Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-10-07

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All times shown according to UTC.

Time Nick Message
06:26 ilbot2 joined #bioclipse
06:26 Topic for #bioclipseis now An open source workbench for chem- and bioinformatics - http://www.bioclipse.net/ | BioclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.org/irclogge​r/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse || Bioclipse2 beta released! See http://bioclipse.blogspot.com/ || http://www.youtube.com/watch?v=ZUBQknWUEYU
06:38 Gpox joined #bioclipse
07:11 egonw joined #bioclipse
07:15 egonw moin
07:15 zarah saluton egonw
07:41 sneumann joined #bioclipse
07:47 jonalv joined #bioclipse
08:09 sneumann joined #bioclipse
08:46 egonw jonalv: got time for a bit of performance testing?
08:46 egonw on CML reading?
08:46 egonw I got a patch which I think would speed up performance...
08:46 jonalv egonw: well not really no
08:46 jonalv egonw: cool
08:46 egonw first time I ran without patch it was 15 secs
08:46 egonw with patch 5...
08:46 jonalv w0t
08:46 egonw but then with master again for some replicates
08:46 jonalv |w00t
08:46 egonw it was 5 secs too :(
08:47 jonalv huh
08:47 egonw so, no improvement...
08:47 jonalv k
08:47 egonw but wondering if eclipse cached classes or so...
08:47 jonalv maybe
08:47 jonalv I don't know
09:22 egonw Gpox: ping
09:22 Gpox egonw: pong
09:23 egonw what names did we come up with for the swt widget plugins?
09:23 egonw can you check my whiteboard?
09:23 Gpox sure
09:26 Gpox egonw: org.openscinece.cdk.swtrender, org.openscinece.cdk.swtcontrol
09:26 egonw mmm...
09:27 egonw so we did not split up for AtomContainerRenderer and ChemModelRenderer yet ...
09:27 egonw ok, what about:
09:27 egonw cdk.swtrender.basic
09:27 egonw cdk.swtrender.full ?
09:27 egonw and perhaps shorten to .swt. ?
09:30 egonw will make it so
09:30 Gpox org.openscinece.cdk.swt.render.basic/extra
09:30 egonw so, four plugins
09:30 egonw basic, extra, OK
09:30 egonw good, following the current module naming
09:31 Gpox now we got cdk.renderawt
09:31 egonw right... because CDK modules cannot have dots...
09:32 Gpox ok, but these are not cdk modules
09:34 egonw no, not yet :)
09:34 egonw we'll do that for 2.4
09:51 egonw Gpox: commiting stubs...
09:52 egonw can you add the appropriate classes there?
09:52 egonw I have packages like:
09:52 egonw Export-Package: org.openscience.cdk.renderswtbasic
09:52 egonw but feel free to change that
09:52 egonw to
09:52 egonw cdk.render.foo
09:52 egonw e.g.
09:52 egonw cdk.render.swt
09:52 egonw or cdk.render.swt.basic
09:53 egonw if you want each bundle to use different java packages...
09:55 CIA-51 bioclipse.cheminformatics: Egon Willighagen master * rd71b977 / (16 files in 8 dirs): Added stubs for the new bundles to containt the SWT widget wrapping the JChemPaint functionality - http://bit.ly/3813Mk
10:42 * jonalv starts Wclipse for the first time in quite some time.
10:43 jonalv wish me luck
10:43 jonalv :)
11:19 * egonw is finally making some backups of his HD again
11:19 egonw been too long
11:19 egonw git++
11:30 jonalv zarah: seen olass
11:30 zarah I have not seen olass
11:30 jonalv zarah: seen olas
11:30 zarah I have not seen olas
11:30 jonalv zarah: seen zarah
11:30 zarah jonalv: I'm right here
11:30 jonalv zarah: seen jonalv
11:30 zarah jonalv was last seen right now in #bioclipse saying 'zarah: seen jonalv'
11:37 samuell joined #bioclipse
11:38 egonw good morning samuell :)
11:44 samuell Good morning :*)
11:44 samuell (Means, *blush* :) )
11:46 samuell egonw: FYI: http://saml.rilspace.com/content/javapro​log-interface-swi-prolog-jpl-up-running
11:46 zarah samuell's link is also http://tinyurl.com/yb7vm9v
11:46 samuell (Had forgot to make the post public...)
