Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-05-20

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All times shown according to UTC.

Time Nick Message
05:24 egonw joined #bioclipse
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07:47 jonalv egonw, olas net.biocliupse.cdk is not compiling right now...
07:48 jonalv I have removed stuff from Manifest.mf and that seems to do the trick
07:48 olas ok, please commit
07:50 CIA-45 bioclipse: jonalv * r5644 /bioclipse2/trunk/plugins/net.bioclipse.cdk/ (.classpath META-INF/MANIFEST.MF): Removed things from cdk manifest and updated classpath in order to keep up with changes in cdk. Hopes nothing in Bioclipse was depending on those parts...
07:56 egonw yeah, I have been cleaning up CDK trunk jar/
07:57 egonw btw, I have set up cdk/trunk/ as a Eclipse org.openscience.cdk plugin
07:57 egonw and hope to replace net.bioclipse.cdk with this new plugin
07:57 egonw but not today
07:58 jonalv egonw, sounds interesting
07:58 jonalv egonw, are you gonna play any more with structuredb? :)
07:59 egonw not today
07:59 egonw we have a university sports day today...
07:59 egonw so, preparing for an afternoon of golf :)
07:59 egonw and tomorrow a MetWare meeting
07:59 egonw which needs some preparations
07:59 jonalv oki
07:59 jonalv golf sounds nice
07:59 jonalv how's the weather?
08:00 egonw good
08:00 egonw 18 degrees C this afternon
08:00 egonw and verry sunny
08:00 jonalv sounds like you will have a nice afternoon then :)
08:03 jonalv creating the structure takes almost as long as persisting it
08:06 jonalv sometimes very much longer
08:10 egonw jonalv: please check out yourkit.com
08:10 egonw that's the company who hands out free licenses for open source projects
08:10 egonw which we use for the CDK
08:10 egonw per Rajarshi
08:10 egonw it's a good profiler
08:11 egonw and should be useful here
08:11 egonw you need to contact them and get a license per user...
08:11 egonw we don't have a CDK security code
08:11 egonw but each user has his/her own
08:11 egonw email Rajarshi Guha for details
08:38 * egonw is off
08:38 egonw have a nice day
08:39 egonw will visit Leiden tomorrow
08:39 egonw bye
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11:44 CIA-45 bioclipse: jonalv * r5645 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Fixed addstrucutrefromsdf in structuredb. It no longer repersists all structures already in the folder each time it persists a new structure in the folder(ooops) btw: It is much quicker now... :)
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14:21 CIA-45 bioclipse: jonalv * r5646 /bioclipse2/trunk/plugins/ (9 files in 6 dirs): Worked around one possible memory leak while importing sdf files in structuredb. It doesn't seem to be the only onw though since it still dies complaining about OUTOFMEMORY when running an SDF file of about 6 MB
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