Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-06-11

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All times shown according to UTC.

Time Nick Message
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07:07 CIA-47 bioclipse: miguelrojasch * r5830 /bioclipse2/trunk/plugins/.classpath: removed file which was commit rev 5809 in the incorrect directory
07:08 CIA-47 bioclipse: miguelrojasch * r5831 /bioclipse2/trunk/plugins/.project: removed file which was commit rev 5809 in the incorrect directory
07:08 CIA-47 bioclipse: miguelrojasch * r5832 /bioclipse2/trunk/plugins/plugin.xml: removed file which was commit rev 5809 in the incorrect directory
07:09 CIA-47 bioclipse: miguelrojasch * r5833 /bioclipse2/trunk/plugins/build.properties: removed file which was commit rev 5809 in the incorrect directory
07:40 olas joined #bioclipse
08:01 CIA-47 bioclipse: ospjuth * r5834 /bioclipse2/trunk/plugins/net.bioclipse​.cdk10.jchempaint/src/net/bioclipse/cdk​10/jchempaint/ui/editor/JCPPage.java: Do not set default tooltip to AtomType, that was just for testing.
08:02 edrin joined #bioclipse
08:02 edrin hi
08:03 edrin http://xkcd.com/435/
08:12 olas hi edrin
08:17 egonw joined #bioclipse
08:18 egonw moin
08:18 jonalv hi egonw
08:21 jonalv eclipse crasc number 3 today :/
08:21 egonw not good
08:21 jonalv nope
08:21 jonalv but I am moving to a Mac real soon now. Leaving Ubuntu.
08:21 jonalv That should work beter
08:21 egonw hahahaha
08:22 jonalv egonw, just laughs. What's the secret?
08:22 jonalv :)
08:27 jonalv eclipse crash number 4 today :(
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08:29 olas right
08:29 olas hi egonw
08:30 egonw jonalv: the trouble with Eclipse here is that it si difficult to get a good stacktrace
08:30 egonw allowing one to file good bug reports
08:30 egonw hi olas
08:30 olas that is a major concern
08:30 olas we should try to sort that out asap
08:31 jonalv olas: We where talking about Eclipse in general but yea I guess the problem transfers to Bioclipse as well...
08:36 olas it does
08:36 olas and is something which is really annoying
08:37 olas if we can describe the problem accurately we could email the Eclipse platform or RCP newsgroup
08:38 jonalv uhm my problem is_: Eclipse crashes wihtout any pattern at all. I ahve seen complaints about permgenspace
08:38 jonalv that's all
08:38 jonalv something is leaking somewhere...
08:38 jonalv not easy to know what and where...
08:38 olas jonalv: you need to start with -Xmx512m
08:39 jonalv I think eclipse takes care about that because I have seen it using 700MB
08:40 olas strange
08:42 stain set permgen space in eclipse.ini
08:43 stain I have
08:43 stain -Xms40m
08:43 stain -Xmx512m
08:43 stain -XX:MaxPermSize=256m
08:43 jonalv what's the las one?
08:48 jonalv eclipse crash number 5 today :( // I don't think this one was memory related actually
08:49 egonw brb
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09:00 jonalv eclipse crash number 6 today
09:05 olas jonalv: you using new mac?
09:05 jonalv not yet
09:07 stain jonalv: the last one is the permgen space, which is basically the space used for Class and ClassLoader instances if I understand correctly.. which could happen easily if you use the Maven plugin or the J2ee modes
09:35 steinbeck joined #bioclipse
09:42 olas hi steinbeck
09:43 * olas is on lunch now
09:44 steinbeck Cheers olas
11:25 jonalv eclipse crash number 7 today
11:41 olas jonalv: get a mac
11:43 jonalv olas: I was working on that yesterday but I ran out of time...
11:43 edrin ... and become a puppet
11:43 edrin :)
11:43 olas MOHAHAHA
11:43 olas puppet on a mac
11:50 egonw yeah, ubuntu hardy must be the most unstable release in ages...
11:50 * egonw has a bloody annoying cold
11:50 egonw :(
12:02 jonalv egonw,  I think I  am running feisty :)
12:25 olas egonw: get some sleep
13:38 jonalv eclipse crash number 8 today. //First time it actually was permgen space
13:38 olas get a mac
13:42 CIA-47 bioclipse: jonalv * r5835 /bioclipse/trunk/playground/plugin​s/net.bioclipse.expression.tests/ (.classpath META-INF/MANIFEST.MF): Added dependency to junit4
13:59 * olas is away for a meeting
14:34 jonalv eclipse crash number 9 today. //Second time it actually was permgen space
14:35 jonalv maybe I should ahck eclipe.ini file :)
14:36 jonalv hm I already have -Xmx512m
14:36 egonw also add those other two lines
14:36 jonalv I had the first too
14:37 jonalv two
14:37 jonalv added the third now. Let's see if it makes any difference
16:14 CIA-47 bioclipse: ospjuth * r5836 /bioclipse2/trunk/plugins/net.bioclipse.pcore/: Initial import.
16:14 olas joined #bioclipse
16:16 CIA-47 bioclipse: ospjuth * r5837 /bioclipse2/trunk/plugins/net.bioclipse.pcore/ (20 files in 8 dirs): Initial import of a plugin to query a set of molecules for pharmacophore queries and visualize results in Jmol. More information: http://wiki.bioclipse.net/index.php​?title=Pharmacophore_visualization
16:18 olas left #bioclipse
16:27 CIA-47 bioclipse: jonalv * r5838 /bioclipse/trunk/playground/plugins/​net.bioclipse.expression/src/net/bio​clipse/expression/Calculator.java: don't throw SuppressedVariableException return Double.NaN instead
17:23 edrin anyone has access to this article: http://stke.sciencemag.org/cgi/cont​ent/abstract/sigtrans;2005/280/pe18 ?
17:30 edrin stain?
17:30 edrin rojasm: ?
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17:43 rojasm yes edrin
17:43 edrin do you have access to this article?
17:44 edrin rojasm: can you send me this article as pdf via mail?
17:44 edrin rojasm: i cannot receive dcc
17:45 edrin johannes.wagener at med.uni-muenchen.de
17:45 rojasm ok! your email?
17:45 rojasm ok
17:45 rojasm one moment
17:45 edrin :)
17:45 edrin great
17:46 rojasm done
17:47 edrin thanks very much
17:48 rojasm not problem
17:49 edrin rojasm: sorry to bug you, but my uni server removed the file 21386.0.pe18.pdf because of the filename... can you rename it to something else and maybe send again
17:49 edrin ?
17:49 rojasm yes
17:51 rojasm done
18:09 stain edrin: ?
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