Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-07-02

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All times shown according to UTC.

Time Nick Message
04:25 masak joined #bioclipse
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09:10 edrin joined #bioclipse
09:11 edrin moin
09:11 egonw hi edrin
09:12 EskilA moin
09:12 egonw busy here today
09:12 * jonalv is fighting against sunversion and loosing. Merge is not something simple.
09:13 egonw merging is not trivial in SVN anyway
09:13 jonalv not trivial = impossbile
09:14 jonalv I think I will redo all the work directly on trunk instead. Branches seems impossible to handle...
09:30 jonalv net.bioclipse.cdk10 suddenly doesn't compile. I think something has changed in cdk repo?
09:32 egonw see #cdk last night
09:32 egonw the logs
09:32 egonw pinged stefan about that
09:32 egonw ping him
09:32 egonw he had been hacking in that code
09:33 jonalv egonw: I just wanted to be sure someone knew about it :)
09:33 egonw email cdk-devel
09:33 egonw then enough people know to expect some action
09:33 jonalv should I?
09:35 egonw better then seeing it get lost on IRC
09:35 egonw stefan is the one to explain what has changed
09:35 egonw I have no idea what he has done
09:36 jonalv oh well it seems as if you know about it so I am sure it will be fixed without me complaiing on mail :)
09:38 rojasm joined #bioclipse
10:06 jonalv I have Bioclipse running with all plugins except the cdk10 ones with the new spring-osgi platform. Commit comming. After updating now please reset the target platform and repport any problems to me. (there shouldn't be any since it works for me, right? :) )
10:10 olas jonalv++
10:10 * olas will test
10:12 jonalv is our commit bot dead?
10:13 * jonalv @lunch (and hopes there won't be too much trouble when he returns...)
10:20 EskilA joined #bioclipse
10:35 egonw joined #bioclipse
10:46 egonw jonalv: cdk10 seems to work for me
10:47 egonw wait... forgot to refresh after svn update
10:52 shk3 joined #bioclipse
11:16 egonw jonalv: cdk10 is fine, but .core gives errors
11:16 egonw such as 'spring' cannot be found
11:17 * egonw will try 'clean' and fix classpath (PDE)
11:24 egonw does not help
11:27 egonw Bundle 'net.sf.cglib' cannot be resolved
11:27 egonw Bundle 'org.springframework.bundle.osgi.core' cannot be found
11:29 egonw any suggestions...
11:29 egonw done the 'Set as Target Platform' multiple times now
11:35 shk3 see you in uppsala next week
11:35 shk3 I will be travalling tomorrow and friday, perhaps I will be in the chat, but not sure
11:35 egonw ack
11:35 egonw cu next week
11:35 olas jonalv: around?
11:35 olas bye shk3
11:36 shk3 olas: what's your office room number in bmc?
11:36 Gpox olas: he is still on lunc
11:36 shk3 ah ok,
11:36 shk3 never ming
11:36 shk3 mind
11:36 shk3 will find it, I think
11:56 * jonalv is back :)
11:57 egonw jonalv: please check my spring problems posted earlier
11:57 egonw can't reproduce your .cdk compile issues
11:58 jonalv egonw: I think olas fixed the cdk problems. Does cdk10 compile for you?
11:59 egonw yes, but .core does not
11:59 egonw neither does .ui and .usermanager
12:01 * jonalv has a feeling something was left behind in the commit...
12:02 egonw http://cdk.pastebin.com/m3341a7a8
12:03 egonw which is for net.bioclipse.usermanager
12:03 egonw but problems are typical for .core and .ui
12:03 olas I have same probs here
12:03 egonw done the 'set target' 'update classpath' and 'clean'
12:04 egonw ok, phew
12:04 egonw so, I'm not an idiot :)
12:04 egonw or, at least not the only one :)
12:04 jonalv it's me. I found the problem
12:04 jonalv not sure about what to do about it yet though
12:05 jonalv I have folders with .svn catalouges in that is from another system
12:05 jonalv I can't add them
12:05 jonalv and they where not added in the commit
12:05 jonalv egonw: if you check your target.platfrom I think you will find it very empty...
12:06 egonw how do I check that?
12:06 egonw I did note that I did not get missing plugins
12:06 egonw even though I don't have delta installed ...
12:10 * jonalv is fixing and feeling a bit ashamed. hang on
12:12 olas jonalv: keep up the good work
12:13 jonalv commit in the pipe :)
12:14 egonw is arzhep also going to handle auto builds for BC2?
12:14 egonw of what's that bot called again?
12:15 * egonw has given up
12:15 egonw too hot and moist to concentrate
12:15 jonalv egonw: you talking about zarah?
