PathVisio / pathvisio

PathVisio - pathway editor, visualization and analysis software
http://www.pathvisio.org
Apache License 2.0
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PathVisio failing to install on Mac #155

Closed ghost closed 4 years ago

ghost commented 4 years ago

Dear all,

I am facing a problem in installing the jar file on my MacBook Pro. it gives an error as follows: y

Can you please help me with this? Thanks in advance!

mkutmon commented 4 years ago

Can you check which Java version you have?

ghost commented 4 years ago

it is java version "14" 2020-03-17.

mkutmon commented 4 years ago

PathVisio currently only works with Java 8. We are working on upgrading the Java version but the current release still requires Java 8

ghost commented 4 years ago

thanks for the information! Please update when you upgrade the java version as working with older versions of java is primarily not advised.

oolonek commented 2 years ago

Pasting here in case it can help someone.

Had Java 17 on macOS so pathvisio complained :

➜  pathvisio-3.3.0 sh pathvisio.sh
Problem creating boot delegation class loader: java.lang.reflect.InaccessibleObjectException: Unable to make protected java.security.SecureClassLoader(java.lang.ClassLoader) accessible: module java.base does not "opens java.security" to unnamed module @49b70bc7
Installing bundles that are embedded in the jar.
Detected embedded bundle: org.apache.batik.svggen_1.7.0.v201011041433.jar
Loading jar:file:/Applications/pathvisio-3.3.0/pathvisio.jar!/org.apache.batik.svggen_1.7.0.v201011041433.jar

Followed these instructions https://medium.com/@brunofrascino/working-with-multiple-java-versions-in-macos-9a9c4f15615a to get jenv installed. Didn't know about this utility which conveniently helps to choose the java version you which to set for a given folder.

You might need to echo eval "$(jenv init -)" >> /Users/username/.zshrc at one point if jenv complains. Alternatively run jenv doctor to be sure.

Then you can navigate to your pathvisio folder and run jenv local 1.8.0.292 (or the java8 version you have)

Like this you can have both java8 and more recent version cohabiting on your computer and linked to different folders.

AlexanderPico commented 2 years ago

Update on linked instructions at medium.com: