Camelia, the Perl 6 bug

IRC log for #bioclipse, 2012-01-09

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All times shown according to UTC.

Time Nick Message
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10:24 CIA-104 bioclipse.cheminformatics: Ola Spjuth master * r183a837 / plugins/net.bioclipse.cdk.ui/src/net/biocli​pse/cdk/ui/handlers/ConvertSMILEStoSDF.java :
10:24 CIA-104 bioclipse.cheminformatics: Allow header size to be less than content.
10:24 CIA-104 bioclipse.cheminformatics: * Added TODO for defining process in wiki - http://git.io/jx5bpA
10:27 CIA-104 bioclipse.core: Arvid Berg 2.5.x * r6f2e1f0 / net.bioclipse.target.platf​orm/target-platform.target : Updated cdk version in TP - http://git.io/0P9wxA
10:36 zaetnick Gpox. olass: I did update core and reset target platform, but still have errors
10:36 zaetnick updated cheminformatics too
10:37 zaetnick we are talking 2.5.x, aren't we
10:37 olass zaetnick: yes
10:37 * olass will update core and set TP too
10:39 Gpox zaetnick: do you have org.openscience.cdk* in workspace?
10:40 zaetnick Gpox: yes, branch bioclipse.2.6
10:43 Gpox remove those
10:45 olass aha
10:45 olass hmm, should we have branch 2.6?
10:45 olass ok
10:46 olass right, I should remove it
10:47 olass zaetnick: have you fixed the statet plugins to work with 1.0?
10:47 olass can I update?
10:49 zaetnick olass: no, bc.statistics comes with the old walware packages on the update site
10:50 zaetnick ok, now org.openscience.cdk are closed and cheminformatics is clean
10:51 Gpox good
10:57 zaetnick a few issues with qsar and rdf
10:57 zaetnick ref depends on some net.bioclipse.biojava.business
10:59 Gpox that is in bioclipse.bioinformatics
11:07 egonw moin moin
11:13 zaetnick and qsar and xws4j cannot resolve net.bioclipse.xws.* imports
11:14 Gpox bioclipse.xws4j, there is lots of inter repo dependencie
11:17 zaetnick I have bioclipse.xws4j, but the XwsManager class complains about the same imports
11:20 olass zaetnick: you can close the qsar-xmpp for now, we don't use it
11:20 olass the list of features I gave you does not include XMPP
11:21 Gpox use cmd+shift+a and check if you have net.sf.xws4j
11:21 Gpox and that all repos is 2.5.x
11:22 egonw Gpox: I have also released cdk-jcp 25
11:22 egonw based on cdk 1.4.7
11:23 zaetnick olass: I have net.sf.xws4j
11:23 Gpox yeah I saw that, reminds me I still have to give you that patch
11:23 egonw :)
11:24 egonw yeah, I can easily make further releases
11:24 egonw there is also the work from Eric(?) about transparency... Gilleain was looking at that
11:28 * olass heads off to consume a healthy lunch-in-a-box
11:43 zaetnick olass: ping me when done with box :)
11:52 olass zaetnick: ping
11:52 olass quick lunch
11:53 zaetnick and healthy :)
11:53 olass very
11:53 zaetnick the ds repo - which branch
11:53 olass zaetnick: how many eggs have you had so far today?
11:53 olass zaetnick: just pushed to 2.5.x before lunch
11:53 zaetnick 0 eggs
11:53 olass what!?
11:53 olass you mean 10 eggs?
11:54 zaetnick 2,5 morroter. 3 st knäckerbröd m smör and a bannan
11:54 olass zaetnick: you health-freak!
11:55 zaetnick no time to boil the eggs
11:55 zaetnick olass: you should've seen me in the evenings during the holidays :)
11:56 olass hundreds of eggs?
11:56 zaetnick … solid and liquid
11:58 zaetnick olass: still error in DenseCDKRModelMatcher
11:59 olass ouch
11:59 olass ok, in ds?
