Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-07-04

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All times shown according to UTC.

Time Nick Message
06:16 rojasm joined #bioclipse
06:18 egonw joined #bioclipse
06:25 Gpox joined #bioclipse
06:37 masak joined #bioclipse
06:38 egonw hi masak, Gpox
06:38 egonw hi berry_k
06:38 masak hello egonw
06:38 egonw berry_k: did you get any wiser on open source bioinformatics already?
06:38 masak egonw: your visit to Sweden coincides with my vacation :/
06:38 * egonw recommends the life science friend feed for nice discussions
06:38 egonw masak: yeah, that happens...
06:39 masak egonw: it would have been good to meet
06:39 masak egonw: yes, but this is the second time around
06:39 egonw http://friendfeed.com/rooms/the-life-scientists
06:39 zarah egonw's link is also http://tinyurl.com/6mw7qr
06:51 egonw zarah: dz
06:51 zarah you're welcome, egonw :)
06:51 egonw zarah: thanx
06:52 masak hm, 'thanx', I'll add that :)
06:53 egonw masak: dz
06:53 egonw :)
06:53 masak :)
07:00 masak zarah: restart
07:00 zarah joined #bioclipse
07:00 masak @clear
07:00 zarah masak: messages cleared
07:00 masak @thanx
07:00 zarah no, YOU'RE the cute one! :)
07:01 masak :)
07:13 rojas1 joined #bioclipse
07:27 egonw @tell olas is there really no way to have CDK's src/test in the build path without the export?
07:27 zarah Consider it noted.
07:53 EskilA joined #bioclipse
08:11 EskilA joined #bioclipse
08:15 jonalv joined #bioclipse
08:16 jonalv hi all
08:16 zarah hi jonalv
08:22 egonw hi jonalv
08:45 EskilA joined #bioclipse
09:52 EskilA joined #bioclipse
10:42 EskilA joined #bioclipse
10:43 EskilA Anyone here know anything about java graphics double buffering? I get flickering problems since i redraw graphics often in a JFreeChart widget
10:44 EskilA which is an awt/swing widget
11:09 egonw have the JFC lib write to a BufferedImage
11:10 egonw and plot the resulting image into your SWT window
11:10 egonw but I'd guess JFC should have double buffering itself too, not?
11:20 jonalv_ joined #bioclipse
14:21 egonw @tell olas making progress with the OWL atom type stuff... getting forward with CDK2Sybyl atom type mapping
14:21 zarah Consider it noted.
14:27 shk3 joined #bioclipse
14:28 shk3 hi
14:28 shk3 still problems running bc2
14:28 shk3 worked yesterday morning,
14:29 shk3 but after shutting down the computer it's no longer working
14:29 jonalv joined #bioclipse
14:29 jonalv hi all
14:29 zarah hi jonalv
14:31 shk3 ah jonalv
14:32 shk3 still can't run bc2 :-(
14:32 jonalv shk3, you can't?
14:32 jonalv what's your problem now?
14:33 shk3 The activator org.eclipse.ui.internal.WorkbenchPlugin for bundle org.eclipse.ui.workbench is invalid
14:33 shk3 but it keeps changing
14:33 shk3 i had
14:33 shk3 java.lang.IllegalArgumentException: The System Bundle's start level can not be modified.
14:33 shk3 first and after a clean it switched to the activator invalid
14:34 jonalv you have the invalid error now?
14:34 shk3 yes
14:34 jonalv shk3, could you give me the complete stack trace for it?
14:34 shk3 and
14:35 shk3 Caused by: java.lang.NoClassDefFoundError: org/eclipse/ui/plugin/AbstractUIPlugin
14:35 jonalv huh
14:35 jonalv never heard of that before...
14:35 jonalv you are running 3.4?
14:35 shk3 http://pastebin.com/m7c0e8e0a
14:35 zarah shk3's link is also http://tinyurl.com/64qxo6
14:35 shk3 yes, 3.4
14:38 jonalv shk3, you have very strange errors...
14:38 jonalv Is this in Ubuntu?
14:39 shk3 kubuntu
15:03 shk3 i can't even check out
15:03 shk3 is the svn repository working?
15:13 jonalv I think so, I just updated on my ubuntu machine
15:39 shk3 ok, working
15:39 shk3 i try a new checkout
15:40 shk3 only thing i can think of right now
15:51 shk3 hm, tried a checkout
15:52 shk3 the bundle org.openscience.cdk is missing
15:52 jonalv missing as in?
15:52 shk3 bundle org.os.cdk cannot be resolved
15:52 shk3 in MANIFEST.MF
15:53 jonalv did you do the checkout from eclipse?
15:53 shk3 eg. in net.bioclipse.cdk.business
