Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-12-04

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All times shown according to UTC.

Time Nick Message
05:01 wins joined #bioclipse
05:02 wins joined #bioclipse
05:59 egonw joined #bioclipse
07:34 egonw joined #bioclipse
07:34 CIA-65 bioclipse.cheminformatics: Egon Willighagen 2.2.x * rcbdf5fd / plugins/net.bioclipse.cdk.business/src/ne​t/bioclipse/cdk/business/CDKManager.java : Removed redundant method stub; cdk.fromSMILES() still works, so it seems that this stub was never reached anyway (fixes #1746) - http://bit.ly/8sl4GV
07:34 zarah bug #1746 | http://tinyurl.com/yf63b6o
07:46 egonw hi wins
08:01 Gpox joined #bioclipse
08:02 egonw hi Gpox
08:02 Gpox hi egonw
08:23 sneumann_ joined #bioclipse
08:26 olass joined #bioclipse
08:27 olass moin
08:27 zarah oh hai olass
08:27 egonw hi olass
08:27 olass hi egonw
08:27 * olass is pulling all egonw's commits
08:29 olass egonw: you are aware that your bioclipse.statistics is a fork of my bioclipse.statistics?
08:29 olass and I already updated version on that
08:29 * olass just wanted to confirm
08:31 egonw olass: no, was not aware...
08:31 egonw check the remotes, but yours was not listed...
08:31 egonw did not check further
08:31 olass see github
08:31 olass ok
08:31 egonw thanks for the ping
08:31 olass now you know :)
08:32 egonw indeed
08:32 olass since not much devel there, it matters little
08:33 * egonw is attempting to run the RDF plugin unit tests...
08:33 olass egonw: so are we good to go with RC2?
08:33 egonw but it fails...
08:33 egonw :(
08:33 olass oh :(
08:33 egonw with some weird JVM dump
08:33 egonw while the CDK plugin unit tests run fine
08:33 egonw olass: no, not yet
08:33 olass strange
08:33 olass ok, no worries
08:33 egonw I need to work out RDF issues...
08:33 egonw hence the unit testing...
08:33 olass I need to test some things and make a test build
08:34 egonw olass: please run as many test suites as possible and report in wiki
08:34 olass so no worry for a few hours
08:34 olass if I have time..
08:34 olass will try as much as I can
08:34 olass will primarily test some UI stuff
08:34 olass to see that it runs
08:35 * olass wants nightly!
08:35 * olass wants Hudson
08:35 * olass wants Buckminster
08:36 olass Gpox: any JCP bug fixes scheduled for today that can make it into RC2?
08:36 * olass is just planning his day
08:36 olass egonw: did you ever get to the run-scripts-as-unit-tests?
08:36 olass would be nice to run the scripts before every release...
08:37 olass now this is tedious, manual work
08:37 olass maybe Hudson can do that?
08:37 olass Gpox: do you think we could get Hudson to run scripts in Bioclipse?
08:37 olass gists would be ideal...
08:38 egonw olass: no, not yet
08:38 * olass suspected so
08:38 egonw olass: I think we should annotate manager methods with @MyExperiment("number,number")
08:38 egonw then we can automate that testing
08:38 olass yes
08:39 olass would be nice to have that layer of testing as well
08:39 olass unit testing and script testing
08:39 egonw quite so
08:39 olass and verbose reports of uncovered methods and methods that fail
08:39 olass then we are really on the way...
08:40 * olass looks forward to that day
08:40 egonw but right now, I'd be happy if the bloody AllRDFManagerPluginTests suite would just run :(
08:40 olass indeed
08:41 olass egonw: did you bump version on bioclipse.social feature + plugins?
08:42 egonw yes
08:42 egonw @pz 1758
08:42 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1758
08:42 egonw @pz MyExperiment
08:42 zarah [1758] @MyExperiment annotation for I... http://tinyurl.com/yglda8t
08:42 zarah [1643] StructureDB locks up and refus... http://tinyurl.com/yblv5l8
08:42 zarah Entire list at http://tinyurl.com/yk7t64v
08:43 egonw @tell masak please have @pz NUM also report a title...
08:43 zarah Consider it noted.
08:44 CIA-65 bioclipse.cheminformatics: mark_rynbeek 2.2.x * re8514b0 / cdk-externals/trunk/org.openscience.cdk.​renderbasic/src/org/openscience/cdk/rend​erer/generators/BasicBondGenerator.java :
08:44 CIA-65 bioclipse.cheminformatics: some double bonds were rendered as wedge
08:44 CIA-65 bioclipse.cheminformatics: Signed-off-by: Arvid Berg <goglepox@users.sourceforge.net> - http://bit.ly/8qI5n2
09:04 egonw OK, RDF test suite running again...
09:04 egonw just patiently reseting target platform, refreshing workspace, repeatedly....
09:04 jonalv joined #bioclipse
09:24 egonw damn...
09:24 egonw sparqlRemote is broken :(
09:24 sneumann_ http://en.wikipedia.org/wi​ki/Continuous_integration
09:24 zarah sneumann_'s link is also http://tinyurl.com/6lajga
09:25 sneumann_ Disadvantages
09:25 sneumann_ * Initial setup time required
09:25 sneumann_ * Well-developed test suite required for best utility
09:25 sneumann_ I think bioclipse has covered the 2nd point
09:25 sneumann_ very well already
09:26 jonalv well it can ofcourse always be better...
10:01 miguelrojasch joined #bioclipse
10:04 egonw hi miguelrojasch
10:05 miguelrojasch hi egonw
10:19 jonalv o/
10:42 samuell joined #bioclipse
10:45 CIA-65 bioclipse.structuredb: jonalv master * r9869a42 / (3 files in 2 dirs):
10:45 CIA-65 bioclipse.structuredb: Added faster annotate method to StructureDB
10:45 CIA-65 bioclipse.structuredb: It annotates a molecule directly in the database. Handy when we don't want to collect a complete list of all annotated molecuels in memory. Or don't want to do unecessary loading just to annotate. - http://bit.ly/69ZlaC
10:45 CIA-65 bioclipse.structuredb: jonalv master * re29bce1 / plugins/net.bioclipse.structuredb/src/net/bioclip​se/structuredb/persistency/dao/DBMoleculeDao.java :
10:45 CIA-65 bioclipse.structuredb: Optimized StructureIterator with a cache
10:45 CIA-65 bioclipse.structuredb: It now loads 10 molecules from the database in a go to keep down the number of
10:45 CIA-65 bioclipse.structuredb: database calls. The number could be fine tuned and maybe a WeakHashMap should be
10:46 CIA-65 bioclipse.structuredb: used instead to really avoid memory leaks if the number is made too high.. -
10:46 CIA-65 bioclipse.structuredb: http://bit.ly/6EIq5a
10:46 CIA-65 bioclipse.structuredb: jonalv master * radfd724 / plugins/net.bioclipse.structuredb/src/net/bioc​lipse/structuredb/DBMoleculesEditorModel.java :
10:46 CIA-65 bioclipse.structuredb: cache number of molecules opened in editor
10:46 CIA-65 bioclipse.structuredb: Cache the number of molecules in the label opened in an editor. This number is apharently used a lot in the editor.. - http://bit.ly/7D4I5X
10:55 CIA-65 bioclipse.structuredb: jonalv master * r99ceb72 / (5 files in 5 dirs): set version 2.2.0.RC2 - http://bit.ly/5IhDY7
10:56 CIA-65 bioclipse.core: jonalv 2.2.x * r6652604 / plugins/net.bioclipse.data​bases/META-INF/MANIFEST.MF : Set version 2.2.0.RC2 - http://bit.ly/6UeXAB
10:56 CIA-65 bioclipse.core: jonalv 2.2.x * r599605e / (24 files in 23 dirs): Merge branch '2.2.x' of github.com:olas/bioclipse.core into 2.2.x - http://bit.ly/6hrBMH
11:01 egonw downloadin many more WTP features, hoping to find the one with xerces ... :(
11:03 * egonw is getting lunch, while features are downloading bloody slow
11:48 egonw samuell: ping
11:48 samuell egonw: pong
11:49 egonw your TDB patches broken sparqlRemote()
11:49 egonw so I reverted that
11:49 samuell egonw: Ah, ok
11:49 egonw which actually took some effort because of conflicts due to later commits :)
11:49 egonw patches about to be uploaded
11:49 egonw I added missing unit tests
11:50 egonw so, when you revert the reverts, to add TDB again, please tune things to make all unit tests pass
11:50 egonw in the RDF test suit
11:50 egonw e
11:51 samuell Yep... sure... will probably need some guidance with the unit tests.... but I guess we can take that a day when you're at bmc
11:51 egonw have you already run the unit tests suites?
11:51 egonw particularly, the plugin suites?
11:51 samuell No, I'm not at all familiar with that
11:53 samuell in fact, I was a little bit worried that the TDB stuff got committed, since I know there are things I don't know very well yet (like tests) ...
11:54 samuell Anyway, thanks for sorting out the troubles it caused
11:55 egonw well, it is important functionality, I'd like to see in the final 2.2
11:55 egonw and it worked...
11:55 egonw it's just that there was a side effect :)
11:56 samuell Ok
11:57 egonw samuell: I actually think that it is just the old Xerces used...
11:58 CIA-65 bioclipse.rdf: Egon Willighagen 2.2.x * rec0949c / (6 files):
11:58 CIA-65 bioclipse.rdf: Revert "Added missing jars, required for Jena TDB"
11:58 CIA-65 bioclipse.rdf: This reverts commit 9c7df0e13eee7dfdcfbfdecf7823b477f917c5c9. - http://bit.ly/5UDQfL
11:58 CIA-65 bioclipse.rdf: Egon Willighagen 2.2.x * r58817f1 / (10 files in 5 dirs):
11:58 CIA-65 bioclipse.rdf: Reverted "Added file based RDF Storage, via Jena TDB library"
11:58 CIA-65 bioclipse.rdf: This reverts commit 5260b0f5aea34456021056f6c4fbdd6f4ebfa47d. - http://bit.ly/8YbvoN
11:58 CIA-65 bioclipse.rdf: Egon Willighagen 2.2.x * r31880dc / plugins/net.bioclipse.rdf.tests/src/net/bioclip​se/rdf/tests/AbstractRDFManagerPluginTest.java : Fixed missing close of SELECT in SPARQL query - http://bit.ly/6ta4tD
11:58 egonw samuell: and we should try TDB with 2.9.0
11:59 olass egonw: did these commits fix the broken RDFManager?
11:59 egonw olass: yes
11:59 olass so we are ready to release RC2?
11:59 olass Gpox: any late commits?
11:59 egonw yes, don't think I can do much more
11:59 olass ok, great
11:59 samuell egonw: 2.9.0 is version, of ... ?
12:00 egonw samuell: xerces
12:00 samuell Ok
12:02 egonw olass: can I introduce a org.apache.xerces plugin in bioclipse.core/externals ?
12:02 egonw post RC2
12:02 egonw pre final
12:02 olass if necessary I guess..
12:02 egonw there are two plugins that need it
12:03 olass then fien with me
12:03 olass fine
12:03 olass but is that not part of Eclipse?
12:03 olass should it not go in target platform?
12:03 egonw no of the eclipse core
12:03 egonw no, rather not
12:03 olass why not in TP?
12:03 egonw because xerces is rather API changing
12:03 egonw putting it in target platform is asking for trouble
12:04 olass ok then
12:04 olass hmm, I have a conflict
12:04 olass in structuredb
12:04 olass egonw: how do I resolve conflicts in git?
12:04 olass can I just "override and update"?
12:04 olass how do I achieve that?
12:04 egonw I do not know what that means
12:05 olass overwrite my local with the remote
12:05 olass discarding my local changes
12:05 egonw yes, that is possible
12:05 egonw need to look up how that is done ...
12:05 olass can I do 'git pull --force' or so?
12:06 egonw http://stackoverflow.com/questions/528​659/git-automatic-conflict-resolution
12:06 zarah egonw's link is also http://tinyurl.com/yayvk4v
12:06 egonw http://stackoverflow.com/questions/1501509​/how-to-take-the-version-in-remote-branch-​and-forget-the-change-i-make-in-my-worki
12:06 zarah egonw's link is also http://tinyurl.com/yl4zptw
12:07 egonw that should give some clues
12:07 olass hmm
12:13 egonw alternatively...
12:13 egonw delete the local branch
12:13 egonw and create a new one by cloning the remote one
12:13 egonw that's what I do sometimes
12:22 egonw olass: how do we put binary bundles in the git repository?
12:22 egonw Gpox, jonalv: maybe you know?
12:22 olass no idea
12:22 olass jonalv?
12:23 jonalv binary bundles?
12:23 jonalv I don't understand the question
12:23 egonw like: http://download.eclipse.org/tools/orbit/d​ownloads/drops/S20091026190351/bundles/or​g.apache.xerces_2.9.0.v200909240008.jar
12:23 jonalv what is the problem?
12:23 zarah egonw's link is also http://tinyurl.com/ya29anb
12:23 jonalv yea, what about that one?
12:24 egonw [12/04/09 13:22] <egonw> olass: how do we put binary bundles in the git repository?
12:24 jonalv we usually put such thins in the target.platform.
12:24 jonalv egonw: I thin I would commit it using git add and then git commit
12:24 jonalv egonw: and then push it to the repo usign git push
12:24 * jonalv feels that he has not understood the question
12:25 * egonw thinks so too
12:25 egonw :)
12:25 egonw I don't want it in the target platform; too risky
12:25 egonw will break too much, I'm afraid
12:25 jonalv egonw: too risky?
12:25 jonalv egonw: okey, so where do you want it?
12:25 egonw bioclipse.core/net.bioclipse.target.platform/libs has indeed binary bundle .jars
12:26 egonw I want it in bioclipse.core/externals
12:26 egonw I only want specific plugins to see the bundle
12:26 egonw not all plugins
12:26 jonalv egonw: good luck
12:27 egonw no need, I just want an asnwer
12:27 egonw luck is not part of my working scheme
12:27 jonalv honestly I don't thin you can do what you are trying to do
12:27 egonw why not?
12:27 jonalv this is the reason that OSGI people think you should use version numbers when importing stuff
12:27 egonw indeed
12:27 egonw but xerces sucks anyway
12:28 egonw so, some bundle only needs to see xerces 2.8 or better, and we're screwed
12:28 jonalv then only the bundles that need the xerces version you have here can import them and the other will use some other version
12:28 egonw yes, that's the theory
12:28 egonw xerces practice is not quite like that simple theorem
12:29 jonalv egonw: xerces and logging are the two big questionsmarks in Bioclispe if you ask me
12:31 egonw OK, found the src bundles: http://dev.eclipse.org/viewcvs/index.cg​i/org.eclipse.orbit/?root=Tools_Project
12:31 zarah egonw's link is also http://tinyurl.com/yjtrwpt
12:32 egonw CVS.... lovely
12:32 jonalv ye I can't understand why Eclipse can't join us in the future instead of hanging around with CVS...
12:33 egonw they are moving to git
12:33 jonalv are you sure?
12:34 egonw no
12:35 egonw damn...
12:35 egonw it's now pulling the full orbit archive
12:35 jonalv lol
12:37 egonw I wish I could run 2.6.32 on my karmic...
12:37 egonw user space shared memory blocks...
12:37 egonw just think about that...
12:37 egonw running 10 Eclipse instances in 1GB ...
12:37 egonw or more...
12:37 egonw if the can run 32 VMs with Win XP in 1GB ...
12:39 egonw Gpox: you are also setting up a new fixes branch on Pele?
12:39 egonw Gpox: btw, please take notice that not all patches I could apply.... see my email to cdk-jchempaint
12:39 Gpox for porting cdk-jcp stuff from bc?
12:41 Gpox then yes I will
12:41 egonw yes
12:41 egonw I think at least 80% of current BC2.2 is now in cdk-jchempaint too
12:41 egonw pending those few failing patches, and your stuff of today
12:42 egonw and 'git clone --reference' rocks too
12:44 egonw Gpox: looking at da420ef3917065cd27a5467d476bd5154a2be0cc ...
12:44 egonw Gpox: a non-ring bond cannot be aromatic...
