Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-03-12

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All times shown according to UTC.

Time Nick Message
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08:50 jonalv ho ho
08:50 * jonalv almost expects an echo in this empty place...
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10:23 CIA-23 bioclipse: ospjuth * r5084 /bioclipse2/trunk/plugins/net.bioclipse.services/ (26 files in 7 dirs): Adapted ServiceView to read roots from new Extension point for ServiceRoot. A lot of model and schema changes.
10:28 CIA-23 bioclipse: ospjuth * r5085 /bioclipse2/trunk/plugins/net.bioclipse.services/ (10 files in 3 dirs): Adapted all roots for new EP-system and updated labelprovider to use icon in EP.
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13:26 jonalv net.bioclipse.cdk in bc2 is not compiling for me at the moment... What's up?
13:36 egonw joined #bioclipse
13:43 olas jonalv: repeat the question :-)
13:43 olas egonw just signed on
13:47 jonalv net.bioclipse.cdk in bc2 is not compiling for me at the moment... What's up?
13:47 egonw hang on
14:01 masak joined #bioclipse
14:01 jonalv hi masak
14:02 masak hello
14:03 olas wb masak
14:03 masak thx
14:03 egonw question about Checking_out_Bioclipse_2
14:03 masak http://wiki.bioclipse.net/index.p​hp?title=Checking_out_Bioclipse_2
14:03 egonw would that Missing Plugins message not dissapear when one has the BLA plugin installed?
14:03 * masak plays lambdabot
14:04 egonw olas: what's that plugin again?
14:04 egonw which you need to make a release...
14:04 egonw and which comes with plugins for other platforms?
14:05 olas The Delta pack you mean
14:05 egonw yeah, think so...
14:05 olas you need to download that from eclipse.org
14:05 egonw can't find it on download.eclipse.org
14:06 olas and unpack in your eclipse installation
14:06 olas go to platform
14:06 egonw but that would solve those warnings, not?
14:06 olas most probably
14:06 jonalv egonw, I am not sure
14:06 egonw would be worth checking out...
14:06 olas I get no warnings even without the delta pack
14:10 * egonw is running BC2
14:11 * egonw will now import cdk, jmol, ...
14:15 egonw argh... git-svn does not seem to handle svn:externals properly...
14:15 jonalv borken :(
14:18 * egonw is getting a copy of net.bioclipse.cdk using regular svn
14:19 masak egonw: I hear that is a major problem with groups migrating from svn to git
14:19 egonw yeah, I can imagine...
14:19 egonw svn:externals is quite nice...
14:25 jonalv egonw, you think git is better than svn?
14:25 egonw no, but it does allow me to 'commit' things when offline...
14:25 jonalv ah
14:25 egonw and since I'm on the train quite a lot, that feature is certainly useful
14:26 CIA-22 bioclipse: ospjuth * r5087 /bioclipse2/trunk/plugins/n​et.bioclipse.ui/plugin.xml: Added contexts for Bioinformatics and Chemoinformatics.
14:26 jonalv but you can't use it from within Eclipse or?
14:28 egonw there is a git plugin for eclipse, AFAIK
14:29 jonalv but you don't use it?
14:30 egonw not so far
14:30 * egonw is a command line addict
14:30 jonalv have you tried svk?
14:33 egonw no, what's that?
14:33 jonalv a version control system based on svn it supports offline commits among other stuff
14:34 egonw oh, interessant
14:35 jonalv <http://blog.brautaset.org/2005/05/15/​ditching-gnu-arch-aka-embracing-svk/>
14:36 Dahlo joined #bioclipse
14:37 masak I can attest to svk's greatness
14:37 masak you sense how big it is when you download it
14:39 masak but srsly, it's one of the contenders in the new generation of version control programs (where hg, git, arch and darcs are some others)
14:42 CIA-22 bioclipse: ospjuth * r5088 /bioclipse2/trunk/plugins/n​et.bioclipse.ui/plugin.xml: Cleanup of contexts
14:42 jonalv olas, you doing help stuff?
14:43 olas nja
14:43 olas kinda working on a lot of stuff
14:44 olas making services active only in certain contexts
14:44 jonalv so what's a context in this context anyway? :)
14:44 masak could be context-dependent even within this context :P
14:45 jonalv my head hurts
14:49 olas contexts in Eclipse: http://help.eclipse.org/help33/index.j​sp?topic=/org.eclipse.platform.doc.isv​/guide/workbench_advext_contexts.htm
14:49 olas reallu useful
14:50 olas left #bioclipse
14:50 jonalv so how many are you planning on now?
14:50 jonalv olas?
14:50 olas joined #bioclipse
14:50 jonalv :(
14:50 jonalv ah wb
14:50 egonw one context for one perspective?
14:50 egonw crap...
14:50 olas thinking of it at least
14:51 olas can be multiple
14:51 egonw my Eclipse crashes now on the BC2 workspace...
14:51 olas and one per project seems appropriate as well
14:51 egonw all I did was that I removed a jar from the classpath :(
14:51 olas if you work with QSAR then the QSARcontext is active
14:51 olas and QSARContext is child of Chemoinformatics context
14:51 olas and so on...
14:53 olas jonalv: masak: please read this:
14:53 olas http://help.eclipse.org/help33/index.jsp?topic=​/org.eclipse.platform.doc.isv/guide/search.htm
14:54 olas this is what we should use IMO
14:54 egonw crap...
14:54 egonw it's reproducible...
