diff --git a/doc/Install.md b/doc/Install.md index 6b1b8e12..d2f99d14 100644 --- a/doc/Install.md +++ b/doc/Install.md @@ -22,14 +22,15 @@ environments. 2. Install PyImageJ into a new environment: ``` - mamba create -n pyimagej pyimagej openjdk=8 + mamba create -n pyimagej pyimagej openjdk=11 ``` - This command will install PyImageJ with OpenJDK 8. If you would rather use - OpenJDK 11, you can write `openjdk=11` instead, or even just leave off the - `openjdk` part altogether to get the latest version of OpenJDK. PyImageJ - has been tested most thoroughly with OpenJDK 8, but it is also known to - work with OpenJDK 11, and likely later OpenJDK versions as well. + This command will install PyImageJ with OpenJDK 11. PyImageJ requires a + minimum of OpenJDK 8. PyImageJ has been tested most thoroughly with OpenJDKs + 8 and 11, but it is likely to work with later OpenJDK versions as well. + + *Please note that openjdk=8 from conda-forge is broken on M1 Mac.* + If you are using an M1 Mac, you should use openjdk=11 or newer. 3. Whenever you want to use PyImageJ, activate its environment: ``` @@ -83,7 +84,7 @@ It is possible to dynamically install PyImageJ from within a Jupyter notebook. For your first cell, write: ``` import sys, os -!mamba install --yes --prefix {sys.prefix} pyimagej openjdk=8 +!mamba install --yes --prefix {sys.prefix} pyimagej openjdk=11 os.environ['JAVA_HOME'] = os.sep.join(sys.executable.split(os.sep)[:-2] + ['jre']) ``` @@ -119,7 +120,7 @@ on Google Colab with a wrapped local Fiji installation: 3. Install PyImageJ: ```python - !mamba install pyimagej openjdk=8 + !mamba install pyimagej openjdk=11 ``` You can also install other deps here as well (scikit-image, opencv, etc). @@ -166,7 +167,7 @@ RUN apt-get install -y wget unzip > /dev/null && rm -rf /var/lib/apt/lists/* > / RUN micromamba install -y -n base -c conda-forge \ python=3.8\ pyimagej \ - openjdk=8 && \ + openjdk=11 && \ micromamba clean --all --yes ENV JAVA_HOME="/usr/local" # Set MAMVA_DOCKERFILE_ACTIVATE (otherwise python will not be found) diff --git a/doc/Troubleshooting.md b/doc/Troubleshooting.md index 5639f7ea..095c1f93 100644 --- a/doc/Troubleshooting.md +++ b/doc/Troubleshooting.md @@ -145,6 +145,17 @@ This indicates the Maven executable wasn't found on your system. If you installed `maven` via conda/mamba on Windows, you may have gotten a version that was [briefly broken](https://github.com/conda-forge/maven-feedstock/issues/26). You should be able to simply update with `conda update -n pyimagej maven` (adjusted if you named your environment something other than `pyimagej`). +### Command died with Signals.SIGKILL: 9 + +If you see an error like: +``` +subprocess.CalledProcessError: Command '['.../jre/bin/java', '-version']' died with . +``` +it might be that you are using an M1 Mac, and have OpenJDK 8 installed from conda-forge? +Unfortunately, Version 8 of OpenJDK from conda-forge is known to be broken on Mac M1 machines. + +Try `mamba install openjdk=11` to update to version 11, and this problem should go away. + ### Error in "mvn.CMD -B -f pom.xml" dependency:resolve: 1 This indicates a problem running Maven on your system.