Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-03-17

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All times shown according to UTC.

Time Nick Message
03:51 CIA-33 joined #bioclipse
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08:51 masak jonalv: it is now proven: you can't rebase upstream svn with git-svn.
08:51 masak http://gist.github.com/80408
09:01 shk3 joined #bioclipse
09:02 edrin joined #bioclipse
09:03 edrin hi. good morning
09:07 masak mornin'
09:08 jonalv oh hai
09:08 zarah hello jonalv, you fantastic person you
09:29 sneumann joined #bioclipse
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11:08 edrin olass: http://www.toytowngermany.co​m/lofi/index.php/t8757.html
11:08 edrin and
11:08 zarah edrin's link is also http://tinyurl.com/cplsos
11:08 edrin olass: http://languageandgrammar.com/2008/04/​14/ordinal-numbers-first-not-firstly/
11:08 zarah edrin's link is also http://tinyurl.com/cf76oa
11:08 edrin olass: maybe we should stick to first second third and not firstly ... ?
11:40 egonw joined #bioclipse
11:40 steinbeck joined #bioclipse
11:43 olass edrin: if you say so
11:43 olass I disagree
11:43 olass but you decide
11:44 olass Firstly - it's an adverb, so from a grammar perspective that's the one to go for IMHO.
11:45 egonw I always thought it was "Firstly, we bla..."
11:45 olass me too
11:45 olass on the other hand, it seems first can be used as adverb too
11:46 olass edrin: you decide
11:47 egonw http://www.timesonline.co.uk/tol/life_and_style/r​elated_features/wine_and_dine/article2862463.ece
11:47 zarah egonw's link is also http://tinyurl.com/dm92p3
11:47 egonw a journalist would know, I think
11:47 egonw second sentence, second paragraph
11:47 egonw UK Times
11:50 masak egonw: http://www.youtube.com/watch?v=05hDiLTDkFo
11:50 zarah masak's link is also http://tinyurl.com/lo75l
11:50 egonw masak: tack
11:50 masak egonw: np. :)
12:13 edrin ok, keep it firstly
12:48 egonw guys.... a 1GB SD file... how many structures are that?
12:48 egonw or, a 50K structure SD file, how large would that be?
13:13 egonw joined #bioclipse
13:17 CIA-33 bioclipse: jonalv * r9331 /bioclipse2/trunk/plugins/ (6 files in 3 dirs):
13:17 CIA-33 bioclipse: Created Advice for running manager methods in gui thread. It also does Exception
13:17 CIA-33 bioclipse: management so code like: "ui.open(bioObject, "weee") reports an error to the
13:17 CIA-33 bioclipse: console now. This feature requires "the New Worl Order" on effected managers +
13:17 CIA-33 bioclipse: an extra advice that is only added to the ui manager so far.
13:17 CIA-33 bioclipse: jonalv * r9332 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.smartsmatching/META-INF/MANIFEST.MF: Removed version demands. (olass++ said I could do that)
13:18 CIA-33 bioclipse: jonalv * r9333 /bioclipse2/trunk/plugins/net.bioclipse.scripti​ng.ui/src/net/bioclipse/scripting/ui/business/ (IJsConsoleManager.java JsConsoleManager.java): Added printError( Throwable t ) to the js manager for printing errors to the js console.
13:18 olass jonalv++ //thx for the help
13:22 egonw joined #bioclipse
13:24 egonw joined #bioclipse
13:27 Gpox joined #bioclipse
13:33 jonalv masak++ //java method ending with: "}}});}}));}"
13:33 jonalv :)
13:33 masak jonalv: you should see my intentionally obfuscated Java code. :P
13:34 jonalv yes please :)
13:35 masak jonalv: http://weblogs.java.net/blog/forax/ar​chive/2006/10/obfuscated_java_1.html
13:35 zarah masak's link is also http://tinyurl.com/d277tg
13:48 rajarshi joined #bioclipse
13:48 jonalv hm seems that last commit doesn't work...
13:48 jonalv could someone confirm? olass?
13:52 olass jonalv: what?
13:52 olass how?
