Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-03-09

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All times shown according to UTC.

Time Nick Message
06:32 sneumann joined #bioclipse
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08:28 CIA-57 bioclipse.rdf: Egon Willighagen master * r840437e / (2 files in 2 dirs): Depend on Java5 not Java6 (fixes #1911) - http://bit.ly/9Cylve
08:28 zarah bug #1911 | http://tinyurl.com/y95zd8d
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09:04 * egonw is wondering if he should actually cascade the CDK initialization into multiple threads...
09:04 egonw many people here with more than two cores?
09:07 CIA-57 bioclipse.cheminformatics: Ola Spjuth master * r5625e73 / (2 files in 2 dirs): Implemented toString in getInfo(). Solved #1844. - http://bit.ly/a9sD67
09:07 CIA-57 bioclipse.cheminformatics: Egon Willighagen master * r16fed1b / (2 files): Do some CDK bootstrapping if stuff that is very likely going to be used: isotope, element and atom type lists (fixes #1907) - http://bit.ly/b27qoo
09:07 zarah bug #1907 | http://tinyurl.com/y95hp37
09:14 jonalv egonw: are you home?
09:14 egonw yes
09:15 egonw no sushi this week either
09:15 egonw too busy
09:15 jonalv I thought you said you were joining for sushi///
09:15 jonalv oki
09:15 jonalv egonw: regarding cdk init. about how long does it take?
09:16 egonw depends on how fast your machine is :)
09:16 egonw <10secs
09:16 jonalv egonw: off course, hence the 'about'
09:16 egonw with logging enabled, 5secs on my dual core machine
09:16 egonw how so?
09:16 egonw I should not have used a thread?
09:16 jonalv egonw: you were asking whether we thought you should split it into multiple threads
09:17 egonw it's in Activator.start() now
09:17 egonw it just fires up the thread
09:17 egonw so should still return quickly
09:17 egonw and observations in the log indicate it does so properly
09:17 jonalv egonw: yea good, which Activator is this?
09:17 egonw cdk.business
09:18 jonalv egonw: oh, what was the symptom that made yo ustart looking at this?
09:18 egonw olas
09:19 jonalv egonw: okey, I am still a bit unsure what it is you are doing. Do you want to exlain?
09:19 egonw no, I don't want to...
09:19 egonw (but I will answer questions about it :)
09:20 jonalv what does init. mean in this case? And have you taken precautions if someone asks for unintilialised resources (is that even possible?)
09:25 egonw annzi, samuell, jonalv, s_wolf, sneumann: please read your bioclipse-devel email on the Google Summer of Code ...
09:29 sneumann http://dbkgroup.org/
09:29 sneumann http://www3.imperial.ac.uk/people/t.ebbels
09:29 zarah sneumann's link is also http://tinyurl.com/yfqflto
09:29 sneumann http://users.aber.ac.uk/nwh/
09:30 sneumann http://www.metabolomicscentre.nl/
09:30 zarah sneumann's link is also http://tinyurl.com/y8ao49b
09:30 sneumann (sorry, kinda wrong window :-)
09:30 sneumann There is someone here looking for a job ...
09:30 egonw ah :)
09:31 egonw I wish we had open positions in our group :(
09:31 sneumann He just finished diploma thesis
09:31 sneumann and is availably from August  on
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10:06 CIA-57 bioclipse.cheminformatics: Egon Willighagen master * r4ddd089 / (2 files): Added helper methods to convert CDK into Bioclipse molecules lists and visa versa (implements #1854) - http://bit.ly/cGwyxu
10:06 egonw sneumann: that was your bug
10:06 egonw feature request
10:06 egonw now time for coffee
10:11 sneumann thanks
10:31 jonalv egonw: ping
10:31 egonw pong
10:32 jonalv egonw: do you have a pull request or something? I have compile error is cdk...
10:32 jonalv cdk.business
10:32 jonalv BioclipseLoggingTool to be exact
10:33 jonalv egonw: oh hang on, I missed a git error message in that last merge
10:33 * jonalv tries agan
10:33 egonw and make sure you have the bioclipse24 branch for org.openscience.cdk
10:34 jonalv egonw: why not master?
10:34 egonw 1. because we use cdk+cdk-jchempaint
10:34 egonw 2. I had to squash in a commit not in the 1.3.3 release
10:35 jonalv egonw: oki
10:36 jonalv egonw: yup now that is compiling, thanks
