Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-11-10

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All times shown according to UTC.

Time Nick Message
05:16 s_wolf left #bioclipse
05:17 s_wolf joined #bioclipse
07:22 olass joined #bioclipse
08:06 Gpox joined #bioclipse
08:17 egonw joined #bioclipse
08:35 egonw moin
08:35 zarah saluton egonw
08:58 olass hi
08:58 zarah hi olass
12:42 masak joined #bioclipse
12:50 CIA-84 bioclipse.rdf: Egon Willighagen master * r4e49a2e / .gitignore : Ignore .settings/ folders - http://bit.ly/cluxUY
12:50 CIA-84 bioclipse.rdf: Egon Willighagen master * rcd94ab6 / (2 files): Added an update site - http://bit.ly/d4kTcX
13:25 egonw Gpox: where can Eclipse find Xerces?
13:28 egonw Gpox: Ola and I really need your help now...
13:29 Gpox any particular version?
13:30 egonw no, 2.9 should do
13:30 egonw that worked in the past
13:30 egonw but Eclipse cannot find the 2.9
13:30 egonw (or any)
13:31 Gpox 2.9.1 is in the targetplatform
13:32 egonw yeah, that's what I thought...
13:32 egonw so why can't Eclipse it then with Import-Package: ?
13:33 Gpox It seams to be a fragment to org.apache.xmlcommons
13:37 egonw so, how does that help eclipse to find xerces?
13:37 egonw OK, dunnot what changed...
13:37 egonw but your mental support helped
13:37 egonw no red crosses no more
13:38 egonw Gpox++
13:38 egonw Gpox: and you get extra ++'s if you can tell me what you did to fix it here :)
13:38 olass Gpox++
13:41 Gpox dunno it shouln't work as the targetplatform is missing org.apache.xmlcommons, so i started to download it
13:42 egonw :)
13:42 egonw here it got it from com.springsource.org.apache.xerces
13:42 Gpox there is another bundle with xerces in core.git/externals that it could pick up
13:42 egonw yeah, after I removed that from my Eclipse is started working
13:42 egonw so, it might have been a conflict
13:43 Gpox yeah, I will add the required bundle to the platform anyways
13:44 egonw olass: I also created a new workspace
13:44 olass ok
13:44 egonw so, importing all the opentox deps now
13:44 egonw that may also have helped
13:45 Gpox because it is a import-package it doesn't care where it gets it from
13:48 CIA-84 bioclipse.rdf: Arvid Berg master * rc29111a / (3 files): Added p2 site feature - http://bit.ly/dq3rYk
13:51 egonw Gpox: but that's just a feature?
13:51 egonw what in the patch makes it a p2 site?
13:52 egonw (just curious)
13:52 Gpox some magic springles in the build.properties file
13:55 egonw and can't those just be added to the existing features?
13:55 egonw allowing us to get rid of these sites?
13:56 Gpox only the features referenced from the site_feature is published on the p2 site
13:57 Gpox maybe, there is a flag to allso include the containing feature.
13:58 egonw ok
13:58 Gpox But take the chemoinformatics repo, there we could create a site contianting many features that could be installed instead of installing everything with the chemoinformatics feature
14:09 egonw ack
14:20 CIA-84 bioclipse.ds: Ola Spjuth master * r9111de6 / (9 files in 5 dirs): Updated chiral signatures code. - http://bit.ly/dwf03b
14:20 CIA-84 bioclipse.ds: Ola Spjuth master * r8060c55 / (3 files in 3 dirs): Implemented en extension point for model discovery - http://bit.ly/aIi5HS
14:22 CIA-84 bioclipse.qsar: Ola Spjuth master * r7789d9d / (8 files in 7 dirs): Added extension point for QSAR provider discovery. - http://bit.ly/aKibrC
14:26 egonw Gpox: still around?
14:26 Gpox yes
14:26 egonw Gpox: no red crosses for Xerces anymore
14:26 egonw but Bioclipse platform does not boot anymroe
14:26 egonw MESSAGE Missing required bundle org.eclipse.core.databindin​g.observable_[1.2.0,2.0.0).
14:26 egonw stuff like that...
14:26 egonw any clue?
14:28 CIA-84 bioclipse.core: Arvid Berg master * rfb5f0d8 / (2 files):
14:28 CIA-84 bioclipse.core: Added org.apack.xmlxommons to target platform
14:28 CIA-84 bioclipse.core: Required by com.springsource.org.apacke.xerces. - http://bit.ly/auk3ph
14:29 egonw has anything changed wrt to the target platform?
