Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-08-26

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All times shown according to UTC.

Time Nick Message
05:27 egonw joined #bioclipse
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07:26 olas joined #bioclipse
07:27 olas moin
07:27 zarah hi olas
07:29 jonalv joined #bioclipse
07:30 olas hi jonalv
07:30 rojasm joined #bioclipse
07:30 jonalv hi olas
07:52 EskilA joined #bioclipse
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09:39 olas tell egonw: I urgently need help with OWL and the # or no # question!
09:43 olas @tell egonw: I urgently need help with OWL and the # or no # question!
09:43 zarah Consider it noted.
09:44 CIA-51 bioclipse: jonalv * r6736 /bioclipse2/trunk/plugins/net.bioclipse.core.​tests/src/net/bioclipse/core/MockIFile.java: added file ending to name of MockIFile
09:46 CIA-51 bioclipse: jonalv * r6737 /bioclipse2/trunk/plugins/ (6 files in 5 dirs): [structuredb] fixed a few more tests. Still one important thing that doesn't work...
09:49 egonw joined #bioclipse
09:55 olas egonw: that is my dirty solution too
09:55 olas but need to go to bottom of this
09:56 olas when you have more time
09:56 egonw actually, this is the best solution
09:56 zarah egonw: You have new messages. Write '@messages' to read them.
09:56 egonw olas: I'll bring you up to speed when in Uppsala
09:56 egonw @msg
09:56 zarah egonw: olas said I urgently need help with OWL and the # or no # question!
09:56 egonw zarah: tack
09:56 zarah egonw: eh... wha'?
09:57 egonw lunch
09:58 CIA-51 bioclipse: carl_masak * r6738 /bot/trunk/zarah.pl: [zarah] new synonym "tack" for "thanks"
10:06 shk3 joined #bioclipse
10:28 olas hi shk3
10:32 CIA-51 bioclipse: ospjuth * r6739 /bioclipse2/trunk/plugins/net.bioclipse.qsar/ (32 files in 7 dirs): Updated to use Blue Obelisk descriptor-algorithms OWL ontology for defining decsriptors. Parsing with Jena. Renamed old Descriptor to DescriptorImpl. Added libs for Jena as well.
10:33 CIA-51 bioclipse: ospjuth * r6740 /bioclipse2/trunk/plugins/net.bioclipse.qsar.test/ (2 files in 2 dirs): Adapted tests for new Descriptor model based on BO descriptor ontology.
10:38 shk3 hi olas
10:38 CIA-51 bioclipse: ospjuth * r6741 /bioclipse2/trunk/plugins/net.bioclipse.q​sar.ui/src/net/bioclipse/qsar/ui/editors/ (DescriptorContentProvider.java DescriptorLabelProvider.java): Updated to show Descriptors, not DescriptorImpls.
10:39 CIA-51 bioclipse: ospjuth * r6742 /bioclipse2/trunk/plugins/net.bioc​lipse.qsar/src/net/bioclipse/qsar/​descriptor/model/Descriptor.java: Added new Descriptor class.
10:39 CIA-51 bioclipse: ospjuth * r6743 /bioclipse2/trunk/plugins/net.bioclipse.qsar.​ui/src/net/bioclipse/qsar/ui/Activator.java: Corrected pluginID
10:52 CIA-51 bioclipse: ospjuth * r6744 /bioclipse2/trunk/plugins/net.bioclipse.qsar/ (8 files in 4 dirs):
10:52 CIA-51 bioclipse: * Removed name attribute of Descriptor as it refers to an entry in BO ontology.
10:52 CIA-51 bioclipse: * Renamed descriptor to descriptorImpl in extension point.
10:52 CIA-51 bioclipse: * Also removed category from DescriptorImpl.
10:52 CIA-51 bioclipse: * Updated XSD and regenerated model code.
10:55 CIA-51 bioclipse: ospjuth * r6745 /bioclipse2/trunk/plugins/net.bioclipse.qsar.edit/ (3 files in 3 dirs): Regenerated edit code and updated test that writes out example placed on wiki.
10:56 CIA-51 bioclipse: ospjuth * r6746 /bioclipse2/trunk/plugins/net.​bioclipse.cdk.qsar/plugin.xml: Removed category from all descriptorImpl in cdk. Also renamed descriptor to descriptorImpl as required by EP.
11:05 olas left #bioclipse
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11:06 olas egonw: pong
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12:14 olas egonw: no worries!
12:14 maclean joined #bioclipse
12:50 masak people! if you haven't read the Javadoc manual yet, do it! it's for your own good.
12:50 egonw URL?
12:50 masak hold on
12:50 egonw zarah: why don't you spit useful tips every now and then?
12:50 zarah egonw: are you making fun of me?
12:51 masak http://java.sun.com/j2se/javado​c/writingdoccomments/index.html
12:51 masak I think that's it
12:52 masak also, http://java.sun.com/j2se/1.5.0/do​cs/tooldocs/solaris/javadoc.html
12:53 CIA-51 bioclipse: egonw * r6747 /bot/trunk/zarah.pl: Added some DeNiro
12:53 egonw zarah: reboot
12:53 egonw zarah: kill yourself, then boot ?
12:53 zarah egonw: I'm just a bot, you expect me to understand that?
12:54 masak @reboot
12:54 zarah joined #bioclipse
12:55 egonw tack!
12:55 masak zarah: tack
12:55 zarah masak: no, YOU'RE the cute one! :)
12:55 masak :)
13:05 edrin @reboot