11:49 * jonalv is stuck in the dependency swamp... :(
11:56 egonw samuell: excellent!
11:57 samuell So, now have to start figuring out how to connect things.
11:59 egonw yes
11:59 egonw have a look at the balloon plugin
11:59 egonw and see how Ola has hooked in .so libs
12:00 samuell Ok!
12:00 samuell Good tip
12:00 masak joined #bioclipse
12:01 samuell Will check balloon...
12:02 samuell Any links to reading about balloon?
12:03 samuell (Googling "balloon" potentially can give some irrelevant results :) )
12:03 egonw see if Ola added docs to the plugins
12:03 egonw look for toc.xml's
12:04 jonalv where is olass when I need him
12:04 samuell egonw: Ok
12:04 egonw selling Bioclipse licenses, I guess
12:05 jonalv hehe
12:32 * samuell will go to the optician in ~10 min
12:37 * samuell still has some issues getting blipkit connected to swi-prolog after switch from ubuntu repos to building from source (but hopefully will resolve that soon)
12:49 * jonalv can't get the Brunn update site to work :(
12:49 egonw :(
12:49 egonw what's the problem
12:49 jonalv it installs okey but it won't start the plugins
12:49 jonalv they are only in resolved status
12:49 jonalv and Eclipse doen't give any error message or anything
12:54 egonw but the update site is not involved in plugins getting loaded...
12:55 * egonw is not understanding what jonalv is telling
12:55 jonalv egonw: I can't get things to run from my update site
12:55 egonw but things don't run on an update site
12:55 jonalv egonw: no, have I claimed that_
12:55 jonalv ?
12:56 egonw do they *install* from your update site?
12:56 jonalv egonw: as I said a while ago yes "it installs okey"
12:56 jonalv but it won't start the plugins when trying to run it after it has installed them
12:57 egonw OK...
12:57 jonalv I am guessing there is some deps problem but I don't get any error messages or anything..
12:57 egonw you made me think you meant the update site was causing your plugins not to run
12:57 jonalv egonw: yes that's sort of what is going on
12:58 jonalv egonw: it seems that having the plugins going though the update site makes them not work
13:03 egonw mmm...
13:03 egonw sounds unlikely
13:03 egonw but perhaps the update site is eating away important chars
13:04 jonalv egonw: sounds very unlikely
13:07 CIA-51 bioclipse.cheminformatics: Egon Willighagen master * r06255c5 / (3 files in 3 dirs): Removed local settings from the git repository - http://bit.ly/2anm66
13:09 jonalv egonw: When I try to start the plugin boundles manually I get: org.osgi.framework.BundleException: The bundle could not be resolved. Reason: Missing Constraint: Require-Bundle: org.junit4; bundle-version="0.0.0"
13:09 jonalv that feels like a clue...
13:09 jonalv but why is not the junit4 boundle there...
13:10 egonw ah...
13:10 egonw a clue indeed
13:10 egonw did you see that blog I bookmarked today about 3.5.1 and plugin versions
13:10 egonw maybe that helps
13:10 egonw I have had such problems too
13:11 egonw but as with many incomprehendible eclipse issues, it disappeard at some point
13:11 egonw as if it never happened
13:12 * jonalv wonders if it might be better to import the junit stuff then actually depending on a certain plugin...
13:15 egonw joined #bioclipse
13:34 CIA-51 bioclipse.rdf: Egon Willighagen master * radbd95b / .gitignore : Ignore plugin customizations - http://bit.ly/hexhL
13:46 egonw samuell: I think you might find this blog interesting: http://www.w3.org/QA/2009/10/rif_and_owl.html
13:46 zarah egonw's link is also http://tinyurl.com/yavvjxk
13:49 egonw jonalv: does the Bioclipse Agenda have a public URL?
