Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-05-25

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All times shown according to UTC.

Time Nick Message
05:26 egonw joined #bioclipse
07:01 olass joined #bioclipse
07:02 olass moin
07:02 zarah oh hai olass
07:06 Gpox joined #bioclipse
07:18 egonw olass, Gpox: where is perl typically found in a Max?
07:20 olass egonw: good question
07:20 olass guess it depends on how you install it
07:20 olass mbpro:~ ola$ which perl
07:20 olass /usr/bin/perl
07:20 egonw ack, tack
07:20 olass but that is just mine
07:27 Gpox in the PATH, i got it in /usr/bin and /opt/local/bin since i use ports. But because /opt/local/bin is first in the path i get that one
07:28 CIA-40 bioclipse: egonw * r10712 /bioclipse2/trunk/externals/org.mindswap.pellet/ (14 files in 2 dirs): Uploaded Pellet 2.0.0 RC6
07:31 CIA-40 bioclipse: egonw * r10713 /bioclipse2/trunk/externals/com.hp.hpl.jena/ (5 files in 2 dirs): Uploaded Jena 2.5.7
07:31 CIA-40 bioclipse: egonw * r10714 /bioclipse2/trunk/plugins/ne​t.bioclipse.doc.developers/ (.classpath build.xml jars/ jars/ant-contrib-1.0b3.jar):
07:31 CIA-40 bioclipse: Tuned up building process (fixes #1089):
07:31 CIA-40 bioclipse: * detect platform
07:31 CIA-40 bioclipse: * pick a suitable perl location (overwritable with -Dperl.exec=/foo/bar/perl)
07:31 CIA-40 bioclipse: * ensure the output folder is created
07:31 CIA-40 bioclipse: * add ant-contrib for the use of <if>
07:31 zarah bug #1089 | http://tinyurl.com/of5f72
07:33 rojasm joined #bioclipse
07:37 rojasm moin all
07:37 zarah saluton rojasm
07:38 edrin joined #bioclipse
07:38 edrin hi
07:38 zarah hello edrin, you fantastic person you
07:47 olass hi edrin
07:56 edrin hi olass
07:57 CIA-40 bioclipse: goglepox * r10715 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/plugin.xml:
07:57 CIA-40 bioclipse: Added check so Delete menu option is only visible when atom or bond is selected.
07:57 CIA-40 bioclipse: Fixes bug #1069
07:57 zarah bug #1069 | http://tinyurl.com/ov2fuu
07:59 egonw olass: behold the future: http://pele.farmbio.uu.se/cgi-bin/g​itweb.cgi?p=bioclipse.git;a=summary
07:59 zarah egonw's link is also http://tinyurl.com/p793tr
08:00 olass egonw: looks very nice!
08:00 egonw debian rulez!
08:00 egonw apt-get install gitweb
08:00 egonw :)
08:01 olass egonw: is this a report of git, svn or git-svn
08:01 olass ?
08:01 egonw a git mirror
08:01 egonw last update 15 days ago
08:01 egonw http://pele.farmbio.uu.se/cgi-bin/gitweb.cgi
08:01 zarah egonw's link is also http://tinyurl.com/qzsq4u
08:01 egonw there's jonalv's bioclipse repos too
08:01 egonw where he did his NWO thing
08:02 egonw oh, and the bugzilla copy of Pelezilla :)
08:02 egonw and two CDK mirrors
08:03 egonw so, we can easily have multiple git repositories for the various features bundles
08:08 masak joined #bioclipse
08:09 jonalv joined #bioclipse
08:10 jonalv joined #bioclipse
08:55 egonw jonalv: the general pattern is this:
08:55 egonw using a manager from another manager
08:56 egonw but I could not think of a way to discover inside the calling manager whether it is called as IJava- or IJavaScriptFooManager
08:56 jonalv egonw: yea we need to figure out the best way of dong that
08:56 egonw so, can not decide whether to use for the called manager:
08:56 egonw Activator.getDefault().getJava- or .getJavaScriptFooManager
08:57 jonalv I personally would probably have manager methods taking the manager as a paramater and passing the right one using AOP
08:58 jonalv so if the JavaScript manager is called it get\s a ref to for example the cdk javascript manager
09:03 jonalv egonw: which managers are you having this situtation in?
