Hi John,
Thanks for the reply...
On 12/17/2012 12:29 PM, John May wrote:
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.
I haven't ported chemViz to 3.0, yet, so this is definitely not an OSGi
issue.
System.out.println(System.getProperty("user.home"));
Yeah, I'll give that a try and see if something is clobbering the system
properties completely...
Thanks!
-- scooter
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]
<mailto:[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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