Hi Scooter,
Do you have build, I can test on another machine if you like?
Thanks,
J
On 17 Dec 2012, at 21:40, Scooter Morris <[email protected]> wrote:
> Hi all,
> Just a quick update... I checked and the user.home property is correctly
> set both before and after the attempt to call jni-inchi.
>
> -- scooter
>
> On 12/17/2012 01:30 PM, Scooter Morris wrote:
>> 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...
> Nope, the user.home property is correctly set
>>
>> 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]> 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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>>
>>
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