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steineggerlab / ufcg

UFCG: Universal Fungal Core Genes
https://ufcg.steineggerlab.com
GNU General Public License v3.0
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Could not initialize class envs.config.GenericConfig #15

Open jungleblack007 opened 1 year ago

jungleblack007 commented 1 year ago

I have intalled ufcg on WSL, however, when I used the same way (mamba install -y ufcg) to install it on ubuntu 22.04.2 LTS, it got wroing. ufcg -u Exception in thread "main" java.lang.NoClassDefFoundError: Could not initialize class envs.config.GenericConfig at envs.toolkit.Prompt.print(Prompt.java:31) at pipeline.UFCGMainPipeline.main(UFCGMainPipeline.java:289) I checked my java is openjdk-17-jdk, how can I process it?

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endixk commented 1 year ago

Hi, I tried to reproduce your error in both conda and docker environment, but both worked fine from my side.

Could you please try to create a clean conda environment and install the package again to see if the issue persists?

JuliaPlewka commented 11 months ago

Hi, I have the same error, also on Ubuntu systems, after installing it with mamba in clean conda envs. Do you have any solution?

endixk commented 11 months ago

Hey @JuliaPlewka, could you please run java --version and which java on the system from which you encountered the error? I suspect this occurs in specific version(s) of JDK/JRE.

Muzixibeijin commented 4 months ago

Hi, I have the same error,

java -version openjdk version "21.0.2-internal" 2024-01-16 OpenJDK Runtime Environment (build 21.0.2-internal-adhoc.conda.src) OpenJDK 64-Bit Server VM (build 21.0.2-internal-adhoc.conda.src, mixed mode, sharing)

which java /home/zmz/miniconda3/envs/ufcg_env/bin/java @endixk Do you have any solution?

endixk commented 4 months ago

@Muzixibeijin I recommend you to compile the program from source instead of using conda, as described in https://github.com/steineggerlab/ufcg?tab=readme-ov-file#build-from-source.

Alternatively, you can install older versions of JDK (8 or 11), which should work consistently.

I suppose the pre-compiled JAR included in the conda package raises such exceptions in some environments. I will try to make it consistent in the later versions.