Perl 6 - the future is here, just unevenly distributed

IRC log for #bioclipse, 2014-08-20

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All times shown according to UTC.

Time Nick Message
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07:02 egonw_ DS devs...
07:02 egonw_ just updated target platform, repositories, etc
07:02 egonw_ got Problem in net.bioclipse.ds.libsvm.tests
07:02 egonw_ with a Require-Bundle in the manifest on org.junit4
07:03 egonw_ lin 22
07:03 egonw_ that should just be org.junit
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07:43 egonw Gpox: how are we doing with depending which Java version for Bioclispe?
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10:45 egonw crap... Bioclipse doesn't boot at all...
11:04 egonw error:
11:04 egonw "org.osgi.service.resolver.ResolutionException: Uses constraint violation. Unable to resolve resource net.bioclipse.core [osgi.identity; osgi.identity="net.bioclipse.core"; type="osgi.bundle"; version:Version="2.6.2.qualifier"; singleton:="true"] because it is exposed to package 'javax.xml.transform' from resources org.eclipse.osgi [osgi.identity; osgi.identity="org.eclipse.osgi"; type="osgi.bundle"; version:Version="3.10.0.v20140606-
11:04 egonw 1445"; singleton:="true"] and com.springsource.org.apache.xmlcommons [osgi.identity; osgi.identity="com.springsource.org.apache.xmlcommons"; type="osgi.bundle"; version:Version="1.3.4"] via two dependency chains."
11:05 egonw I have no idea how to handle this...
11:38 Gpox egonw: have you updated the target platform?
11:38 egonw yes
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11:53 Gpox if you are running a launch configuration with plugins remove javax.xml from the list of plugins
11:55 egonw I'm using features
11:55 egonw I do get a red marker for java.something.soap missing
11:55 egonw one sec... booting up Eclipse (4.4) again
11:56 egonw but I am also now on a 64bit system, so not really surprised it doesn't directly work...
11:56 egonw there are 64bit builds, right? so, in itself, that should not be a problem, correct?
11:57 Gpox yes, it should work
11:58 Gpox you could try and remove java.xml formt he target platform, uncheck it from the content tab
12:04 egonw this is the soap error: Unsatisfied version constraint: 'javax.xml.soap: 1.3.0'
12:04 egonw in net.bioclipse.webservices
12:05 egonw I can solve that by removing the version constraint
12:05 egonw but maybe that's the cause of the fail to boot...
12:05 egonw will try removing java.xml...
12:06 Gpox The addition of version constrainst is automatic and I don't think it should affect anything
12:07 egonw mmm... it's written in the MANIFEST.MF file...
12:13 egonw OK, it boots now
12:15 egonw getting a lot of "14:15:18.778 WARN  [n.b.ui.ApplicationWorkbenchAdvisor] Unknown perspective id null"
12:16 egonw and I note this one:
12:16 egonw "ERROR [net.bioclipse.scripting.JsEnvironment] Faild to find "JavaScript" scripting engine. Available engins are Groovy, python"
12:17 egonw that may be my bad, though I had previously all three working simultaneously
12:18 Gpox yeah, I belive it has to do with the latest version of Java not providing it in the same way.
12:18 Gpox from what I remember we use the version shiped with java.
12:19 egonw sounds familiar...
12:19 egonw Gpox: one tiny patch emailed
12:22 egonw engineManager.getEngineByName("nashorn")
12:27 Gpox do that work in bioclipse?
12:27 egonw no, not yet...
12:29 egonw first catching some exceptions as a fail safe...
12:39 egonw mmm... it only sees those we explicitly add to the classpath :(
12:44 egonw mmm...
12:44 egonw the nashorn.jar is on the JRE definition list in Eclipse...
12:44 egonw so, that doesn't seem to be the problem
12:47 egonw trying the dirty way and add this nashorn.jar to net.bioclipse.scripting/libs :)
12:48 egonw yes, that works
12:49 egonw confirmed
12:49 egonw that works fine
12:50 egonw how about adding it for now?
12:50 egonw it's open source: http://openjdk.java.net/projects/nashorn/
12:53 Gpox or http://aries.apache.org/modules/spi-fly.html I belive that is how they are suppose to be found
12:54 egonw what I understands from the docs, that's what ScriptEngineManager should be doing, indeed...
12:54 egonw but if I run a list .getEngineFactories() on that manager it doesn't list anything
12:55 egonw I do not have the impression we should be using SPI ourselves...
12:55 egonw see http://docs.oracle.com/javase/8/docs/technotes/guides/scripting/prog_guide/api.html#CDEGJDJF
12:55 zarah egonw's link is also http://tinyurl.com/l7ww653
13:00 egonw Gpox: https://github.com/egonw/bioclipse.core/commits/feature/nashorn
13:00 egonw since Java 1.8 is not out yet (right?), so take of this what you like and do not like
13:02 egonw and thanx for the support... happy that Bioclipse is booting again...
13:02 egonw for some reason, if you think along, the target platform starts working again...
13:02 egonw I don't grasp the physics of that, but who cares ;)
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14:42 commitbot [bioclipse.rdf] egonw opened pull request #5: Feature/compare models (develop...feature/compareModels) http://git.io/uGTPAQ
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14:42 egonw Gpox: a pull request for some additional RDF functionality https://github.com/bioclipse/bioclipse.rdf/pull/5
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14:53 commitbot [bioclipse.rdf] goglepox closed pull request #5: Feature/compare models (develop...feature/compareModels) http://git.io/uGTPAQ
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14:53 egonw Gpox++
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