-packages for you. To install R and the the required packages through Anaconda:

conda install -c conda-forge r r-base r-lmertest r-emmeans rpy2

For the latest stable release

After either option you can pip install pymer4

pip install pymer4

For the latest development release

Install via github:

pip install git+

Making sure the install worked

You can test the installation by running the following command in a terminal

python -c "from pymer4.test_install import test_install; test_install()"

Installation Issues

If you have installed via pip it’s recommended you try the conda method described above prior to raising an issue on github. Otherwise the following solutions may help.

Missing R packages

If you follow step 2 in the prerequisites above (i.e. let Anaconda install R for you), some users have reported that the conda install command above sometimes doesn’t install everything you need; for example the matrix package. You can fix this by either installing any missing packages from within R directly by first launching R at a terminal using R, then adding the package with install.packages("Matrix") or by using Anaconda and prepending r- infront of the lowercase name of the package: conda install -c conda-forge r-matrix.

Compiler Issues on macOS

Some of the more cryptic error messages you might encounter on macOS are due to compiler issues that give rpy2 (a package dependency of pymer4) some issues during install. Here’s a fix that should work for that:

  1. Install homebrew if you don’t have it already by running the command at the link (it’s a great pacakage manager for macOS). To check if you already have it, do which brew in your Terminal. If nothing pops up you don’t have it.

  2. Fix brew permissions: sudo chown -R $(whoami) $(brew --prefix)/* (this is necessary on macOS Sierra or higher (>= macOS 10.12))

  3. Update homebrew brew update

  4. Install the xz uitility brew install xz

  5. At this point you can try to re-install pymer4 and re-test the installation. If it still doesn’t work follow the next few steps below

  6. Install an updated compiler: brew install gcc, or if you have homebrew already, brew upgrade gcc

  7. Enable the new compiler for use:

    export CC="$(find `brew info gcc | grep usr | sed 's/(.*//' | awk '{printf $1"/bin"}'` -name 'x86*gcc-?')"
    export CFLAGS="-W"
  8. If the above results in any error output (it should return nothing) you might need to manually find out where the new compiler is installed. To do so use brew info gcc and cd into the directory that begins with /usr in the output of that command. From there cd into bin and look for a file that begins with x86 and ends with gcc-7. It’s possible that the directory ends with gcc-8 or a higher number based on how recently you installed from homebrew. In that case, just use the latest version. Copy the full path to that file and run the following:

    export CC= pathYouCopiedInQuotes
    export CFLAGS="-W"
  9. Finally install rpy2 using the new compiler you just installed: pip install rpy2 if you have R/RStudio or conda install -c conda-forge rpy2 if you don’t.

  10. Now you should be able to pip install pymer4 :)

Kernel Crashes in Jupyter Notebooks/Lab

Sometimes using pymer4 interactively can cause the Python kernel to crash. This is more likely to happen if you have multiple interactive sessions running simulatenously. One way around this is to put this at the top of your notebook/code:

import os

Or set the following environment variable prior to launching your interactive sessions: