Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-01-19

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All times shown according to UTC.

Time Nick Message
07:22 sneumann joined #bioclipse
07:52 masak joined #bioclipse
08:10 Gpox joined #bioclipse
08:32 egonw joined #bioclipse
08:54 egonw moin
08:54 zarah privet egonw
09:00 jonalv joined #bioclipse
09:30 jonalv egonw: ping
09:30 egonw pong
09:31 jonalv egonw: I am trying to run the cheminforamtics plugin JUnit tests
09:31 jonalv egonw: do they work for you?
09:31 egonw last time I checked...
09:31 egonw let me tru
09:31 egonw y
09:31 jonalv egonw: for me they get stuck at testGenerate3DCoordinates
09:31 jonalv oh now it moved on
09:31 jonalv did it time out?
09:32 egonw loading the db can be slow
09:32 jonalv I ran out of memory on that test
09:33 jonalv that is usually not so good becuase anything can happen after OutOfMemoryException... :(
09:34 egonw 3D generation was working for me last week...
09:34 egonw when writing book chapters
09:34 jonalv egonw: okey
09:34 jonalv egonw: do you know how much memory you are gicing the jvm when you run the tests?\
09:34 egonw but we should record this... please file a bug report
09:34 egonw mom, checking...
09:37 egonw no special mem settings
09:48 samuell joined #bioclipse
10:06 jonalv egonw: strange
10:14 * jonalv tried with the Bioclispe mem settings and then it worked..
10:56 * egonw just finished a conf call
10:56 egonw since 11:00
10:56 egonw perhaps it inherits the mem settings of the running eclipse?
10:56 egonw those are increased in my case
11:41 egonw jonalv: feedback on your patch...
11:41 egonw jonalv: we're using JUnit4 which has means to expect exceptions
11:41 egonw and
11:41 egonw that string may not be stable... particularly in the i18n world of 2.4
11:41 CIA-37 bioclipse.cheminformatics: jonalv 2.2.x * r00341ec / plugins/net.bioclipse.cdk.business.te​st/src/net/bioclipse/cdk/business/tes​t/AbstractCDKManagerPluginTest.java : test for bug 1813 - http://bit.ly/55Sxf3
11:41 zarah bug #1813 | http://tinyurl.com/ybngu7m
11:59 jonalv egonw: oh did you make the apropriate changes then I take it?
11:59 egonw sure not
12:00 egonw it's just feedback
12:00 jonalv egonw: on another note. Do you remember how you create the 'New Molecule' action?
12:00 egonw depends on the amount of detail
12:00 jonalv egonw: ah I thought since you accepted the commit...
12:00 egonw I think I used Eclipse
12:00 egonw but not sure anymore :)
12:00 jonalv egonw: do you know which plugin.xml I should look?
12:00 egonw no, but you can look for the matching commit...
12:01 egonw and see what I changed at the time
12:01 jonalv I found 'Molecule from SMILES' in cdk.ui
12:01 jonalv egonw: 'look for mathcing commit'? how?
12:01 egonw with git, of course...
12:02 jonalv and matching what?
12:02 egonw mom...
12:02 egonw git log -S
12:02 egonw is an option
12:02 egonw and add the name of the class
12:03 egonw also check the log --grep option
12:03 egonw and/or -i and -E
12:03 egonw well, try: git log --help
12:03 egonw and look for the 'Commit Limiting' section
12:04 jonalv I am just not sure what to look for... :(
12:05 jonalv egonw: do you ahve a feeling about what you called it? :)
12:05 egonw no
12:05 egonw mom
12:06 egonw net.bioclipse.cdk.jchempaint
12:06 egonw so:
12:07 egonw git log -- plugins/net.bioclipse.cdk.jchempaint/src/net/biocl​ipse/cdk/jchempaint/wizards/NewMoleculeWizard.java
12:07 egonw (if I made not typo's)
12:07 egonw -- <- is intended !
12:07 jonalv ah thanks I will start by checking the plugin.xml in that plgujin. *much easier start)
12:09 jonalv found it, thanks egonw++
12:11 egonw yw
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14:44 sneumann joined #bioclipse
14:50 user420396 joined #bioclipse
14:50 masak zarah: tell user420396 let's meet up at 14:00 on Tuesday.
14:50 zarah Consider it noted.
14:51 user420396 I'm just demoing the @tell function in zarah.
14:51 zarah user420396: You have new messages. Write '/msg zarah @messages' to read them.
14:51 user420396 @messages
14:51 zarah user420396: 54 s ago, masak said let's meet up at 14:00 on Tuesday.
14:52 jonalv google things
14:52 zarah jonalv: http://culturedcode.com/things/
14:53 jonalv @pz Javascript
14:53 zarah [761] JsEditor edits a file backend, ... http://tinyurl.com/np3zzr
14:53 zarah [1811] Add a method js.lastException(... http://tinyurl.com/y9abozl
14:53 zarah [1422] Managers should be able to clo... http://tinyurl.com/yedkpbw
14:53 zarah [1443] Managers initialized in backgr... http://tinyurl.com/yzn393r
14:53 zarah [1723] Gist 95189 fails with exceptio... http://tinyurl.com/y9y2car
14:53 zarah Entire list (20) at http://tinyurl.com/y984qc2
14:53 masak @plan
14:53 zarah masak: bc2/console-test-jcterm: 1 h planned
14:53 zarah masak: bc2/managerdocs-improvements: 45 m planned
14:54 jonalv @help
14:54 zarah jonalv: avaliable commands are ask bcwiki botsnack clear-messages gist google help hi hug karma messages pelezilla ping plan planet pong ps replan restart seen slap start stop tell thanks tutorial unplan
14:55 masak @slap jonalv
14:55 * zarah jabs jonalv with a C pointer
14:55 jonalv zarah: why did you do that?
14:55 zarah jonalv: I did not understand that
14:55 jonalv zarah: you never seem to do...
14:55 zarah jonalv: I did not understand that
14:55 masak zarah: you're a smart girl.
14:55 zarah masak: So smart I'm looking for another job. Over.
14:59 user420396 left #bioclipse
15:55 sneumann Cool, just had a "private" conversation with zarah :-)
15:56 masak no details :P
15:56 jonalv sneumann++
16:06 masak zarah++
16:23 egonw jonalv: interesting post on mem usage by Java: http://www.unixville.com/~moazam/stories/2004/05/1​7/maxpermsizeAndHowItRelatesToTheOverallHeap.html
16:23 zarah egonw's link is also http://tinyurl.com/4gewq
16:24 jonalv egonw: looks itresting
16:25 egonw thanx to peter maas who hangs on here every now and then
16:39 jonalv Do anyone know of a manager method that opens the texteditor with a String?
16:41 ilbot2 joined #bioclipse
16:41 Topic for #bioclipseis now An open source workbench for chem- and bioinformatics - http://www.bioclipse.net/ | BioclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.org/irclogge​r/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse || Bioclipse2 beta released! See http://bioclipse.blogspot.com/ || http://www.youtube.com/watch?v=ZUBQknWUEYU
16:42 masak zarah: netsplit?
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