09:04 egonw ummm...
09:04 egonw I know the MedeaManager is calling other manager
09:04 egonw CDKDebugManager too
09:04 egonw OWLManager
09:05 jonalv egonw: okey
09:05 jonalv egonw: so it's a general problem...
09:05 egonw yes
09:05 egonw and related to this
09:05 jonalv uisng the java one is probably not right
09:05 egonw is that one likely want something to do with progress monitors
09:05 jonalv better to use the javascript I think
09:05 egonw where calls to other methods allow passing monitors...
09:06 jonalv but yes there is the problem with passing monitors...
09:06 egonw yes, I know
09:06 egonw just wanted to link it to this here
09:06 egonw as I see a link
09:06 jonalv I am not 100% sure but I think using the Javascript one should work
09:07 jonalv or using the java one for java calls and the javascript one for javascript calls. But that might generate many jobs...
09:07 jonalv in the java casae
09:27 * egonw failed to isolate the problem why rednael just stops working at some point in time...
09:31 olass jonalv: what are you working on now?
09:31 jonalv @pz 1105
09:31 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1105
09:31 olass jonalv: excellent
09:32 olass would be happy if you could look at my BioclipseUIJob problem also
09:32 jonalv olass: uhm which one is that?
09:32 olass the one I told you about last week
09:32 olass mom, locating bug
09:34 maclean joined #bioclipse
09:35 egonw hi maclean
09:35 maclean hi egonw
09:36 egonw maclean: http://friendfeed.com/chemistry-development-kit​/6b0ee8ed/simplest-example-1-methylcyclobutane
09:36 zarah egonw's link is also http://tinyurl.com/qoddk4
09:36 egonw unfortunately no response
09:37 egonw yeah, better that ol' ass
09:37 maclean oh, well. thanks for asking though, egonw.
09:37 maclean I should probably know the answer myself, if I understood the maths in the papers I've been reading :)
09:38 olass egonw-- //making fun of people's names like that
09:38 * olass is in a picky mode today
09:38 olass mood and mode ;)
09:38 maclean set olass unpicky
09:38 jonalv maclean +1
09:38 * olass is now unpicky
09:39 egonw and yet I do not see this translated into bug reports about coding (style) by others
09:39 maclean :)
09:39 masak maclean: dang! I should have thought of that! so simple! :)
09:39 olass egonw: please rephrase or stop trying to be witty
09:39 masak *lol*
09:39 rednael2 joined #bioclipse
09:39 * olass is now in bot mode
09:40 olass hi rednael2, you fantastic bot, you
09:40 maclean masak : too many years of rasmol for me, I suppose.
09:44 olass jonalv: bug #1109
09:44 jonalv @pz 1109
09:44 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1109
09:44 olass There is a unit test
09:45 olass and a way to reproduce in GUI
09:45 rednael2 [Bioclipse Twitter] me is wondering if #rednael is more happy about twits about #cdk #bioclipse and #metware now  http://twitter.com/egonwill​ighagen/statuses/1911120949
09:45 zarah rednael2's link is also http://tinyurl.com/o2mkdj
09:45 jonalv olass: oki
09:45 olass rednael: who is 'me' ?
09:45 olass rednael2: who is 'me' ?
09:45 jonalv is it just me or can someone understand how the ui manager works?
09:48 masak olass: maybe it should be more obvious who is twittering.
09:48 masak olass: but you can see it through the URL.
09:48 CIA-40 bioclipse: miguelrojasch * r10716 /bioclipse2/trunk/plugins/ (7 files in 4 dirs): Method working with ICDKReactionScheme instead of ICDKReaction
09:48 * olass still doesn't see the point of twitter
09:49 maclean you're not alone, ola
09:49 egonw neither do I, but maybe I might in the future...
