Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-05-11

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All times shown according to UTC.

Time Nick Message
04:13 egonw joined #bioclipse
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06:20 egonw joined #bioclipse
06:43 Gpox joined #bioclipse
06:54 annzi joined #bioclipse
06:54 egonw annzi: http://www.techscreencast.com/tool/vers​ioncontrol/git--interactive-adding/791
06:54 zarah egonw's link is also http://tinyurl.com/2wx4gbf
07:09 jpansanel joined #bioclipse
07:21 egonw hi jpansanel
07:21 egonw jpansanel: what's your progress with porting MyChem to the newer MySQL?
07:22 egonw Gpox: this is the same bnd, correct? http://njbartlett.name/blog/2010/05/10/announcing​-bndtools-simple-powerful-osgi-tools-for-eclipse/
07:22 zarah egonw's link is also http://tinyurl.com/38yn4oh
07:23 sneumann joined #bioclipse
07:24 Gpox yes, and a nice tool for using it.
07:28 egonw yeah, gonna have to look at it
07:56 faceface joined #bioclipse
07:56 faceface hi
07:56 zarah hello faceface, you fantastic person you
07:56 egonw hi faceface
07:56 faceface why ty
07:56 egonw zarah is a bot
07:56 faceface hello
07:56 zarah saluton faceface
07:56 faceface ;-)
07:56 egonw never mind here :)
07:56 faceface Bioclipse is a free and open source workbench for the life sciences.
07:56 faceface interesting!
07:57 egonw thanx :)
07:57 faceface Samuel Lampa about?
07:57 faceface I'm reading his GSoC project
07:58 faceface sorry to say I only just heard about bioclipse
07:58 egonw no, have not seen him yet
07:58 egonw but got an appointment with him later this morning
07:58 egonw faceface: no worries :)
07:58 egonw welcome!
07:58 faceface cool
07:58 egonw you're his mentor?
07:58 faceface Cheminformatics and Metabolism Team at the European Bioinformatics Institute
07:58 faceface nice
07:58 faceface no
07:58 faceface just a person :-)
07:58 egonw EBI is one part of the development team
07:58 faceface awesome
07:59 egonw Uppsala University is the other part
07:59 egonw where Bioclipse originates
07:59 egonw and the largest developer concentration
07:59 faceface one thing that attracts me here is the connection between semantic mediawiki and eclipse... SMW despirately needs an IDE
08:00 * faceface grabs the paper
08:00 faceface its all java I guess?
08:00 egonw yeah, the core parts yes
08:00 egonw some plugins use C/C++ code in the background
08:00 egonw but not the Bioclipse core
08:00 egonw faceface: there are now two Bioclipse papers
08:00 egonw both OA
08:01 faceface my colleagues are developing an interesting java library - do you think that kind of java analysis toolkit can be easily added to bioclipse? (sorry for nieve questions)
08:01 egonw yes
08:01 faceface 2009?
08:01 egonw yes
08:01 faceface oic
08:01 faceface 2007 / 2009
08:01 faceface cheminformatics is so cool
08:02 egonw :)
08:02 egonw yeah, I think so too :)
08:02 egonw what's the library about?
08:02 jonalv joined #bioclipse
08:02 faceface protein structure analysis and prediction
08:02 egonw sounds interesting...
08:03 egonw not too much of that in Bioclipse yet
08:03 faceface yeah, the core devs are great
08:03 egonw so, would be a welcome addition, I'd say
08:04 faceface http://www.bioinformatics.​org/groups/?group_id=1014
08:04 zarah faceface's link is also http://tinyurl.com/3ynxxh4
08:04 faceface ty zarah
08:05 egonw are you present on the social web?
08:05 faceface erm...
08:05 faceface I have a twitter account, but its mostly me spamming music I like ;-)
08:05 faceface danbolser
08:05 egonw :)
08:05 egonw PDBHighlight
08:05 egonw that's cool!
08:05 faceface :-P
08:06 egonw I have been thinking about that for a very long time
08:06 faceface check the year
08:06 faceface hehehe
08:06 egonw well, with Jmol script then
08:06 faceface right
08:06 egonw with make a very nice Bioclipse plugin too!
08:06 egonw 2003 :)
08:06 faceface back then I was also talking to ... bernstein and .... the spanish jmol developer(?) about standardizing the scripting language for molecular interaction
08:06 egonw angel
08:06 faceface right
08:07 egonw bernstein?
08:07 faceface rasmol dude
08:07 egonw ah, ic...
08:07 faceface we talked about writing a grant to develop the idea of a query language based on sql
08:07 egonw yeah, have been talking to the late Warren about it too
08:07 faceface but I didn' thave time
08:07 faceface ...
08:07 egonw same here
08:07 faceface he's still on irc?
08:08 egonw warren? no, don't think so
08:08 egonw or angel?
