Unexpected error: 'void sun.misc.Unsafe.registerNatives()' with IGV_Linux_2.19.5

[qyGitHub]

igv0.log

[jrobinso]

I have no idea what that means.

[qyGitHub]

Sorry. I downloaded IGV_Linux_2.19.5, started with igv.sh. This unexpected error popped up when IGV opened. My Linux is Ubuntu 22.04.4 LTS.

[qyGitHub]

Here is the error report,
INFO [Jul 28,2025 12:15] [Main] Startup IGV Version 2.19.5 07/09/2025 01:47 PM
INFO [Jul 28,2025 12:15] [Main] Java 21.0.4 (build 21.0.4+7-LTS) 2024-07-16
INFO [Jul 28,2025 12:15] [Main] Java Vendor: Eclipse Adoptium https://adoptium.net/
INFO [Jul 28,2025 12:15] [Main] JVM: OpenJDK 64-Bit Server VM Temurin-21.0.4+7
INFO [Jul 28,2025 12:15] [Main] OS: Linux 5.15.0-134-generic amd64
INFO [Jul 28,2025 12:15] [Main] IGV Directory: /net/wei/vol1/home/qyi/igv
INFO [Jul 28,2025 12:15] [OAuthUtils] Loading Google oAuth properties
INFO [Jul 28,2025 12:15] [CommandListener] Listening on port 60151
INFO [Jul 28,2025 12:15] [GenomeManager] Loading genome: https://raw.githubusercontent.com/igvteam/igv-genomes/refs/heads/main/json/hg38.json
SEVERE [Jul 28,2025 12:30] [LongRunningTask] Exception running task
SEVERE [Jul 28,2025 12:30] [LongRunningTask] java.lang.UnsatisfiedLinkError: 'void sun.misc.Unsafe.registerNatives()'
at sun.misc.Unsafe.registerNatives(Native Method)
at sun.misc.Unsafe.(Unsafe.java:28)
at java.base/java.lang.Class.forName0(Native Method)
at java.base/java.lang.Class.forName(Unknown Source)
at java.base/java.lang.Class.forName(Unknown Source)
at com.google.gson@2.8.9/com.google.gson.internal.reflect.UnsafeReflectionAccessor.getUnsafeInstance(UnsafeReflectionAccessor.java:70)
at com.google.gson@2.8.9/com.google.gson.internal.reflect.UnsafeReflectionAccessor.(UnsafeReflectionAccessor.java:34)
at com.google.gson@2.8.9/com.google.gson.internal.reflect.ReflectionAccessor.(ReflectionAccessor.java:36)
at com.google.gson@2.8.9/com.google.gson.internal.ConstructorConstructor.(ConstructorConstructor.java:51)
at com.google.gson@2.8.9/com.google.gson.Gson.(Gson.java:209)
at com.google.gson@2.8.9/com.google.gson.Gson.(Gson.java:188)
at org.igv/org.broad.igv.feature.genome.load.GenomeConfig.fixChromosomeOrder(GenomeConfig.java:320)
at org.igv/org.broad.igv.feature.genome.load.GenomeConfig.fromJson(GenomeConfig.java:67)
at org.igv/org.broad.igv.feature.genome.load.JsonGenomeLoader.loadGenomeConfig(JsonGenomeLoader.java:69)
at org.igv/org.broad.igv.feature.genome.load.JsonGenomeLoader.loadGenome(JsonGenomeLoader.java:40)
at org.igv/org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:169)
at org.igv/org.broad.igv.feature.genome.GenomeManager.loadGenomeById(GenomeManager.java:142)
at org.igv/org.broad.igv.ui.IGV$StartupRunnable.run(IGV.java:1981)
at org.igv/org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:73)
at org.igv/org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:43)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)

[jrobinso]

I can't reproduce the error with Ubuntu 14.04. Try installing Java 21 independently, then using the "All platforms" bundle. This sometimes resolves errors on Linux.