09:49 egonw I have not played enough with it to appreciate the scope
09:49 egonw I don't like SMS either
09:49 olass seems like something you do if you don't have anything else to do, in order to waste time
09:50 olass SMS has its uses
09:50 egonw true: spending money
09:50 egonw and a lot of that per character
09:50 olass no, all normal people have cellphones
09:50 egonw rather efficient way of spending money
09:50 olass hence is reachable
09:50 olass not all people are always online
09:50 * egonw looks at masak
09:50 egonw and awaits reply in esperanto
09:51 olass there are of course exceptions
09:51 olass but they are rare these days
09:51 * egonw enjoyed seeing Carl clean patatos
09:51 egonw ha, holiday
09:51 masak egonw: :)
09:51 * egonw looks at another half filled box
09:52 masak egonw: those local newspaper reports are quite harmless, but it's fun to try to get them right.
09:52 egonw :)
09:52 maclean texting is very useful viz : "where the hell are you - I am standing outside!"
09:52 egonw they were not potatos ?
09:52 masak this time we managed to have an article with no grave factual errors. \o/
09:52 masak egonw: yes, they were. but I didn't have to clean them, someone else did that.
09:53 masak me cutting up potatoes: http://www.dt.se/nyheter/b​orlange/article431855.ece
09:54 zarah masak's link is also http://tinyurl.com/ppxds9
09:58 CIA-40 bioclipse: miguelrojasch * r10717 /bioclipse2/trunk/plugins/net.bioclips​e.reaction/src/net/bioclipse/reaction/​editor/ReactionMultiPageEditor.java: changed the update method to ICDKRection..
10:27 maclean "Both [google] App engine and Windows Azure boast a promise of automatic scalability to developers, in the same fashion that a traveling salesman in the early American 1800s with his straw hat, red and white pinstripe suit, and assistant midget boast that their secret-recipe tonic will cure all that ails you."
10:52 jonalv who is Rob Schellhorn?
10:52 rednael2 [Leander Git] Only check feeds when something happened on the IRC channel, to reduce traffic  http://github.com/egonw/rednael/commit/9​f83251942f57ffe720309c9d0a71516db240d68
10:52 zarah rednael2's link is also http://tinyurl.com/qkm8j5
10:52 * jonalv gets a merge conflict in StochasticStructureElucidationJob...
10:53 jonalv I don't understand why...
10:54 maclean I think he was the guy that made the compute plugin
10:54 egonw jonalv: a former student of mine
10:54 maclean the bioclipse wiki says he's "Working on integrating Ghemical (http://bioinformatics.org/gh​emical/ghemical/index.html) into Bioclipse"
10:54 zarah maclean's link is also http://tinyurl.com/re4pq4
10:59 egonw architect of .compute
10:59 egonw and indeed the Ghemical integration
10:59 egonw which was the goal
10:59 egonw also did the hacking on calling the Ghemical (C or C++) code directly from Bioclipse
11:00 egonw which the auto plugin building and sorts
11:00 jonalv egonw: I get conflictis in medea when I try to rebase my local branch...
11:00 jonalv egonw: why is that?
11:01 jonalv egonw: sry seneca
11:01 * egonw does not have supercow powers
11:01 jonalv egonw: I get merge conflicts in seneca
11:01 egonw I cannot peak into the mem space of your laptop
11:02 jonalv I guess that makes sense...
12:04 CIA-40 bioclipse: egonw * r10718 /bioclipse2/trunk/plugins/net.bio​clipse.doc.developers/.gitignore: Ignore the autogenerated doc/ dir
12:05 CIA-40 bioclipse: egonw * r10719 /bioclipse2/trunk/plugins/ne​t.bioclipse.doc.developers/ (.classpath build.xml jars/ant-contrib-1.0b3.jar): OK, the <if> solution did not work; use env.PATH instead (fixes #1089 again)
12:05 zarah bug #1089 | http://tinyurl.com/of5f72
12:27 egonw masak: what was the reason again there is no js.println() ?
12:27 egonw (in addition to js.print()
12:27 egonw )
12:28 masak egonw: there is. it's just shortened to 'js.say()'.
12:28 egonw oh...