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12:21 egonw_ olass: perfect timing!
12:21 olass hi
12:21 zarah saluton olass
12:22 egonw_ olass: I think I found the problem with sparqlRemote() not working for you
12:22 olass nice!
12:22 egonw_ apparently, that Jena bit does require Java6
12:22 egonw_ the missing class is part of Java6
12:22 egonw_ but not Java5
12:22 egonw_ I found a jar and will add it to the target platform
12:22 egonw_ but I need you to test it
12:24 olass I'll be happy to
12:24 olass how?
12:24 egonw_ testing if the sparqlRemote() call you used earlier now works...
12:24 egonw_ but
12:24 egonw_ I need to make the patch first :)
12:25 olass how do I make the patch?
12:25 egonw_ I'm making it...
12:29 egonw_ I only need to put the jars in the lib/ to get them in the target platform, right?
12:29 egonw_ no adding to some config file, right?
12:30 olass don't think so...
12:30 olass not sure
12:30 egonw_ ok, we know soon enough
12:30 egonw_ olass: please check bug #1906 for the patch
12:35 olass will do
12:35 olass after tel call
12:37 egonw np
12:41 olass egonw: ok, setting new TP after applying patch
12:45 olass egonw: nop, still same error
12:45 olass will confirm I have new jar it in CP
12:45 olass hmm, how do I check that?
12:47 * egonw does not know
12:50 * olass will try again
12:53 olass hmm, it seems I did not refresh target platform first
12:53 * olass will try again
12:54 olass no, same error
13:02 olass hmm
13:02 olass seems we cannot put jars in TP which are not OSGI bundles
13:02 olass egonw: we will try to resolve it here
13:02 olass egonw: I assume this jar needs to be on CP for jena plugins?
13:02 olass which ones?
13:02 olass can you not import it there directly?
13:02 olass on classpath?
13:03 olass Gpox is looking for an OSGI bundle as we speak...
13:03 egonw ah, no those are likely not OSGi bundles
13:03 olass Gpox: stax-1.2.0.jar and stax-api-1.0.1.jar
13:03 * egonw had no clue that was expected..!
13:04 egonw it's not too difficult to fix, though:
13:04 egonw http://rajakannappan.blogspot.com/2010/02/eclipse​-rcp-converting-dependencies-to.html?utm_source=f​eedburner&amp;utm_medium=feed&amp;utm_campaign=Fe​ed:+RajaKannappansBlog+(Raja+Kannappan's+Blog)
13:04 zarah egonw's link is also http://tinyurl.com/y8nvr9x
13:04 egonw but I guess we should then better look at Orbit or so...
13:09 CIA-57 bioclipse.rdf: Egon Willighagen master * r6e3f2d1 / (2 files): Now removes NaN values, and entries without SMILES (fixes #1912)
13:09 zarah bug #1912 | http://tinyurl.com/yat544e
13:23 olass egonw: if I want to add the jar files directly, what plugins need them?
13:23 olass stax that is..
13:23 egonw can't find suitable osgi bundles
13:23 egonw I'll try your option
13:25 egonw I have no idea what is up with my network connection :(
13:25 egonw but it's on off all the time :(
13:25 olass egonw: if I want to add the jar files directly, what plugins need them?
13:25 olass I can add them myself I you cannot test..
13:25 olass but I guess you can test running Java 1.5
13:25 olass or..?
13:27 egonw true
13:27 egonw bioclipse.rdf/externals/com.hp.hpl.jena
13:27 egonw that's where they would need to be added
13:33 olass ok, will try
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14:15 olass egonw_: problem solved
14:15 olass will send you a patch
14:15 egonw_ good!
14:16 egonw_ olass++
14:16 egonw_ so much for java's platform indepdency :)
14:16 egonw_ when Gpox is done with setting up hudson/buckminster, we need to set up nodes for all supported platforms
14:34 olass egonw_: pull request sent for resolving 1906
14:39 CIA-57 bioclipse.rdf: Ola Spjuth master * rd347093 / (5 files in 4 dirs):
14:39 CIA-57 bioclipse.rdf: Added stax jar and exported packages.
14:39 CIA-57 bioclipse.rdf: Solves #1906. -
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22:29 CIA-57 bioclipse.rdf: Egon Willighagen master * r6ef7e1d / plugins/net.bioclipse.chembl/src/net/bioc​lipse/chembl/business/IChEMBLManager.java : Fixed params signature to match the match the actual method - http://bit.ly/bmraIu

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