Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-05-27

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All times shown according to UTC.

Time Nick Message
04:06 egonw joined #bioclipse
04:13 slyrus egonw: my initial attempts to get bioclipse working didn't go so well...
04:13 egonw eclipse can be a pain
04:14 egonw even us seasoned developers are struggling with it now and then
04:14 slyrus and, once again, I remember that I need either bioclipse or JCP as what I really want is a 2-d molecule layout engine
04:14 egonw layout and depiction?
04:14 slyrus from my naive perspective, it would be cool if there were an application-independent 2d layout engine that, say, returned the coordinates of the molecules but didn't actually draw it
04:15 slyrus not sure i know the difference between layout and depiction
04:15 egonw the first generates the 2D coords
04:15 egonw layout is in the cdk as org.openscience.cdk.layout
04:15 slyrus oh, great!
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06:24 egonw slyrus: how did you install bioclipse? and what problems did you run into?
06:25 slyrus I tried to follow the instructions to do so. I ran into some problems building the project, or whatever you call it.
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06:56 egonw slyrus: the instructions from the wiki, I guess?
06:56 egonw so, using the git repository(-ies)?
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08:19 CIA-71 bioclipse.core: Ola Spjuth 2.4.x * r85cbeb2 / plugins/net.bioclipse.logback/src/logback.xml :
08:19 CIA-71 bioclipse.core: Set logging for org.mortbay to warn.
08:19 CIA-71 bioclipse.core: Birt flushes the log if not. - http://bit.ly/aVISXT
08:19 CIA-71 bioclipse.core: Ola Spjuth 2.4.x * ra6e400d / features/net.bioclipse.platfo​rm_feature/bioclipse.product : Removed the -32 in product for mac os X. - http://bit.ly/9XCFc7
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13:48 slyrus egonw: yes. I tried both 2.2.x and HEAD but neither worked.
13:48 slyrus I'll try again though.
13:52 egonw please email your error messages to the mailing list...
13:52 egonw then others can perhaps give you suggestions
13:57 slyrus should i be using HEAD or the 2.4.x branch?
13:59 egonw 2.4.x branch
13:59 egonw which should be present in most repositories
13:59 egonw did you 'set the target platform' ?
14:00 slyrus ok, I'm using the branch
14:01 slyrus yes, I "Set as Target Platform" the thing in net.bioclipse.target.platform
14:02 slyrus then I get a bunch (20) java build path warnings and 505 java problems. the first of which is DescriptionResourcePathLocationType
14:02 slyrus The import net.bioclipse.cdk cannot be resolvedAbstractWebservicesManagerPluginT​est.java/net.bioclipse.webservices.tests/​src/net/bioclipse/webservices/testsline 20Java Problem
14:09 egonw mmm
14:09 egonw ok, please also get the bioclipse.cheminformatics repository too then
14:11 slyrus oh, how do I do that?
14:11 slyrus http://github.com/egonw/bio​clipse.cheminformatics.git ?
14:11 zarah slyrus's link is also http://tinyurl.com/3956bk2
14:15 egonw yes
14:17 slyrus I suppose there's some way to add this directory I just checked out to the eclipse project?
14:18 egonw I always check out git repositories from the command line
14:18 slyrus well, yeah, of course
14:18 egonw and then import the project from it via File -> Import -> Exisiting Protject
14:19 slyrus right, but I assume I do the import from the bioclipse.core directory and then somehow add the bioclipse.cheminformatics files to that?
14:21 egonw I use File -> Import for both of them
14:21 egonw (in the future, Buckminster will take care of all this... but that's not set up yet)
14:21 slyrus ok, sorry for the newbie eclipse questions!
14:22 egonw not at all
14:22 egonw we've *all* been there
14:22 egonw and most of us still struggle with Eclipse now and then
14:22 egonw at least, I do
14:24 slyrus Ok, now I get: DescriptionResourcePathLocationType
14:24 slyrus AbstractSelection cannot be resolvedJChemPaintEditor.java/net.​bioclipse.cdk.jchempaint/src/net/b​ioclipse/cdk/jchempaint/editorline 444Java Problem
14:24 egonw you have the 2.4.x branch for both of them
14:25 slyrus ah, I had just figured that out ;)
14:27 slyrus umm... I suppose I have to the cdk sources as well, right?
