Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-12-03

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Time Nick Message
06:23 Gpox joined #bioclipse
08:03 egonw joined #bioclipse
08:51 jonalv joined #bioclipse
09:17 shk3 joined #bioclipse
09:57 shk3 can't start bioclipse any longer.
09:57 shk3 getting java.lang.ClassNotFoundException: org.eclipse.core.runtime.adaptor.EclipseStarter
09:57 shk3 anybody some tips except set target platform, update classpath and clean?
09:57 shk3 I even did a new checkout, but that doesn't help either
10:00 egonw did you try removing all features, save, then add them again, save again?
10:02 shk3 yes
10:02 egonw then I have no clue
10:02 shk3 that removed this java vm bug, but lead to the classnotfound
10:03 edrin joined #bioclipse
10:30 CIA-32 bioclipse: jonalv * r7929 /bioclipse2/trunk/plugins/ (2 files in 2 dirs):
10:30 CIA-32 bioclipse: [structuredb]
10:30 CIA-32 bioclipse: Created testmethods needed for CoverageTest to pass
10:33 egonw edrin: ping
10:33 CIA-32 bioclipse: jonalv * r7930 /bioclipse2/trunk/plugins/ (2 files in 2 dirs):
10:33 CIA-32 bioclipse: [structuredb]
10:33 CIA-32 bioclipse: Fixed problem introduced to testing suite after switching to CACHED tables. Might also fix problem with deleting of databases from the gui.
10:33 egonw edrin: you're at Muenchen University, right?
10:33 egonw I know I should know...
10:40 gilleain joined #bioclipse
11:43 edrin egonw: yes
11:43 egonw tack
11:43 edrin Why?
12:02 shk3 joined #bioclipse
12:02 shk3 Since i am no longer able to run Bioclipse, I have to stop working on it.
12:02 shk3 was nice with you.
12:02 shk3 bye
12:02 egonw you give up quickly...
12:03 egonw do you have more clues?
12:03 egonw it's a bit hard to see from Uppsala what goes wrong on your machine?
12:03 egonw I can throw in some unfounded, time consuming suggestions, which *might* helps...
12:04 egonw but not sure it really will...
12:04 egonw try: please reinstall your OS, JVM and Eclipse...
12:04 shk3 quickly?
12:04 shk3 i trid 3 days
12:04 egonw no, take your time :)
12:04 egonw seriously...
12:04 egonw I really have no clue why it does not work for you
12:04 shk3 i reinstalled eclipse
12:05 shk3 the only thing I did not reinstall is the os
12:05 egonw the ClassNotFoundException does not ring any bell for me
12:05 shk3 but don't want to do that, I must admit
12:05 egonw :)
12:05 egonw nah... please don't do that...
12:05 shk3 well, I had it from time to time, but update classpath and cleaning helped
12:06 egonw please copy/paste the full stacktrace somewhere...
12:06 egonw and let us know the exact plugin and/or feature set you are running
12:07 egonw and try running just the bioclipse_feature
12:07 egonw without any add_on features
12:07 shk3 i checked out the required minimum
12:08 shk3 and even then i get the error
12:08 shk3 http://pastebin.com/m60ef467f
12:11 egonw try to delete all Run Configurations related to Bioclipse
12:11 egonw then do that bioclipse.product thing again...
12:11 egonw remove all features, save (really important), add features, save again
12:11 egonw but before that:
12:11 egonw and after deleting all Run Configs, do another set platform target
12:13 egonw ok, I got one other orthodox approach... as it is common knowledge that demos always fail (Murphey's law), please demo gilleaint that everything you try of the above things does not help and still give you the error
12:13 egonw per 'demo's always fail', it should fix your problem :)
12:13 egonw but you really must want it to fail... that's important
12:13 egonw sort of reverse psychology thing
12:14 egonw that stack trace is rather uninformative, but I think matches to what I have prior to the above steps, which always solved it for me...
12:14 egonw and since it did, I have few other clues :(
12:16 shk3 nothing helps
12:29 jonalv shk3: I whish I knew what to do... It sounds like something to do with target platform or related plugins...
12:32 egonw shk3: you don't have build errors, do you?
12:32 shk3 egonw: how do i do a dist upgrade of kubuntu?