12:45 egonw @pz 1523
12:45 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1523
12:45 Gpox so whats the problem?
12:46 egonw I don't think aromatic bonds should be drawn as single...
12:46 egonw ring or non-ring
12:47 CIA-65 bioclipse.cheminformatics: Arvid Berg 2.2.x * rabc0b92 / (2 files in 2 dirs): Added icon for rotate - http://bit.ly/8ppi0b
12:47 CIA-65 bioclipse.cheminformatics: Arvid Berg 2.2.x * r86a69bf / cdk-externals/trunk/org.openscience.cdk.r​endercontrol/src/org/openscience/cdk/rend​erer/generators/SelectBondGenerator.java : Uses RingGenerator when generating selections - http://bit.ly/60CoV2
12:47 Gpox If you render one bond that is part of a ring and thus is aromatic, it would be drawn as a double bond before
12:48 egonw the BasicBondGenerator is not for drawing selection, or is it?
12:52 Gpox no, I realsize it can be done better
12:52 Gpox could you checkout that commit again
12:53 egonw yes, that looks like a better match with the bug report :)
12:53 egonw Gpox++
12:54 egonw what about stefan's comment on using the rendering parameter
12:54 egonw that tells if the ring should be draw as kekule or with an inner ring?
12:55 * egonw is checking BasicBondGenerator
12:55 Gpox that only applies for complete rings, the slection uses the same generator but that relies on there being a ring
12:56 egonw yeah ....
12:56 egonw one more reason for double looping
12:56 egonw of
12:56 egonw generation of the drawing elements...
12:56 egonw the selection should be able to mirror what is being drawn for atoms/bonds already
12:57 Gpox yeah, selection should use the already generated elements
12:57 egonw indeed
12:57 egonw but not in 2.2
12:57 egonw ok, thanx for the explanation
12:58 CIA-65 bioclipse.cheminformatics: Arvid Berg 2.2.x * rd80fb67 / cdk-externals/trunk/org.openscience.cdk.r​endercontrol/src/org/openscience/cdk/rend​erer/generators/SelectBondGenerator.java :
12:58 CIA-65 bioclipse.cheminformatics: Render aromatic bonds as single if they are not part of a ring
12:58 CIA-65 bioclipse.cheminformatics: Solves bug #1523 - http://bit.ly/5aHLXW
12:58 zarah bug #1523 | http://tinyurl.com/ygzk6x5
13:01 egonw argh... those orbit cvs folder are all empty :(
13:03 jonalv that sounds strange
13:03 sneumann_ wrong branch ?
13:04 egonw yes, perhaps...
13:05 egonw yes...
13:05 egonw I need to set a tag
13:05 egonw cvs up -j ?
13:08 egonw hope, that's not it...
13:08 egonw nope
13:09 egonw ah, up -r
13:14 olass egonw, Gpox: ok, no more commits to cheminfo?
13:14 olass I will now build, then tag, and send pull requests for tags. ok?
13:14 egonw ack
13:15 olass let's hope no more probs :)
13:26 jonalv olass: I am fiddling around with update sites prefereces page. There was a bug on that. I must admit that they have made SWT-builder worse than it was...
13:26 olass jonalv: ok?
13:26 jonalv olass: I am not sure I dare to suggest this patch for 2.2 though...
13:26 jonalv olass: considering how it did last time I was doign fancy layout stuff... :/
13:27 jonalv @pz 1210
13:27 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1210
13:27 jonalv olass: that is the bug
13:48 jonalv olass: how much longer can I squeese in a commit in core?
13:50 olass now?
13:51 olass jonalv: this is just RC2
13:51 olass you can get it in RC3 or even release if we just confirm the fix
13:51 jonalv olass: you are not supposed to think like that.
13:51 olass I know
13:51 olass so, why did you ask then?
13:51 olass ok, I give you 10 minutes, ok?
13:52 jonalv olass: nah I don't dare that. I need to test run it on Windows before throwing this in
13:52 jonalv I will wait for RC3 or 2.4
13:52 jonalv it's jsut an enhancement
13:52 olass how long do you need to test on win?
13:52 * olass likes enhancements
13:52 olass but seriously, an RC3 is likely to happen..