13:52 jonalv olass: well for starters. Can you start Bioclipse using head?
13:53 olass updating now
13:53 olass ask me in 5 mins again :)
13:55 jonalv 5 min?
13:55 jonalv it takes that long for you to update Bioclipse?!
13:56 olass ok
13:56 olass I can run it
13:56 olass now?
13:57 olass ui.open?
13:57 jonalv olass: yea...
13:57 olass hmm, exception
13:57 jonalv I can't even start the jsconsole any longer...
13:57 jonalv Gpox seems to be bale to though...
13:57 olass DEBUG - org.mozilla.javascript.WrappedException: Wrapped java.lang.NullPointerException
13:57 olass at org.mozilla.javascript.Context.throw​AsScriptRuntimeEx(Context.java:1654)
13:58 olass is that intentional?
13:58 olass I was hoping to get the message: "No editor with such ID"
13:58 olass or so
13:59 egonw joined #bioclipse
14:00 jonalv olass: wil fix that later on...
14:09 edrin masak: could you figure out how to extract the nested exceptions of a js script ?
14:10 masak edrin: yes, we finally came up with a solution.
14:10 edrin masak: ok, how does it look like?
14:10 masak plugins/net.bioclipse.scripting.ui/src/net/bi​oclipse/scripting/ui/views/JsConsoleView.java line 74
14:15 edrin masak: ok, but this does not print a stack trace, does it?
14:15 masak no, it prints an appropriate message to the console.
14:15 masak we log the stack trace.
14:15 edrin masak: ok
14:15 jonalv my solution is broken. I didn't finish it...
14:15 jonalv it's not finished
14:16 jonalv and now Bioclipse is not woring for me
14:16 jonalv |working
14:16 * jonalv is not having a good day...
14:16 edrin masak: if you compare it to when running a complete script, how is the output different? output in sense of exception
14:17 masak edrin: I think running in console and running from an editor are two different things.
14:17 masak haven't thought much about the latter, though.
14:17 edrin ok
14:32 masak http://ktown.kde.org/~zrusin/g​it/git-cheat-sheet-medium.png
14:32 zarah masak's link is also http://tinyurl.com/3xdyys
14:47 CIA-33 bioclipse: ospjuth * r9334 /bioclipse2/trunk/plugins/net.bioclipse.cdk.sm​artsmatching/src/net/bioclipse/cdk/smartsmatch​ing/prefs/SmartsMatchingPrefsInitializer.java: Updated default smarts. Solves #678.
15:01 CIA-33 bioclipse: ospjuth * r9335 /bioclipse2/trunk/plugins/​net.bioclipse.qsar.model/: Initial import. Refactored out EMF model to its own plugin.
15:03 CIA-33 bioclipse: ospjuth * r9336 /bioclipse2/trunk/plugins/​net.bioclipse.qsar.model/ (59 files in 9 dirs): Refactored out QSAR EMF model to its own plugin.
15:04 CIA-33 bioclipse: ospjuth * r9337 /bioclipse2/trunk/plugins/net​.bioclipse.qsar.model.edit/: Initial import. Refactored out QSAR EMF EDIT model to its own plugin.
15:06 * jonalv is commiting untested copde now. His Bioclipse refuses to start...
15:06 CIA-33 bioclipse: jonalv * r9338 /bioclipse2/trunk/plugins/net.bioclipse.script​ing/src/net/bioclipse/scripting/JsThread.java: Moved initations to declarations. removed "BIG UGLY HACK". :)
15:06 CIA-33 bioclipse: ospjuth * r9339 /bioclipse2/trunk/plugins/​net.bioclipse.qsar.edit/: Replaced by net.bioclipse.qsar.model.edit.
15:06 jonalv olass, masak: could you please update and see that thigns still starts after my commits? ;)
15:06 * masak updates
15:06 * olass too
15:06 CIA-33 bioclipse: jonalv * r9340 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java: removed some superfluos lines
15:06 CIA-33 bioclipse: ospjuth * r9341 /bioclipse2/trunk/plugins/ne​t.bioclipse.qsar.model.edit/ (83 files in 11 dirs): Refactored out QSAR EMF EDIT model to its own plugin.