12:15 masak egonw: arzhep? :)
12:15 * egonw is going to do some stuff he does not have to think for
12:15 egonw yeah, zarah, I guess :)
12:15 masak it will likely not handle builds, no
12:16 jonalv egonw: hang on a minute and the commit should be there. Then you can update for a while. That doesn't take much thinking. Hopefully it will just work after that :)
12:16 egonw jonalv: that's fine
12:16 egonw no, it's the peak fitting I was working on...
12:17 jonalv left #bioclipse
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12:31 * jonalv is gonna fix the bioclipse.product too now :)
12:31 jonalv it works on masak's machine now btw so egonw please confirm that it works for yoiu :)
12:33 * egonw will update
12:36 egonw oi...
12:36 egonw me sees many, many new spring osgi files :)
12:37 egonw including docs :)
12:39 olas egonw: are you a dot?
12:39 egonw no, I'm a dr
12:39 olas :-)
12:39 olas • (2:40:18 PM): oi... < dr named as a dot
12:40 jonalv egonw: yea I guess maybe I should have cleaned away the docs...
12:40 jonalv live and learn...
12:41 egonw yeah, it works here too now
12:41 egonw that is, no more compile errors
12:42 jonalv did you get the latest commit with a working .product in it? (where is that commit bot?)
12:42 egonw think so
12:42 egonw r6039
12:42 jonalv in that case you should be able to start from the new product and just have everything working :)
12:42 egonw ah, no
12:43 egonw 6040 is the latest commit
12:43 egonw ah, and forgot to 'svn update' cdk10/src/org
12:43 egonw :(
12:43 egonw yes, I can confirm the compile errors
12:43 jonalv yup
12:44 jonalv and yea if you hae 6040 the bioclipse.product in ui should get you up and running
12:45 egonw please update cdk10
12:45 egonw to 6041
12:45 jonalv cd ..
12:45 jonalv gah
12:45 olas cd ../gah
12:45 masak jonalv: no such directory
12:46 egonw might have to do the same for .cdk
12:46 egonw hang on
12:50 egonw ok, no idea about the AtomEditor problem
12:50 jonalv hm too bad
12:52 olas can we do a dirty solution?
12:52 egonw this change first changed the API:
12:53 egonw http://cdk.svn.sourceforge.net/viewvc/​cdk/cdk/branches/cdk-1.0.x/src/org/ope​nscience/cdk/applications/swing/editor​/AtomEditor.java?r1=10410&amp;r2=11447
12:53 olas is it used in jcp in bioclipse?
12:53 egonw yeah, the dirty solution would be to do without the AtomEditor
12:53 olas what does it do?
12:53 olas edit atoms?
12:53 olas how?
12:53 egonw give a popup to change atoms
12:53 olas not sure if it even works in BC
12:54 olas but maybe
12:54 olas compiles here too with new TP
12:54 olas jonalv++
12:54 masak jonalv++
12:56 olas jonalv: one thing though
12:57 olas in the bioclipse.product
12:57 olas on COnfiguration tab
12:57 olas I get a red cross over org.apache.log4j
12:58 olas egonw: can you do the dirty changes?
12:58 olas remove the AtomEditor and place FIXME for shk3?
12:58 egonw yes, working on that :)
12:59 olas let us know here
12:59 olas since the commit bot seems down
13:00 olas who added that?
13:00 olas egonw: you?
13:00 olas how?
13:00 olas hmm, I think maybe edrin did that
13:00 egonw I did
13:00 olas how?
13:00 egonw will check the web page, mom
13:00 olas and how can you restart it?
13:00 egonw http://sourceforge.net/tracker/inde​x.php?func=detail&amp;aid=2008779&a​mp;group_id=150681&amp;atid=778609
13:01 olas jonalv: gone?
13:02 masak olas: jonalv is afk, yes
13:02 olas ok
13:02 olas jonalv: ping me when back
13:03 jonalv olas: ping
13:04 olas ok
13:04 olas my bc.product lacks log4j
13:04 jonalv log4j is in net.bioclipse.logger
13:05 olas ?
13:05 jonalv what plugin has a direct dependency on it?
13:05 olas I have a red cross in bioclipse.product config page
13:05 jonalv net.bioclipse.logger exports the log4j interfaces
13:06 olas ok, so that's the problem?
13:06 jonalv hm interesting
13:06 jonalv could you try by just removing it?
13:06 olas yes, seems to work
13:06 olas however, clicking add req plugins adds one more
13:07 olas mom
13:07 olas it adds: org.springframework.osgi.log4j.osgi
13:07 jonalv hm interesting
13:07 olas can I include it?
13:07 jonalv I don't think so
13:08 olas left #bioclipse
13:08 olas joined #bioclipse
13:08 olas not?