12:32 shk3 no, no build errors
12:32 egonw sudo aptitude dist-upgrade
12:32 egonw but first:
12:32 egonw sudo nano /etc/apt/sources.list
12:32 shk3 I even created a new user and downloaded a new eclipse for that user
12:32 egonw and change gutsy to hardy
12:33 shk3 will do an upgrade after lunch
12:33 shk3 might be usefull anyway
12:33 egonw shk3: you have all plugins use Java5?
12:43 Gpox gilleain: do the jcp application supports draging from an atom drawing a bond and creating atom on release?
13:05 gilleain Gpox : no, don't think so.
13:06 shk3 egonw: do i need to change gutsy to hardy everywhere in the file?
13:07 gilleain Gpox : currently, the AddBondModule just adds a bond (IE : an atom bonded to an existing atom) on a click, not a click-drag-release.
13:13 CIA-32 bioclipse: jonalv * r7931 /bioclipse2/trunk/plugins/net.bioclipse.s​tructuredb/src/net/bioclipse/structuredb/ (3 files in 2 dirs): [structuredb] replaces ugly create database dialog with a shiny new one :)
13:18 egonw jonalv++
13:22 CIA-32 bioclipse: jonalv * r7932 /bioclipse2/trunk/plugins/net.bioclipse.s​tructuredb/src/net/bioclipse/structuredb/​dialogs/CreateNewStructureDBDialog.java: [structuredb] perfected layout for the create new database dialog.
13:22 jonalv doing some cross platform fiddling here... :)
13:27 CIA-32 bioclipse: jonalv * r7933 /bioclipse2/trunk/plugins/net.bioclipse.s​tructuredb/src/net/bioclipse/structuredb/​dialogs/CreateNewStructureDBDialog.java: [structuredb] attempting to make things look good at both Mac and Windows...
13:42 CIA-32 bioclipse: jonalv * r7934 /bioclipse2/trunk/plugins/net.bioclipse.s​tructuredb/src/net/bioclipse/structuredb/​dialogs/CreateNewStructureDBDialog.java: [structuredb] attempting to make things look good at both Mac and Windows...
13:45 jonalv gah, I officially give up
13:45 jonalv platform indepent, nope...
13:45 egonw :(
13:46 egonw jonalv--
13:54 jonalv egonw: oh hang one... :)
13:54 jonalv |on
13:54 CIA-32 bioclipse: jonalv * r7935 /bioclipse2/trunk/plugins/net.bioclipse.s​tructuredb/src/net/bioclipse/structuredb/​dialogs/CreateNewStructureDBDialog.java:
13:54 CIA-32 bioclipse: [structuredb] attempting to make things look good at both Mac and Windows...
13:54 CIA-32 bioclipse: ...on last attempt... :)
13:59 Gpox got the drawing of bonds working without the preview function
14:00 Gpox i leave some unconnected bonds here and there though
14:04 gilleain preview function?
14:04 CIA-32 bioclipse: jonalv * r7936 /bioclipse2/trunk/plugins/​net.bioclipse.structuredb/ (.classpath baseline.jar swt-grouplayout.jar): [structuredb] jar files for that last attempt...
14:11 CIA-32 bioclipse: jonalv * r7937 /bioclipse2/trunk/plugins/​net.bioclipse.structuredb/ (META-INF/MANIFEST.MF build.properties): [strucutredb] added those jar in manifest as well. It's is not 100% perfect now but it's a bit better, good enough for now...
14:14 CIA-32 bioclipse: goglepox * r7938 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint.view/src/net/bioclipse/cd​k/jchempaint/view/JChemPaintWidget.java:
14:14 CIA-32 bioclipse: Moved margin controll to widget from Renderer and
14:14 CIA-32 bioclipse: added dispose listener instead of overriding method.
14:14 CIA-32 bioclipse: goglepox * r7939 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint.view/src/net/bioclipse/cd​k/jchempaint/view/SWTFontManager.java: Chagnged font / scale relationship
14:14 egonw gilleain: yes, the phantom bond shown while dragging the mouse around
14:15 CIA-32 bioclipse: goglepox * r7940 /bioclipse2/trunk/plugins/ (5 files in 5 dirs): Moved Java2DRendererView to n.bc.cdk.jcp.view
14:15 CIA-32 bioclipse: goglepox * r7941 /bioclipse2/trunk/plugins/ (5 files in 5 dirs): Added CML & MDL editor and fixed popupmenu for this
14:15 gilleain oh, right.