15:07 CIA-33 bioclipse: jonalv * r9342 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): added the advice in the cml config files (forgot that..., ups...)
15:07 jonalv bu
15:07 CIA-33 bioclipse: jonalv * r9343 /bioclipse2/trunk/plugins/net.bioclipse​.scripting.ui/src/net/bioclipse/scripti​ng/ui/business/JsConsoleManager.java: changed the printError method in the js console to write the correct exception
15:08 CIA-33 bioclipse: ospjuth * r9344 /bioclipse2/trunk/plugins/net.bioclipse.qsar.test/ (5 files in 4 dirs): Updated tests for Schema updates.
15:08 CIA-33 bioclipse: ospjuth * r9345 /bioclipse2/trunk/plugins/net.bioclipse.qsar.ui/ (10 files in 4 dirs): Updated UI for API, scherma, and model updates. This breaks functionality but at least compiles.
15:08 CIA-33 bioclipse: ospjuth * r9346 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): Updates for API and chema changes.
15:09 masak olass: project description file missing in n.b.qsar.edit
15:09 masak olass: what did you do? :)
15:09 olass I deleted that plugin
15:09 masak oh.
15:10 shk3 the sdf viewer was done by arvid, right?
15:10 olass you mean MoleculesTable?
15:10 shk3 yes
15:10 olass yes
15:10 masak yes
15:10 zarah yes
15:10 masak :)
15:10 olass :)
15:10 jonalv :)
15:10 zarah :)
15:11 masak :)
15:11 masak zarah: you are a smart girl.
15:11 zarah masak: But we _can't_ go on meeting like this!
15:11 olass jonalv: things donät look good now...
15:11 masak mm, donuts...
15:11 jonalv olass: yey
15:11 jonalv donuts
15:12 olass jonalv: please fix things fast
15:12 jonalv olass: I have no idea what is wrong...
15:12 olass revert the commit then?
15:13 jonalv well either that or ficing it...
15:15 masak fic it!
15:15 masak jonalv: I can haz you error now. :/
15:15 CIA-33 bioclipse: ospjuth * r9347 /bioclipse2/trunk/plugins/net.bioclipse.qsar/ (39 files in 7 dirs): Refactored out QSAR EMF model to its own plugin.
15:18 olass jonalv: ETA for ficing the thingy? I cannot run now...
15:19 jonalv olass: we are working on it
15:19 egonw_ joined #bioclipse
15:20 egonw_ zarah: do you read RSS? that is, can we inform you of an RSS feed, and you copy new messages here on IRC?
15:20 zarah egonw_: eh... wha'?
15:20 egonw_ mmm... I guess not
15:22 CIA-33 bioclipse: ospjuth * r9348 /bioclipse2/trunk/features/net.bi​oclipse.qsar_feature/feature.xml: Updated feature with new EMF model plugins.
15:35 CIA-33 bioclipse: jonalv * r9349 /bioclipse2/trunk/plugins/net.bioclipse.script​ing/src/net/bioclipse/scripting/JsThread.java:
15:35 CIA-33 bioclipse: Revert "Moved initations to declarations. removed "BIG UGLY HACK". :)"
15:35 CIA-33 bioclipse: This reverts commit 64aa6ef321ba2f0c5b7b413656267b7a2f7a71e3.
15:36 jonalv olass: that should help things a little, not 100% though...
15:37 * olass is updating
15:41 jonalv we have too many plugins
15:42 egonw we have too few plugin sets with assigned responsible people we can kick
15:43 rajarshi :)
15:43 olass jonalv: still does not run
15:43 jonalv olass: it should
15:44 olass jonalv: well, it doesn't
15:44 jonalv olass: but not 100%
15:44 jonalv commit pending...
15:44 olass ok
15:44 jonalv sourceforge is very slow right now...
15:45 olass so is my mind
15:45 jonalv olass: what does that mean?
15:45 CIA-33 bioclipse: jonalv * r9350 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): fixed a bunch of typos. The ui.open stuffs errors should work now...