14:29 egonw open target-platform.target
14:29 egonw and hit Set as Target Platform...
14:29 egonw right?
14:30 Gpox yes but wait for it to resolve first
14:38 egonw Gpox: I deleted my site again
14:38 CIA-84 bioclipse.rdf: Egon Willighagen master * r886c9c5 / (2 files): Removed bad site - http://bit.ly/bp2fqt
14:39 egonw for bioclipse.rdf
14:39 egonw as it was wrong, as you pointed out
14:43 CIA-84 bioclipse.rdf: Arvid Berg master * r6674fe4 / sites/net.bioclipse.rdf_site/feature.xml : Added net.bioclipse.rdf_feature to site - http://bit.ly/a2tt6b
14:45 egonw nooooooooooooooo !!!!!
14:45 egonw (now it is failing on Xerces again)
14:53 egonw Gpox: please do continue with getting bioclipse.rdf building on hudson
14:53 egonw there is something really fishy in some of the dependencies...
14:53 egonw I'm back to square zero
14:53 egonw cannot find Xerces
15:17 CIA-84 bioclipse.rdf: Arvid Berg master * r852e169 / sites/net.bioclipse.rdf_site/feature.xml :
15:17 CIA-84 bioclipse.rdf: Added correct feature to rdf site
15:17 CIA-84 bioclipse.rdf: Removed bioinformatics.rdf feature and added
15:17 CIA-84 bioclipse.rdf: net.bioclipse.rdf_feature - http://bit.ly/bukIte
15:38 egonw Gpox: should I be using Eclipse 3.5 or 3.6?
15:39 egonw I know that it theoretically does not matter...
15:39 egonw but what are you using?
15:39 Gpox I am using 3.6
15:40 Gpox and I have changed bioclipse over to 3.6 in my local p2 branch
15:41 egonw ok, that will be my next attempt then
15:47 Gpox there seams to be some depedency on net.bioclipse.core_feature version 2.4.0.RC1 in rdf
15:53 Gpox thre is a lot of product definition files in the rdf repo
15:54 egonw ignore those
15:54 egonw those are there for convenience
15:54 Gpox sure I can but I don't think buckmisnter can :)
15:54 * egonw dislikes having to change bioclipse.product all the time
15:54 egonw oh...
15:54 egonw buckminster--
15:57 Gpox there is support for launch configurations base on features in 3.6
16:01 egonw it's resolving the target platform
16:01 egonw and, of course, downloading considerable amount of stuff now
16:06 CIA-84 bioclipse.rdf: Arvid Berg master * r0157c54 / features/net.bioclipse.rdf_feature/rdf.product : Removed version from features in rdf.product - http://bit.ly/9sGVHD
16:10 Gpox and we got success, rdf site is now building
16:17 egonw Gpox++
16:17 egonw well done!
16:23 olass egonw: what is still not working with your Eclipse?
16:23 olass Gpox: can you help egonw?
16:23 egonw olass: he is
16:24 olass ok..
16:33 egonw arghh...
16:33 egonw eclipse 3.6 is not helping either
16:40 egonw Gpox: in Eclipse 3.6 I get org.eclipse.core.runtime cannot be resolved
16:40 egonw I repeatedly reset target platform...
16:40 egonw suggestions?
16:42 olass egonw: try to reload the TP
16:43 Gpox I assume clean all too
16:43 olass have you tried that from the Preferences?
16:43 egonw yeah, just doing that
16:43 egonw olass: ?
16:43 olass open Preferences
16:43 olass search for "target"
16:43 olass there is a button there saying "reload"
16:43 olass do you find it?
16:44 egonw yes
16:44 egonw Spring-osgi-1.0.2 (Active)
16:44 olass yup
16:44 egonw reload that one?
16:44 olass yes
16:44 olass I have found that it does things differently than when clicking "set target platform" sometimes
16:45 egonw no, not helping
16:45 olass that ws quick..
16:45 olass clean all?
16:45 egonw what branches should I be using?
16:45 olass hmm, how about changing TP on the prefs dialog and then change back to Spring-osgi-1.0.2 ?
16:46 egonw bioclipse.core master seems to still have some stuff now in the TP
16:46 Gpox you can try shift-ctrl-a and typing in org.eclipse.core.runtime and see if it finds anything
16:46 egonw some plugins, like net.bioclipse.xom
16:46 olass I am not up to date completely
16:46 olass Gpox: do you use master?