14:16 CIA-32 bioclipse: goglepox * r7942 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint/src/net/bioclipse/cdk/jch​empaint/editor/SWTMosueEventRelay.java: Only relay drag if left mouse button
14:16 CIA-32 bioclipse: goglepox * r7943 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jchem​paint/src/net/bioclipse/cdk/jchempaint/handlers/ (AbstractJChemPaintHandler.java ChangeModuleHandler.java): Added handler for changing contorller module
14:16 CIA-32 bioclipse: goglepox * r7944 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/plugin.xml: Added DrawModule action
14:41 shk3 joined #bioclipse
15:47 CIA-32 bioclipse: jonalv * r7945 /bioclipse2/trunk/plugins/net.bioclipse.s​tructuredb/src/net/bioclipse/structuredb/ (4 files in 3 dirs): [structuredb] Fixed deletion of labels from the gui
15:48 egonw jonalv: ping, still here
15:48 egonw ?
15:48 egonw can I show you something?
15:48 jonalv egonw: yea
15:50 jonalv egonw: should I join you?
15:50 egonw please
15:53 egonw http://www.crossref.org/labs/cr_ubiquity.html
15:53 zarah egonw's link is also http://tinyurl.com/5nrazk
16:09 egonw gilleain, shk3: added removeBond(IBond) the the interface
16:09 gilleain ok, cool.
16:09 egonw gilleain: got a sec?
16:09 gilleain I'm just tracking down a bug, but yes
16:10 egonw was discussing drawing with arvid
16:10 gilleain ok
16:10 egonw of new bonds
16:10 gilleain saw his new module, yes
16:10 egonw and the fact of phantom atoms, bonds
16:10 egonw things which might be added...
16:10 egonw like clicking an atom (not releasing)
16:10 gilleain sure
16:11 egonw and dragging around, which will draw a suggested (phantom) bond...
16:11 gilleain suggested?
16:11 egonw possible hit an existing atom
16:11 gilleain yes, we don't have merge yet
16:11 egonw yes, not the single click atom add
16:11 egonw right...
16:11 egonw but there is addBond(IAtom, IAtom)
16:11 egonw which you could very well use for that
16:11 gilleain yes, true
16:11 egonw which brings us to phantom atoms...
16:12 gilleain ok
16:12 egonw arvid suggested that a suggested bond actually is a phantom things...
16:12 gilleain riiight.
16:12 egonw so one can just add an atom to the model, but mark it as phantom
16:12 gilleain is there such a thing?
16:12 egonw so that a clearPhantoms() would delete this phantom stuff again
16:12 gilleain hmm.
16:12 egonw no, but we'd like to add it
16:12 gilleain PseudoAtom?
16:13 gilleain I mean, it would be a model-level thing, like an IAtom, right?
16:13 egonw no, that's different
16:13 egonw yes
16:13 gilleain Huh.
16:13 egonw oh, implement the phantom atom as pseudo atom...
16:13 egonw possible...
16:13 gilleain Well, whatever, that sounds ok.
16:14 egonw arvid will go on holiday after friday
16:14 egonw until next year...
16:14 gilleain ah right.
16:14 egonw so we are focusing on BC2.0.0 release now
16:14 gilleain Ok.
16:15 gilleain There have been some developments in the renderer that JCP uses, that the BC one might benefit from.
16:15 egonw might you please summarize those in your blog?
16:15 gilleain such as not fitting-to-screen
16:15 gilleain ok, sure
16:16 gilleain arvid's original idea was that we would only use one renderer for both, not sure how possible that actually is, but a reasonable goal.
16:17 egonw yes, we should aim at as much shared code as possible
16:20 gilleain true but I didn't want to keep breaking arvid's swt-jcp with changes that were essential for the awt/swing-jcp.
16:20 egonw right... and vice versa, I think...
16:21 egonw those bits need to be in platform specific bits...
16:21 egonw so, where are those bits exactly?
16:21 egonw the visitors?
16:21 gilleain yes
16:21 egonw because, I guess, ideally the visitors are shared too, not?
16:21 egonw so, that there is common base of visitors
16:22 egonw so, we should think how to factor out platform details from those shared visitors...
16:22 egonw would that not be possible?
16:22 gilleain oh, right, the idea was that the renderer has a paint(IRenderingVisitor v) method
16:22 gilleain and then its called like:
16:23 gilleain paint(new AWTRenderingVisitor(g))
16:23 gilleain and
16:23 gilleain paint(new SWTRenderingVisitor(gc))
16:23 egonw right, and we can tune the level of detail in the API of these visitors...
