Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-10-15

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All times shown according to UTC.

Time Nick Message
06:04 sneumann joined #bioclipse
06:29 egonw joined #bioclipse
06:57 egonw moin
06:57 zarah hello egonw, you fantastic person you
06:57 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
07:09 sneumann joined #bioclipse
07:13 egonw @msg
07:13 zarah egonw: 18 h 3 m 12 s ago, Gpox said My patches are in more-edit-patches http://pele.farmbio.uu.se/git/gpox-jchempaint.git
07:14 egonw @tell Gpox thanx!
07:14 zarah Consider it noted.
08:13 miguelrojasch joined #bioclipse
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08:23 jonalv oh hai
08:23 zarah hi jonalv
08:25 samuell joined #bioclipse
08:40 edrin joined #bioclipse
08:42 CIA-51 bioclipse.structuredb: jonalv master * r8c2fb5e / plugins/net.bioclipse.structuredb/src/net/biocli​pse/structuredb/business/StructuredbManager.java :
08:42 CIA-51 bioclipse.structuredb: fireAnnotationChanged when annotations change.
08:42 CIA-51 bioclipse.structuredb: The databases view is now updated when a new annotation is created. Fixes bug: #1644. - http://bit.ly/1VeHLE
08:43 zarah bug #1644 | http://tinyurl.com/yzalor3
08:54 CIA-51 bioclipse.structuredb: jonalv master * rac7a3c5 / plugins/net.bioclipse.structuredb/src/​net/bioclipse/structuredb/viewer/Struc​tureDBLightweightLabelDecorator.java :
08:54 CIA-51 bioclipse.structuredb: try catch in decorate method
08:54 CIA-51 bioclipse.structuredb: If an exception is thrown here the decorators are turned off. Now they at least
08:54 CIA-51 bioclipse.structuredb: stay on but we might end up with a long stack trace in the log but if someone
08:54 CIA-51 bioclipse.structuredb: finds that we know what went wrong at least.. - http://bit.ly/1hdZwl
09:02 sneumann joined #bioclipse
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09:13 CIA-51 bioclipse.rdf: Egon Willighagen 2.2.x * rc06a0b4 / (2 files): Implemented searching for BSLs on MyExperiment (implements #1655) - http://bit.ly/4hODnU
09:40 masak joined #bioclipse
09:47 olass joined #bioclipse
09:48 jonalv egonw: ping
09:48 egonw pong
09:49 masak oh hai
09:49 zarah hi masak
09:49 jonalv egonw: I don't wanna disturb olass and maybe you can help
09:49 * egonw is disappointed in the swedish culture
09:49 masak ok, here's the deal.
09:49 egonw I'll try
09:49 masak I created a branch 2.2-releng in .core
09:49 masak I've been committing bug fixes to that branch.
09:49 * egonw feels an urge to become a swedish politician
09:49 jonalv the core repo conatins the folloowing branches: 2.0.x, 2.2-releng, and master
09:49 jonalv what do I commit where?
09:49 masak egonw: I know. I'm sorry too.
09:50 egonw masak: 2.2-releng?
09:50 masak egonw: 2.2-releng.
09:50 jonalv egonw: shouldn't master contain all new stuff fancy stuff including bug fixes?
09:50 egonw what does the releng refer too?
09:50 masak release engineering.
09:50 egonw master will inherit everything from the branch
09:50 masak exactly.
09:50 egonw so, anything you put in the 2.2 branch will be part of 2.4 too
09:51 masak aye.
09:51 egonw that's up to the branch managers to take care of
09:51 masak jonalv's question is about backporting features.
09:51 jonalv egonw: so when I make a commit to 2.2 I should chreey-pick it into master?
09:51 egonw ouch...
09:51 egonw jonalv: no
09:51 masak I feel slightly doubtful about cherry-picking to master.
09:51 masak I would like to merge, preferably once.
09:52 egonw jonalv: but we have not made a policy of how to and how often to merge 2.2 with master
09:52 egonw masak: same here...
09:52 jonalv egonw: but, you jsut said that everything in 2.2 should go into 2.4 and master is 2.4 now right?
09:52 egonw makes automerging more tricky
09:52 egonw jonalv: yes, but the *branch manager* will do that
09:52 jonalv egonw: oh you have a policy? Can you explain this policy to me please?
09:53 egonw actually... cherry-picking should be OK, *if and only if* the patches are identical
09:53 egonw then the 'git merge' should (TM) recognize that
09:53 egonw you know... what possibly could go wrong ...
09:54 egonw I have a policy?!
