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drivenbyentropy / aptasuite

A full-featured bioinformatics software collection for the comprehensive analysis of aptamers in HT-SELEX experiments.
https://drivenbyentropy.github.io/
GNU General Public License v3.0
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Issue in running the AptaSuite program #80

Closed psomdeb25 closed 4 years ago

psomdeb25 commented 4 years ago

Hello. I downloaded the pre-compiled version and extracted it using the tar command. After which I tried running using: java -jar aptasuite-0.9.4.jar. However, I am presented with errors which I wasn't really able to understand.

This is error that shows up on first running the program:

Exception in thread "main" java.lang.NoClassDefFoundError: javafx/application/Application at java.base/java.lang.ClassLoader.defineClass1(Native Method) at java.base/java.lang.ClassLoader.defineClass(ClassLoader.java:1016) at java.base/java.security.SecureClassLoader.defineClass(SecureClassLoader.java:174) at java.base/jdk.internal.loader.BuiltinClassLoader.defineClass(BuiltinClassLoader.java:802) at java.base/jdk.internal.loader.BuiltinClassLoader.findClassOnClassPathOrNull(BuiltinClassLoader.java:700) at java.base/jdk.internal.loader.BuiltinClassLoader.loadClassOrNull(BuiltinClassLoader.java:623) at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:581) at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178) at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521) at aptasuite.Aptasuite.main(Aptasuite.java:89) Caused by: java.lang.ClassNotFoundException: javafx.application.Application at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:583) at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178) at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521) ... 10 more

So, I ran with verbose (-v) flag and this shows up: Unrecognized option: -v Error: Could not create the Java Virtual Machine. Error: A fatal exception has occurred. Program will exit.

Is there any missing dependencies?

psomdeb25 commented 4 years ago

I forgot to mention that I am running macOS v 10.14.6

Bioanalytica commented 4 years ago

Are you sure that you are running the correct version of Java and that it was installed correctly (is written into PATH)? I'm using Version 8.0.202.8

psomdeb25 commented 4 years ago

@Bioanalytica This is the java version that I am running - java 11.0.1 2018-10-16 LTS Java(TM) SE Runtime Environment 18.9 (build 11.0.1+13-LTS)

But it came built into my OS.

Edit: I installed the latest LTS version of Java (as shown below) but I still get the same error: java 11.0.6 2020-01-14 LTS Java(TM) SE Runtime Environment 18.9 (build 11.0.6+8-LTS)

drivenbyentropy commented 4 years ago

The error suggests that JavaFX is not present on your system. I do not have a Mac available but I suspect JavaFX does not ship with the Java version installed on your computer.

You could start here and check the installation instructions specific to your environment.

drivenbyentropy commented 4 years ago

I am closing this issue due to inactivity. Feel free to reopen should the problem persist.