14:32 slyrus I seem to be getting closer. now the first error is: DescriptionResourcePathLocationType
14:32 slyrus Project 'org.openscience.cdk' is missing required library: 'develjar/doccheck.jar'org.openscience.cdkBuild pathBuild Path Problem
14:33 egonw ah, good
14:33 egonw that's yet another repos
14:33 egonw http://github.com/egonw/org.openscience.cdk/
14:33 zarah egonw's link is also http://tinyurl.com/34gyz2c
14:33 egonw take the bioclipse2.4 branch please
14:34 egonw we're not making it easy... sorry about that...
14:37 slyrus so does that mean I use that repo instead of the cdk I checked out earler?
14:40 slyrus oh, no, I guess not
14:43 slyrus I still can't find this doccheck jar it seems to be looking for
14:43 egonw no
14:43 egonw both
14:43 slyrus right. i got that much :)
14:43 egonw org.openscience.cdk has the eclipse bundles for the CDK
14:43 egonw remove docheck.jar from the classpath
14:43 egonw should not be there
14:43 egonw will be fix in the next release
14:44 egonw already fixed in the CDK git repos
14:44 slyrus ah, I should have pulled first...
14:50 slyrus how do I remove doccheck.jar from the classpath?
14:50 egonw right click on the project
14:50 egonw -> Build Path
14:51 egonw then the Libraries tab, or so
14:54 slyrus this is the problem with GUIs. it's hard to reason about actions to be taken on them. shell scripts and emacs-lisp-fu may be arcane, but at least they're easily communicated via a text-only channel
14:54 slyrus I don't know what you mean by "right click on the project"
14:54 egonw agreed
14:54 egonw in the project navigator
14:54 slyrus project explorer?
14:54 egonw yes, that's the one
14:55 * egonw does not have an eclipse open
14:55 slyrus there are a whole bunch of things in that hierarchical list panel. is there a particular item I should be clicking on?
14:55 egonw mmm...
14:55 egonw the one project that is complaining about the missing doccheck.jar
14:56 slyrus ah, now we're getting somewhere :)
14:57 egonw note the red crosses on some projects
14:57 slyrus yes, quite a few of them!
14:57 slyrus but fewer now!
14:58 slyrus DescriptionResourcePathLocationType
14:58 slyrus The import org.eclipse.birt cannot be resolvedStartup.java/net.bioclips​e.birt/src/net/bioclipse/birtline 17Java Problem
14:58 egonw ah...
14:58 egonw what project is that?
14:58 egonw try closing that project
14:58 egonw BIRT is not needed for the core
14:58 slyrus net.bioclipse.birt
14:59 egonw ok, close that one
14:59 egonw right click on the project in the Explorer
14:59 slyrus ok, 0 errors
14:59 slyrus 4804 warnings, but I suppose that's for another day!
15:00 egonw yeah, no worry about those
15:02 slyrus hrm: java.lang.RuntimeException: Application "net.bioclipse.ui.application" could not be found in the registry. The applications available are: org.eclipse.equinox.app.error, org.eclipse.equinox.p2.artifact​.repository.mirrorApplication, org.eclipse.equinox.p2.director.app.application, org.eclipse.equinox.p2.director, org.eclipse.equinox.p2.gar​bagecollector.application, org.eclipse.equinox.p2.metad
15:02 slyrus ata.generator.EclipseGenerator, org.eclipse.equinox.p2.metadata​.repository.mirrorApplication, org.eclipse.equinox.p2.publisher.InstallPublisher, org.eclipse.equinox.p2.publisher.ProductPublisher, org.eclipse.equinox.p2.publishe​r.FeaturesAndBundlesPublisher, org.eclipse.equinox.p2.reconciler.application, org.eclipse.equinox.p2.repository.repo2runnable, org.eclipse.equinox.p2.updatesite.UpdateSitePu
15:02 slyrus blisher, org.eclipse.equinox.p2.publ​isher.UpdateSitePublisher, org.eclipse.equinox.p2.pub​lisher.CategoryPublisher, org.eclipse.help.base.infocenterApplication, org.eclipse.help.base.helpApplication, org.eclipse.help.base.indexTool, org.eclipse.update.core.standaloneUpdate, org.eclipse.update.core.siteOptimizer.
15:02 slyrus whoops, sorry about the miniflood
15:02 egonw using the bioclipse.product?