13:49 egonw if so, can you please blog that? and perhaps embed the agenda in that blog??
13:50 jonalv egonw: what is that?
14:00 egonw you made that agenda, not?
14:00 egonw with feature freeze etc?
14:00 jonalv egonw: agenda?
14:00 jonalv egonw: didn't we make that at that meeting?
14:00 jonalv egonw: I only created a google calendar for te dates
14:00 egonw mmm... who made that google agenda then?
14:01 egonw yes, right
14:01 egonw ah... calendar, not agenda
14:01 egonw ok, I'll rephrase :)
14:01 * jonalv is stuck with this damn update site still...
14:01 egonw jonalv: does that Bioclipse Calendar have a public URL?
14:01 jonalv egonw: I have no idea
14:02 egonw yes, it has...
14:02 egonw OK, hacking...
14:02 jonalv I am beginning to think that Eclipse does not rebuild the plugins although I hit the "Build All" button...
14:04 egonw http://pele.farmbio.uu.se/agenda/
14:04 zarah egonw's link is also http://tinyurl.com/y8a8xun
14:05 jonalv cute
14:05 egonw I'll ask Ola for http://agenda.bioclipse.net
14:05 jonalv egonw: good plan
14:06 egonw so, who has rights to add stuff?
14:06 jonalv egonw: I don't know
14:06 jonalv egonw: me?
14:06 egonw :) yes, guess so
14:07 * jonalv is quickly getting into a terrible mood here... :/
14:07 egonw yes, Eclipse can be a real pain...
14:07 egonw but you can do it...
14:08 egonw double check all classpath related stuff...
14:08 egonw as you said, there probably is a file missing or so...
14:08 egonw check the 'Classpath Horror' page in our wiki
14:08 jonalv egonw: but it runs fine from inside Eclipse
14:09 egonw yes, that happens
14:09 egonw this is why Ola always needs so much time for the exporting...
14:10 jonalv it still thinks that it needs junit4
14:10 jonalv even though I have added the jar file and removed all requirepackage lines
14:10 jonalv It's as if I am not running the changed files
14:11 masak egonw: your script only does 'git fetch'. so you still have to merge your branches manually?
14:11 egonw yes
14:11 egonw intentionally
14:12 egonw for example, I may be working in a branch
14:17 * jonalv give up
14:18 jonalv I will have to ask olass for help. He has the most experience with update sites I think...
14:18 masak egonw: fair enough.
14:18 egonw jonalv: I don't think he has the answer... I think he just tweaks until it works too
14:18 samuell egonw: Thanks for the link. Will check
14:18 jonalv egonw: I have tried everything I can think of
14:19 jonalv egonw: I donät know what elese to try...
14:19 egonw then start trying to think of things you would never try
14:19 egonw or, unzip everything in the jars downloaded from the update site
14:19 jonalv egonw: thatäs what I have been doing for the last couple of hours...
14:19 egonw and inspect the content
14:19 egonw and see what is missing
14:19 jonalv egonw: but I am not even sure how they should look...
14:20 egonw oh, just look at something that is working
14:20 egonw plenty of such plugins around
14:21 masak egonw: http://pele.farmbio.uu.se/agenda/ -- "This content cannot be displayed in a frame - To protect your security, the publisher of this content does not allow it to be displayed in a frame." wtf?
14:21 zarah masak's link is also http://tinyurl.com/y8a8xun
14:21 masak I've never seen that warning before. I cannot imagine what would cause it.
14:21 egonw what browser is that?
14:21 masak Fx3.5.2
14:22 egonw mmm...
14:22 jonalv -me canät unpack jar files
14:22 egonw works here
14:22 egonw don't seem to need to be logged in...