16:46 Gpox yes
16:46 egonw indeed, there is no org.eclipse.core.runtime
16:47 egonw there are many .runtime.foo artifacts...
16:47 olass must be a TP error in some way..
16:47 olass Gpox: what do you think?
16:47 egonw but the .runtime itself is missing
16:47 Gpox try restarting
16:48 olass you can also try changing TP and then change back...
16:48 egonw ok
16:48 egonw will try both
17:06 egonw both failed
17:06 egonw I am returning to Eclipse 3.5
17:21 masak left #bioclipse
18:41 Gpox left #bioclipse
19:04 egonw olass: do you have all projects in bioclipse.core in your eclipse workspace?
19:04 egonw including those in externals/ ?
19:08 egonw I'm pretty sure not...
19:15 olass egonw: ping
19:15 egonw ping
19:15 egonw pong
19:15 olass pong
19:15 egonw :)
19:15 olass :)
19:15 olass ok, I'm back..
19:16 olass yes, I include all projects
19:16 olass from the core repo
19:17 egonw then you should have gotten a compile error on net.bioclipse.xml
19:17 olass I am afraid to update master...
19:17 egonw ah
19:18 olass so sticking to my current checkout..
19:18 olass what are our current problems in eclipse?
19:22 egonw dunno yet
19:22 egonw started from scratch (again)
19:22 egonw from master
19:22 egonw not good?
19:22 egonw should I use the branch?
19:23 olass I use master
19:24 olass hmm, no...
19:24 olass I use branch 2.4.x...
19:31 egonw OK
19:31 egonw master has many more patches
19:31 egonw olass: can you give me bioclipse.core write access?
19:32 olass you don't have that?
19:32 olass sure
19:32 egonw apparently not
19:33 olass done
19:34 olass seems you were not in that group in the bioclipse account
19:34 olass you are now
19:34 egonw tack
19:38 CIA-84 bioclipse.core: Egon Willighagen master * r7422608 / (1427 files in 87 dirs): Removed obsolete Xerces plugins now provided by the target platform - http://bit.ly/bmviU0
19:38 CIA-84 bioclipse.core: Egon Willighagen master * r2b19b2a / plugins/net.bioclipse.xml/META-INF/MANIFEST.MF : Removed dependency on Xerces externals/ project - http://bit.ly/c5wO3f
19:48 egonw olass: OK, I think I have an idea now why running from master fails
19:48 egonw and no clue why it works for Gpox
19:48 olass ok, why?
19:48 olass did you manage to fix it?
19:49 egonw version numbers are messed up
19:49 egonw it seems
19:49 olass oh
19:49 olass you got it fixed now?
19:49 egonw ah, no...
19:49 egonw wrong plugin...
19:49 egonw version number is right
19:50 egonw oh... it's likely that I don't have bioclipse.cheminformatics yet
19:50 egonw and bioclipse.statistics
19:50 egonw ok, will have to import those first too then
19:50 egonw fingers crossed
19:58 CIA-84 bioclipse.cheminformatics: Egon Willighagen master * r0655741 / plugins/net.bioclipse.cdk.smartsmatchin​g/.settings/org.eclipse.jdt.core.prefs : Removed .settings/ files - http://bit.ly/czcFqv
19:58 CIA-84 bioclipse.cheminformatics: Egon Willighagen master * r39d5409 / (3 files): Added a test feature - http://bit.ly/ayBBEx
19:58 CIA-84 bioclipse.cheminformatics: Egon Willighagen master * r68621a2 / plugins/net.bioclipse.cdk.ui.sdfedito​r/src/net/bioclipse/cdk/ui/sdfeditor/​CDKFingerPrintPropertyCalculator.java : Merge branch '2.4.x' - http://bit.ly/a2hInh
19:59 CIA-84 bioclipse.cheminformatics: Egon Willighagen master * r34c3c5b / (27 files in 27 dirs): Merge branch '2.4.x' - http://bit.ly/boWpJt
20:11 egonw ok, I now have imported:
20:11 egonw bioclipse.core, bioclipse.cheminformatics, bioclipse.statistics, org.openscience.cdk, bioclipse.balloon
20:11 egonw opened target-platform.target
20:11 egonw waiting for it to finish resolving...
20:11 egonw now resetting...
20:12 olass I usually just import core then set target platform
20:12 egonw via prefs...