11:59 zaetnick line 105 DenseDataset dataset = qsar.calculate(mols, descriptors);
11:59 olass did you update QSAR to latest branch 2.5.x?
11:59 olass ok, what is the error?
12:00 zaetnick I updated QSAR earlier today, wait a second
12:01 zaetnick it's up to date yes
12:01 zaetnick the error is Type mismatch: cannot convert from DescriptorCalculationResult to DenseDataset DenseCDKRModelMatcher.java /net.bioclipse.ds.r/src/net/bioclipse/ds/r line 105 Java Problem
12:02 olass no error on imports?
12:03 zaetnick not here in net.bioclipse.ds.r
12:04 zaetnick imports error in net.bioclipse.ds.sdk
12:04 zaetnick import core.Server;
12:04 olass close that project
12:04 olass Gpox: ping
12:04 zaetnick closed
12:04 Gpox olass: pong
12:04 olass Gpox: how should we treat projects that are deprecated or just postponed?
12:04 olass should we move them from a repo to somewhere else?
12:05 Gpox not have tem in the feature/site
12:05 olass but they would still be imported in eclipse..
12:05 olass and show up as red
12:06 Gpox why do you have such project in the 2.5.x branch?
12:06 Gpox shouldn't they be in a feature branch
12:06 olass ok, how/where do I move them?
12:06 olass they are in the repo
12:06 olass should they be moved to a branch?
12:06 olass I guess that is the best thing to do?
12:07 * olass does that for ds now
12:09 olass done
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12:11 olass zaetnick: please pull ds branch 2.5.x
12:12 olass zaetnick: still problems?
12:15 olass zaetnick: I will relocate to a more quit room for a TC, please ping me if problems persist
12:20 zaetnick olass: the same error in DenseCDKRModelMatcher in *ds.r
12:20 zaetnick olass: the rest is fine
12:23 olass joined #bioclipse
12:23 * olass is now relocated
12:24 olass zaetnick: ping
12:24 zaetnick olass: pong
12:24 olass still problems?
12:24 zaetnick DenseCDKRModelMatcher in *ds.r
12:24 zaetnick the same error
12:25 olass plese explain error
12:25 olass is it runtime?
12:25 zaetnick DescriptionResourcePathLocationType
12:25 zaetnick Type mismatch: cannot convert from DescriptorCalculationResult to DenseDatasetDenseCDKRModelMatcher.java/net​.bioclipse.ds.r/src/net/bioclipse/ds/rline 105Java Problem
12:27 CIA-104 bioclipse.qsar: Ola Spjuth 2.5.x * red4eaed / (9 files in 7 dirs): Merged master into 2.5.x - http://git.io/7l8ZdQ
12:27 olass zaetnick: sorry, I forgot to push
12:27 olass please update bioclipse.qsar
12:27 egonw :)
12:30 zaetnick olass: now there are errors in net.bioclipse.qsar.test net.bioclipse.cdk.qsar.test
12:30 olass hmm
12:31 olass but tests you can ignore
12:31 olass thanks for the pointer however
12:31 zaetnick DescriptionResourcePathLocationType
12:31 zaetnick Type mismatch: cannot convert from DenseDataset to DescriptorCalculationResultTestQsarMan​ager.java/net.bioclipse.qsar.test/src/​net/bioclipse/qsar/test/businessline 570Java Problem
12:31 olass same problem??
12:31 zaetnick aha
12:32 zaetnick I closed them
12:33 zaetnick should be ok for the moment
12:53 olass zaetnick: so problem disappeared now?
12:54 olass else you need to share screen with me in skype...
12:54 zaetnick olass: no problems in the workspace now
12:54 olass *phew*
12:55 zaetnick when I try Generate 3D > Balloon I get this one Balloon: failed: Balloon execution failed. Native BalloonRunner returned false.
12:56 zaetnick it was the same the first time I tested
13:03 olass zaetnick: you run from within eclipse?
