JVM crash on Cartera 23, JNA-Inchi 1.3.1

[ctapobep]

When upgrading from JNA Inchi 1.1 to 1.3.1 my JVM crashes when parsing InChI. Environment:

• https://hub.docker.com/_/amazoncorretto (amd64 architecture)
• Cortera 23

Error excerpts (the full log is attached):

C  [jna11626777807323842640.tmp+0x7aceb]  GetStructFromINCHIEx+0x195
Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
j  io.github.dan2097.jnainchi.inchi.InchiLibrary.GetStructFromINCHI(Lio/github/dan2097/jnainchi/inchi/tagINCHI_InputINCHI;Lio/github/dan2097/jnainchi/inchi/tagINCHI_OutputStruct;)I+0
j  io.github.dan2097.jnainchi.JnaInchi.getInchiInputFromInchi(Ljava/lang/String;Lio/github/dan2097/jnainchi/InchiOptions;)Lio/github/dan2097/jnainchi/InchiInputFromInchiOutput;+26
j  io.github.dan2097.jnainchi.JnaInchi.getInchiInputFromInchi(Ljava/lang/String;)Lio/github/dan2097/jnainchi/InchiInputFromInchiOutput;+4
j  org.openscience.cdk.inchi.InChIToStructure.<init>(Ljava/lang/String;Lorg/openscience/cdk/interfaces/IChemObjectBuilder;Lio/github/dan2097/jnainchi/InchiOptions;)V+43

I see errors like this down in the dump:

Event: 60.846 Thread 0x00007fff994f0ef0 Exception <a 'java/lang/UnsatisfiedLinkError'{0x00000000c4b1c110}: Error loading shared library libjnainchi.so: No such file or directory> (0x00000000c4b1c110) 

Seems relevant, but the dependencies look ok:

io.github.dan2097:jna-inchi-api:1.3.1
io.github.dan2097:jna-inchi-core:1.3.1
io.github.dan2097:jna-inchi-darwin-aarch64:1.3.1
io.github.dan2097:jna-inchi-darwin-x86-64:1.3.1
io.github.dan2097:jna-inchi-linux-aarch64:1.3.1
io.github.dan2097:jna-inchi-linux-arm:1.3.1
io.github.dan2097:jna-inchi-linux-x86:1.3.1
io.github.dan2097:jna-inchi-linux-x86-64:1.3.1
io.github.dan2097:jna-inchi-win32-x86:1.3.1
io.github.dan2097:jna-inchi-win32-x86-64:1.3.1

I'm using a maven-shade-plugin, so eventually it all ends up in a single JAR as folders in the root:

linux-aarch64
linux-arm
linux-x86
linux-x86-64

[dan2097]

Just to double check, you're saying JNA InChI 1.1 worked correctly in that environment?

Alpine appears to differ from nearly all other Linux distro's by using musl rather than glibc and I've heard that some applications need to be recompiled to work with musl, so I'm speculating but I wonder whether that be the underlying cause. InChI does appear to be tested with musl (IUPAC-InChI/InChI#6) but I don't know whether the default binaries are built to work with it.

[ctapobep]

Yep, JNA InChI 1.1 works perfectly in exactly same conditions :)