Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-04-22

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All times shown according to UTC.

Time Nick Message
03:56 egonw joined #bioclipse
04:56 egonw_ joined #bioclipse
06:19 egonw joined #bioclipse
06:45 Gpox joined #bioclipse
06:57 Gpox hio
07:10 mgerlich joined #bioclipse
07:14 egonw hi Gpox
07:15 * Gpox got bioclipse almost running with logback
07:16 egonw logback?
07:17 Gpox logging backend for slf4j, which in turn captures the log4j messages
07:17 egonw what is good about this? that is, I sense it solves something, but not sure what precisely
07:18 Gpox works with apache.commons.logging and java.util.Logging too
07:18 egonw does it also mean we get rid of Import: clauses in our manifest files?
07:18 Gpox so all logging is loged to one place
07:19 Gpox no, still using log4j. We could use java logging to avoid that dependencie
07:19 sneumann joined #bioclipse
07:22 Gpox I now get lots of Spring debug messages, dunno where they whent before
07:30 Gpox http://logback.qos.ch/reasonsToSwitch.html
07:30 zarah Gpox's link is also http://tinyurl.com/2fefrj4
07:39 egonw Gpox++
07:39 egonw do you think this can be backported to 2.4 ?
07:39 egonw sounds like it will make debugging a lot easire
07:39 egonw sounds like it will make debugging a lot easier
07:41 egonw wow -> http://logback.qos.ch/reason​sToSwitch.html#packagingData
07:41 zarah egonw's link is also http://tinyurl.com/2fefrj4
07:41 egonw love to see that in action on bioclipse!
07:42 egonw cool licensing too!
07:44 Gpox The eclipse plugin is outdated :/
07:44 egonw eclipse--
07:44 egonw well, Gpox...
07:44 egonw why not make a eclipse patch ? :)
07:45 Gpox is is the logback plugin, colored logging output
08:06 olass joined #bioclipse
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08:49 jonalv joined #bioclipse
09:05 masak joined #bioclipse
09:06 egonw moin all
09:06 zarah ni hao egonw
10:06 jkutzer joined #bioclipse
10:06 s_wolf joined #bioclipse
11:16 jonalv` joined #bioclipse
11:34 CIA-61 bioclipse.brunn: jonalv master * r9aeb23b / (4 files in 2 dirs): wrote help for master plate - http://bit.ly/bUKCgo
11:34 CIA-61 bioclipse.brunn: jonalv master * r8dffa76 / (4 files in 2 dirs): help text for plates - http://bit.ly/bSIgEi
12:01 olass joined #bioclipse
12:22 samuell joined #bioclipse
13:32 egonw olass: http://chem-bla-ics.blogspot.com/2010/​04/cip-rules-for-stereochemistry.html
13:32 zarah egonw's link is also http://tinyurl.com/2d844lc
13:34 olass I take it he replied with a yes then to go public?
13:34 egonw quite so :)
13:34 olass did you get more input?
14:09 egonw good... pellet burner refilled, wood chopped for the kachel...
14:10 egonw so, ready for some CDK hacking
14:25 edrin BioTorrent reads almost like BioTerror
14:26 egonw :)
14:27 egonw masak: did you make progress with your header/javadoc-fix script?
14:27 masak was just going to look at that :)
14:27 egonw masak++
15:06 masak mail's away.
15:08 jonalv egonw: how do I install Sun Java 5 on Ubuntu 9.10?
15:08 egonw compile from source, I think
15:11 jonalv egonw: oh, so I am guessing you haven't done it?
15:19 jonalv egonw: but how are you doing then? You simply live with a broken Bioclipse?
15:29 jonalv egonw: ping
15:43 egonw jonalv: indeed
15:44 egonw jonalv: but it just the editor that is really visible broken
15:44 egonw got to go for dinner now
15:44 egonw bbl
15:44 egonw bye
15:44 jonalv egonw: hm
16:14 egonw joined #bioclipse
16:15 egonw jonalv: ping, I'm back from dinner
16:16 jonalv egonw: I am building an Ubuntu image for test running  Bioclipse Brunn
16:16 jonalv egonw: I just thorugh mayeb we want Jav 5 for that...
16:16 egonw image?
16:17 jonalv uhm virtual box
16:17 egonw ah, ack
