Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-05-28

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All times shown according to UTC.

Time Nick Message
05:23 sneumann joined #bioclipse
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07:57 jonalv joined #bioclipse
07:59 jonalv oh hai
07:59 zarah ni hao jonalv
08:08 CIA-71 bioclipse.bioinformatics: jonalv master * r5d873db / plugins/net.bioclipse.align.k​align.ws/META-INF/MANIFEST.MF :
08:08 CIA-71 bioclipse.bioinformatics: Removed strange imports which couldn't be resolved
08:08 CIA-71 bioclipse.bioinformatics: They didn't seem to be needed... - http://bit.ly/cfqQZR
08:26 jonalv Gpox: do you know anything about org.apache.log4j 1.2.15?
08:27 jonalv Gpox: like for example what version we have...
08:27 Gpox remove the version
08:27 zarah Gpox: You have new messages. Write '/msg zarah @messages' to read them.
08:27 jonalv Gpox: and if we should import org.apache.log4j without giving version numbers?
08:27 * jonalv removes the version numbers then...
08:29 jonalv Gpox: what about org.xmlcml.cmlxom_2.0.0. then?
08:30 Gpox import pacakge without the version
08:30 jonalv Gpox: for log4j?
08:31 Gpox org.xmlcml.cml.element
08:31 Gpox rog.xmlcml.*
08:32 jonalv okey I don't understand this, how come I can build the update site but I can't start Bioclispe from Eclipse with all those features
08:32 jonalv there are lot's and lot;s of plugins importing log4j wiht a version number...
08:33 annzi joined #bioclipse
08:33 Gpox because you can compile it, but the plugins can't be resolved at runtime
08:34 jonalv Gpox: okey, should I remove net.bioclipse.logger from my workspce or are we still using that plugin?
08:34 Gpox no we are not
08:34 jonalv Gpox: so maybe remove it from git entirely?
08:35 Gpox probably
08:37 jonalv Gpox: now that changed thigns a bit, quite a few things not compiling now
08:37 * jonalv fixes but does not look forwards to getting all patches into all the right repos... :(
08:39 * Gpox only did it for core, chemoinformatics and balloon
08:41 jonalv ah oki
08:43 jonalv Gpox: do you have org.openscience.cdk.log4j?
08:43 jonalv Gpox: it is not compiling for me, should I be worried?
08:43 Gpox yeah :/
08:44 Gpox it is looking for log4j stuff not pressent in the sl4j implementation
08:44 jonalv Gpox: you see problem too?
08:44 jonalv oh joy
08:44 jonalv Gpox: and I am guessing we are using that bundle?
08:45 jonalv Gpox: yes we do
08:46 jonalv Gpox: suggestions?
08:48 jonalv Gpox: ping?
08:48 * Gpox thinking
08:49 jonalv Gpox: did you not remove net.bioclipse.logger from your worksbench so you have been running with it all the time or how did we end up here?
08:49 * jonalv can't quite understand where that other implementation of log4j could have comre from otherwise...
08:50 Gpox cmd+a, search for org.apache.log4j
08:51 Gpox I gont have every project checked out
08:51 jonalv Gpox: cmd+a selects all...
08:51 Gpox sry, shit+cmd+a
08:54 Gpox *shift
08:54 Gpox was org.openscience.cdk.log4j used somewhere?
09:10 jonalv Gpox: sry I had a talk with egand yes it was used in another cdk bundle but we have fixed that now... (I hope)
09:11 * jonalv tries to start again
09:12 jonalv okey I stil lhavea long list of errors but I am suprised about Cannot load 32-bit SWT libraries on 64-bit JVM
09:33 masak joined #bioclipse
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10:29 * jonalv switches to only get the main updates features to start on his machine...
10:30 egonw that sounds like a good decision to me
10:30 jonalv still problem with org.xmlcml.cmlxom_2.0.0. though
10:30 jonalv Gpox: did you say you knew somethign about that?
10:31 Gpox import pacakge without the version
10:32 jonalv Gpox: instead of depending on bundle org.xmlcml.cmlxom?
10:32 Gpox yes
10:32 * jonalv tries that
10:32 Gpox the buindleis now net.bioclipse.org.cmlxom, but using import package allows that to be changed
10:33 jonalv Gpox: seems I don't have that package in my workspace
10:33 egonw import package does not take a buncle name, but java packages names, correct?
10:34 jonalv or do I want org.xmlcml.cmllxom.managers?
10:34 jonalv egonw: correct
10:34 Gpox I belive it is org.cmlxom.cml.elements and base that is the mose used packages
10:35 jonalv Gpox: yea that seems right
10:35 jonalv Gpox: am I doing studd that you ahve already done?
10:36 Gpox depends which plugin
10:36 jonalv net.bioclipse.cdk.qsar.xmpp
10:38 Gpox then no
10:38 Gpox does it use xom?
10:39 jonalv Gpox: yea that is my next question...
10:39 Gpox I have aded it to the target platform but in another bundle, net.bioclipse.xom is not used any more
10:40 jonalv what feature should provide xom? What is xom?
10:40 jonalv Gpox: oh okey, so what do I depend on?
10:40 jonalv Gpox: or do I import package again?