13:06 edrin hm
13:06 masak edrin: all users are equal, but some are more equal than others :)
13:06 edrin ic
13:06 jonalv &me likes being equal :)
13:07 jonalv zarah: booh!
13:07 zarah jonalv: you've just exceeded my capabilities :/
13:07 jonalv zarah: you on my isde. come an!
13:07 zarah jonalv: please rephrase or stop trying to be witty :)
13:07 jonalv zarah: boo!
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13:52 * jonalv needs help
13:52 jonalv can someone help?
13:58 egonw 42
14:00 masak jonalv: it's in the top drawer in the great hall, on the second floor, in the abandoned building in the field, behind the barn where you start the game.
14:00 jonalv okey you are bit intrested at least.... :)
14:00 jonalv 2 things.
14:00 jonalv cdk only works with jhava 1.6 for me
14:01 masak interesting.
14:01 jonalv I can\t get cdk to read my sdf file in my test
14:01 masak ok.
14:01 jonalv We are suposed to use java 1.5...
14:04 masak ues.
14:04 masak yes.
14:17 egonw jonalv: stacktraces pleae
14:17 egonw jonalv: nightly is using Java 1.5 for compiling etc...
14:17 egonw jonalv: so, "should work" tm
14:17 olas egonw: we are REALLY stuck with this CML issue
14:18 jonalv egonw: http://pastebin.com/f1860d264
14:18 olas it appeared after we included last Jumbo
14:18 olas egonw: can we inform the CML people?
14:18 olas will be hard to produce a small junit test
14:18 egonw jonalv: we did check that the files was in the jumbo jar, not?
14:18 olas egonw: yes
14:18 olas I did that
14:19 olas (please verify that)
14:19 egonw ok, you double checked, perfect
14:19 egonw yeah, I have no clue...
14:19 * jonalv was gonna try it on windwos but cdk did'nt build in windows...
14:19 jonalv egonw: does it build on windows now?
14:19 egonw no idea
14:19 egonw I don't have windows
14:19 * egonw notes that his next laptop will require good support for virtualizatino
14:20 olas egonw: you'll get a Mac in Uppsala
14:20 jonalv let rephrase that. Does it use bash?
14:20 olas with parallels
14:20 egonw olas: nooooooo
14:20 maclean The latest checkout of cdk builds on XP in eclipse for me.
14:20 egonw please don't make me use a mac
14:20 egonw don't want too...
14:20 olas you have to
14:20 olas you must
14:20 egonw no, we need multi-osing development environments...
14:21 olas run parallels
14:21 egonw we really need my lcaol Ubuntu installation
14:21 * masak admires egonw for using a free OS
14:21 jonalv egonw: You and me should work on running Ubuntu on this mac's...
14:21 jonalv I want to be free too :)
14:21 egonw ok, could live with that :)
14:21 egonw no more vendor lock in...
14:21 jonalv (but it's good to be able to test in all systems...)
14:21 egonw no more java bugs the vendor does not want to fix
14:21 masak I would, too, but I'm too weak. Apple has me in its grip.
14:21 egonw maclean: might you please try it from the command line too?
14:22 maclean As an ant task? Which?
14:22 egonw ant clean dist-all test-dist-all dist-large
14:22 egonw and if you have a few minutes: ant test
14:23 maclean Come to think of it, I should install ant on this machine first...
14:23 egonw :)
14:36 maclean Ugh. no not possible. no admin rights on a windows machine means my ability to do anything on the command line is virtually 0. :(
14:41 jonalv maclean: you don't have admin rights to your own computer?
14:41 jonalv that must suck
14:41 maclean no.
14:42 maclean I mean no I don't, and yes that does suck.
14:55 masak maclean: there should be a t-shirt for that situation
14:56 masak something along the lines of "got root? -- no :("
15:03 maclean That would be an extremely geeky t-shirt. But yes, I could have one of those. Luckily I am root on my mac.
15:23 * jonalv is testrunning on Windos. Things woirk terriffyinlgy bad
15:25 jonalv egonw: got the can not index schema error pn wondows using java 1.6 now...
15:25 egonw ok, excellent
15:25 egonw so, not Java1.5/1.6 related
15:25 egonw got to go home
15:25 egonw email the CML community
15:25 egonw it's their library tripping up...
15:26 egonw I might bring it in on Monday, at the EBI, where I'll meet with Jim...
15:26 egonw if not solved by then
15:29 jonalv egonw: where should I mail the problemds?
15:30 egonw cml-discuss@lists.sf.net
15:31 jonalv oki
15:31 egonw going home
15:31 egonw bye!
15:32 edrin btw.
15:32 edrin in the evening
15:32 edrin when i get online
15:32 edrin it's always very lonely here
15:38 edrin :/
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22:54 CIA-51 bioclipse: edrin_t * r6748 /xws/trunk/xws4j/src/net/b​ioclipse/xws/client/xmpp/ (8 files in 4 dirs):

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