12:28 egonw yes, logical
12:28 masak for me as a perl6er, it is. :)
13:00 edrin hi egonw
13:00 rednael2 [Bioclipse Twitter] now analyzing the #metware SKOS ontology with #bioclipse  http://twitter.com/egonwill​ighagen/statuses/1912074697
13:00 zarah rednael2's link is also http://tinyurl.com/ppgxzg
13:00 edrin egonw: do you have a minute for a chemical question?
13:02 egonw yes
13:03 CIA-40 bioclipse: jonalv * r10720 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): removed monitors from IUIManager interface
13:04 CIA-40 bioclipse: jonalv * r10721 /bioclipse2/trunk/plugins/net.bioclips​e.ui.business.tests/src/net/bioclipse/​ui/business/tests/UIManagerTest.java: non plugin tests are testing the manager not the proxied one that implements the interface
13:06 jonalv svn--
13:06 CIA-40 bioclipse: jonalv * r10722 /bioclipse2/trunk/plugins/net.bioclipse.ui.busine​ss/src/net/bioclipse/ui/business/IUIManager.java: layout
13:07 jonalv karma svn
13:07 zarah svn has a karma of -11
13:07 jonalv karma SVN
13:07 rednael2 [Bioclipse Twitter] Updating my local copy. #bioclipse  http://twitter.com/carlmasak/statuses/1912137100
13:07 masak SVN--
13:07 CIA-40 bioclipse: jonalv * r10724 /bioclipse2/trunk/plugins/ (8 files in 4 dirs): Made ui into New World order. Sadly enough a few plugin tests fail. I think they have to be rewritten or something. I don't know how to fix it... :(
13:07 zarah SVN has a karma of -11
13:07 zarah rednael2's link is also http://tinyurl.com/o52xzj
13:09 egonw jonalv: file bug reports
13:09 rednael2 [Bioclipse Twitter] @carlmasak++ for using the #bioclipse hashtag  http://twitter.com/egonwill​ighagen/statuses/1912153540
13:09 zarah rednael2's link is also http://tinyurl.com/ot2cp8
13:09 egonw btw, I am not sure why having a progress monitor on ui.remove  is bad
13:10 egonw jonalv: can you explain that?
13:12 jonalv egonw: sry exlain what?
13:12 egonw why having a progress monitor on ui.remove  is bad
13:13 jonalv egonw: have I said that it is bad?
13:14 egonw you removed them
13:14 * jonalv feels a bit confused
13:14 egonw ah...
13:14 egonw you removed them from the interface
13:14 egonw sorry... overlooked that
13:14 jonalv egonw: oh yes
13:14 jonalv aha
13:14 jonalv I c
13:16 sneumann quick question, I am trying to fix my BC2 checkout after NWO.
13:16 sneumann IBioclipseManager cannot be resolved
13:16 sneumann where should that one be ?
13:17 sneumann I have net.bc.managers checked out, but it is empty
13:17 sneumann i.e. no java files
13:17 * jonalv afk
13:17 egonw yes, that plugin no lnger exists
13:18 egonw IBioclipseManager is in net.bioclipse.core again
13:24 sneumann net.bioclipse.inchi can not be resolved in cdk.business
13:25 egonw is it in your workspace?
13:26 sneumann now it is :-)
13:26 sneumann only leaves
13:27 sneumann to add the import to CDKMolecule.java
13:27 sneumann in cdk.business
13:28 sneumann exception launching the eclipse platform
13:28 sneumann setting now as target plattform running
13:28 egonw ok,
13:28 egonw reset target platform
13:28 egonw Ctrl-Shift-R
13:28 egonw then type:
13:28 shk3 joined #bioclipse
13:28 sneumann java.lang.ClassNotFoundException: org.eclipse.core.runtime.adaptor.EclipseStarter
13:29 egonw tar
13:29 egonw and pick target-platform.target
13:29 * sneumann typing shk3 has joined this channel
13:29 egonw click the Set as Target Platform in the top right corner
13:29 shk3 hi all
13:29 zarah ni hao shk3
13:29 egonw hi shk3
13:29 maclean hi shk3
13:39 shk3_ joined #bioclipse
13:55 CIA-40 bioclipse: jonalv * r10723 /bioclipse2/trunk/plugins/net.bioclipse.cor​e/src/net/bioclipse/jobs/BioclipseJob.java: don't remove null from the paramaterlist if no uiJob can be found
14:15 shk3__ joined #bioclipse
14:24 egonw I wonder if rednael is also listening for new gists...
