dennishendriksen opened a new issue, #2635:
URL: https://github.com/apache/fory/issues/2635
### Question
I'm struggling with an error using my graalvm 25 native image with fory
v0.12.2.
any thoughts on how to debug this issue?
```
error: Failed to deserialize input
org.apache.fory.exception.DeserializationException: Failed to deserialize
input
at
org.apache.fory.util.ExceptionUtils.handleReadFailed(ExceptionUtils.java:66)
at org.apache.fory.Fory.deserializeJavaObject(Fory.java:1226)
<cut>
at
java.base@25/java.lang.invoke.LambdaForm$DMH/sa346b79c.invokeStaticInit(LambdaForm$DMH)
Caused by: java.lang.RuntimeException: java.lang.NoSuchMethodException:
org.molgenis.vipannotate.annotation.SequenceVariantAnnotationIndexBig.<init>([Ljava.math.BigInteger;)
at
org.apache.fory.util.record.RecordUtils$3.computeValue(RecordUtils.java:142)
at
org.apache.fory.util.record.RecordUtils$3.computeValue(RecordUtils.java:129)
at
java.base@25/java.lang.ClassValue.get(JavaLangSubstitutions.java:542)
at
org.apache.fory.util.record.RecordUtils.getRecordConstructor(RecordUtils.java:198)
<cut>
at
org.apache.fory.serializer.Serializers.newSerializer(Serializers.java:101)
at
org.apache.fory.resolver.ClassResolver.createSerializer(ClassResolver.java:1402)
at
org.apache.fory.resolver.ClassResolver.getClassInfo(ClassResolver.java:1276)
at org.apache.fory.Fory.deserializeJavaObject(Fory.java:1218)
... 9 more
Caused by: java.lang.NoSuchMethodException:
org.molgenis.vipannotate.annotation.SequenceVariantAnnotationIndexBig.<init>([Ljava.math.BigInteger;)
at
java.base@25/java.lang.Class.checkConstructor(DynamicHub.java:1356)
at java.base@25/java.lang.Class.getConstructor0(DynamicHub.java:1565)
at
java.base@25/java.lang.Class.getDeclaredConstructor(DynamicHub.java:2491)
at
org.apache.fory.util.record.RecordUtils$3.computeValue(RecordUtils.java:140)
... 33 more
class in question:
public record SequenceVariantAnnotationIndexBig(BigInteger[]
encodedVariants) {
public @Nullable IndexRange findIndex(SequenceVariant variant) {
BigInteger encodedVariant = SequenceVariantEncoder.encodeBig(variant);
return IndexRangeFinder.findIndexes(encodedVariants, encodedVariant);
}
}
```
I've followed https://fory.apache.org/docs/guide/graalvm_guide/ (not
thread-safe Fory):
```
public class ForyFactory {
private static final Fory fory;
static {
fory =
Fory.builder().withLanguage(Language.JAVA).requireClassRegistration(true).registerGuavaTypes(false).build();
fory.registerSerializer(SortedIntArrayWrapper.class,
SortedIntArrayWrapperSerializer.class);
fory.register(SequenceVariantAnnotationIndexSmall.class, true);
fory.register(SequenceVariantAnnotationIndexBig.class, true);
fory.register(SequenceVariantAnnotationIndex.class, true);
fory.ensureSerializersCompiled();
}
private ForyFactory() {}
public static Fory createFory() {
return fory;
}
}
```
native-image.properties:
```
$ cat
src/main/resources/META-INF/native-image/org.molgenis/vip-annotate/native-image.properties
Args=--initialize-at-build-time=org.molgenis.vipannotate.serialization,\
me.lemire.integercompression,\
org.molgenis.vipannotate.annotation.SequenceVariantAnnotationIndexBig,\
org.molgenis.vipannotate.annotation.SequenceVariantAnnotationIndexSmall,\
org.molgenis.vipannotate.annotation.SequenceVariantAnnotationIndex
```
build shows some warnings, might this be relevant?
```
[1/8] Initializing...WARNING: A terminally deprecated method in
sun.misc.Unsafe has been called
WARNING: sun.misc.Unsafe::arrayBaseOffset has been called by
org.apache.fory.memory.Platform
(file:/home/dhendriksen/.m2/repository/org/apache/fory/fory-core/0.12.2/fory-core-0.12.2.jar)
WARNING: Please consider reporting this to the maintainers of class
org.apache.fory.memory.Platform
WARNING: sun.misc.Unsafe::arrayBaseOffset will be removed in a future release
Warning: Unknown attribute(s) [methods, fields] in serialization descriptor
object
Warning: "customTargetConstructorClass" is deprecated in
serialization-config.json. All serializable classes can be instantiated through
any superclass constructor without the use of the flag.
Build resources:
2025-09-19 06:17:10 INFO Fory:172 [ForkJoinPool.commonPool-worker-1] -
Created new fory org.apache.fory.Fory@7ae10962
<cut>
2025-09-19 06:17:10 INFO CompileUnit:55 [ForkJoinPool.commonPool-worker-1]
- Generate code for
org.molgenis.vipannotate.annotation.SequenceVariantAnnotationIndexBigForyCodec_0
took 14 ms.
