Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-08-16

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All times shown according to UTC.

Time Nick Message
04:03 sneumann_ joined #bioclipse
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06:45 egonw moin
06:45 zarah privet egonw
06:46 egonw @tell dsurdyk I was, but had not noted your question...
06:46 zarah Consider it noted.
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07:48 jonalv hi
07:48 zarah hello jonalv, you fantastic person you
07:48 egonw_ hi jonalv
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11:44 dsurdyk Ola - are you here?
11:44 zarah dsurdyk: You have new messages. Write '/msg zarah @messages' to read them.
11:45 dsurdyk left #bioclipse
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11:48 olass hi dsurdyk
11:49 egonw hi dsurdyk
11:49 egonw [08/16/10 13:44] <zarah> dsurdyk: You have new messages. Write '/msg zarah @messages' to read them.
11:49 egonw but I think just typing @msg will do fine
11:49 egonw @msg
11:49 zarah egonw: You have no new messages.
11:53 sneumann_ If you want to keep your messages private, /msg zarah @messages is far better ...
11:53 egonw ah... good point
11:56 dsurdyk hi - yes i read that.  accidentally sent a "/ msg" so that's what likely published it.  sorry
11:56 dsurdyk and hi all
11:57 olass dsurdyk: did you get my replies?
11:57 olass makes sense?
12:00 dsurdyk i did
12:00 dsurdyk looks like i'm just good at finding bugs -
12:00 dsurdyk the google sites said that jar was in a subfolder
12:00 dsurdyk but it looks like it was just redirecting it to the root "/cibaupdatesite" folder
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13:23 dsurdyk hey all - what is the update site for installing Biojava 2.2.0 into a clean install of bioclipse?
13:23 dsurdyk i can't seem to find that in the wiki
13:27 egonw does bioclipse even have 2.2 ?
13:28 egonw ummm... dsurdyk: do you mean Bioclipse 2.2?
13:28 egonw as biojava seems to be at 1.7.1
13:28 egonw http://www.biojava.org/wiki/BioJava:Download
13:28 egonw and don't think bioclipse has that version
13:28 egonw last jar upload was from 2008 it seems:
13:29 egonw 2009:
13:29 egonw http://github.com/bioclipse/bioclipse.bi​oinformatics/commits/master/plugins/net.​bioclipse.biojava/jars/biojava-live.jar
13:32 dsurdyk I C - I just looked at it deeper, and the error seems to be a bit vague -
13:33 dsurdyk the biojava-for-bioclipse (as ola pointed out in an email) is part of the Bioinformatics_2.2.0 plugin
13:33 dsurdyk I guess that's what I was looking for - hopefully!
13:34 egonw yes, that's the one
13:34 egonw ping masak and me if you need a more recent BioJava
13:35 masak aye.
13:35 dsurdyk no the only issue I can see - is that I tried instaling my plugin, which requires Bioinformatics 2.2.0
13:35 dsurdyk only the update component didn't resolve the dependency correctly, and displayed an error - I have to get going, but I'll confirm that tonight.
13:37 dsurdyk Ok - so my plugin depends on net.bioclipse.logger
13:38 dsurdyk is that not part of the default bioclipse install?  or is that a developer only thing?
13:39 masak urgh, logging trouble again... :/
13:39 masak dsurdyk: it's not a developer-only thing. should be included.
13:41 dsurdyk well i just looked, and all my code uses the apache logger
13:42 dsurdyk "import org.apache.log4j.Logger"
13:42 dsurdyk so when I clicked on the "Compute" button in the feature
13:43 dsurdyk (i.e. on the feature's "dependencies" tab) ... it puts net.bioclipse.logger in there
13:43 dsurdyk is that reminants of old-version bioclipse stuff?
13:44 egonw something changed between BC 2.2 and BC 2.4
13:44 egonw let me check
13:45 dsurdyk ok - thanks.  for now I have to get to work - I'll check the logs later today.
13:45 egonw dsurdyk: better ask on the ML
13:45 egonw should not be checking this out right now
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16:18 CIA-71 bioclipse.brunn: jonalv jasper * r1101350 / (17 files in 3 dirs):
16:18 CIA-71 bioclipse.brunn: Work on the 384 wells plate report
16:18 CIA-71 bioclipse.brunn: Two troubles left. Can't get columns working in subreport and how to generate logarithmic axes on the diagram? - http://bit.ly/abDg8j
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