Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-07-23

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All times shown according to UTC.

Time Nick Message
05:21 rojasm joined #bioclipse
06:19 Gpox joined #bioclipse
06:41 egonw joined #bioclipse
07:17 jonalv joined #bioclipse
07:17 olas joined #bioclipse
07:18 olas hi all
07:18 zarah hi olas
07:18 jonalv moin
07:18 zarah hi jonalv
07:18 olas moin
07:18 zarah hi olas
07:18 olas moin?
07:18 olas @msg
07:18 zarah olas: You have no new messages.
07:19 olas zarah: I know
07:19 zarah olas: I'm just a bot, you expect me to understand that?
07:19 jonalv yea learned that word during my week off :)
07:19 olas in germany?
07:19 jonalv yea
07:20 olas zarah: guten morgen
07:20 zarah olas: I did not understand that
07:20 jonalv olas: http://en.wikipedia.org/wiki/Moin
07:20 zarah jonalv's link is also http://tinyurl.com/39azxx
07:21 olas :-)
07:31 egonw moin
07:31 zarah hi egonw
07:32 egonw @msg
07:32 zarah egonw: You have no new messages.
07:32 egonw damn, we pass around too few messages
07:32 egonw my blog of last night was a hit
07:32 egonw 68 reads on the first day
07:33 masak joined #bioclipse
07:35 olas egonw: nice
07:35 CIA-40 bioclipse: ospjuth * r6217 /bioclipse2/trunk/plugins/net.bioclipse.molfilter​.editor/src/net/bioclipse/molfilter/presentation/ (MolfilterActionBarContributor.java MolfilterEditor.java): Added global action to add new analysis.
07:43 jonalv olas: CAn you export Bioclipse from OSX? I get a strange IllegalArgumentException...
07:43 olas that has ahppened to me as well
07:44 olas I'll try again today
07:44 jonalv any ideas?
07:44 olas no
07:44 olas somehow I got rid of it
07:44 olas have no idea how
07:44 olas restart eclipse :-) ?
07:45 * jonalv is trying from Windows
07:45 olas actually, export seems buggy in ganymede
07:45 olas jonalv: should we have a pring-feature?
07:45 olas spring
07:45 olas to hold the spring plugins?
07:46 jonalv the target platfrom holds the Spring plugins
07:46 jonalv or?
07:46 jonalv which are you thinking off?
07:46 olas yes, but that is not included when you export
07:46 olas now it's packed into the product
07:46 egonw @tell shk3 that nmrshiftdb.ice.mpg.de is down in some kind: header, footer but no front page content
07:46 zarah Consider it noted.
07:47 olas so in the bioclipse-fearure
07:47 olas I just thought it would be wise to separate it from Bioclipse
07:47 olas to me it feels like a new feature
07:48 olas but hey, it matters not much
07:48 jonalv olas: I don't really know. Isn't all plugins from the target platform included?
07:48 jonalv when exporting?
07:48 olas we now move to feature-based build
07:48 jonalv then again if we switch to a feature oriented export than maybe we must make a feature for them?
07:49 olas so all plugins are listed in a feature
07:49 olas now all are in one single feature, bioclispe-feature
07:49 olas which could be split in more, if we deem it necessary
07:49 jonalv I don't think it's wrong to have them all in a core feature...
07:50 olas no, definitely not wrong
07:50 olas just makes that feature large and hard to navigate
07:50 olas try debugging errors in the feature and you'll see :-)
07:50 olas maybe for the future then
07:51 jonalv I must admit that I haven\t used features at all so I don't know...
07:51 jonalv Brunn is plugin oriented you know :)
07:52 olas ok, we should try to set up the list of things for the first alpha release
07:52 olas there is a wiki page
07:52 olas http://wiki.bioclipse.net/index.p​hp?title=Bioclipse2_release_plan
07:52 zarah olas's link is also http://tinyurl.com/5guree
07:52 jonalv link?
07:52 olas it's old
07:52 olas and needs updating
07:52 jonalv okey
07:52 olas but let's do that together
07:52 olas and list things that we want tested as well
07:53 olas hmm
07:53 olas I need to update the versions
07:53 olas since we decided it should be 2.0RC1-alpha
07:53 olas I will edit now
07:54 jonalv yey
07:57 * jonalv can report succesfull export from Windows
08:03 olas nice
08:03 olas ok, I have updated the page
08:03 olas http://wiki.bioclipse.net/index.p​hp?title=Bioclipse2_release_plan
08:03 zarah olas's link is also http://tinyurl.com/5guree
08:04 olas what do you think?