14:22 jonalv argh
14:23 ilbot2 joined #bioclipse
14:23 Topic for #bioclipseis now An open source workbench for chem- and bioinformatics - http://www.bioclipse.net/ | BioclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.org/irclogge​r/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse || Bioclipse2 beta released! See http://bioclipse.blogspot.com/ || http://www.youtube.com/watch?v=ZUBQknWUEYU
14:23 * jonalv can't unpack jar files
14:23 egonw jar xvf ?
14:23 jonalv on good operating systems one just double click them and they open up for browsing...
14:24 jonalv on this one I don't know how to do it...
14:24 egonw jar xvf ?
14:25 jonalv egonw: okey
14:25 jonalv b0rken shit
14:26 jonalv argh
14:26 jonalv It unpacked it in the same catalouge
14:26 jonalv now there is total havoc here!
14:26 egonw catalogue ?
14:26 jonalv directory/folder/catalogue
14:26 * egonw feels an utter OS/X novice
14:26 jonalv map
14:26 egonw ah, database?
14:27 jonalv egonw: database?
14:27 egonw nevermind :)
14:29 jonalv Do anyone see any metnioning of requiring the bundle junit4 in this:
14:29 jonalv Manifest-Version: 1.0
14:29 jonalv Bundle-ManifestVersion: 2
14:29 jonalv Bundle-Name: net.bioclipse.brunn.core
14:29 jonalv Bundle-SymbolicName: net.bioclipse.brunn.core;singleton:=true
14:29 jonalv Bundle-Version: 0.9.3.v20091007
14:29 jonalv Bundle-ClassPath: .,
14:29 egonw oh no
14:29 egonw pastebin
14:29 jonalv mysql-connector-java-3.1.13-bin.jar,
14:29 jonalv hibernate3.jar,
14:29 egonw pastebin
14:29 egonw pastebin
14:29 jonalv lib/ant-1.6.5.jar,
14:29 egonw pastebin
14:29 egonw please!
14:29 jonalv lib/ant-antlr-1.6.5.jar,
14:29 jonalv lib/ant-junit-1.6.5.jar,
14:29 jonalv lib/ant-launcher-1.6.5.jar,
14:29 jonalv lib/antlr-2.7.6rc1.jar,
14:29 jonalv lib/ant-swing-1.6.5.jar,
14:29 jonalv lib/asm.jar,
14:29 jonalv lib/asm-attrs.jar,
14:29 jonalv lib/c3p0-0.9.0.jar,
14:29 egonw ChanServ: kick jonalv
14:29 jonalv lib/cglib-2.1.3.jar,
14:29 jonalv lib/cleanimports.jar,
14:30 jonalv lib/commons-collections-2.1.1.jar,
14:30 egonw jonalv--
14:30 jonalv lib/concurrent-1.3.2.jar,
14:30 egonw for each line
14:30 jonalv lib/connector.jar,
14:30 egonw everyone please
14:30 jonalv lib/dom4j-1.6.1.jar,
14:30 jonalv lib/ehcache-1.1.jar,
14:30 jonalv lib/jaas.jar,
14:30 jonalv lib/jacc-1_0-fr.jar,
14:30 egonw jonalv: really, I understand you hate eclipse
14:30 egonw everyone does
14:30 jonalv lib/jaxen-1.1-beta-7.jar,
14:30 jonalv lib/jboss-cache.jar,
14:30 jonalv lib/jboss-common.jar,
14:30 egonw but please don't make *us* suffer for that! :(
14:30 jonalv lib/jboss-jmx.jar,
14:30 jonalv lib/jboss-system.jar,
14:30 jonalv lib/jdbc2_0-stdext.jar,
14:30 jonalv lib/jgroups-2.2.8.jar,
14:30 jonalv lib/jta.jar,
14:30 jonalv lib/oscache-2.1.jar,
14:30 jonalv lib/proxool-0.8.3.jar,
14:30 egonw jonalv--
14:30 jonalv lib/swarmcache-1.0rc2.jar,
14:30 jonalv lib/syndiag2.jar,
14:30 jonalv lib/versioncheck.jar,
14:31 jonalv lib/xerces-2.6.2.jar,
14:31 jonalv lib/xml-apis.jar,
14:31 jonalv lib/dbunit-2.1.jar,
14:31 jonalv lib/spring.jar,
14:31 jonalv lib/commons-dbcp-1.2.1.jar,
14:31 egonw why do you have xerces in there??