13:52 jonalv I am only 95% done then I need to export it and test it and perahsp fix any problems found on Windows...
13:53 olass next week
13:53 egonw this is experimental material, right?
13:53 egonw who care about win then?
13:53 olass egonw: no
13:53 olass core
13:53 egonw ah
13:53 egonw :)
13:53 jonalv I am trying to get the table in the update sites preferences page to scale when that dialog window is scaled
13:54 jonalv I had it working but thne it turned out that it only was visible after a resize in Bioclispe. I hate when that happend. A missing re something somewhere. Calling pack made it show but also made it look slightly not so perfect... :/
14:04 jonalv olass: can you build? I get an error message... :(
14:04 jonalv |export I mean
14:08 olass yes, export works here on mac at least
14:08 olass testing now
14:21 CIA-65 bioclipse.core: Ola Spjuth 2.2.x * r7392b8c / features/net.bioclipse.platfo​rm_feature/bioclipse.product :
14:21 CIA-65 bioclipse.core: Set version of product to 2.2.0.RC2.
14:21 CIA-65 bioclipse.core: I always forget this. - http://bit.ly/5ooHa6
14:21 CIA-65 bioclipse.core: Ola Spjuth 2.2.x * rd50a8c6 / (2 files): Updated sample scripts that queried PDB from WS. - http://bit.ly/4Gv0Ft
14:34 jonalv Windows copy dialog, 51 mins remaining, oh now 3 min, 4, 5 hm...
14:35 jonalv it\s counting the wrong way...
14:40 * jonalv is trying to set up a work environment in Windows... :(
14:45 * egonw is getting coffee...
14:46 sneumann_ good luck guys!
14:46 sneumann_ bye
14:46 egonw if there is urgent need for me in the next 30 minutes... use skype
14:46 * jonalv will try to manage :)
15:06 olass how can I recursively list all files from a starting directory and search for a string in the contents?
15:06 * olass has forgot how..
15:06 olass anyone?
15:06 olass jonalv?
15:06 olass Gpox?
15:09 jonalv olass: file names? You mean i Java?
15:11 jonalv olass: http://java.sun.com/j2se/1.4.2/doc​s/api/java/io/File.html#list%28%29
15:11 zarah jonalv's link is also http://tinyurl.com/2wn6q
15:11 jonalv olass: that method looks intresting
15:11 olass jonalv: in linux/OS X
15:11 jonalv olass: oh from the command line?
15:11 olass and no, contents of the file
15:11 olass yes
15:11 jonalv I c
15:12 jonalv I whish I knew...
15:12 jonalv olass: have you tried Spotlight?
15:12 jonalv :)
15:12 olass yup
15:12 olass no luck
15:13 jonalv I got git runnign on Windoes now at least :)
15:14 Gpox find . -name *.java -exec grep something {} +
15:14 Gpox that should work
15:14 jonalv Gpox: you are good with bash, can't you help olass ?
15:14 jonalv ah
15:14 jonalv hehe
15:14 jonalv Gpox++
15:15 Gpox grep -r is enough if it all files
15:16 olass Gpox: what does the {} + do?
15:16 olass Gpox: what does the part '{} +' do?
15:16 Gpox {} instert the file form find, + execute in the same direcory as the file
15:18 Gpox you can check the man file for find to find out the specifics
15:19 jonalv olass: have you built yet? :)
15:19 jonalv :)
15:20 olass jonalv: fixing bugs :(
15:20 jonalv olass++
15:29 CIA-65 bioclipse.core: jonalv jonalv-updatesitesLayout * rba39c5a / plugins/net.bioclipse.ui/src/net/biocli​pse/ui/prefs/UpdateSitesEditDialog.java : test to get it right - http://bit.ly/5G4JdB
15:45 CIA-65 bioclipse.core: jonalv 2.2.x * r28448d7 / plugins/net.bioclipse.ui/src/net/bioclips​e/ui/prefs/UpdateSitesPreferencePage.java :
15:45 CIA-65 bioclipse.core: Reworked layout for UpdateSitePreferences page.