08:16 CIA-40 bioclipse: carl_masak * r6218 /bioclipse2/trunk/plugins/n​et.bioclipse.ui.scripting/: [net.bioclipse.ui.scripting] removed in favor of scripting.ui
08:16 masak jonalv++, olas++ # turns out I had the plugin marked up for deletion, but uncommitted
08:17 olas masak: can zarah detect msg from teh commit bot?
08:17 masak olas: not yet
08:17 olas ok
08:17 * masak is planning to add it
08:28 CIA-40 bioclipse: ospjuth * r6219 /bioclipse2/trunk/plugins/net.bioclip​se.cdk.business/META-INF/MANIFEST.MF: Moved up cdk in deps list.
08:31 egonw christoph has breaking news: http://friendfeed.com/e/ee963266-52a​9-4bf5-8850-559b89dac162/Breaking-Ne​ws-Open-access-to-large-scale-drug/
08:31 zarah egonw's link is also http://tinyurl.com/555uvu
08:34 olas very cool
08:35 masak the URL itself is a bit unfortunate :)
08:35 CIA-40 bioclipse: ospjuth * r6220 /bioclipse2/trunk/features/net.bioclipse-feature/: Initial import of bioclipse-feature. Needs some work.
08:36 CIA-40 bioclipse: ospjuth * r6221 /bioclipse2/trunk/features/net.bioclipse-feature/ (.project build.properties feature.xml): Added some preliminary content.
08:39 masak egonw: could you please approve me as a bioclipse dev in launchpad?
08:40 egonw done, for Gpox too
08:40 masak thanks, egonw++
08:42 CIA-40 bioclipse: ospjuth * r6222 /bioclipse2/trunk/features/net.​bioclipse-feature/feature.xml: Updated deps.
08:42 olas no olas++?
08:42 zarah shame on you, olas, giving yourself karma like that
08:42 CIA-40 bioclipse: ospjuth * r6223 /bioclipse2/trunk/features/net.bio​clipse.chemoinformatics-feature/: Initial import.
08:42 olas zarah: that was a question
08:42 zarah olas: you've just exceeded my capabilities :/
08:42 olas zarah: karma
08:42 zarah olas has a karma of 5
08:43 olas karma masak
08:43 zarah masak has a karma of 8
08:43 olas karma egonw
08:43 zarah egonw has a karma of 5
08:43 masak karma zarah
08:43 zarah zarah has a karma of 11
08:43 masak zarah is in the lead! :)
08:43 olas zarah--
08:43 zarah masak: you've just exceeded my capabilities :/
08:43 masak woah! :)
08:43 olas karma zarah
08:43 zarah zarah has a karma of 10
08:43 olas @slap zarah
08:43 zarah why on earth would I slap zarah?
08:43 masak hehe
08:44 CIA-40 bioclipse: ospjuth * r6224 /bioclipse2/trunk/features/net.bi​oclipse.chemoinformatics-feature/ (.project build.properties feature.xml): Added preliminary list of plugins in chemoinformatics feature.
08:46 CIA-40 bioclipse: carl_masak * r6225 /bot/trunk/zarah.pl: [zarah] now refuses self-slap
08:50 CIA-40 bioclipse: jonalv * r6226 /bioclipse2/trunk/plugins/net.bioclipse.core/src​/net/bioclipse/core/domain/SmilesMolecule.java: added empty constructor needed for proxying
08:50 olas I successfully exported from mac
08:50 olas plugin-based
08:50 olas will now try feature-based
08:53 egonw_ joined #bioclipse
08:57 CIA-40 bioclipse: carl_masak * r6227 /bioclipse2/trunk/plugins/net.bioclipse.s​cripting.ui/META-INF/spring/context.xml:
08:57 CIA-40 bioclipse: [sprint/context.xml]
08:57 CIA-40 bioclipse: * more adaptations to the actual use
08:59 olas joined #bioclipse
09:04 jonalv olas: give me a ping when it is set up for feature based export and I will test it from Windows too :)
09:05 olas right
09:05 olas just installed the delta pack
09:05 olas wil ltry to expoert for mult pltaforms first
09:07 zarah joined #bioclipse
09:08 olas export for mult complete with no errors
09:08 olas will now do feature based
09:09 CIA-40 bioclipse: ospjuth * r6228 /bioclipse2/trunk/plugins/net.b​ioclipse.ui/bioclipse.product: Added plugins for delta pack.
