Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-12-08

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All times shown according to UTC.

Time Nick Message
06:27 sneumann joined #bioclipse
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08:51 egonw moin
08:51 zarah hi egonw
08:52 sneumann__ hi there
08:53 sneumann__ somebody was recently asking for a 2.6.32 kernel for better virtualisation memory efficiency ?
08:53 sneumann__ https://launchpad.net/~kernel-ppa/+archive/ppa
08:53 sneumann__ although that does not have too many details,
08:53 sneumann__ there is 2.6.32 in there: http://kernel.ubuntu.com/~k​ernel-ppa/mainline/v2.6.32/
08:53 zarah sneumann__'s link is also http://tinyurl.com/ylqtcoh
08:53 sneumann__ No clue about dependencies, though
08:54 egonw oh... thanx for the link...
08:54 egonw should be good for having multiple JVMs running too...
09:01 * egonw is amused by the fact that file name patterns change for bioclipse releases all the time
09:01 egonw sometimes bioclipse-2.x.y
09:02 egonw sometimes bioclipse2.x.y
09:11 egonw @pz ubuntu
09:11 zarah [1722] Patch boot scripts for platfor... http://tinyurl.com/yafe5c9
09:11 zarah [1559] R Console does not run on Ubun... http://tinyurl.com/yjtltxv
09:11 zarah Entire list at http://tinyurl.com/yeotm44
09:30 jonalv joined #bioclipse
09:38 jonalv oh hai
09:38 zarah oh hai jonalv
09:40 egonw hej jonalv
09:41 * jonalv rushes through that SADI slideshow
09:52 egonw Gpox: can you come over for a sec?
09:52 egonw I lost the JCP icons...
10:20 CIA-65 bioclipse.cheminformatics: Arvid Berg 2.2.x * rf13c578 / (2 files in 2 dirs):
10:20 CIA-65 bioclipse.cheminformatics: Added menu option for taking a snapshot.
10:20 CIA-65 bioclipse.cheminformatics: Solves bug #1732 - http://bit.ly/8bzQ4O
10:20 zarah bug #1732 | http://tinyurl.com/yaf7tgk
10:20 CIA-65 bioclipse.cheminformatics: Arvid Berg 2.2.x * r2c508ed / (7 files in 4 dirs):
10:20 CIA-65 bioclipse.cheminformatics: Added preference for showing 'Generated' label
10:20 CIA-65 bioclipse.cheminformatics: Fixes bug #1629 - http://bit.ly/5896d1
10:20 zarah bug #1629 | http://tinyurl.com/ygedkmc
10:37 egonw jonalv: ping
10:38 CIA-65 bioclipse.cheminformatics: jonalv 2.2.x * r9907e2a / plugins/net.bioclipse.cdk.business/src/ne​t/bioclipse/cdk/business/ICDKManager.java :
10:38 CIA-65 bioclipse.cheminformatics: added saveSDF with IProgressMonitor
10:38 CIA-65 bioclipse.cheminformatics: Can be used to call the saveSDFile with an already constructed monitor. - http://bit.ly/8VlekU
11:18 jonalv joined #bioclipse
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11:46 * egonw will reboot into a 2.6.32 kernel and try booting 10 Eclipse instances...
11:54 egonw_ joined #bioclipse
11:55 egonw_ so far, so good
11:55 egonw_ booted into 2.6.32
11:56 egonw_ looking nice
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12:02 egonw_ got 2 eclipses booted, and still got 2GB free mem (out of 4)
12:03 egonw_ booting instance 4 now
12:03 egonw_ grmph...
12:03 egonw_ I need to start making new workspaces... :)
12:04 egonw_ got 4 eclipse's running now... 1.3GB free
12:04 egonw_ 1.4
12:04 egonw_ it also seems to speed up booting
12:05 egonw_ (of eclipse)
12:05 egonw_ so, it seems to know what eclipse libs are already in memory?
12:06 jonalv joined #bioclipse
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12:06 egonw_ 6 instances running now :) 0.7GB free mem
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13:12 samuell egonw: I have errors reasoning with numerical values in pellet whatever I try.
13:12 samuell egonw: Maybe the problem is that I import the RDF data with Jena (rdf manager), while the reasoning is done with pellet?
13:12 samuell egonw: The error message I get seems to point in that direction: SPARQL syntax error: Found class com.hp.hpl.jena.graph.impl.LiteralLabel, but interface was expected
13:40 sneumann__ egonw is lost in virtual machines ...
13:40 sneumann__ trying to escaoe ...
15:37 egonw_ joined #bioclipse
15:37 egonw_ jonalv: ping
15:38 jonalv egonw_: pong
15:38 egonw_ jonalv: sdf reading problem was false alarm
15:38 egonw_ I'd forgotten to gunzip the file
15:38 jonalv egonw_: which one?
15:38 jonalv ah
15:38 jonalv hehe
15:38 egonw_ was under the impression that it did that automatically...
15:38 egonw_ which is only the case when using the ReaderFactory
15:50 jonalv egonw_: no idea
16:24 egonw_ jonalv: it is not calculating FPs for all ChEMBL structures
16:25 jonalv egonw_: uh, no the bucky ball of bor fails horribly
16:25 egonw_ hopefully
16:25 egonw_ it's around 250k structures now
16:26 jonalv egonw_: more things that fail?
16:27 egonw_ no, it's still running
16:27 egonw_ just takes time :)
16:28 jonalv ah hehe
16:34 CIA-65 bioclipse.structuredb: jonalv master * r5956532 / plugins/net.bioclipse.structuredb/src/net/b​ioclipse/structuredb/domain/DBMolecule.java : use a method call insted to be on the safe side - http://bit.ly/8hWBIy
16:44 egonw_ jonalv: it's still busy
16:44 egonw_ where's the code in structuredb that fails?
16:44 jonalv egonw_: Start StructureDB and try to import that file
16:45 jonalv I don't really remmeber. Did I post a stacktrace with the bug report perhaps?
17:00 egonw_ it's still running...
17:00 egonw_ the output to STDOUT does not really improve performance...
17:00 egonw_ will keep it running...
17:00 egonw_ but no crash so far
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17:33 egonw_ jonalv: it completed without problems
17:33 egonw_ now going back to dinner
17:33 jonalv egonw_: awesome, could you please check the problem instead of things that work? :)
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18:15 egonw_ jonalv: that was not amusing
18:15 egonw_ jonalv: you're a PhD... find the problem yourself? :)
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