Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-03-17

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All times shown according to UTC.

Time Nick Message
07:14 Annzi joined #bioclipse
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07:34 egonw joined #bioclipse
08:37 olas joined #bioclipse
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09:36 CIA-22 bioclipse: carl_masak * r5103 /bioclipse2/trunk/plugins/net.bioclipse.ui/sr​c/net/bioclipse/ui/views/NavigatorRoot.java:
09:36 CIA-22 bioclipse: [NavigatorRoot.java]
09:36 CIA-22 bioclipse: * whitespace
10:09 CIA-22 bioclipse: carl_masak * r5104 /bioclipse2/trunk/plugins/net.biocl​ipse.ui/src/net/bioclipse/ui/views/ (JsConsoleView.java ScriptingConsoleView.java):
10:09 CIA-22 bioclipse: [JsConsoleView.java]
10:09 CIA-22 bioclipse: * implemented "clear" command
10:09 CIA-22 bioclipse: [ScriptingConsoleView.java]
10:09 CIA-22 bioclipse: * new method `clearConsole` executes the above command
10:33 Annzi left #bioclipse
10:40 CIA-22 bioclipse: carl_masak * r5105 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/n​et/bioclipse/ui/views/ScriptingConsoleView.java:
10:40 CIA-22 bioclipse: [ScriptingConsoleView.java]
10:40 CIA-22 bioclipse: * adressed bug 1909650:
10:40 CIA-22 bioclipse:  "Some pasted commands give
10:40 CIA-22 bioclipse:  StringIndexOutOfBoundsException"
10:40 CIA-22 bioclipse: * this solution is questionable but works
10:41 Annzi joined #bioclipse
10:57 masak I'm troubled by the way ActionHistoryView imports classes with "discouraged access", in order to create views without file resources
10:57 masak I think we should go to the Eclipse people and try to resolve that differently
11:10 egonw lunch, bbl
11:36 steinbeck joined #bioclipse
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14:07 CIA-22 bioclipse: jonalv * r5106 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Cleaned up code in BioList and started implementing tests for it (I know I am doing this in a somewhat reversed order (better to write tests first) please forgive me)
14:14 steinbeck joined #bioclipse
14:35 CIA-22 bioclipse: egonw * r5107 /bioclipse2/trunk/plugins/net.bioclipse.cdk10/ (9 files in 4 dirs): Starting to add stuff for a CDK 1.0 plugin
14:42 olas egonw++
14:50 egonw crap
14:50 egonw Java on Ubuntu hardy sucks
14:51 egonw it looks like Java on OS/X
14:51 egonw looks := tries-to-run
14:52 jonalv huh?
14:53 egonw you remember I had those crashes last week?
14:53 egonw when I wanted to update some .cdk problem...
14:53 egonw well, I still got them...
14:53 egonw making Eclipse practically useles
14:53 jonalv okey
14:53 jonalv aouch
14:58 olas install from eclipse.org?
15:00 egonw yes
15:08 egonw any change I make to the build path crashes the system...
15:08 egonw seems to have to do with the Navigator tree update...
15:08 egonw error log shows some font lib problem...
15:10 * egonw will try the 3.2 that comes with Ubuntu
15:15 egonw and discovers that BC2 *really* needs 3.3 :(
15:15 egonw OK, no BC2 development possible at Hardy :(
15:15 * jonalv will not upgrade
15:15 jonalv hang on btw. HArdy? that's not even released is it?
15:16 egonw no, not until some weeks...
15:16 jonalv lol, well I hope you have filled apropiate error rapport about this...
15:16 egonw I tend to switch about 1 month in advance, to be able to give some bug feedback...
15:16 egonw well, Hardy is more unstable four weeks ahead than gutsy and feisty combined
15:16 egonw this one is really to deep...
15:17 jonalv I tend to switch 1-6 months after in order to have a smoth ride :)
15:17 egonw the error log shows 100+ trace lines...
15:17 jonalv aouch
15:17 egonw this one is too deep
15:17 egonw I have absolutely no hope this will be fixed before the release, or after it, for that matter...
15:18 * jonalv is still running feisty btw :)
15:23 CIA-22 bioclipse: jonalv * r5108 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): More work on Biolist. 3 tests fail. 2 of them are really complicated to fix and will not work for quite some time, if ever.
15:24 * jonalv is gonna check out complete bioclipse 2 trunk from commendline now. Do it the egonw way :)
15:24 egonw at least 3.2 will allow him to get net.bioclipse.cdk10 in order, in terms of compile errors...
15:24 egonw but the rest of BC2 fails
15:24 jonalv hm I think I will not only take the trunk but the the complete bc2 part :)
15:29 rojasm left #bioclipse
15:44 CIA-22 bioclipse: egonw * r5109 /bioclipse2/trunk/plugins/net.bioclipse.cdk10/ (. .classpath META-INF/MANIFEST.MF): Cleaned up classpath: I don't have white crosses on red boxes anymore
15:46 egonw ok, enough BC2 for now
15:46 olas NOOO
15:46 olas egonw: mor eBC2
15:46 jonalv egonw, Do you not like us any longer? :(
15:47 egonw not today, no
15:47 * masak cries bitterly
15:47 egonw please try net.bioclipse.cdk10 for your installs...
15:47 egonw next step would be to make
15:47 egonw cdk10.jchempaint
15:48 egonw with a new cdk10-based, BC2-oriented JCP editor
15:48 egonw but got really no clue how to approach that
15:48 egonw as I have hardly been involved in the BC1 JCP editor
15:48 jonalv what's in cdk10?
15:48 egonw CDK 1.0 tree
15:48 olas a tree?
15:48 egonw n.b.cdk is CDK from trunk
15:48 egonw branch
15:48 olas right
15:48 egonw no, tree...