15:53 shk3 yes
15:53 shk3 via subclipse
15:53 jonalv is org.openscience.cdk there? (Becaue I don't think subclipse handles the external correct)
15:54 shk3 where should it come from?
15:55 shk3 there is no such plugin, right?
15:55 jonalv that's cdk
15:55 jonalv from the cdk repo
15:55 jonalv or did I not understand the question?
15:56 shk3 I don't know
15:56 shk3 but cdk should not be required separatly in bioclipse
15:57 shk3 it should be in some plugin?
15:57 jonalv cdk is an osgi bundle these days I think
15:57 shk3 ok, so it should be there?
15:57 jonalv but can you run bioclipse without cdk?
15:58 jonalv (that would be a start at least) :)
16:01 shk3 yes
16:01 shk3 !!!!!
16:01 shk3 it runs!!!!!
16:02 shk3 i get errors on console, but it runs
16:02 jonalv what errors?
16:03 shk3 No suitable Log constructor [Ljava.lang.Class;@ec115b for org.apache.commons.logging.impl.Log4JLogger (Caused by java.lang.NoClassDefFoundError: org/apache/log4j/Category) (Caused by org.apache.commons.logging.​LogConfigurationException: No suitable Log constructor [Ljava.lang.Class;@ec115b for org.apache.commons.logging.impl.Log4JLogger (Caused by java.lang.NoClassDefFoundError: org/apache/log4j/Category))
16:03 shk3 seems to be logging
16:04 jonalv yey you got the logger error...
16:05 jonalv you are somehow running the wrong plugins... :(
16:06 jonalv Is that from the product or by addeing required plugins in the run dialog?
16:08 shk3 i added the minmal set from http://wiki.bioclipse.net/index.p​hp?title=Checking_out_Bioclipse_2
16:08 zarah shk3's link is also http://tinyurl.com/58kmzp
16:08 jonalv shk3, try by just launching the product in net.bioclipse.ui
16:08 jonalv you know how to do that?
16:09 shk3 that complains about errors in plugins
16:10 jonalv errors in pluigns?
16:10 jonalv lol
16:10 jonalv how many different error have you got now? :)
16:11 shk3 and if I proceed, i get similar errors to those in my old checkout
16:11 jonalv what does error in plugins mean?
16:12 shk3 it's this popup
16:12 shk3 saying "the following plugins have errors: ..."
16:12 jonalv doesn't it only come when some polkugin isn't compiling?
16:12 shk3 it's the plugins which don't compile
16:12 shk3 yes,
16:12 shk3 exactly
16:12 jonalv okey, what plugin doesn't compile?
16:14 shk3 lots
16:14 shk3 all net.bc.cdk ones
16:14 shk3 except
16:14 shk3 net.bc.cdk10
16:15 shk3 and
16:15 shk3 net.bc.cdk10.*
16:15 jonalv hm, why is that?
16:15 shk3 I think somehow stuff from net.bc.cdk10 isn't exported
16:15 shk3 all are missing the net.os.cdk bundle,
16:15 jonalv Didn't that cdk ant build fix all errors?
16:15 shk3 which should come from net.bc.cdk0
16:16 shk3 cdk ant buildÄ
16:16 shk3 ?
16:16 shk3 what's that?
16:16 shk3 I have no cdk checkout
16:16 shk3 do I need this?
16:16 jonalv in order to run the cdk stuff yea
16:16 shk3 hmpf, ok, will do this
16:17 shk3 but now i have to leave
16:17 shk3 sorry
16:17 shk3 hope in monday in uppsala we will get things running
16:17 jonalv http://wiki.bioclipse.net/index.php?title=Instruc​tion_for_how_to_check_out_and_compile_Bioclipse_2
16:17 zarah jonalv's link is also http://tinyurl.com/6nh6qk
16:17 shk3 ok, thanks
16:17 jonalv yea I am sure Gpox will get it running. He always does :)
16:17 jonalv cya
16:32 jonalv zarah, seen egonw?
16:32 zarah egonw was last seen 2008-07-04T14:21:42 in #bioclipse saying '@tell olas making progress with the OWL atom type stuff... getting forward with CDK2Sybyl atom type mapping'
16:44 jonalv zarah, tell shk3 I have Bioclipse 2 running on Ubuntu Feisty Fawn with Eclipse 3.3. I think you should try to remove org.apache.commons.logging from your run configuration when you get the logging error. BTW: structuredb requires Eclipse 3.4 :)
16:44 zarah Consider it noted.
17:34 egonw joined #bioclipse
17:34 egonw @messages
17:34 zarah egonw: You have no new messages.
17:34 egonw zarah: dz
17:34 zarah you're welcome, egonw :)
22:00 rojasm joined #bioclipse

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