15:45 * olass is tired
15:45 olass slept badly
15:46 * jonalv is in pain :/
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15:48 leander joined #bioclipse
15:48 egonw @time
15:48 leander egonw: The time is now Tue Mar 17 16:48:35 CET 2009
15:48 egonw leander: thanx
15:48 jonalv leander: hi
15:49 egonw jonalv: he, you scared her away
15:49 jonalv egonw: who was she?
15:49 masak egonw: new bot?
15:49 egonw masak: yes, a Java bot
15:49 masak :)
15:49 egonw I need something to monitor RSS feeds...
15:49 egonw and post entries here...
15:49 masak good idea.
15:49 masak egonw++
15:50 masak I'm sure she and zarah can learn to get along.
15:50 egonw yes, I'll make them occasionally chat...
15:50 egonw anyway... being Java...
15:50 egonw who wants a net.bioclipse.leander ?
15:50 olass jonalv++ //It works now
15:50 jonalv :)
15:50 jonalv phew...
15:50 olass nice!
15:50 olass I like the output
15:51 jonalv olass: good
15:51 olass is it general?
15:51 olass please document on wiki
15:51 jonalv olass: uhm how do you mean?
15:51 olass needs annotations?
15:51 jonalv olass: I am not very happy aboutthe current solution
15:51 olass ok, write up on wiki
15:51 olass instructions for manager maintainers
15:51 olass (and developers)
15:52 jonalv I think we should create a PoincutAdvisor for annotations, as things are now the advices check for the annotations and act according to it...
15:52 masak jonalv++ # locating and fixing circularity
15:52 masak Gpox-- # introducing it :)
15:53 jonalv would be better to only run the advice if the annotation is really there...
15:53 jonalv do anyone understand what I am talking about?
15:54 jonalv gah who's who?
15:54 masak jonalv: you're talking about running the advice only if the annotation is there.
15:54 jonalv masak: yes...
15:54 masak egonw is testing nick availability...
15:55 masak 'haraz' sounds a bit negative. :)
15:55 haraz masak++
15:55 haraz :)
15:55 haraz leander was taken
15:55 masak and not very imaginative...
15:56 masak egonw: what about 'mikaela'?
15:59 egonw ok, forget it...
15:59 egonw no registered account...
16:00 masak egonw: why not?
16:00 egonw because I cannot get it worked out...
16:00 masak :/
16:00 egonw it keeps complaining about me already being egonw :)
16:06 jonalv olass: there is a good pdf explaining generics...
16:06 olass there probably are
16:19 leander joined #bioclipse
16:19 egonw @blog
16:21 leander joined #bioclipse
16:21 egonw @blog
16:22 egonw mmm
16:22 leander joined #bioclipse
16:22 egonw @blog
16:24 rednael joined #bioclipse
16:24 egonw @blog
16:25 rednael joined #bioclipse
16:25 egonw mmm
16:25 egonw @blog
16:25 egonw OK, eddy sucks
16:40 egonw trying rome
16:40 rednael joined #bioclipse
16:40 egonw @blog
16:40 rednael Retrieving feed http://bioclipse.blogspot.com/feeds/posts/default
16:40 rednael Feed Polled. URL = http://bioclipse.blogspot.com/feeds/posts/default
16:40 zarah rednael's link is also http://tinyurl.com/c8x6tj
16:40 zarah rednael's link is also http://tinyurl.com/c8x6tj
16:44 rednael joined #bioclipse
16:44 egonw @blog
16:44 rednael Retrieving feed http://bioclipse.blogspot.com/feeds/posts/default
16:44 rednael Feed Polled. URL = http://bioclipse.blogspot.com/feeds/posts/default
16:44 zarah rednael's link is also http://tinyurl.com/c8x6tj
16:44 zarah rednael's link is also http://tinyurl.com/c8x6tj
16:45 egonw grmph
16:45 rednael joined #bioclipse
16:45 egonw @blog
16:45 rednael Retrieving feed http://bioclipse.blogspot.com/feeds/posts/default
16:45 rednael Feed Polled. URL = http://bioclipse.blogspot.com/feeds/posts/default
16:45 rednael Feed Retrieved. URL = http://bioclipse.blogspot.com/feeds/posts/default
16:45 rednael http://bioclipse.blogspot.com/feeds/posts/default retrieved
16:45 zarah rednael's link is also http://tinyurl.com/c8x6tj
16:45 rednael http://bioclipse.blogspot.com/feeds/posts/default has a title: BioclipseBlog and contains 25 entries.