09:54 egonw no, I just said we do *not* have a policy on how to keep master up to date with the current stable branch
09:54 egonw -es
09:55 egonw I'm pretty sure I need to port a few patches from 2.0 into 2.2
10:30 CIA-51 bioclipse.core: jonalv 2.0.x * rbdcd980 / plugins/net.bioclipse.ui/src/net/biocli​pse/ui/prefs/UpdateSitesEditDialog.java :
10:30 CIA-51 bioclipse.core: Made UpdateSitesdialog resizable.
10:30 CIA-51 bioclipse.core: Makes it easier to write really long paths to update sites. Fixes bug: #1652. - http://bit.ly/jkTDn
10:30 CIA-51 bioclipse.core: jonalv 2.2-releng * ra8f02fd / plugins/net.bioclipse.ui/src/net/biocli​pse/ui/prefs/UpdateSitesEditDialog.java :
10:30 zarah bug #1652 | http://tinyurl.com/yz98yle
10:30 CIA-51 bioclipse.core: Made UpdateSitesdialog resizable.
10:30 CIA-51 bioclipse.core: Makes it easier to write really long paths to update sites. Fixes bug: #1652. - http://bit.ly/4emaEN
10:30 zarah bug #1652 | http://tinyurl.com/yz98yle
10:30 CIA-51 bioclipse.core: jonalv master * r5ced915 / plugins/net.bioclipse.ui/src/net/biocli​pse/ui/prefs/UpdateSitesEditDialog.java :
10:30 CIA-51 bioclipse.core: Made UpdateSitesdialog resizable.
10:30 CIA-51 bioclipse.core: Makes it easier to write really long paths to update sites. Fixes bug: #1652. - http://bit.ly/1jFh2i
10:30 zarah bug #1652 | http://tinyurl.com/yz98yle
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14:18 edrin hm...
14:41 jonalv hm...?
14:41 masak hm...!
14:50 edrin definitely :)
15:24 edrin joined #bioclipse
15:28 jonalv java.lang.LinkageError: loader constraints violated when linking org/apache/log4j/Logger class
15:28 jonalv I think we have multiple versions of log4j around sudeenly
15:35 CIA-51 bioclipse.structuredb: jonalv master * r9baa3d4 / plugins/net.bioclipse.structuredb/s​rc/net/bioclipse/structuredb/intern​albusiness/LoggedInUserKeeper.java :
15:35 CIA-51 bioclipse.structuredb: class synchronized, no null return but exception
15:35 CIA-51 bioclipse.structuredb: Synchronized the whole class and made the method throw an exception instead complaining about no user logged in instead of returning null - http://bit.ly/4s5e2v
15:35 CIA-51 bioclipse.structuredb: jonalv master * rbb90e26 / (2 files in 2 dirs):
15:35 CIA-51 bioclipse.structuredb: Speeded up and added time est. to drop db
15:35 CIA-51 bioclipse.structuredb: Only remove the file and then drop the entire database file. Also added estimating time remaining text. - http://bit.ly/47lgDS
15:35 CIA-51 bioclipse.structuredb: jonalv master * raf5aea2 / (3 files in 3 dirs): Rename Annotation action - http://bit.ly/1egaZ0
15:41 jonalv guys we have log4j all over the palce again
15:42 jonalv egonw: ping
15:43 egonw pong
15:43 jonalv egonw: do you know which log4j jar file we should use?
15:44 jonalv egonw: try openining a class named Logger in you Bioclispe checkout. How many do you have?
15:44 jonalv org.apache.log4j.Logger that is. I have it at 4 different places
15:44 jonalv and that is what give me java.lang.LinkageError: loader constraints violated when linking org/apache/log4j/Logger class
15:51 egonw mom, booting eclipse
16:27 egonw jonalv: yes, I see multiple apache log4j's too...
16:28 jonalv egonw: that is just one of the problems I am having right now
16:28 egonw file bug reports...
16:28 jonalv egonw: it's structuredb
16:28 * egonw thought he had already removed the one from hp.hpl.jena
16:28 egonw sorry about that...
16:28 jonalv I think I am going to give up
16:29 jonalv for the moment nothing worlks
16:29 egonw on export? or when running from eclipse?
16:30 jonalv from eclipse
16:31 egonw but structuredb is not depending on rdf, is it?
16:31 egonw bbl
16:38 * jonalv get OutOfMemoryExceptions now
16:39 jonalv YourKit points me in the directions of a Logger instance inside JsEnvironment. I don't understand at all. I give up now
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