09:26 CIA-40 bioclipse: ospjuth * r6229 /bioclipse2/trunk/features/net.​bioclipse-feature/feature.xml: Added fragment constraints. Really stupid this is not autogenerated.
09:27 olas Successfully built bioclipse by feature.
09:27 olas trying multiple platform build by feature now
09:27 jonalv something regarding cml generation has become broken
09:27 olas ask shk3
09:27 olas in cdk?
09:27 olas I committed a fix to cdk about cml generation, updated jars to jumbo5.4.2
09:28 jonalv probably but I am not sure
09:28 olas please update
09:28 olas and update CP
09:28 jonalv "CP"?
09:28 olas successfully built feature-based for multiple platforms
09:28 olas classpath
09:28 olas :-)
09:28 olas ok jonalv, please try feature-based export after installing delta pack
09:28 jonalv w00t
09:29 jonalv I need delta pack first?
09:29 CIA-40 bioclipse: carl_masak * r6230 /bioclipse2/trunk/plugins/ (20 files in 7 dirs):
09:29 CIA-40 bioclipse: [net.bioclipse.ui] -> [net.bioclipse.scripting.ui]
09:29 CIA-40 bioclipse: Moved the views ActionHistoryView, GroovyConsoleView, JsConsoleView,
09:29 CIA-40 bioclipse: RubyConsoleView, ScriptingConsoleView and VirtualView
09:29 jonalv can\t I just try without delta pack?
09:31 CIA-40 bioclipse: carl_masak * r6231 /bioclipse2/trunk/plugins/net.bioclipse.s​cripting.ui/icons/logo/logo_16_trans.gif:
09:31 CIA-40 bioclipse: [net.bioclipse.scripting.ui]
09:31 CIA-40 bioclipse: copied logo_16_trans.gif from net.bioclipse.ui
09:38 CIA-40 bioclipse: carl_masak * r6232 /bioclipse2/trunk/plugins/ (6 files in 4 dirs):
09:38 CIA-40 bioclipse: [net.bioclipse.scripting.ui]
09:38 CIA-40 bioclipse: * exported net.bioclipse.scripting.ui.views
09:38 CIA-40 bioclipse: [net.bioclipse.structuredb]
09:38 CIA-40 bioclipse: * chased s/net.bioclipse.ui/net.bioclipse.scripting.ui/ restructuring
10:56 CIA-40 bioclipse: ospjuth * r6233 /bioclipse2/trunk/plugins/net.b​ioclipse.ui/bioclipse.product: Use feature-based product.
11:24 CIA-40 bioclipse: carl_masak * r6234 /bioclipse2/trunk/plugins/net.bioclipse.scrip​ting.ui/src/net/bioclipse/scripting/ui/views/ (JsConsoleView.java ScriptingConsoleView.java):
11:24 CIA-40 bioclipse: [ScriptingConsoleView]
11:24 CIA-40 bioclipse: * renamed variable
11:24 CIA-40 bioclipse: * added overridable method tabCompletionHook
11:24 CIA-40 bioclipse: [JsConsoleView]
11:24 CIA-40 bioclipse: * removed unneeded imports
11:24 CIA-40 bioclipse: * tabCompletionHook takes job of adding '(' and '()' now
11:27 edrin joined #bioclipse
11:27 edrin hi
11:27 zarah hi edrin
11:27 masak hi edrin
11:28 CIA-40 bioclipse: carl_masak * r6235 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java:
11:28 CIA-40 bioclipse: [JsConsoleView]
11:28 CIA-40 bioclipse: * tab completing on managers now gives a period ('.') too
11:44 CIA-40 bioclipse: carl_masak * r6236 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java:
11:44 CIA-40 bioclipse: [JsConsoleView]
11:44 CIA-40 bioclipse: * more comments
11:44 CIA-40 bioclipse: * added exception for when user writes "help" or "man"
11:52 masak olas: I was about to remove the stacktraces written to the Eclipse console every time someone makes a syntax error in the Js Console... remember we discussed it and I said they should be there? well, I've been using the console a bit now, and they bug me too :)
11:52 jonalv I sense a "but"
11:53 masak but when I was about to remove them, I saw that they are logged as debug messages
11:53 masak and I think that's fine
11:53 jonalv besides I really fell that I used those stack traces so I want them somewhere please
11:53 masak end users are not going to run at debug level anyway
11:53 masak jonalv: yes.