16:17 egonw @google bioclipse wiki ubuntu karmic
16:17 zarah egonw: http://saml.rilspace.com/content/runni​ng-ubuntu-karmic-koala-and-sun-java-6
16:17 egonw @google ubuntu karmic site:wiki.bioclipse.net
16:17 zarah egonw: http://wiki.bioclipse.net/ind​ex.php%3Ftitle%3DUbuntuKarmic
16:17 egonw that's better :)
16:18 egonw jonalv: check that page for pointers
16:18 jonalv egonw: yea I saw that after you left
16:18 jonalv I even tried to build it
16:18 jonalv nost successfull though :(
16:18 jonalv |not
16:18 jonalv now I am fighting wtih your shell script
16:20 egonw ah, for the gtk workarouond?
16:20 jonalv yea
16:23 jonalv egonw: also we don't have a Bioclispe icon for linux?
16:23 egonw what's that?
16:23 egonw a bioclipse icon for linux?
16:23 jonalv google icon
16:23 zarah jonalv: http://www.rideicon.com/
16:24 jonalv uhm lol
16:24 jonalv egonw: yea there is no icon for bioclispe in linux
16:24 jonalv how bad is that?
16:24 egonw last time I checked, icon's were not platform dependent
16:24 egonw icons
16:24 egonw no '
16:24 jonalv egonw: I mean in the build for linux
16:25 egonw oh
16:25 egonw dunno about that
16:25 egonw never noticed
16:25 jonalv gtg
16:25 Gpox /net.bioclipse.ui/icons/molecule3D.xpm
16:30 jonalv Gpox: cool /I wil try with that one tomorrow
16:30 Gpox that what is set in the bioclipise.product
16:30 Gpox for linux
16:30 jonalv zarah: tell jonalv /net.bioclipse.ui/icons/molecule3D.xp
16:30 zarah jonalv: You can tell yourself that.
16:30 jonalv zarah--
16:30 egonw Gpox: do you know if some git am --directory trick is available to strip some folders from the patch?
16:31 egonw if someone, say masak, did not use --relative?
16:31 notjonalv zarah: tell jonalv /net.bioclipse.ui/icons/molecule3D.xp
16:31 zarah Consider it noted.
16:31 Gpox zarah: tell jonalv /net.bioclipse.ui/icons/molecule3D.xpm
16:31 zarah Consider it noted.
16:31 masak --relative?
16:31 egonw notjonalv++
16:31 jonalv okey now zarah will remind me tomorrow
16:31 zarah jonalv: You have new messages. Write '/msg zarah @messages' to read them.
16:31 egonw masak: yeah, is cool git magic I learned from Gpox++
16:31 masak ah, nice option.
16:31 masak will do next time :)
16:32 egonw :)
16:32 Gpox git am --directory=cdk-externals/trunk/org​.openscience.cdk.controlbasic/src/ ../patches/*
16:32 Gpox it is in the git wave
16:33 egonw yeah, but that's if the patch has paths like main/org/openscience/cdk/... etc, not?
16:34 CIA-61 bioclipse.ds: Ola Spjuth master * rf4871ff / (7 files in 5 dirs): Added a stub for Generator-based visualization. - http://bit.ly/dt1qwU
16:34 CIA-61 bioclipse.ds: Ola Spjuth master * r7fffc87 / plugins/net.bioclipse.ds/src/net/​bioclipse/ds/ui/views/DSView.java :
16:34 CIA-61 bioclipse.ds: Updated DSView to copy properties from clone
16:34 CIA-61 bioclipse.ds: and turn on Generators. - http://bit.ly/9quKTs
16:34 CIA-61 bioclipse.ds: Ola Spjuth master * ra5a33d6 / (11 files in 7 dirs): Switched to Generator-based rendering of results in JCP. - http://bit.ly/9ik0O2
16:34 CIA-61 bioclipse.ds: Ola Spjuth master * r333fcf3 / (87 files in 38 dirs): Added bursi and cpdb endpoints to DS. - http://bit.ly/bLaUVA
16:35 Gpox -p<n> but that might only take slashes
16:35 egonw will try that
16:37 egonw git am --directory=src/main -p4 ~/Desktop/0001-plugins-de-Jav​adoc-numerous-comments.patch
16:37 egonw works
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20:18 edrin_ joined #bioclipse
20:19 edrin_ hi egon
20:19 edrin_ do you know this ? http://www.youtube.com/watch?v=​eFjXgsCcN9Q&amp;feature=related
20:19 zarah edrin_'s link is also http://tinyurl.com/25yxc2a
20:19 edrin_ ok, maybe you have better things to do ;)
22:13 samuell joined #bioclipse

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