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This is my first time posting, so I'm sorry for any mistakes in formating or exposing the problem. I am also a Linux beginner.

I am trying to run a bioinformatics program called Caver Analyst. Whenever I call it on the terminal, I get the following output:

dgesto@jarvis ~: caver_analyst

Jul 24, 2019 5:24:39 PM cz.caver.Main main
INFO: Using default userdir: /home/dgesto/.caver_analyst/2.0b2
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.netbeans.ProxyURLStreamHandlerFactory (file:/usr/local/lib/caver_analyst2/platform/lib/boot.jar) to field java.net.URL.handler
WARNING: Please consider reporting this to the maintainers of org.netbeans.ProxyURLStreamHandlerFactory
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
Inconsistency detected by ld.so: dl-lookup.c: 111: check_match: Assertion `version->filename == NULL || ! _dl_name_match_p (version->filename, map)' failed!

I'm running Linux Mint 19.1 (Tessa) with OpenJDK version 11.0.3. I thought it might have somethig to do with java, and tried downgrading to version 8 with no luck.

If you need anymore information about my system please let me know.

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  • Hi, not sure this will be of help, but here's a related Launchpad bug report with the same problem with another Java app. – undercat applauds Monica Jul 25 '19 at 9:57
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Solved it, it really was a problem with some java update. I purged OpenJDK 11 following these instructions and installed OpenJDK 8. It seems to be working fine now.

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I don't want to purge OpenJDK from my box, so you can download Oracle JDK 8 from Oracle and run the following command:

$ PATH=<oracle_jdk_path>/bin:$PATH JDK_HOME=<oracle_jdk_path> ./caver_analyst

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