11:53 masak so I'll leave them as they are
11:54 masak before release we'll have to remember to change the log level
11:56 masak olas: I'm moving the alignment editor into net.bioclipse.biojava.ui now
11:56 masak but it clashes with the sequence editor; the both read files of the same type
11:56 masak should I remove the sequence editor from plugin.xml for now?
11:56 stain any biologists here?  What is this blue thingie..? http://picasaweb.google.com/armazme/SnailThing
11:56 zarah stain's link is also http://tinyurl.com/6xt8vx
11:57 masak olas: I can comment it out if you prefer ;)
12:00 masak stain: this could be related: http://www.aquariacentral.com/​forums/showthread.php?t=113175
12:00 zarah masak's link is also http://tinyurl.com/5cdqxz
12:04 CIA-40 bioclipse: carl_masak * r6237 /bioclipse2/trunk/plugins/ (9 files in 5 dirs):
12:04 CIA-40 bioclipse: [net.bioclipse.ui] -> [net.bioclipse.biojava.ui]
12:04 CIA-40 bioclipse: * moved Aligner, AlignmentEditor and related dependencies
12:08 olas masak: comment out it from plugin.xml
12:08 masak olas: already did that
12:09 masak I second-guessed that that was what you wanted
12:09 olas :-)
12:09 olas it will most loikely be compåletely replaced
12:09 olas just might be some code snippets that are valuable there
12:09 masak (I toyed with the idea of removing it outright, but I haven't checked what sequenceeditor does)
12:09 masak exactly.
12:10 olas if you check that you can remove it
12:10 olas or give me a SF bug and I'll look at it later
12:11 * masak checks that
12:26 masak olas: SequenceEditor seems completely harmless to me. I'm less sure about SequenceEditorContribution
12:26 olas remove that too
12:30 * olas hates eclipse
12:30 olas grrrr
12:30 olas reinstallation did not solve problem
12:30 olas soon I will give up
12:31 jonalv we all know that giving up isn't an option... :(
12:31 olas I know
12:31 olas just very angry for the moment
12:32 olas I have a new eclipse
12:32 olas checking out into new workspace
12:32 olas if this does not work I will install leopard
12:32 masak olas: what be the matter, arr?
12:32 masak what is it that doesn't work?
12:33 olas my resourcesPlugin won't start
12:33 olas even after reinstallation
12:33 olas (which is scary)
12:34 masak ...and strange
12:36 olas no
12:36 olas no luck
12:36 olas still same problem
12:37 masak :/
12:48 jonalv @seen shk3
12:48 zarah I have not seen shk3
12:48 jonalv @seen egonw
12:48 zarah I have not seen egonw
12:48 CIA-40 bioclipse: jonalv * r6238 /bioclipse2/trunk/plugins/ (6 files in 5 dirs): Created a mocked version of IFile for the manager tests in cdk. Probably many testplugins is going to need this class so maybe it should be in some test-utils plugin?
12:48 jonalv @seen masak
12:48 zarah masak was last seen 2008-07-23T12:38:59 in #farmbio saying 'ska bara starta om, straxt tillbaka'
12:50 masak joined #bioclipse
12:57 * olas fixed the build problem in bc2
12:57 olas *phew*
12:59 jonalv olas++
12:59 masak olas++
12:59 stain that snail thing was their.. sex organs. http://snegler.bioforsk.no/nb/node/25
13:00 zarah stain's link is also http://tinyurl.com/5z46bu
13:01 masak stain: another thing to be glad about today, that my sex organs aren't blue
13:01 jonalv aha I could have guessed that :)
13:05 stain it seems they both ahve two sexes, and so they both get pregnant
13:05 jonalv this sounds familiar
13:06 CIA-40 bioclipse: jonalv * r6239 /bioclipse2/trunk/ (51 files in 51 dirs): Updated all classpath on olas++ suggestion
13:14 olas karma olas
13:14 zarah olas has a karma of 8
13:14 olas nice
13:14 CIA-40 bioclipse: ospjuth * r6240 /bioclipse2/trunk/features/net.​bioclipse-feature/feature.xml: Updated feature with required plugins for help system.