10:40 Gpox import package
10:40 Gpox nu.xom
10:41 egonw Gpox: can bioclipse.cheminformatics/e​xternals/org.xmlcml.cmlxom be removed from the repos?
10:42 jonalv Gpox: sometimes I feel we should go through and set the right versions on all iport package statements...
10:42 Gpox Yes I belive so. net.bioclipse.cml.xom should export those packages
10:43 egonw Gpox: ok, I will remove that project from the externals then
10:44 Gpox yes with [1.2.0,1.3.0) foramt
10:45 egonw ./bioclipse.core/plugins/net.biocl​ipse.logger/log4j/log4j-1.2.15.jar ??
10:46 jonalv egonw: yea in my oppinion net.bioclipse.logger should be removed from all repos everyehwere
10:46 CIA-71 bioclipse.cheminformatics: Egon Willighagen 2.4.x * rb59b4ff / (10 files in 5 dirs): Removed org.xmlcml.cmlxom of which the packages are now provided by net.bioclipse.cml.xom - http://bit.ly/aZs7O1
10:48 jonalv okey now it seems I can start Bioclispe with the main update sites features
10:48 * jonalv moves on with the experimental ones
10:53 jonalv hm that worked
10:53 jonalv cool
10:53 jonalv :)
10:53 egonw jonalv++
10:53 egonw jonalv will make one fine Bioclipse release manager!
10:54 jonalv so next step is trying to export it again and see what happends :)
10:54 egonw jonalv: you'll like these 12 recommendations: http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=2441
10:54 zarah egonw's link is also http://tinyurl.com/3ywaxtd
10:55 jonalv egonw: yea I will read it when I get to it on my googe reader feeds :)
11:42 jonalv Gpox: do you remember the log file location by heart?
11:42 jonalv my Bioclpse keeps crashign now... :(
11:43 Gpox on mac? ~/Library/Logs/Bioclipse/bioclipse.log
11:43 egonw masak: http://groovy.codehaus.org/J​SR+223+Scripting+with+Groovy
11:43 zarah egonw's link is also http://tinyurl.com/3tuht4
11:43 masak egonw: ok.
11:46 jonalv Gpox: are you sure?
11:46 jonalv Gpox: it doesn't seem to be working on my machine
11:50 Gpox ~/bioclipse.log?
11:54 jonalv Gpox++ yup that's it
11:55 Gpox hopefully it picks up the right location in the error dialog
11:55 jonalv Gpox: we have a quite extensive logging for the moment...
11:55 jonalv anyway, from time to time things are working for now
11:56 Gpox spring stuff?
11:57 jonalv I don't know, a few times it just plain didn't work but now it does
11:57 jonalv hard to find errors when it's working...
11:58 jonalv I think I am gonna try in Windows
12:08 egonw so, how do I turn off all that debug info from OSGi again?
12:21 egonw Gpox, jonalv: ping
12:21 egonw how do I turn that off?
12:21 jonalv egonw: yea?
12:21 * jonalv doesn't know
12:21 Gpox net.bioclipse.logback
12:25 jonalv hm strange wrrors when attempting to run local update site in windows
12:25 * jonalv hopes that can simply be ignored
12:25 * egonw did not have .logback in his workspace yet
12:26 egonw and nothing seemed to have complained
12:26 jonalv that sounds nice
12:30 egonw Gpox: and then?
12:30 egonw Gpox: should I change something in logback?
12:31 Gpox no
12:31 egonw ok, sounds simple enough
12:31 egonw testing
12:31 Gpox logback should pick up the logback.xml and use that configuration
12:33 egonw Caused by: java.lang.ClassCastException: Script1 cannot be cast to groovy.lang.GroovyObject
12:33 egonw at org.codehaus.groovy.runtime.InvokerHelp​er.createScript(InvokerHelper.java:421)
12:33 egonw masak: that's what I get right now
12:33 egonw Gpox: ic... well, it works fine :)
12:33 egonw Gpox++
12:33 masak egonw: ok.
12:34 egonw interesting results...
12:35 egonw it seems to be set up correctly
12:35 egonw but fails with missing methods
12:35 egonw Caused by: groovy.lang.MissingMethodException: No signature of method: Script4.clear() is applicable for argument types: (Script4$_run_closure1) values: {Script4$_run_closure1@23053693}
12:37 CIA-71 bioclipse.bioinformatics: jonalv master * r52a9162 / (3 files in 3 dirs): fixes for logging changes in 2.4 - http://bit.ly/9qaJIa
12:43 CIA-71 bioclipse.cheminformatics: jonalv 2.4.x * r96355fb / features/net.bioclipse.chemoin​formatics_feature/feature.xml :
12:43 CIA-71 bioclipse.cheminformatics: rm org.[...].cdk.log4j frm cheminformatics feature
12:43 CIA-71 bioclipse.cheminformatics: It org.openscience.cdk.log4j is not something that Bioclipse need and there were loggign trouble with it so removed it from the chemoinformatics feature. - http://bit.ly/c29Gfr
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12:53 jonalv egonw: maybe it would be easier if you gave me commit bit for bioclipse.joelib?
13:51 egonw jonalv, masak: want to see something cool?
13:51 jonalv egonw: yes
13:51 masak egonw: we'll be over :)
13:51 egonw then you have to hurry
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