Camelia, the Perl 6 bug

IRC log for #bioclipse, 2011-01-14

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All times shown according to UTC.

Time Nick Message
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11:37 egonw jonalv: btw, I am working on updating the CDK version in Bioclipse
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12:18 edrin hi all
12:18 zarah ni hao edrin
12:18 zarah edrin: You have new messages. Write '/msg zarah @messages' to read them.
12:23 olass hi edrin
12:31 egonw hi edrin
13:42 CIA-40 bioclipse.core: jonalv HEADLESS * r6598032 / plugins/net.bioclipse.browser.tests​/src/net/bioclipse/browser/tests/Ab​stractBrowserManagerPluginTest.java : added Expected to error message from test - http://bit.ly/h8ghEd
13:42 CIA-40 bioclipse.core: jonalv HEADLESS * re26bda8 / plugins/net.bioclipse.browser.tests​/src/net/bioclipse/browser/tests/Ab​stractBrowserManagerPluginTest.java : ignore bad test - http://bit.ly/ejrZv0
13:44 CIA-40 bioclipse.core: jonalv master * r6467cea / plugins/net.bioclipse.browser.tests​/src/net/bioclipse/browser/tests/Ab​stractBrowserManagerPluginTest.java : added Expected to error message from test - http://bit.ly/ervLOX
13:44 CIA-40 bioclipse.core: jonalv master * r9a3fd72 / plugins/net.bioclipse.browser.tests​/src/net/bioclipse/browser/tests/Ab​stractBrowserManagerPluginTest.java : ignore bad test - http://bit.ly/gUi34O
13:44 CIA-40 bioclipse.core: jonalv master * ra313c52 / (2 files): Merge branch 'master' of github.com:bioclipse/bioclipse.core - http://bit.ly/f1Ehar
13:44 egonw Gpox, jonalv: it would be very helpful if one of you can blog (or wiki) about how to build and play with 'headless'...
13:44 egonw really, be friendly to potential early adoptors
13:45 jonalv egonw: yea I will as soon as there is something to actually play with
13:45 egonw it complies, not?
13:45 egonw that's qualifies to me as 'ready to play with'
13:45 jonalv egonw: for the moment I am stuck fixing things in standard Bioclipse which broke during the refactoring
13:45 jonalv as for actual headless there is not very much yet
13:46 egonw what is there?
13:46 jonalv egonw: a loop that does JavaScript
13:46 jonalv nothing bioclipse related
13:47 jonalv or rather a lot of Bioclispe related things which does nto yet work... :)
13:47 jonalv if I recall correctly
13:47 egonw but that is already pretty something, not?
13:48 jonalv egonw: you might have a point...
13:48 egonw so, I can run .js files from the cmd line with bioclipse now?
13:48 jonalv egonw: no
13:48 egonw (not being sarcastic here)
13:48 jonalv you can not
13:48 egonw ok, it's JSConsole in action?
13:48 jonalv or I guiess if you pipe it
13:48 jonalv yea maybe
13:48 egonw piping sounds good to me
13:49 jonalv I have not tried that
13:49 jonalv + I have not managed to build it in such a way that it does actually work from commandline
13:49 jonalv I have only run it from Eclipse
13:50 jonalv and right now not even that
13:50 jonalv I think my workspace suffer from bit rot
13:50 jonalv it worked the other day...
13:51 jonalv I can't quite remember which target.platform I am supposed to be running now
13:51 jonalv Gpox: do you?
13:52 Gpox no
13:53 jonalv An internal error occurred during: "Launching bslrunner.product".
13:53 jonalv java.lang.NullPointerException
13:53 jonalv :(
13:54 jonalv eclipse--
13:55 jonalv guys, which target platform are you using these days?
13:55 jonalv I keep getting errors about not being able to locate things on the helios update site...
13:58 * egonw is using the old one
13:58 egonw wait, and hit reset again...
13:58 egonw alternatively, do it via the prefs windows...
13:59 jonalv egonw: what reset would that be?
13:59 jonalv egonw: it fails when I open the editor...
13:59 egonw Project -> Prefs -> search for 'target' -> select the target.platform from bioclipse, and hit the apply button
13:59 egonw you might variate that, and select another platform first, and then the bioclispe one again
13:59 egonw that did miracles for me
14:00 egonw not sure anymore who adviced me this route
14:00 jonalv okey
14:00 * jonalv tries
14:00 jonalv okey I need water while that builds
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14:07 jonalv nah still red crosses
14:07 * jonalv tries some more...
14:08 jonalv Gpox: didn't you export a TP to file or something?
14:09 jonalv do I need to update eclipse?
14:09 jonalv oh how I hate this
14:09 * jonalv updates Eclipse
14:09 egonw no need
14:09 egonw the target platform should pull in the right stuff...
14:10 jonalv hm seems I am runnign the latest
14:10 egonw have you tried to set it to the wrong target first?
