Camelia, the Perl 6 bug

IRC log for #bioclipse, 2012-02-20

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All times shown according to UTC.

Time Nick Message
05:32 sneumann joined #bioclipse
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07:23 Gpox joined #bioclipse
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09:24 CIA-98 bioclipse.balloon: Arvid Berg 2.5.x * r83cdbf1 / (3 files in 3 dirs): Added touchpoint for chmod for balloon executable - http://git.io/K22K6Q
09:24 CIA-98 bioclipse.balloon: Arvid Berg 2.5.x * r6b86a49 / (2 files in 2 dirs): Changed verso of cdk bundle and cleaned up dependencies - http://git.io/LxxZvw
09:42 CIA-98 bioclipse.core: Arvid Berg 2.5.x * r4732ae1 / features/net.bioclipse.pla​tform_feature/feature.xml : Removed some bundles from required and added net.bioclipse.logback - http://git.io/lhi7sA
09:42 CIA-98 bioclipse.core: Arvid Berg 2.5.x * r356ae92 / features/net.bioclipse.platfo​rm_feature/bioclipse.product : removed version in product for platform feature - http://git.io/x5hdeQ
09:44 egonw Gpox: ping
09:44 egonw Gpox: how do you do SDF parsing?
09:44 egonw a bug in the CDK SDF parser was found
09:45 egonw affecting Bioclipse
09:58 Gpox with the mdl reader
10:04 Gpox_ joined #bioclipse
10:04 egonw ok, good
10:04 egonw so, if the MDL reader throws an exception, it will happily continue?
10:11 Gpox_ in the sdfeditor it will return null for that molecule but will continue to show the rest
10:11 zaetnick joined #bioclipse
10:13 egonw Gpox: the cdk manager has a SDF parser yet... that one is not using your code, right? because I am seeing the problem there
10:13 egonw does that make sense?
10:18 Gpox yes they are different
10:25 egonw so, what version is Bioclipse using at this moment? that is, after you upgraded the way the CDK is packaged?
10:25 egonw I guess I can see that from Hudson :)
10:28 egonw Gpox: did the links to the artifacts get removed?
10:29 Gpox probably never added for cdk, it publishes the bundels to http://pele.farmbio.uu.se/bioclipse/cdk
10:29 egonw and I also discovered that the Workspace is only visible when logged in
10:30 egonw which I normally am, but not until a sec ago :)
10:30 egonw ok, thanx!
10:30 egonw 14.6.1... excellent!
10:31 egonw that should make upgrading to 1.4.8 trivial... :)
10:31 egonw it has some other MDLV2000Reader robustness fixes too
10:32 egonw Gpox: what is the time line? is it ok if I try to get a few more fixes in for 1.4.8, or is it better if I release 1.4.8 asap?
10:32 egonw (with a matching CDK-JChemPaint)
10:38 Gpox I think it would be ok, but I have not tried to update the cdk version since the 1.3 -> 1.4 upgrade
10:41 egonw I also worked on getting renderextra ready for submission as CDK patch
11:25 egonw masak++ (for RTing the new logger levels)
11:25 egonw @tell jonalv http://pele.farmbio.uu.se/nightly-jonalv/
11:25 zarah Consider it noted.
11:34 amarillion joined #bioclipse
11:34 amarillion Hi egonw
11:36 amarillion Hey guys, egon tells me you know a bit about OSGi
11:36 amarillion Do you have any idea how I can get eclipse to stop loading outdated bundles that were generated on the command line?
11:36 amarillion This has bitten me many times
11:37 amarillion for some reason eclipse prefers to load an outdated jar that was generated with ant, and ignores the project that I set up that provides the same bundle
11:38 egonw both have the same version?
11:45 amarillion yes
11:45 amarillion the trouble is, I don't point eclipse to those bundles anywhere
11:45 amarillion they just get picked up automagically
11:46 amarillion so there seems also to be no way to prevent them from being picked up