13:14 olas so, only update system deps left
13:14 olas which are troublesome
13:14 olas hmm
13:15 olas that was never 100% solved in bc1...
13:15 jonalv we just got a mail about that on the Bioclispe list btw...
13:26 olas about update sites?
13:26 olas I got no such mail...
13:26 jonalv yea about updates and proxies in 1.2
13:26 olas did we?
13:26 olas not me :-(
13:27 olas to devel?
13:27 olas or users?
13:27 jonalv olas see the mailing list please.
13:27 olas I am looking at it
13:27 olas I see no mail
13:27 jonalv users
13:27 olas maybe I'm not subscribed to users
13:29 jonalv well we should answer...
13:29 olas plz fwd to me
13:29 olas I now also registered to users
13:29 olas hmm
13:29 jonalv And since it is bioclipse 1 realted I don't feel qualified... :)
13:29 olas I am already subscribed
13:30 olas why did I not get that mail?
13:30 jonalv good question
13:30 jonalv I forwarded it now anyway...
13:30 jonalv please answer to the list too :)
13:30 olas sure
13:36 olas got that mail now
13:36 olas really late
13:46 egonw joined #bioclipse
14:20 CIA-40 bioclipse: ospjuth * r6241 /bioclipse2/trunk/features/net.​bioclipse-feature/feature.xml: Added feature deps for proxy and password storage.
14:22 CIA-40 bioclipse: ospjuth * r6242 /bioclipse2/trunk/plugins/net.b​ioclipse.ui/bioclipse.product: Updated deps for plugin-based product.
14:27 olas jonalv: around?
14:27 jonalv mm
14:27 olas jonalv: I'd like us to remove the search menu for now, until we implement it.
14:27 olas ok?
14:27 jonalv @seen egonw
14:27 zarah I have not seen egonw
14:27 olas could you please?
14:28 jonalv olas: We have a serch menu?
14:28 olas or was it masak who di that?
14:28 olas search accross databases
14:28 olas masak?
14:28 olas a mocked GUI I assume
14:30 * masak hardly remembers that
14:30 masak I remember we talked about it...
14:30 olas :-)
14:30 olas do you want to see it?
14:30 olas run BC, in edit menu select "search..."
14:30 masak oki
14:31 masak oh right
14:31 masak it's all coming back...
14:31 masak :/
14:31 masak I'm sorry :)
14:31 masak should I delete it?
14:32 jonalv well, it is simething that we will wanan have...
14:32 masak it is a mocked GUI, from some wiki page I think
14:33 masak I made it and tried to learn about SWT at the same time
14:39 olas masak: there's a JSeditor on SF for Eclipse: http://sourceforge.net/projects/jseditor
14:39 zarah olas's link is also http://tinyurl.com/5gd3u7
14:39 olas that would be easiest probably
14:39 olas but please also look at the new JSEditor in Ganymede
14:39 olas I'll provide a link here asap
14:40 olas http://wiki.eclipse.org/index.php/ATF/JSDT
14:40 zarah olas's link is also http://tinyurl.com/5uuo89
14:40 olas could be too much functionality
14:40 olas so the first project might suit us better
14:42 masak olas: dz. will look at it tomorrow
14:43 olas great
14:43 CIA-40 bioclipse: jonalv * r6243 /bioclipse2/trunk/plugins/net​.bioclipse.usermanager.tests/ (.classpath build.properties): class path and build.properties fixed...
14:58 CIA-40 bioclipse: ospjuth * r6244 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (14 files in 7 dirs): Added update site functionality in Bioclipse2 and commented out unused search... menu.
14:59 olas karma
14:59 zarah olas has a karma of 8
15:18 CIA-40 bioclipse: jonalv * r6245 /bioclipse2/trunk/plugins/net.bioclipse​.structuredb/src/net/bioclipse/structur​edb/business/StructuredbManager.java: fix for bug #2025774
16:32 CIA-40 bioclipse: ospjuth * r6246 /bioclipse2/trunk/features/net.​bioclipse-feature/feature.xml: Updated with OS/arch info for added features (net+update).
16:48 olas left #bioclipse
17:38 edrin left #bioclipse
19:22 egonw joined #bioclipse
22:06 ilogger2 joined #bioclipse

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