15:49 egonw major branch with a few tags...
15:49 egonw it does currently not really contain smaller branches though
16:04 jonalv bah eclipse crash :(
16:04 egonw yeah? you too?
16:05 egonw cool :)
16:05 jonalv egonw,  that cdk10 doesn't work pwrfectly
16:05 jonalv I have manifest problems
16:05 jonalv in it
16:05 egonw brilliant
16:05 egonw so it might not be my Eclipse that is bad...
16:05 egonw bad the plugin content?
16:05 egonw but the...
16:05 jonalv I don't think any mapis set as source
16:07 egonw ah, might that be the reason...
16:08 egonw cdk10 only has a svn:externals in src/
16:08 egonw ok... will add the missing Activator class...
16:09 egonw and let's see if that helps...
16:09 egonw btw, Eclipse3.2 does not crash on the cdk10/ plugin
16:09 jonalv you don't have any build.properies either
16:09 egonw btw, I too am totally lost in this OSGi/Spring boot system mango-tango
16:10 jonalv yea I feel somewhat lost too....
16:10 jonalv But I think Richard has some good ideas
16:10 egonw yeah, it seems so
16:10 egonw which is good :)
16:10 egonw this is how OS works
16:10 jonalv yea :)
16:13 jonalv egonw, there is also an issue with org.apache.commons in cdk10...
16:13 egonw umm... no
16:13 egonw should not be
16:13 egonw those classes should be in Exclude from Build Path
16:13 jonalv okey but I have :/
16:14 jonalv okey I did something here maybe I messed taht up..
16:14 egonw yeah, likely :)
16:14 egonw hehehehe
16:14 CIA-22 bioclipse: egonw * r5110 /bioclipse2/trunk/plugins/net.bioclipse.cdk10/ (5 files in 4 dirs): Added some missing stuff
16:14 * jonalv is reverting
16:14 egonw ok, please update
16:15 * egonw will try E3.3
16:16 egonw no, EC3.3 still crashes
16:16 egonw on start up again :)
16:18 jonalv egonw, now I have only one problem left
16:18 egonw which is?
16:18 jonalv org.openscience.cdk.iupac can not be located
16:18 egonw what needs it?
16:18 jonalv export package in manifest
16:20 egonw I'm sure I removed that...
16:21 egonw and it does not show up here...
16:21 egonw no, it does...
16:21 jonalv olas, ping
16:22 CIA-22 bioclipse: egonw * r5111 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk10/META-INF/MANIFEST.MF: Removed .iupac
16:23 jonalv great, now it compileas. What's next? :)
16:23 egonw jonalv: please try now
16:23 egonw ah... porting the old jchempaint plugin
16:23 egonw from BC1
16:23 egonw but that's not for today...
16:23 egonw got to make dinner now
16:23 jonalv nope
16:23 jonalv okey
16:24 jonalv olas, ping
16:26 egonw bbl
16:30 rklancer joined #bioclipse
16:31 egonw hi rklancer
16:31 rklancer hiya
16:31 egonw jonalv: turns out I don't need to help with dinner
16:31 rklancer It's dumb of me to go on irc I should put my head down and work :)
16:32 egonw he, IRC is not about chatting...
16:32 rklancer true
16:32 egonw it's about getting things done
16:32 egonw (and chatting, hahahaha)
16:32 rklancer and that's why I'm on it
16:32 jonalv =)
16:32 jonalv rklancer, I just read you mail
16:33 rklancer And yes that applies to both of your comments egonw
16:33 rklancer :)
16:33 * egonw too is clueless about all this OSGi and Spring booting stuff... and is looking forward to what rklancer is coming up with
16:33 rklancer okay, well my first job is to get logging startup in a good place so I can put that to bed for a while
16:33 rklancer I'm happy Grant is interested in the Ant build stuff
16:34 rklancer getting to that was my initial motivation for working on the logging stuff b/c logging issues seemed to block further progress on exporting
16:36 * egonw is downloading E3.4 M5
16:36 egonw maybe that does not crash
16:37 steinbeck 'course it does
16:37 rklancer after that (s/b very soon) I'd love to sort out the Spring startup thing ... I do have to read up on Spring and study n.b.core though
16:37 egonw rather do that than install a Ubuntu gutsy (K)VM
16:37 egonw steinbeck: that meeting... will that be about metabolites too?
16:37 egonw that is, how does ChEBI fit in your metabolomics plans?
16:38 rklancer am I crazy or does even 3.3
16:38 rklancer oops
16:39 rklancer 3.3 does just lose its mind occasionally right?
16:39 egonw my E3.3 crashes on net.bioclipse.cdk and .cdk10 for BC2
16:40 rklancer okay well glad I don't need to work on those yet :(
16:40 egonw hehehe
16:40 rklancer (all that maintenance of state...sometimes I'm amazed that any complex software keeps running for more than a week)
16:42 egonw :)
16:44 rklancer oops gotta run...so much for work :(
16:47 steinbeck egonw: it will be not much more than mentioning the metabolomics context.
16:47 steinbeck no deep discussions
16:47 egonw ack
16:54 egonw EC3.4 is booting
16:55 jonalv cool
16:55 egonw no crash so far
16:55 egonw building at 33%
16:55 jonalv yey
16:55 egonw 34%
16:55 egonw 35
16:56 egonw done
16:56 egonw including the crash :)
16:56 jonalv you crashed again?
16:56 egonw well, Eclipse did
16:56 egonw ok, dinner time
16:56 egonw bye, cu later
16:56 jonalv cya
16:57 CIA-22 bioclipse: jonalv * r5112 /bioclipse2/trunk/plugins/net.​bioclipse.usermanager.tests/: svn ignore on generated file
19:08 Annzi left #bioclipse
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