13:08 olas someone declared it as a dependncy
13:08 olas obviously
13:08 jonalv nope I think it will interfere with the on in net.bioclipse.logger but I am not 100%
13:09 jonalv olas: not necessary
13:09 jonalv necessarily
13:09 olas I thought that was what "add required plugins" did
13:09 jonalv there are two ways...
13:10 jonalv either you depend directly on a plugin
13:10 jonalv or you import a package exported by any plugin
13:10 jonalv But I guess you already knew this...
13:10 egonw please update cdk10.jchempaint
13:11 egonw commented out code, and filed bug report
13:11 egonw assigned to stefan
13:11 olas update cdk10 right?
13:11 olas or cdk10.jcp?
13:12 olas jonalv: I get some errors running on new TP
13:12 jonalv olas: errors?
13:12 jonalv like what?
13:12 olas Error creating bean with name 'cdkManagerTarget'
13:13 jonalv is it missing something?
13:14 jonalv uhm guys now jmol doesn't compile for me...
13:14 egonw update cdk10.jcp
13:14 olas http://pastebin.com/m59439f5e
13:14 jonalv egonw: I just updated everything
13:14 egonw good :)
13:15 * jonalv is updating everything again...
13:15 olas cdk10.jcp compiles, but no cdk10
13:15 egonw cdk10 is fine here
13:16 jonalv olas: row 47 seems to be the intersting one:
13:16 jonalv Caused by: java.lang.NoClassDefFoundError: org/openscience/cdk/interfaces/IChemObjectBuilder
13:17 olas does it run for you?
13:18 egonw 'cdkManagerTarget' is usign cdk10 or cdk?
13:18 olas cdk
13:18 olas cdk10 has no manager with spring
13:18 egonw .jmol fails to compile here too
13:19 egonw PharmacophoreBond constraint=provider.getConstraint();
13:19 egonw undefined
13:19 olas oops
13:19 olas my bad
13:20 olas update cdk.business
13:20 olas missing commit from my hand
13:21 egonw Bioclipse boots for me
13:21 egonw not without trouble
13:21 olas without errors?
13:21 egonw but that's because I did not reset the perspective
13:21 olas that's normal
13:21 egonw and did not have all the views available
13:21 egonw yes
13:26 * jonalv can run structuredb now. Are you still having problems?
13:29 egonw mom
13:30 jonalv olas: is there a reason for calling the services view for "Installed Services"? Couldn't we go with simply "Services"?
13:31 olas please rename it
13:41 jonalv so everything works now?
13:43 egonw well, except some log4j problems
13:43 egonw and CDKManager not findable, it seems...
13:44 jonalv I can't re-create those problems
13:44 egonw how can I test the structuredb?
13:44 jonalv as in run the tersts or as in run the plugin?
13:45 egonw either
13:46 jonalv to run the tests. right klick net.bioclipse.structuredb.tests and select run as junit tests
13:46 jonalv or you could just start bioclipse with the plugin.
13:46 jonalv then you should have structuredb in the javascript console
13:46 jonalv as for gui I have just started with that
13:47 egonw ok
13:47 egonw from the bc console...
13:47 egonw what do I type again?
13:47 jonalv There is also great plans for a generic annotation system
13:47 jonalv structuredb. and hi tab :)
13:47 jonalv hit
13:47 olas jonalv: could you not write up structuredb commands on the wiki?
13:47 olas and blog about it when you have a screenshot with GUI?
13:48 * egonw would be happy with a blog with the console commands
13:48 jonalv yea I am gonna blog about it when there's some kind of a gui :)
13:48 jonalv maybe I should work a little bit more on the help structuredb command :)
13:48 egonw org.mozilla.javascript.EcmaError: ReferenceError: "structuredb" is not defined.
13:49 jonalv hm
13:49 egonw Plug-in "net.bioclipse.core" was unable to execute setInitializationData on an instance of "net.bioclipse.core.busines​s.MoleculeManagerFactory".
13:49 egonw that is in the console...
13:49 egonw among many others...
13:49 jonalv you are running the plugin and you didn't get any stack trace or errors on the termianl in eclipse?
13:49 egonw org.eclipse.core.runtime.CoreException[1]: java.lang.NullPointerException
13:49 egonw at net.bioclipse.core.Activator.getMo​leculeManager(Activator.java:126)
13:49 jonalv hm
13:50 jonalv could you paste the complete log somewheere?
13:50 egonw hang on
13:50 egonw will first change that code to catch null services
13:50 egonw mom
13:51 egonw } else if (service == null) {
13:51 egonw logger.error( "MolecularManager service was null...");
13:51 egonw ok, if I commit that?
13:52 jonalv yea
13:52 egonw http://cdk.pastebin.com/m6ec8b2c6
13:52 egonw pre-commit
13:52 jonalv egonw:  which plugin was that in btw?