16:23 gilleain think so
16:24 gilleain and also some parameters in the renderer, like rescaleEachTime and stuff.
16:24 gilleain which are actually ideal for the old Renderer2DModel :)
16:25 gilleain (as you might want to scaleToFit when drawing lots of images, for example)
16:25 egonw oh... what was this bug report about a margin about?
16:25 egonw arvid's code has a margin...
16:26 egonw that should not be too difficult to share between AWT and SWT, right?
16:26 CIA-32 bioclipse: egonw * r7946 /bioclipse2/trunk/cdk-externals/trunk/ (2 files in 2 dirs): Added missing removeBond(IBond)
16:26 gilleain I have a margin, if scaledToFit.
16:26 egonw ok
16:27 gilleain if natural scale, then not.
16:27 gilleain it gets a little tricky
16:28 egonw mmm... I need to start writing JavaDoc for IChemModelRelay...
16:29 gilleain by-the-way should there be a setChemModel method in IChemModelRelay?
16:29 gilleain I wondered if it was left out as a design descision, or...
16:30 egonw good question...
16:37 CIA-32 bioclipse: egonw * r7947 /bioclipse2/trunk/cdk-externals/trunk/ (2 files in 2 dirs): Added experimental concept of phantoms, for temporary atoms and bonds which might be drawn
16:47 egonw gilleain: about setChemModel(IChemModel)
16:47 gilleain yes
16:47 egonw is that something we want to express at this level?
16:48 gilleain I don't know - why would we not?
16:48 egonw dunno
16:48 egonw will add it
16:48 gilleain the alternative is to re-create the hub every time
16:48 egonw but feels a bit too low level...
16:48 egonw true
16:48 gilleain which is possible
16:49 gilleain there's the danger (we found) of storing the chemmodel in the hub AND elsewhere
16:49 gilleain and then not updating both
16:50 egonw ack
16:51 CIA-32 bioclipse: egonw * r7948 /bioclipse2/trunk/cdk-externals/trunk/ (2 files in 2 dirs): Made getChemMOdel() symmetric
16:51 gilleain you have to do paint(hub.getIChemModel())
16:53 egonw ok, got to catch the bus
16:53 egonw cu tomorrow or tonite
16:53 gilleain okbye
16:53 egonw bye
16:53 egonw have fun with the imrpvoed API :)
18:00 gilleain joined #bioclipse
19:04 CIA-32 bioclipse: carl_masak * r7949 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint/src/net/bioclipse/cdk/jch​empaint/editor/SWTMosueEventRelay.java: [SWTMosueEventRelay] fixed typo
19:06 CIA-32 bioclipse: carl_masak * r7950 /bioclipse2/trunk/manager-apido​cs/parse-file-for-annotations:
19:06 CIA-32 bioclipse: [manager-apidocs]
19:06 CIA-32 bioclipse: * fixed a few issues with YAML output
19:06 CIA-32 bioclipse: * adapted regexes to handle multiline ignorable annotations
19:07 CIA-32 bioclipse: carl_masak * r7951 /bioclipse2/trunk/manager-apidocs/ (render-as-html run-the-whole-thing): [manager-apidocs] added render-as-html
19:16 gilleain carl_mask you fixed a typo in MosueEventRelay, but didn't change the name!! Oh noes.
19:18 egonw joined #bioclipse
19:18 egonw moin
19:18 zarah hi egonw
19:18 gilleain 'ning.
19:19 gilleain I may have changed a few things.
19:20 egonw +            bondLength = 2.5;       // XXX Or some sensible default?
19:20 egonw 1,4 angstrom?
19:20 egonw that's a better educated guess, I think
19:21 gilleain for a C-C bond?
19:21 gilleain fair enough.
19:22 egonw yeah... it's not that people will do geometry optimizatio on 2D structures )
19:22 gilleain Well, model space is 1:1 with angstrom, I thought.
19:22 edrin hi again
19:23 gilleain hi
19:23 zarah hi gilleain
19:43 egonw joined #bioclipse
19:46 egonw going offline...
19:46 egonw can't focus anyway...
19:46 egonw cu tomorrow
19:47 gilleain cu
20:19 edrin left #bioclipse

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