14:10 egonw until that is finished, and then the bioclipse one?
14:10 egonw all via prefs?
14:10 jonalv egonw: there are very many target platforms there
14:10 jonalv I tried two
14:10 jonalv not sure which one is the bioclipse one
14:11 egonw ah, make sure...
14:11 egonw here it gives a patch at the end of each line
14:11 egonw path, not patch
14:11 jonalv egonw: yea but which one am I supposed to be running?
14:11 jonalv bioclispe 2.5?
14:11 jonalv probably...
14:12 egonw it here says:
14:12 egonw "Spring-osgi-1.0.2 (Active) - /net.bioclipse.target.platf​orm/target-platform.target"
14:13 egonw crap...
14:13 egonw I think I should have said "hit the Reload button"
14:13 egonw rather then the Apply button...
14:13 egonw "oops"
14:13 jonalv Problems occurred getting the plug-ins in this container
14:13 jonalv Unable to locate installable unit org.eclipse.platform.sdk
14:13 jonalv
14:14 egonw that sounds nasty indeed
14:16 jonalv yea
14:16 jonalv I am basicly fucked
14:18 jonalv Gpox: have you made changes to the target.platform in master since headless was branched of?
14:20 Gpox jonalv: you mean rebased
14:20 jonalv Gpox: yea
14:20 jonalv I guess
14:20 jonalv I don't really know what to do right now
14:20 jonalv I am out of ideas...
14:20 Gpox no, updated target platform is the last
14:20 jonalv it is supposed to download things from eclipse right?
14:21 jonalv only, it sais that those things can't be found
14:21 Gpox before the branching
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14:21 Gpox don't you have another target platform that points to a local directory?
14:22 jonalv Gpox: I can't find such a thing, maybe I am looking at the wrong location?
14:22 jonalv I havea buckminister default TP
14:22 jonalv could that be it?
14:23 jonalv sounds strange but that is all I find...
14:23 Gpox if you download the stuff from here http://pele.farmbio.uu.se/buckminster/tp/ and creates a targetplatform with local that points to it you should be ok
14:24 jonalv okey I will try that then, so I create a new target platform and set it to point somehow?
14:29 Gpox jonalv: Add->Directory
14:38 jonalv Gpox: I don't understand, I have to create the target platform inside a project or?
14:40 * jonalv guesses so
14:47 jonalv hm I think a few less red crosses now
14:47 jonalv still many though
14:47 egonw no worries... I'm about to make a commit :)
14:49 CIA-40 bioclipse.cheminformatics: Egon Willighagen master * r8fde21d / (3 files in 3 dirs): Removed use of the browser.scraper extension point, which seems only available from master, not 2.4.x - http://bit.ly/ev2PaX
14:49 CIA-40 bioclipse.cheminformatics: Egon Willighagen master * r5d7ee35 / (10 files in 6 dirs): Added a new from IUPAC name wizard based on OPSIN - http://bit.ly/exme07
14:50 jonalv egonw: that confuses me
14:50 jonalv why remove something from master that is only avilable in master?
14:50 CIA-40 bioclipse.cheminformatics: Egon Willighagen master * rb4e9971 / (3 files in 3 dirs):
14:50 CIA-40 bioclipse.cheminformatics: Revert "Removed use of the browser.scraper extension point, which seems only available from master, not 2.4.x"
14:50 CIA-40 bioclipse.cheminformatics: This reverts commit 8fde21d28a37326cc8d07223ead963c8c48f70ee.
14:50 CIA-40 bioclipse.cheminformatics: Oops, that should not have been commited... :( - http://bit.ly/hDKxBf
14:50 jonalv ah
14:50 egonw jonalv: yes, that commit was on the wrong branch...
14:50 jonalv hehe
14:50 egonw olass: btw, I'd love a blog about the scraper functionality...
15:10 olass egonw: yes, all in due time
15:15 jonalv egonw: okey you can now read me blog post about headless
15:16 egonw jonalv++
15:16 egonw bbl
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15:46 egonw jonalv: yeah, I sort of does...
15:46 jonalv egonw: sry? what do you do?
15:46 egonw replying to your answer on the ML
15:47 jonalv egonw: it answers your questions or it does nit?
15:48 egonw it does to sufficient levels
15:48 jonalv good
15:49 egonw now, if only bioclipse would automatically file  bug reports ... :)
15:53 jonalv egonw: lol
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16:29 jonalv Gpox: ping
16:30 Gpox jonalv: pong
16:31 jonalv Gpox: when running the bsl-runner it seems I don't get any logging from Spring
16:31 jonalv Gpox: do you have any idea how I can turn that on?
16:31 Gpox check the logback.xml file
16:32 jonalv ah
16:32 jonalv testing
16:32 egonw_ jonalv: I totally get your target platform problems!
16:32 egonw_ it seems I still had 2.4.x for .core
16:32 jonalv ah
16:33 jonalv noiw I get some ClassNotFoundExceptions
16:33 jonalv \o/
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