16:45 rednael Polling http://bioclipse.blogspot.com/feeds/posts/default again to test conditional get support.
16:45 rednael Feed Polled. URL = http://bioclipse.blogspot.com/feeds/posts/default
16:45 zarah rednael's link is also http://tinyurl.com/c8x6tj
16:45 rednael Feed Unchanged. URL = http://bioclipse.blogspot.com/feeds/posts/default
16:45 rednael If a "Feed Unchanged" event fired then the server supports conditional gets.
16:46 zarah rednael's link is also http://tinyurl.com/c8x6tj
16:46 zarah rednael's link is also http://tinyurl.com/c8x6tj
16:46 zarah rednael's link is also http://tinyurl.com/c8x6tj
16:46 zarah rednael's link is also http://tinyurl.com/c8x6tj
16:46 zarah rednael's link is also http://tinyurl.com/c8x6tj
16:46 zarah rednael's link is also http://tinyurl.com/c8x6tj
16:47 masak zarah: reboot
16:48 masak egonw: what just happened?
16:48 zarah joined #bioclipse
16:48 egonw masak: how so?
16:48 masak aha, no worries.
16:48 egonw zarah just saw a lot of URLs coming bye
16:48 masak I thought zarah had started misbehaving. not so.
16:48 masak zarah: no worries.
16:48 zarah masak: I see.
16:50 jonalv egonw: seeems my advice does in fact not at all translate from String IFile if no progressmonitor is in the method... :(
16:51 jonalv must fix that...
16:51 jonalv right now it seems to only work for methods with progressmonitors...
16:52 * egonw is leaving in 3 minutes
16:52 egonw ok
16:52 * jonalv needs to work with the new worlkd order...
16:52 jonalv This means Jmol won't happend for a while...
16:53 egonw ok, bye all
16:53 jonalv bye
16:57 masak bye
18:26 shk3 what's the release plan for BC2?
18:26 shk3 still 23rd?
18:40 egonw joined #bioclipse
19:52 olass joined #bioclipse
19:52 olass g'evenin
19:53 egonw hi olass
19:53 olass hi egonw
19:53 egonw http://github.com/egonw/rednael/tree/master
19:53 zarah egonw's link is also http://tinyurl.com/ddrrga
19:54 CIA-33 bioclipse: ospjuth * r9351 /bioclipse2/trunk/plugins/net.bioc​lipse.qsar/src/net/bioclipse/qsar/ (4 files in 2 dirs): Rewrote QSAR calculator to work on arbitrary descriptors for molecules
19:54 CIA-33 bioclipse: ospjuth * r9352 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Adapted CDK QSAR for new API, boosting performance.
19:54 CIA-33 bioclipse: ospjuth * r9353 /bioclipse2/trunk/plugins/net.bioclipse.qsar.test/​src/net/bioclipse/qsar/test/DummyCalculator.java: More tests for arbitrary molecules and descriptors.
19:55 CIA-33 bioclipse: ospjuth * r9354 /bioclipse2/trunk/plugins/net.bioclipse.qsar.ui/sr​c/net/bioclipse/qsar/ui/builder/QSARBuilder.java: Making proress completely reworking the QSARBuilder.
19:56 olass edrin: will work on XMPP wiki tomorrow
19:56 olass egonw: any progress with CML bindings in Bioclipse?
19:56 egonw no
19:57 olass that is sort of the only major thing left I guess
19:57 olass the rest is just thiings to do
19:57 egonw will try tonie
19:58 olass super
19:58 olass ok, will run off to dinner now
19:58 olass see you later
19:58 olass bye
20:54 edrin left #bioclipse
22:39 CIA-33 bioclipse: egonw * r9355 /bioclipse2/trunk/features/net.bi​oclipse.rdf_feature/feature.xml: Added missing chart plugin

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