2025-09-19 06:17:10 INFO JaninoUtils:121 [ForkJoinPool.commonPool-worker-1]
- Compile [SequenceVariantAnnotationIndexBigForyCodec_0] take 23 ms
<cut>
2025-09-19 06:17:10 INFO JaninoUtils:121 [ForkJoinPool.commonPool-worker-1]
- Compile [SerializedLambdaForyCodec_0] take 76 ms
2025-09-19 06:17:10 WARN ObjectStreamSerializer:93
[ForkJoinPool.commonPool-worker-1] - class java.lang.IndexOutOfBoundsException
customized jdk serialization, which is inefficient. Please replace it with a
org.apache.fory.serializer.Serializer or implements java.io.Externalizable
<cut>
2025-09-19 06:17:10 INFO JaninoUtils:121 [ForkJoinPool.commonPool-worker-1]
- Compile [ThrowableForyCodecCompatible_0] take 61 ms
2025-09-19 06:17:10 WARN ObjectStreamSerializer:93
[ForkJoinPool.commonPool-worker-1] - class java.lang.Throwable customized jdk
serialization, which is inefficient. Please replace it with a
org.apache.fory.serializer.Serializer or implements java.io.Externalizable
2025-09-19 06:17:10 WARN ObjectStreamSerializer:93
[ForkJoinPool.commonPool-worker-1] - class java.lang.NullPointerException
customized jdk serialization, which is inefficient. Please replace it with a
org.apache.fory.serializer.Serializer or implements java.io.Externalizable
<cut>
2025-09-19 06:17:10 INFO JaninoUtils:121 [ForkJoinPool.commonPool-worker-1]
- Compile [Collections_ReverseComparatorForyCodec_0] take 7 ms
2025-09-19 06:17:10 WARN ObjectStreamSerializer:93
[ForkJoinPool.commonPool-worker-1] - class
java.util.concurrent.LinkedBlockingQueue customized jdk serialization, which is
inefficient. Please replace it with a org.apache.fory.serializer.Serializer or
implements java.io.Externalizable
<cut>
2025-09-19 06:17:10 INFO JaninoUtils:121 [ForkJoinPool.commonPool-worker-1]
- Compile [StackTraceElementForyCodec_0] take 25 ms
2025-09-19 06:17:10 WARN ObjectStreamSerializer:93
[ForkJoinPool.commonPool-worker-1] - class java.lang.Exception customized jdk
serialization, which is inefficient. Please replace it with a
org.apache.fory.serializer.Serializer or implements java.io.Externalizable
2025-09-19 06:17:10 WARN ObjectStreamSerializer:93
[ForkJoinPool.commonPool-worker-1] - class java.lang.RuntimeException
customized jdk serialization, which is inefficient. Please replace it with a
org.apache.fory.serializer.Serializer or implements java.io.Externalizable
2025-09-19 06:17:10 WARN ObjectStreamSerializer:93
[ForkJoinPool.commonPool-worker-1] - class java.lang.IllegalArgumentException
customized jdk serialization, which is inefficient. Please replace it with a
org.apache.fory.serializer.Serializer or implements java.io.Externalizable
<cut>
2025-09-19 06:17:10 INFO JaninoUtils:121 [ForkJoinPool.commonPool-worker-1]
- Compile [IllegalArgumentExceptionForyCodecCompatible_0] take 10 ms
2025-09-19 06:17:10 WARN ObjectStreamSerializer:93
[ForkJoinPool.commonPool-worker-1] - class
java.util.concurrent.ArrayBlockingQueue customized jdk serialization, which is
inefficient. Please replace it with a org.apache.fory.serializer.Serializer or
implements java.io.Externalizable
<cut>
2025-09-19 06:17:11 INFO JaninoUtils:121 [ForkJoinPool.commonPool-worker-1]
- Compile [ArrayBlockingQueueForyCodecCompatible_0] take 63 ms
2025-09-19 06:17:11 WARN ObjectStreamSerializer:93
[ForkJoinPool.commonPool-worker-1] - class java.lang.IllegalStateException
customized jdk serialization, which is inefficient. Please replace it with a
org.apache.fory.serializer.Serializer or implements java.io.Externalizable
<cut>
2025-09-19 06:17:11 INFO JaninoUtils:121 [ForkJoinPool.commonPool-worker-1]
- Compile [IllegalStateExceptionForyCodecCompatible_0] take 16 ms
2025-09-19 06:17:11 WARN ObjectStreamSerializer:93
[ForkJoinPool.commonPool-worker-1] - class java.io.IOException customized jdk
serialization, which is inefficient. Please replace it with a
org.apache.fory.serializer.Serializer or implements java.io.Externalizable
<cut>
2025-09-19 06:17:11 INFO JaninoUtils:121 [ForkJoinPool.commonPool-worker-1]
- Compile [IOExceptionForyCodecCompatible_0] take 29 ms
2025-09-19 06:17:11 WARN ObjectStreamSerializer:93
[ForkJoinPool.commonPool-worker-1] - class
java.lang.ArrayIndexOutOfBoundsException customized jdk serialization, which is
inefficient. Please replace it with a org.apache.fory.serializer.Serializer or
implements java.io.Externalizable
<cut>
```
any of your thoughts are highly appreciated!
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