14:25 CIA-40 bioclipse: egonw * r10725 /bioclipse2/trunk/plugins/net.bioclipse.rdf/sr​c/net/bioclipse/rdf/business/RDFManager.java: Catch more exceptions and report in the JavaScript console
14:25 egonw no, she is not
14:26 CIA-40 bioclipse: egonw * r10726 /bioclipse2/trunk/plugins/net.bioclipse.rdf/sr​c/net/bioclipse/rdf/business/RDFManager.java: Be happy with any XML: needed for http://www.w3.org/TR/rdf-schema/rdfs-namespace which gives a HTTP 406 otherwise
14:26 zarah CIA-40's link is also http://tinyurl.com/6gww9y
16:08 edrin left #bioclipse
16:50 Gpox joined #bioclipse
19:19 edrin joined #bioclipse
19:19 CIA-40 bioclipse: egonw * r10727 /bioclipse2/trunk/plugins/net.bioclipse.rdf/sr​c/net/bioclipse/rdf/business/RDFManager.java: Catch QueryParseExceptions to give user feedback when the SPARQL is broken
19:22 CIA-40 bioclipse: egonw * r10728 /bioclipse2/trunk/plugins/net.bioclipse.rdf/sr​c/net/bioclipse/rdf/business/RDFManager.java: Fixed using namespaces in the output which were defined in the PREFIX parts of the SPARQL
19:22 sneumann_ joined #bioclipse
19:23 sneumann_ Hm. running bioclipse.project from n.b.ui
19:23 sneumann_ still fails with an
19:24 sneumann_ java.lang.ClassNotFoundException: org.eclipse.core.runtime.adaptor.EclipseStarter
19:24 sneumann_ on both my eclipse installs
19:24 sneumann_ after svn update as of today / 30 mins ago.
19:27 edrin hm
19:27 edrin still activity
19:27 edrin at this time?
19:27 sneumann_ Sitting in the garden, with a beer in my hand.
19:27 sneumann_ Maybe that's the problem ?
19:28 sneumann_ Currently trying to clean run configuration and .metadata caches
19:36 egonw mom
19:36 egonw doing the dishes
19:36 egonw brb
19:47 egonw back
19:47 egonw sneumann: did you reset the target platform?
19:48 egonw if not, the above problem is common
19:48 egonw also make sure that the bioclipse.product's first tab has
19:48 egonw :
19:48 egonw ID: net.bioclipse.ui.product
19:48 egonw Application: net.bioclipse.ui.application
19:49 sneumann_ running an eclipse update, will take a while,
19:49 sneumann_ then trying to fix bc2
19:49 egonw ack
19:58 ilogger2 joined #bioclipse
19:59 egonw please also check that Overview tab of bioclipse.product
20:01 sneumann_ Yup. I now get a real BC error message ... getting there
20:15 egonw good :)
20:15 egonw what's the error ?
20:21 sneumann_ first:
20:21 sneumann_ org.osgi.framework.BundleException: The bundle could not be resolved. Reason: Another singleton version selected: org.eclipse.update.configur​ator_3.2.201.R34x_v20080819
20:21 sneumann_ and a few that look similar, with R34x in them
20:21 sneumann_ second
20:21 egonw bla
20:21 sneumann_ SEVERE: Pre refresh error
20:21 sneumann_ org.apache.commons.logging.​LogConfigurationException: org.apache.commons.logging.​LogConfigurationException: No suitable Log constructor [Ljava.lang.Class;@203a16 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;@203a16 for org.apache.commons.logging.impl.