14:31 jonalv lib/commons-pool-1.3.jar,
14:31 jonalv lib/jep-2.4.0.jar,
14:31 jonalv lib/junit-4.7.jar
14:31 jonalv Bundle-Localization: plugin
14:31 jonalv Require-Bundle: org.eclipse.core.runtime,
14:31 jonalv org.eclipse.ui,
14:31 egonw or junit??
14:31 jonalv net.bioclipse.brunn.expression,
14:31 jonalv net.bioclipse.usermanager;bundle-version="0.1.1",
14:31 jonalv net.bioclipse.encryption;bundle-version="0.1.0"
14:31 jonalv Bundle-Activator: net.bioclipse.brunn.Activator
14:31 jonalv Export-Package: net.bioclipse.brunn,
14:31 jonalv net.bioclipse.brunn.HibernateMapping,
14:31 egonw why versioned depends on those plugins?
14:31 jonalv net.bioclipse.brunn.business,
14:31 jonalv net.bioclipse.brunn.business.annotation,
14:31 jonalv net.bioclipse.brunn.business.audit,
14:31 egonw usermanager and encryption??
14:32 jonalv net.bioclipse.brunn.business.exportScript,
14:32 jonalv net.bioclipse.brunn.business.folder,
14:32 jonalv net.bioclipse.brunn.business.operation,
14:32 jonalv net.bioclipse.brunn.business.origin,
14:32 jonalv net.bioclipse.brunn.business.plate,
14:32 jonalv net.bioclipse.brunn.business.plateLayout,
14:32 jonalv net.bioclipse.brunn.business.sample,
14:32 jonalv net.bioclipse.brunn.genericDAO,
14:32 jonalv net.bioclipse.brunn.pojos,
14:32 jonalv net.bioclipse.brunn.results,
14:32 jonalv net.bioclipse.brunn.results.orcaParser,
14:32 jonalv net.bioclipse.brunn.results.parser96
14:32 jonalv Import-Package: org.apache.commons.logging,
14:32 jonalv org.apache.log4j;version="1.2.15"
14:32 jonalv
14:32 jonalv egonw: okey here then: http://pastebin.com/mdd8fa50
14:33 egonw I hope you saw my comments
14:33 jonalv egonw: becasue I have the junit tests there...
14:33 jonalv egonw: what about usermanager and encryption?
14:33 jonalv egonw: I don't understand them...
14:33 egonw I suggest splitting out brunn.test
14:33 jonalv egonw: yes I know. Whenever I find two free weeks I can do that... :/
14:34 egonw but,but ... you are doing a PhD... you have 96 weeks...
14:34 jonalv egonw: We need Brunn up and running last week...
14:35 jonalv egonw: First make it run then make it nice...
14:35 egonw well, isn't this about making it run?
14:36 jonalv but I don't understand how that plugin can depend on the junit4 bundle
14:36 egonw have you tried making it depend on it?
14:36 egonw if it thinks it does, why not formalize that
14:36 egonw if you can't beat them, join them ??
14:37 jonalv egonw: it used to depend on it
14:37 jonalv egonw: but that didn't work
14:37 egonw did you check the feature?
14:37 egonw is that still depending onit?
14:37 jonalv so now I am trying to get rid of that dependency
14:37 egonw http://friendfeed.com/dullhunk/9731c6b1/mo​st-common-hotmail-password-revealed-threat
14:37 zarah egonw's link is also http://tinyurl.com/yapbxv2
14:38 jonalv egonw: I don't understand what you mean. IS the deature depending on what?
14:38 egonw on junit
14:38 egonw what else??
14:39 jonalv egonw: can a feature depend on a bundle?
14:39 egonw sure
14:40 jonalv egonw: it only depends on net.bioclipse.birt_feautre
14:40 jonalv egonw: it contains org.junit4 though...