14:54 egonw can't boot Eclispe anymore :(
14:55 egonw jonalv: might take a while before I fixed that .cdk compile error
14:55 * olas seldom has problems with Eclipse
14:55 jonalv olas: yes that looks interesting
14:55 * olas has 2Gb ram
14:55 * olas soon has 4 Gb ram
14:55 jonalv egonw, ok, what did you do? :)
14:56 egonw [15:51] <egonw> all I did was that I removed a jar from the classpath :(
14:57 jonalv but what jar file was that?
14:57 jonalv can't you just put it back?
14:57 egonw yes and no
14:57 egonw can do it, but don't want to
14:57 egonw not in CDK SVN anyway
14:57 egonw not strictly speaking not adding it to n.b.cdk either
14:58 masak olas: sounds important
14:58 masak is it something that I should take into consideration when mocking the search GUI?
14:58 jonalv masak: YES
14:58 masak ok, good
14:59 masak phew, all these already-invented wheels...
14:59 jonalv yea what about them?
15:01 masak one better learn about them.
15:02 egonw damn...
15:02 egonw stupid Eclipse
15:02 egonw never seen something *so* reproducable...
15:03 jonalv hehe
15:03 egonw ok, can someone else please remove the weka.jar from the export and build deps for net.bioclipse.cdk ?
15:03 jonalv and not be able to start eclipse either?
15:04 egonw right
15:04 jonalv I am on it :(
15:04 jonalv :)
15:04 egonw it crashes when building the project
15:05 jonalv what do you mean by build deps?
15:06 egonw configure build path ->
15:06 egonw Order and Export
15:06 egonw remove the wek.jar there
15:07 egonw and remove it from the Libraries tab too
15:07 jonalv ok
15:08 jonalv it still thinks that it needs it for some reason
15:08 jonalv libraries tab?
15:08 jonalv ok hang on
15:09 jonalv Have you stopped using weka?
15:10 olas weka is GPL
15:10 * jonalv is commiting those changes
15:10 CIA-22 bioclipse: jonalv * r5089 /bioclipse2/trunk/plugins/net.bioclipse.cdk/ (.classpath META-INF/MANIFEST.MF): removed weka
15:12 CIA-22 bioclipse: ospjuth * r5090 /bioclipse2/trunk/plugins/net.bioclipse.services/ (7 files in 3 dirs): ServiceTypes now appear in ServiceView. Also added support to filter by context.
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15:16 jonalv hm we ahve the views Problems and Tasks in bioclipse 2. Are we using them for anything?
15:19 olas nope
15:19 olas but I hope we will
15:20 olas with good editors in the future
15:20 olas indicating problems "3D coordinates missing, cannot calculate descriptor XXX"
15:20 jonalv the Tasks view?
15:20 jonalv I am not sure we should use it
15:20 olas hmm, maybe that should be omitted...
15:21 olas but what if users want to set up tasks and check them after finishing them?
15:21 olas 1) Get the data
15:21 olas 2) analyse
15:21 olas 3) call jonalv and report problems
15:21 olas let's keep it for now
15:21 jonalv hm I think we should integrate it better if we should keep it
15:21 olas true
15:21 olas let's not worry about that now
15:22 olas we have bigger hills to climb :-)
15:22 olas but I'm making progress here
15:22 olas The ServiceView is coming along
15:22 * jonalv is taking a moment to look at whole picture. He is gonna demo Brunn tomorrow and doen't wanna start doing stuff that might break things...
15:23 egonw jonalv: make a tag!
15:23 egonw that's what tags are for
15:23 jonalv yea good point
15:23 egonw make a tag Brunn20080313
15:23 egonw or so
15:23 egonw tags in SVN are cheap
15:24 egonw it does not really make a copy, so SF won't complain
15:24 jonalv it's a bit complicated though cause I have plugins in both brunn and bioclipse repo...
15:30 egonw bbl
15:45 jonalv hm I am thinking about that svn:externals thing. Brunn probably want that for bioclipse plugins. How hard is it?
15:48 olas ask egonw
15:48 * olas has no idea
15:48 * jonalv is looking in to it now
15:48 jonalv I think I would have to set it up using command line svn but that's not such a big problem after all...
15:51 CIA-22 bioclipse: ospjuth * r5091 /bioclipse2/trunk/plugins/net.bioclipse.se​rvices/src/net/bioclipse/services/model/: Removed old model fro services
15:52 CIA-22 bioclipse: ospjuth * r5092 /bioclipse2/trunk/plugins/net.bioclipse.services/ (16 files in 6 dirs): Fully supports ServiceImplementations now in ServiceView.
15:55 egonw jonalv: svn propedit svn:externals <somedir>
15:55 egonw then the content should be like:
15:55 egonw <local DIR> <svnpath>
15:56 jonalv I wanna do version number too
15:56 egonw jonalv: check the prop for net.bioclipse.cdk/src/org
15:56 jonalv (for a tag) :)
15:56 egonw ah, I think I've seen that
15:56 egonw I think append @REV at the end of the SVN path
15:56 jonalv yea I am gonna look in the svn cookbok
15:56 jonalv chenking out brunn from the commandline right now
15:58 jonalv can you commit over externals?
15:59 egonw yes
15:59 jonalv cool
15:59 egonw indeed
16:00 egonw ok, I'm going offline now...
16:00 jonalv cya
16:00 egonw otherwise it's too difficult to get rest
16:00 egonw cu later
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