13:53 egonw .core
13:55 jonalv true, it's in the getMolecoleMAnager method right?
13:55 egonw rigth
13:55 egonw 6048
13:56 jonalv egonw: Could you explain how you selected plugins? It seems to be the usual logging problem...
13:57 egonw select cdk.jchempaint and .structuredb + required
13:57 jonalv ...which I sort of hoped we where rid of :)
13:59 jonalv (you off-course remembered to uncheck Include optional dependencies when computing?)
14:00 egonw I start off with 'unselect all'
14:01 * jonalv thinks that we probably should invest time in building a complete target platfrom so that we all run the same plugins and not base it on what people happen to have in there Eclipse one...
14:02 jonalv hm for me it works both with and without the optional dependencies checked...
14:02 jonalv I left my Ubuntu computer home today...
14:03 jonalv egonw: sry I can't seem to get mine to fail...
14:03 jonalv how many plugins are you running?
14:04 egonw ok, will try structuredb + required only
14:04 egonw (excl optional)
14:04 egonw 70 selected
14:04 jonalv egonw: try just structuredb
14:07 egonw that is just structuredb + required
14:08 jonalv yea select structuredb and clikc the add required button twice :)
14:09 egonw twice?
14:09 jonalv yea
14:09 jonalv don't ask... :)
14:09 jonalv (I have no idea)
14:10 jonalv it adds new plugins both times though...
14:10 egonw the CIA.VC website can't connect to the bots...
14:11 egonw so, the CIA bots are in revision it seems
14:11 jonalv that seems to happen once in a while...
14:11 egonw yes
14:11 egonw no worries
14:11 egonw ok, still tons of traces
14:12 egonw Caused by: java.lang.NoClassDefFoundError: org/apache/log4j/Category
14:12 jonalv okey, let's chech the plugins you are running
14:13 egonw Caused by: java.lang.NoClassDefFoundError: org/apache/log4j/Category
14:13 egonw wrong paste
14:13 jonalv last in the plujgins tab there are two pluings named slf4j somthing.
14:13 egonw ERROR - MolecularManager service was null...
14:13 egonw that's a confirm on the other problem
14:13 jonalv are you running then? and what version are they?
14:13 egonw ok, mom, checking
14:14 egonw "About Bioclipse Plug-ins" reports:
14:14 jonalv sry, did you or did you not miss org/apache/log4j/Category?
14:14 egonw did
14:14 egonw it was missing
14:14 egonw just did not want to paste it twice
14:14 jonalv as in it is missing?
14:15 jonalv ah
14:15 jonalv okey
14:15 egonw I see no slf4j plugins
14:15 egonw in About BC plugins
14:15 egonw but I do see org.apache.log4j
14:15 jonalv where's that? :)
14:15 jonalv could you check tohe run config?
14:15 egonw where's what?
14:15 egonw int he Run Dialog?
14:15 jonalv "About BC plugins"
14:16 jonalv yea in the run dialog
14:16 egonw BIoclipse -> Help
14:16 jonalv oh, never been there :)
14:16 jonalv check in the run dialog
14:16 egonw jcl104.over.slf4j 1.5.0  (not selected by 'required')
14:17 jonalv that's the problem. our plugins import the log4j packages and these are the pluigns that should get added
14:17 jonalv but sometimes another implementation of log4j get's added instead. Then it doesn't work...
14:18 egonw and I have two time selected org.eclipse.osgi
14:18 jonalv can you figure out where your log4j comes from?
14:18 egonw 3.2.2.R32x_v2007bla
14:18 egonw and 3.3.2.R33x_v2008bla
14:19 egonw slf4j.api 1.5.0 (not selected)
14:19 jonalv hm interesting :)
14:19 egonw slf4j.log4j12 1.5.0 (not selected)
14:19 jonalv those two need to be selected
14:20 egonw org.apache.commons.logging is selected
14:20 egonw so is org.apache.log4j
14:20 jonalv org.apache.commons.logging should not be selected
14:21 jonalv log4j I have
14:21 egonw .core and .logging both add log4j upon 'add required'
14:21 jonalv not sure about that one. It might work without it but seem to work with it :)
14:21 egonw and apache.commons.loggin
14:22 jonalv commos.logging is probably not even from the target.platform so just removing it from it will probably not help...
14:22 egonw ok, got to leave now
14:24 jonalv I think we should follow Richard Klancers thoughts from: <http://wiki.bioclipse.net/index.php?title=​General_Issues_with_Logging_in_Bioclipse2>
14:24 jonalv and make a complete target.plattfrom
14:24 jonalv read that page when you find some time
14:24 jonalv cya
14:24 egonw ok, bye
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