20:21 sneumann_ Log4JLogger (Caused by java.lang.NoClassDefFoundError: org/apache/log4j/Category))
20:22 egonw well, let's start with the first
20:22 sneumann_ and
20:22 sneumann_ Caused by: java.lang.NoClassDefFoundError: org/apache/log4j/Category
20:22 egonw first sounds like wrong dep
20:22 sneumann_ somewhat funny
20:22 sneumann_ SEVERE: Unable to create application context for [net.bioclipse.core], unsatisfied dependencies: none
20:22 sneumann_ But in the end
20:22 sneumann_ I have a workspace
20:23 egonw can you put the full output in some pastebin ?
20:23 egonw or on gist.github.com
20:24 sneumann_ org.osgi.framework.BundleException: The bundle could not be resolved. Reason: Another singleton version selected: org.eclipse.update.configur​ator_3.2.201.R34x_v20080819
20:24 sneumann_ at org.eclipse.osgi.framework.internal.core.B​undleHost.startWorker(BundleHost.java:305)
20:24 sneumann_ at org.eclipse.osgi.framework.internal.core.Ab​stractBundle.start(AbstractBundle.java:265)
20:24 sneumann_ at org.eclipse.osgi.framework.internal.core.Ab​stractBundle.start(AbstractBundle.java:257)
20:24 sneumann_ at org.eclipse.equinox.internal.simpleconfigurator.C​onfigApplier.startBundles(ConfigApplier.java:317)
20:24 sneumann_ at org.eclipse.equinox.internal.simpleconfigurato​r.ConfigApplier.install(ConfigApplier.java:86)
20:24 sneumann_ at org.eclipse.equinox.internal.simpleconfig​urator.SimpleConfiguratorImpl.applyConfig​uration(SimpleConfiguratorImpl.java:124)
20:24 sneumann_ at org.eclipse.equinox.internal.simpleconfig​urator.SimpleConfiguratorImpl.applyConfig​uration(SimpleConfiguratorImpl.java:138)
20:24 sneumann_ at org.eclipse.equinox.internal.simpleconfig​urator.Activator.start(Activator.java:48)
20:24 sneumann_ at org.eclipse.osgi.framework.internal.core.Bundle​ContextImpl$2.run(BundleContextImpl.java:1009)
20:24 sneumann_ at java.security.AccessController.doPrivileged(Native Method)
20:24 sneumann_ at org.eclipse.osgi.framework.interna​l.core.BundleContextImpl.startActi​vator(BundleContextImpl.java:1003)
20:24 sneumann_ at org.eclipse.osgi.framework.internal.core.Bundl​eContextImpl.start(BundleContextImpl.java:984)
20:24 sneumann_ at org.eclipse.osgi.framework.internal.core.B​undleHost.startWorker(BundleHost.java:346)
20:24 sneumann_ at org.eclipse.osgi.framework.internal.core.Abs​tractBundle.resume(AbstractBundle.java:355)
20:24 sneumann_ at org.eclipse.osgi.framework.internal.core.F​ramework.resumeBundle(Framework.java:1074)
20:24 sneumann_ at org.eclipse.osgi.framework.internal.core.StartLeve​lManager.resumeBundles(StartLevelManager.java:616)
20:24 sneumann_ at org.eclipse.osgi.framework.internal.core.StartL​evelManager.incFWSL(StartLevelManager.java:508)
20:24 sneumann_ at org.eclipse.osgi.framework.interna​l.core.StartLevelManager.doSetStar​tLevel(StartLevelManager.java:299)
20:24 sneumann_ at org.eclipse.osgi.framework.internal.core.StartL​evelManager.launch(StartLevelManager.java:247)
20:24 sneumann_ at org.eclipse.osgi.framework.internal.core.S​ystemBundle.resume(SystemBundle.java:201)
20:25 sneumann_ at org.eclipse.osgi.framework.internal.cor​e.Framework.launch(Framework.java:644)
20:25 sneumann_ at org.eclipse.osgi.framework.intern​al.core.OSGi.launch(OSGi.java:51)
20:25 sneumann_ at org.eclipse.core.runtime.adaptor.Eclipse​Starter.startup(EclipseStarter.java:313)