20:12 egonw done, no red crosses
20:12 olass nice
20:12 egonw opening bioclipse.prodict
20:12 egonw opening bioclipse.product
20:12 egonw removed all
20:12 egonw saved
20:13 egonw adding _platform
20:13 egonw saved again
20:13 egonw starting
20:13 egonw failed
20:13 egonw f***, f***, f***
20:13 olass why?
20:13 olass what is the error?
20:13 egonw "MESSAGE Product net.bioclipse.ui.product could not be found"
20:14 olass you started from the product?
20:14 egonw bioclipse.product, yes
20:14 olass must be more errors than that?
20:14 egonw yes
20:14 egonw Missing required bundle org.eclipse.equinox.p2.metadata
20:14 egonw that's the last of the first batch
20:15 olass why do you run 3.5?
20:15 olass why not 3.6?
20:15 olass (helios)?
20:15 egonw because 3.6 did not work what so ever
20:15 egonw and master is still based on 3.5, AFAIK
20:16 egonw it isn't?
20:16 olass I guess it should not matter, the TP sets what it needs
20:16 olass and yes, it's 3.5 I guess
20:16 olass you run 2.4.x branch now?
20:16 egonw no, master
20:16 olass try switching to 2.4.x
20:16 olass master might be in flux by Gpox
20:17 olass since error says something about p2...
20:17 egonw true
20:17 olass and he is adding p2 for the 2.6 release
20:17 olass try 2.4.x
20:17 egonw ok, will switch back to 2.4.x
20:17 olass then set target platform
20:17 egonw sure
20:27 egonw yes, we got a logo
20:27 egonw oh...
20:27 egonw and a crash
20:27 egonw oh, wow
20:27 egonw that's something I saw earlier today
20:27 egonw "!MESSAGE Missing required bundle org.eclipse.core.databinding​.observable_[1.2.0,2.0.0)."
20:29 olass hmm, can you maybe install that from Eclipse update site?
20:29 olass databinding that is...
20:29 egonw it's installed...
20:29 olass hmm
20:29 olass
20:29 egonw right version too
20:29 egonw but I got a better error now...
20:30 egonw ah, no, I don't
20:30 egonw "!MESSAGE Missing required bundle org.eclipse.equinox.p2.engine_[1.0.100,2.0.0)."
20:31 egonw but also a better one:
20:31 egonw no application id found...
20:31 olass the latter is just follows from the first I guess..
20:32 egonw what did the plugins tab have to look like again?
20:32 egonw that was just for running the test suite, correct?
20:32 olass sorry?
20:33 olass if you press ctrl + shift + a, a dialog "open plugin artefact " opens, right?
20:34 olass if you type *.p2.e
20:34 olass do you see p2.engine there?
20:35 olass just confirming you have it installed...
20:35 egonw yes
20:35 olass hmm, how about "add required plugins" in the run config? An old trick which we don't use anymore...
20:35 egonw let me try something
20:35 egonw this might be something really stupid
20:36 olass what JDK do you use?
20:36 egonw oracle's
20:36 olass ok, that used to work?
20:36 egonw sure
20:37 egonw that's what I used to write the bloody opentox code
20:37 olass right..
20:37 olass you lost the red crosses now but BC won't start, is it so?
20:37 olass very very strange and annoying...
20:38 egonw yes
20:38 egonw I move the workspace now
20:38 egonw from one partition to another...
20:38 * olass will go out for some jogging now but will continue in 30 minutes or so
20:38 olass have not left this room for 24 hours...
20:39 olass ned some air..
20:39 olass be back soon
20:44 egonw ok, that did not help either
20:51 CIA-84 bioclipse.cheminformatics: Egon Willighagen 2.4.x * rbe1d42f / plugins/net.bioclipse.cdk.business/src/ne​t/bioclipse/cdk/business/ICDKManager.java : Fixed @params of published methods - http://bit.ly/aOHoPS
20:53 egonw olass: it now complains about "!MESSAGE Missing required bundle org.eclipse.equinox.p2.core_[1.0.100,2.0.0)."
20:55 egonw installed some equinox feature
20:55 egonw rebooting, and hoping it helps
21:05 egonw :(
21:08 olass oh no, not the sad face!
21:09 olass Let us rely on Gpox competence tomorrow to solve your problems
21:09 egonw I'm downloading a new Eclipse
21:09 olass sounds good..
21:09 egonw maybe my eclipse install got broken or so...
21:09 olass 3.6?
21:09 egonw last thing I can reasonably think of
21:10 egonw yeah, 3.6.1
21:10 olass good
21:10 * olass will take a shower now
21:19 olass egonw: any luck?