11:47 egonw minor.minor version bump?
11:49 amarillion That's very impractical\
11:50 amarillion not only do I have to update the version no for every code-compile-run cycle
11:50 amarillion I have to do that for the bundle itself, as well as all the users of that bundle
11:50 egonw oh... so, Ant creates a new osgi jar each time?
11:50 amarillion No...
11:50 amarillion My solution at the moment is that I just run dist-clean before starting wokring with eclipse
11:51 amarillion but if I forget by mistake
11:51 amarillion I end up wasting half an hour
11:51 amarillion worse
11:51 amarillion students who try out eclipse, have the same problem as well
11:51 amarillion And they waste a lot of time as well
11:51 egonw have you tried marking those jars as explicitly excluded from the classpath?
11:52 jonalv joined #bioclipse
11:52 amarillion How would I do that? They're not even in the project space
11:52 egonw ok ...
11:52 amarillion they are one level below that
11:57 amarillion Another problem then...
11:57 amarillion I get java.lang.NoClassDefFoundError: org/sbgn/Language
11:57 amarillion Even though the bundle providing it is clearly there
11:58 jonalv google providence
11:58 zarah jonalv: http://www.providenceri.com/
11:58 zarah jonalv: You have new messages. Write '/msg zarah @messages' to read them.
11:59 amarillion lunch, BBL
12:00 jonalv egonw: that CDK nightly is runnign on new pele now? Nice. egonw++
12:00 egonw yeah, everything was copied
12:00 jonalv so it worked as planned
12:00 egonw beanshell and libxslt was missing earlier, but installed those
12:01 jonalv awesome
12:01 jonalv egonw: I read you mail but I am not sure I understood it completely
12:01 jonalv you kep using a word
12:01 jonalv providence or something like that
12:02 egonw which email?
12:02 egonw mom, brb
12:02 jonalv about publishing BSL
12:03 egonw ah!
12:03 egonw provenance?
12:03 egonw brb
12:14 egonw joined #bioclipse
12:16 egonw back
12:19 jonalv wb
12:25 CIA-98 bioclipse.cheminformatics: Arvid Berg 2.5.x * r9e78f07 / (3 files in 2 dirs):
12:25 CIA-98 bioclipse.cheminformatics: Moved ContentTypesPluginTest to cml.tests
12:25 CIA-98 bioclipse.cheminformatics: The tested content types are define in the net.bioclipse.cml plugin - http://git.io/2ach-w
12:25 CIA-98 bioclipse.cheminformatics: Arvid Berg 2.5.x * rd831f62 / features/net.bioclipse.chemoin​formatics_feature/feature.xml : Added cmlxom to included plugins - http://git.io/takV-w
13:10 CIA-98 bioclipse.cheminformatics: Arvid Berg 2.5.x * r38641a1 / features/net.bioclipse.cheminfor​matics.test_feature/feature.xml : Updated test feature with platform and core - http://git.io/7ZdsJw
13:27 olass joined #bioclipse
14:03 olass hi
14:03 zarah oh hai olass
14:04 egonw hi olass
14:05 olass hi egonw
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20:17 olass joined #bioclipse
21:34 amarillion joined #bioclipse
21:35 amarillion Hey,
21:35 amarillion is there anybody here who could give some pointers for an OSGi problem?
21:36 amarillion I'm trying to figure out why eclipse won't load a class from a  certain bundle, while it's in the jar
22:11 amarillion oh well
22:35 olass joined #bioclipse
22:36 olass amarillion: you should ask tomorrow during daytime (Europe)
22:36 olass Gpox can probably give you a hand
22:37 amarillion thanks
22:37 amarillion I think I figured it out, partly
22:37 amarillion but it would be great to get some pointers on osgi troubleshooting
22:38 amarillion because I'm stuck with using witchcraft
22:38 amarillion I'll ask again tomorrow

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