13:03 olass zaetnick: fragments only works if installed in binary build, so if running from eclipse you need to manually remove some plugins from balloon_feature
13:04 olass namely those not suitable for your system
13:04 olass Gpox: ping
13:04 zaetnick olass: I see
13:04 olass Gpox: in plugin net.bioclipse.xws4j I get missing imports for net.bioclipse.xws
13:04 olass how come?
13:05 zaetnick olass: I ran into this earlier today
13:05 olass and?
13:06 olass solution?
13:06 zaetnick closed them
13:06 olass Gpox: can you suggest a more robust solution?
13:09 zaetnick olass: *phew*: it worked after removing some stuff
13:14 CIA-104 bioclipse.qsar: Ola Spjuth 2.5.x * rec92801 / (5 files in 2 dirs): Cleaned up tests for new API, added TODOs - http://git.io/RXYn_w
13:14 olass Gpox: ping me when back regarding xws4j
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14:26 egonw olass, Gpox: should I try the TP again then?
14:26 egonw what's the minimal set up repositories to check out?
14:31 Gpox olass: xws4j compile for me.
14:33 Gpox egonw: minimal for what? I got core,chemoinformatics, ds, ballon, statistics,qsar,rdf,bioinformatics,xws4j
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14:36 egonw Gpox: minimal to get the TP working...
14:36 egonw Gpox: I have/d core, cheminf, balloon, rdf
14:36 egonw that did not work
14:36 egonw oh, and + stats
14:37 Gpox I updated the tp today that might help
14:37 egonw ok...
14:37 egonw I
14:38 egonw I'm relocating to another room, and will update things then...
14:48 olass Gpox: ok, will try again for xws4j
14:51 olass Gpox: ping
14:51 Gpox olass: pong
14:51 olass Gpox: who provides the packages "net.bioclipse.xws.*"
14:51 Gpox net.sf.xws4j
14:51 olass hmm, maybe there is a missing import package here...
14:53 olass Gpox: should we really import net.sf.xws4j bundle or import its packages?
14:53 olass see manifest in bioclipse.qsar.xmpp
14:54 olass well, for me it does not pick up the net.bioclipse.xws packages
14:55 Gpox have you search for it with cmd-shift-a ?
14:55 olass yes, and found it
14:55 Gpox it should be in net.bioclipse.target.platform/libs
14:56 olass yes, it's there
14:56 olass well, it matters little to me right now
14:56 olass just wanted things to compile
14:56 olass I can live with these projects closed now and we look at it on thursday
14:57 Gpox where do you get the error?
14:57 zaetnick I have it in net.bioclipse.xws4j.business XwsManager
14:59 olass me too
14:59 olass and also in CdkXMPPDescriptorCalculator.java
14:59 olass (latter in bioclipse.qsar)
15:00 Gpox strange
15:00 zaetnick I confirm the last one
15:14 CIA-104 bioclipse.core: Arvid Berg 2.5.x * rc341390 / (5 files in 3 dirs): Removed marketplace wizard and added default p2 discovery ui - http://git.io/AfPeYw
15:14 CIA-104 bioclipse.core: Arvid Berg 2.5.x * r27dd321 / net.bioclipse.target.platf​orm/target-platform.target : Updated TP to 3.7 - http://git.io/hPBenw
15:14 CIA-104 bioclipse.core: Arvid Berg 2.5.x * rd28e4a8 / features/net.bioclipse.platfo​rm_feature/bioclipse.product : Added launchers to the product - http://git.io/J67r5A
15:25 egonw Gpox: thanx...
15:26 egonw got these three patches too, and now Eclipse is happy
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18:59 CIA-104 bioclipse.cheminformatics: Arvid Berg 2.5.x * r9c62987 / features/net.bioclipse.chemoin​formatics_feature/feature.xml : Updated dependencies for cheminformatics feature - http://git.io/eYl92g
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