Hi Scooter,
I'm on OS X 10.8.2 and have no problems on either Apple's 1.6.0_37 or Oracle's
Java 7. I can't give a definite answer but some possible pointers:
- I haven't done any Cytoscape development but I heard that in Cyctoscape 3
they were now using OSGi (which I also don't know loads about). However,
something like not having "user.home" set in the system properties sounds very
much like an OSGi problem. Try printing the home in an isolated java class and
again with the plugin.
> System.out.println(System.getProperty("user.home"));
It seems strange this would only happen on OS X but it may well be the case.
Bioclipse use OSGi so it might be worth asking them if they have had any issues
with JNI-InChI and OSGi.
- If you're really desperate you could complete the InChI source to java byte
code using nestedvm. JChemPaint needed to do this as you can't use JNI in
applets. Rich Apodaca has a post about it here:
http://depth-first.com/articles/2007/12/03/from-c-source-code-to-platform-independent-executable-jarfile-using-nestedvm-to-build-jinchi/
Thanks,
J
On 17 Dec 2012, at 18:12, Scooter Morris <[email protected]> wrote:
> Hi all,
> I'm trying to release a new version of the Cytoscape plugin: chemViz, and
> have run into a major issue with JNI-InChI on MacOS-X. For some reason, on
> MacOSX the user.home property is never initialized. As a result, whenever I
> try to create a molecule from an InChI string, I get a failure:
> java.lang.UnsatisfiedLinkError: Expecting an absolute path of the library:
> ${user.home}/.jnati/repo/jniinchi/1.03_1/MAC-X86_64/JniInchi-1.03_1-MAC-X86_64
> Has anyone seen this, and any suggestions on a workaround? I'm on MacOS X
> 10.8.2 with Java version 1.6.0_37. Any help would be greatly appreciated.
>
> -- scooter
>
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