15:03 slyrus yes
15:03 egonw did you reset target platform after the 0 error?
15:03 slyrus nope
15:03 slyrus "Set as Target Platform" again?
15:04 slyrus bah... now I get a bunch of different errors
15:04 slyrus DescriptionResourcePathLocationType
15:04 slyrus AbstractCoverageTest cannot be resolved to a typeCoverageTest.java/net.bioclipse.cdk.busines​s.test/src/net/bioclipse/cdk/business/testline 23Java Problem
15:06 jonalv does anyone know anything about net.bioclipse.chembl? I am having compilation errors in my version...
15:06 egonw close it
15:06 egonw it should have been removed already
15:06 egonw not sure why it is still showing up
15:07 jonalv egonw: so does not feature depend on it?
15:07 egonw no
15:07 jonalv |no feature
15:07 jonalv egonw: becuase when I attempt to build the update site I get: Unable to find plug-in: net.bioclipse.chembl_0.0.0. Please check the error log for more details.
15:07 jonalv
15:08 egonw ah, for you it is different
15:08 egonw it's part of the experimental update site
15:08 jonalv egonw: it's listed in the rdf feature
15:08 egonw checkout bioclipse.chembl repository
15:09 egonw that's bad
15:09 egonw sorry about taht
15:09 jonalv egonw: ah it's moved there?
15:09 egonw should not be part of the RDF feature
15:09 egonw yes
15:09 jonalv egonw: so remove it from the rdf feature?
15:09 egonw 'yes, please
15:13 jonalv egonw: btw why does bioclipse.rdf depend on structuredb? Or does it? The README claims so anyway...
15:14 slyrus egonw: what's an AbstractHandler?
15:14 slyrus DescriptionResourcePathLocationType
15:14 slyrus AbstractHandler cannot be resolved to a typeAbstractJChemPaintHandler.java/ne​t.bioclipse.cdk.jchempaint/src/net/bi​oclipse/cdk/jchempaint/handlersline 33Java Problem
15:17 egonw mom
15:18 slyrus mom?
15:22 egonw short for 'one moment'
15:22 egonw http://www.acronymfinder.com/Slang/MOM.html
15:22 zarah egonw's link is also http://tinyurl.com/2vb9c8f
15:27 CIA-71 bioclipse.rdf: jonalv 2.4.x * r0b1d3be / features/net.bioclipse.rdf_feature/feature.xml :
15:27 CIA-71 bioclipse.rdf: removed chembl from rdf feature
15:27 CIA-71 bioclipse.rdf: Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> - http://bit.ly/axTvFR
15:28 CIA-71 bioclipse.rdf: Egon Willighagen 2.4.x * r9e88a71 / (2 files): Now remove all of the ChEMBL manager - http://bit.ly/bXGs7N
15:39 slyrus ah, ok :)
15:47 slyrus so it looks like somehow I'm missing the org.eclipse classes/jars/whathaveyous
15:47 * egonw has to catch a bus right now
15:47 egonw please email the ML otherwise
15:48 slyrus ok, thanks for your help!
16:01 jonalv zarah: tell gpox Okey I have managed to build both the experimental update site and the main one, and I can install at least some stuff and restart and it works. However there are some deps to and version numbers left to fix. Also when I installed EVERYTHING the JavaScript cnsole went crazy so we have some stuff left to fix I think.
16:01 zarah Consider it noted.
16:01 jonalv zarah: tell Gpox Okey I have managed to build both the experimental update site and the main one, and I can install at least some stuff and restart and it works. However there are some deps to and version numbers left to fix. Also when I installed EVERYTHING the JavaScript cnsole went crazy so we have some stuff left to fix I think.
16:01 zarah Consider it noted.
16:02 jonalv zarah: you shouldn't be so case sensitive...
16:02 zarah jonalv: Hokay. You provide the commits, I provide the "should"-ing
16:06 slyrus well, eclipse is now automagically downloading untold MB of various random-seeming jar files. I suppose that's a good thing.
16:07 slyrus sometimes I think the world's java development/deployment environments are all part of an evil plot for world domination by seagate. seems to be working...
16:08 slyrus i have bioclipse splash screen
16:08 slyrus d/oh!
16:08 slyrus getting closer...
16:09 slyrus Application "net.bioclipse.ui.application" could not be found in the registry.
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