15:45 CIA-65 bioclipse.core: Need to test this on Windows... - http://bit.ly/7sf1FS
15:45 CIA-65 bioclipse.core: jonalv 2.2.x * rba39c5a / plugins/net.bioclipse.ui/src/net/biocli​pse/ui/prefs/UpdateSitesEditDialog.java : test to get it right - http://bit.ly/5G4JdB
15:45 CIA-65 bioclipse.core: jonalv 2.2.x * r8a49008 / (3 files in 2 dirs): Merge branch '2.2.x' of github.com:olas/bioclipse.core into 2.2.x - http://bit.ly/60qKgr
15:45 jonalv olass: fix commited, sry for the merge but I don't think I could avoid it without extra job...
15:45 olass jonalv: is problem solved on windows and also on mac?
15:46 jonalv olass: yup
15:46 olass jonalv++ //never mind the merge
15:46 jonalv olass: I have tested on Windows and Mac
15:46 olass great
15:46 jonalv egonw: could you try on linux?
15:46 olass hope it works on linux then  :)
15:46 olass Gpox: I did this 'grep -r "Install New Software..."' but no luck :(
15:47 egonw I can test 32 bit linux on Pele
15:47 olass did I misunderstand you?
15:47 egonw and 64 bit at home...
15:47 olass egonw: test the binary instead when I get them done
15:47 olass later today
15:47 egonw yes, I though that's what you were talking about
15:47 olass jonalv: was it?
15:47 jonalv egonw: okey checkout core 2.2.x and have a look at the gui for update sites, both the preference page and the edit dialog
15:47 olass sorry then
15:48 egonw ah... still talking about that...
15:48 egonw my bad
15:48 jonalv egonw: if you are infornt of yout linux machine with Eclispe then it would go fast... :)
15:50 Gpox olass: it is picky you sure you wrote it correct
15:50 olass did I not?
15:51 Gpox I meen the text you searching for
15:52 jonalv egonw: you could not help me check that now? :(
15:52 Gpox and yo should indicate where you want to search at the end
15:52 egonw jonalv: if your design works on linux?
15:52 egonw I'm updating repos checkout now
15:52 olass Gpox: ok
15:52 jonalv egonw: yea it's gui stuff and linux, osx, and windows are very different I am afraid...
15:53 egonw what should I be looking at precisely...=
15:53 egonw ?
15:53 jonalv egonw: that the preferences page for update sites looks decent
15:53 jonalv egonw: and the dialog for editing updates sites too
15:54 egonw pref page looks decent, but a bit too large
15:54 egonw so, I get scrollbars
15:54 jonalv egonw: too large?
15:54 jonalv egonw: hm okey but you see all buttons?
15:54 jonalv egonw: try resizing it and see if that works too
15:55 egonw I can enlarge the dialog
15:55 egonw don't think all buttons showed up on first opening the dialog
15:55 jonalv egonw: and the table rezises and everything else moves along nicely around it?
15:55 egonw needed to enlarge the dialog for that
15:55 egonw no beyond the minimum table size
15:55 egonw which was too large for my instance
15:56 jonalv hm maybe we can make the first column for name a bit smaller so the buttons are visible from the start
15:56 egonw or wrap?
15:56 jonalv egonw: wrap?
15:56 egonw wrap the text
15:56 jonalv wghow do you mean?
15:56 egonw Bioclipse
15:56 egonw Update
15:56 egonw Site
15:56 jonalv egonw: hm..
15:56 egonw but likely in between:
15:56 egonw Bioclipse Update
15:56 jonalv I don't really know how to handle that
15:56 egonw Site
15:56 egonw neither do I
15:57 jonalv those names are user defined
15:57 egonw indeed
15:57 jonalv egonw:  are you sure the buttons to the right weas nto visible when you opened it ?
15:57 egonw what about hiding the URL in the initial screen?
15:57 jonalv they are on both mac and Windows...
15:57 egonw no, I am not
15:58 egonw and I do not know the initial size
15:58 jonalv egonw: maybe you could restart and test again?
15:58 egonw so, can't recreate the original situation
15:58 egonw yes, can try
16:04 olass Gpox: ping
16:04 olass Gpox: do you know how one plugin can disable a menu that another plugin adds?