14:40 jonalv egonw: maybe if I remove that...
14:40 egonw masak: does this link work for you?
14:41 egonw http://www.google.com/calendar/embed?src​=doln7r7fhn50ceuqac58fbsvlg@group.calend​ar.google.com&ctz=Europe/Amsterdam
14:41 zarah egonw's link is also http://tinyurl.com/ydayrk8
14:41 egonw jonalv: there you go...
14:41 egonw problem fixed
14:41 jonalv yes
14:41 masak egonw: aye.
14:41 jonalv egonw: I trust that when I see it
14:41 masak egonw: ah. with "Agenda", you meant "time plan".
14:42 masak I'd be slightly wary of using "Agenda" in describing one's own projects. it's slightly negatively tainted (as something hidden or malicious).
14:43 egonw masak: yeah, perhaps you are correct
14:43 egonw suggest something else in the bug report, please
14:43 egonw @pz bioclipse agenda
14:43 zarah [1653] Create http://agenda.bioclipse... http://tinyurl.com/yefyjbj
14:43 zarah Entire list at http://tinyurl.com/ybfxkr6
14:43 egonw calendar may be way better
14:44 masak +1
14:44 jonalv dz
14:44 egonw calendar.bioclipse.net
14:44 jonalv +1
14:44 masak wai~!
14:45 egonw wia?
14:45 egonw wai?
14:46 jonalv egonw: it was a good thought but it didn't work... :(
14:46 egonw ok, well, perhaps there a more files around you have not checked yet...
14:47 jonalv like what?
14:47 egonw have you tried:
14:47 egonw grep -ri junit *
14:48 egonw jonalv: you're not telling me that you let a computer win from you that easily?
14:48 jonalv egonw: that will give too much I think, (what does ri do?)
14:48 egonw you have only been trying <1 day
14:48 egonw grep -ri junit * | grep -v "I don't want lines to contain this sentence"
14:49 jonalv egonw: but on what are you sugggesting I do that?
14:50 egonw your computer
14:50 egonw your local brunn check out
14:50 egonw on the files in that check out
14:53 jonalv egonw: realise that I get HUGE amounts of hts...
14:53 jonalv + I don't even know what I am looking for
14:53 egonw for anything that might cause the problem
14:57 * jonalv takes a walk
15:06 jonalv now it won't even start from eclipse
15:06 egonw ah, excellent!
15:07 egonw that means there must be *another* dependency!
15:07 * egonw likes Cluedo :)
15:08 * jonalv likes when things work
15:08 * egonw suggests to get drunk and try again tomorrow
15:08 * egonw needs just one beer to get drunk, mind that :)
15:09 jonalv I was gonna demo this aftr lunch tomorrow but I guess that will have to be a demo of last version...
15:10 egonw yes, never wait with doing crucial steps until the last day before the deadline
15:10 egonw unless you have very good stress capacity
15:10 jonalv egonw: well I had a back up plan...
15:10 egonw had?
15:11 egonw that vaporated?
15:11 jonalv egonw: have
15:11 egonw ah :)
15:11 egonw dinner
15:11 egonw time
15:11 egonw bbl
15:12 * jonalv can't even get bioclipse.core + bioclipse.birt to run now
15:14 * jonalv need help...
15:23 samuell egonw: Wrote a small blog post about the link on RIF and OWL: http://saml.rilspace.com/content/o​n-the-two-main-approaches-for-know​ledge-handling-on-the-semantic-web
15:23 zarah samuell's link is also http://tinyurl.com/y95c669
15:36 * samuell goes for dinner
16:19 masak samuell++ # blog post
16:40 egonw ah, Open Access for all vr.se funded research: http://scienceblogs.com/clock/2009/1​0/the_swedish_research_council_m.php
16:40 zarah egonw's link is also http://tinyurl.com/ydv4z94
16:53 jonalv w00t
17:58 sneumann joined #bioclipse
18:04 * samuell need to re-login
18:06 samuell joined #bioclipse

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