21:19 egonw 7 download minutes left
21:40 olass egonw: getting there?
21:41 egonw yeah, unpacking
21:42 olass egonw: do you have a paragraph about yourself and CDK which you could send me now?
21:42 olass I have written some in teh doc I want to send to barry...
21:42 egonw tomorrow
21:42 olass ok
21:42 egonw really bad day
21:42 olass I know
21:42 olass sorry
21:42 olass '
21:47 olass egonw: will you send your own partner profile from KI?
21:47 egonw yes
21:47 olass if so, can I remove you from the UPPSALA partner?
21:47 olass ok
21:47 olass will do so then
21:51 egonw it's resolving target platform
21:51 egonw for a while now already...
21:51 egonw but then agian, moving from 3.5 to 3.6
21:52 olass TP sometimes takes quite a while
21:52 egonw it's downloading quite a bit
21:52 olass yes, much more when you run 3.6
21:52 olass since TP makes use of 3.5 plugins
21:52 egonw indeed
21:52 egonw hopefully eclipse can make sense of all of it now...
22:02 egonw it's still 'resolving'...
22:03 egonw I guess another 200MB
22:06 olass you have slow connection there?
22:06 egonw not that bad...
22:06 egonw ~180KB
22:06 egonw it's just a lot of eclipse to download...
22:06 egonw and EMF
22:07 egonw and GEF
22:07 egonw ...
22:07 egonw ...
22:08 egonw but it is done now
22:08 egonw resetted platform
22:08 egonw it's now building the workspace (again)
22:13 egonw yeah! I see a boot progress bar!!!
22:13 egonw finally...
22:13 egonw bloody hell
22:13 egonw what a nightmare
22:14 egonw ok, that was with the core and cheminformatics features
22:14 egonw next stop:
22:14 egonw rdf
22:23 egonw ok, good... no red crosses about xerces...
22:24 egonw ok, still booting...
22:27 egonw importing bioclipse.opentox
22:28 egonw mmm... will import bioclipse.qsar too...
22:28 egonw olass: ping
22:28 egonw olass: qsar -> also 2.4.x branch?
22:28 olass no, master
22:28 egonw I need master there, right?
22:28 egonw ah, right :)
22:29 olass but most important is to run opentox standalone from JS console
22:29 olass for now at least..
22:29 olass glad you got it working!
22:29 olass so it WAS a faulty installation...
22:30 * olass is happy that egonw can continue with opentox now
22:30 egonw haven't booted it yet
22:30 olass egonw++ //for being persistent
22:30 olass uh-oh..
22:32 egonw qsar will likely bring in some new deps...
22:32 egonw resolving again...
22:32 egonw that was quick
22:32 egonw it's done
22:33 egonw reseting target platform...
22:33 egonw rebuilding...
22:33 egonw still no red crosses
22:33 egonw attempting a boot with core, cheminfo, qsar
22:34 egonw ok, let's do ambitous and not remove rdf
22:34 egonw booting
22:34 olass not remove?
22:34 egonw looking good... got a progress bar
22:35 egonw autobuilding qsar project :)
22:35 olass :)
22:35 olass *puh*
22:35 egonw ok, good
22:35 egonw now the opentox feature
22:35 egonw without qsar
22:38 olass finally you can reproduce my reported bug!
22:38 egonw let's hope so
22:38 egonw I got an opentox. manager :)
22:39 egonw service = "http://apps.ideaconsult.net:8080/ambit2/";
22:39 egonw serviceSPARQL = "http://apps.ideaconsult.net:8080/ontology/";
22:39 egonw rdf.createInMemoryStore(); // needed to trigger proper class loading of Xerces
22:39 egonw stringMat = opentox.listDescriptors(serviceSPARQL);
22:39 egonw stringMat.getColumn("algo"); // returns the descriptor services
22:39 egonw stringMat.getColumn("desc"); // returns the BO entries
22:39 egonw oops...
22:39 egonw wrong window :)
22:41 egonw ok, my own calculateDescriptor.js works...
22:41 * egonw is reading Ola's report
23:01 olass egonw: do you know how it is possible to restrict parts of a SPARQL endpoint to certain users/roles?
23:01 olass is that even possible?
23:01 egonw server side?
23:01 olass yes
23:01 egonw no idea
23:01 olass ok..
23:03 egonw @tell jonalv please enable cia commit messages for bioclipse.opentox for the #bioclipse bot
23:03 zarah Consider it noted.
23:19 olass left #bioclipse

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