16:04 Gpox no
16:05 olass Gpox: is there a menu registry that you know of?
16:05 olass else I need to go for the general extension registry..
16:07 egonw jonalv: upon restart, everthing fits nicely...
16:07 jonalv egonw: good
16:07 egonw nicely packed now...
16:07 jonalv egonw: thanks
16:07 egonw but did not load new code...
16:07 Gpox http://stackoverflow.com/questions/1415700/disabl​e-plugin-contributions-in-eclipse-rcp-application
16:07 zarah Gpox's link is also http://tinyurl.com/yf77g4g
16:07 egonw so, sounds unstable
16:07 jonalv egonw: sry you lost me?
16:08 olass Gpox: thanks
16:09 egonw jonalv: as in... not sure what it will look like next time :)
16:09 egonw but I am happy with what I see right now
16:09 egonw olass: I can merge in 2.2.x changes into master for bioclipse.core, correct?
16:09 egonw that is, and push, irght?
16:10 egonw I think the JSConsole patches did not make master yet...
16:10 jonalv egonw: if you are happy I am happy
16:10 olass egonw: sure, master is open :)
16:20 CIA-65 bioclipse.core: Ola Spjuth 2.2.x * r3409b92 / plugins/net.bioclipse.ui/src/net/biocli​pse/ui/ApplicationActionBarAdvisor.java : Removed outcommented code. - http://bit.ly/7aCuxR
16:20 CIA-65 bioclipse.core: Ola Spjuth 2.2.x * r4e63c99 / plugins/net.bioclipse.ui/plugin.xml : Disabled p2 update menus using an Activity. - http://bit.ly/7KE6zY
16:20 CIA-65 bioclipse.core: Ola Spjuth 2.2.x * r9b76511 / (2 files): Merge branch '2.2.x' of git@github.com:olas/bioclipse.core into 2.2.x - http://bit.ly/6qOL4f
16:21 olass will test an update and then build
16:21 olass damn, feature deps are wrong :(
16:30 CIA-65 bioclipse: ospjuth * r11738 /bioclipse2/trunk/ (2 files in 2 dirs): Updated versions to 2.2.0.RC2.
16:30 CIA-65 bioclipse.qsar: Ola Spjuth 2.2.x * r1b2fddf / features/net.bioclipse.qsa​r.xmpp_feature/feature.xml : Set deps to version 2.2.0.RC2. - http://bit.ly/5ngDvf
16:33 * egonw is heading to dinner
16:38 CIA-65 bioclipse.ds: Ola Spjuth 2.2.x * re697e74 / (2 files in 2 dirs): Set feature deps to 2.2.0.RC2. - http://bit.ly/6A0Hz8
16:48 olass egonw: ping
16:48 olass egonw: ping urgent
16:49 olass egonw: joelib still has classes excluded from classpath
16:49 olass egonw: please remove all classes not on classpath
17:25 egonw pong
17:25 egonw still in time?
18:05 CIA-65 bioclipse.joelib: Egon Willighagen 2.2.x * r88217de / (57 files in 9 dirs): Deleted source that was previously excluded from the source .classpath; however, exporting is not happy about such excluded. - http://bit.ly/5VdiV9
18:10 egonw olass: ping
18:10 egonw @tell olass I hope that commit helps
18:11 zarah Consider it noted.
18:19 olass @just tell me
18:20 zarah olass: You have new messages. Write '/msg zarah @messages' to read them.
18:20 olass @msg
18:20 zarah olass: 9 m 6 s ago, egonw said I hope that commit helps
18:20 * olass too
18:21 olass egonw: yes, that helped a lot
18:50 * olass is now uploading stuff
18:52 sneumann_ joined #bioclipse
19:15 sneumann__ joined #bioclipse
19:40 egonw_ joined #bioclipse
19:45 egonw__ joined #bioclipse
20:23 olass joined #bioclipse
22:14 sneumann__ congrats to RC2 ;-)
22:14 sneumann__ Good night,
22:14 sneumann__ cu
22:21 egonw joined #bioclipse
22:24 sneumann__ congrats to RC2 ;-)
22:25 sneumann__ Good night,

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