20:25 sneumann_ at org.eclipse.core.runtime.adaptor.Eclip​seStarter.run(EclipseStarter.java:175)
20:25 sneumann_ at sun.reflect.NativeMethodAc​cessorImpl.invoke0(Native Method)
20:25 sneumann_ at sun.reflect.NativeMethodAccessorImpl.in​voke(NativeMethodAccessorImpl.java:39)
20:25 sneumann_ at sun.reflect.DelegatingMethodAccessorImpl.in​voke(DelegatingMethodAccessorImpl.java:25)
20:25 sneumann_ at java.lang.reflect.Method.invoke(Method.java:597)
20:25 sneumann_ at org.eclipse.equinox.launcher.Mai​n.invokeFramework(Main.java:549)
20:25 sneumann_ at org.eclipse.equinox.launcher.​Main.basicRun(Main.java:504)
20:25 sneumann_ at org.eclipse.equinox.launche​r.Main.run(Main.java:1236)
20:25 sneumann_ at org.eclipse.equinox.launche​r.Main.main(Main.java:1212)
20:25 sneumann_ joined #bioclipse
20:26 egonw ok, anywhere but here ... :)
20:26 sneumann_ <sneumann_> http://pastebin.com/d759604e5
20:26 sneumann_ I am currently running with all plugins in workspace.
20:27 sneumann_ I remember a wiki page saying to use only x,y and z and calc required plugins
20:29 egonw just to check
20:29 egonw you did run set target platform, right?
20:29 egonw which eclipse version are you using?
20:31 egonw ok, can you please check this...
20:31 egonw Help -> About Eclipse SDK -> Plug-in Details...
20:32 egonw sort on column Plug-in Id
20:32 egonw look up org.eclipse.update.configurator
20:32 egonw and tell me what version you have there...
20:32 sneumann_ http://wiki.bioclipse.net/index.p​hp?title=Checking_out_Bioclipse_2
20:32 sneumann_ net.bioclipse.managers required
20:33 zarah sneumann_'s link is also http://tinyurl.com/58kmzp
20:33 sneumann_ is gone
20:33 egonw right
20:33 egonw mom, will fix that
20:33 sneumann_ net.bioclipse.recording required ?
20:33 egonw no
20:36 sneumann_ Once I have it working, I'll ask about plugins needed for OWL/SKOS
20:37 sneumann_ Should this page go to the museum ?
20:37 sneumann_ http://wiki.bioclipse.net/inde​x.php?title=Compile_Bioclipse
20:37 zarah sneumann_'s link is also http://tinyurl.com/c5zdvx
20:37 edrin good night
20:37 edrin cu
20:38 sneumann_ good night
20:39 sneumann_ much fewer errors now with reduced plugin set
20:39 sneumann_ http://pastebin.com/m4965c093
20:44 egonw no, the page is about fine
20:44 egonw [22:31:15] <egonw> ok, can you please check this...
20:44 egonw [22:31:39] <egonw> Help -> About Eclipse SDK -> Plug-in Details...
20:44 egonw [22:32:05] <egonw> sort on column Plug-in Id
20:44 egonw [22:32:12] <egonw> look up org.eclipse.update.configurator
20:44 egonw [22:32:30] <egonw> and tell me what version you have there...
20:45 egonw never mind
20:45 egonw you no longer have that error
20:45 egonw how do you run Bioclipse?
20:53 sneumann_ now I run "as product" instead of "as eclipse application" ... getting different problems
20:53 sneumann_ http://pastebin.com/d47facdee
20:56 egonw OK, can you try this:
20:56 egonw open bioclipse.product
20:57 egonw and click the green 'play' button top right
21:03 sneumann__ joined #bioclipse
21:03 egonw [22:56:51] <egonw> OK, can you try this:
21:03 egonw [22:56:56] <egonw> open bioclipse.product
21:03 egonw [22:57:08] <egonw> and click the green 'play' button top right
21:03 sneumann__ <sneumann_> success
21:04 egonw ah, that did not reach Uppsala
21:06 sneumann__ freenode hickup
21:06 egonw ok, glad it is running for you now

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