08:08 faceface egonw: my latest idea is now to develop jmol - structure DAS integration and organize it via a wiki
08:09 faceface oh... 'have been talking', better 'I was previously talking' ...
08:09 egonw right
08:09 egonw sorry
08:09 egonw had been
08:09 faceface :(
08:10 faceface I'm amazed at my dedication to random ideas back then: http://www.bioinformatics.org/pdbHighlight/
08:10 zarah faceface's link is also http://tinyurl.com/2vyy2hq
08:10 faceface zarah: are you judging me, or just trying to be helpfull?
08:10 zarah faceface: please rephrase or stop trying to be witty :)
08:10 faceface ;-P
08:10 egonw annzi: read this: http://blog.madism.org/index.php/2007/09/09/138​-git-awsome-ness-git-rebase-interactive-?cos=1
08:10 zarah egonw's link is also http://tinyurl.com/37mpqm7
08:11 egonw faceface: http://wiki.jmol.org/index.php/Websites_Using_Jmol
08:11 zarah egonw's link is also http://tinyurl.com/2uz6jw5
08:12 egonw faceface: but this one in particular:
08:12 egonw http://www.proteopedia.org​/wiki/index.php/Main_Page
08:12 zarah egonw's link is also http://tinyurl.com/5mafn3
08:12 faceface egonw: I'm vaguely aware of PP ;-)
08:12 egonw all the green links are Jmol script, to emphasize that particular word in the Jmol window
08:12 faceface I'm one of the authors of PDBWiki ... sigh
08:13 faceface We were the first to develop a MW PDB agunct (sp?), but PP has stolen our thunder with that awesome Jmol app
08:13 faceface also they have funding ;-)
08:13 faceface we just work for food
08:14 egonw yeah, these are things in the air... and then it is the one with the most resources immediately available that gets the glory...
08:14 faceface it's a very nice project
08:15 faceface journal commenting systems are really bad
08:16 egonw indeed
08:16 faceface I posted a comment on teh PDBWiki article weeks ago
08:16 egonw DOI?
08:16 faceface setting out why we think we can exist in addition to PP
08:16 mgerlich joined #bioclipse
08:16 faceface doi: 10.1093/database/baq009
08:17 faceface sadly I don't think they give comments DOI
08:17 faceface well.. nice chatting, $job is calling
08:17 egonw ok, same here
08:17 egonw do come back
08:17 faceface have a nice day
08:17 egonw to chat about plugin options!
08:17 * faceface won't leave!
08:33 jonalv egonw: do you have a moment me and Gpox are having some problems...
08:33 jonalv egonw: do you think you could come over?
08:33 egonw hang on
08:34 egonw annzi: http://www.arthurkoziel.com/2​008/05/02/git-configuration/
08:34 zarah egonw's link is also http://tinyurl.com/2drowwe
08:48 mgerlich joined #bioclipse
09:00 masak joined #bioclipse
09:03 s_wolf joined #bioclipse
10:29 samuell joined #bioclipse
10:43 egonw http://code.google.com/p/freebase-gridworks/
10:43 zarah egonw's link is also http://tinyurl.com/29t9gfx
10:43 egonw looks pretty cool
11:08 s_wolf joined #bioclipse
11:40 olass joined #bioclipse
12:17 egonw jonalv: http://jni-inchi.sourceforge.net/
12:17 zarah egonw's link is also http://tinyurl.com/2ur8aob
12:19 olas egonw: are you pushing Gpox's cheminfo patches now?
12:20 olas then I can try to export..
12:20 egonw hang on
12:24 * olas is hanging on
12:29 egonw good
12:29 egonw keep hanging
12:29 egonw eclipse is rebuilding
12:30 egonw Gpox: what platform file should I be using?
12:30 egonw the new- one?
12:30 Gpox yes
12:30 egonw can you make a patch then to have it replace the old target platform file?
12:32 egonw Gpox: can you join? it does not work here...
12:37 egonw olas: ping
12:37 egonw olas: cannot build here...
12:37 egonw I can commit Gpox' patches, but no clue if they compile properly
12:37 egonw Gpox is looking into the set target platform problem jonalv is seeing too
12:49 egonw fika
12:49 egonw who joins?
13:02 egonw Gpox: might it just be a timing issue?
13:02 egonw Gpox: it now seems to work
13:02 egonw the difference seems to be that the http:// folders are now populated
13:23 CIA-61 bioclipse.core: jonalv 2.4.x * r7fdbe2d / plugins/net.bioclipse.ui.business/src/net/b​ioclipse/ui/business/PasteAsNewTester.java :
13:23 CIA-61 bioclipse.core: fix for bug: 1964
13:23 CIA-61 bioclipse.core: If GUI stuff is null then we might as well not show it. At least that seems like the reasonable action right now. - http://bit.ly/abs7W0
13:23 zarah bug #1964 | http://tinyurl.com/2voe4pc
13:49 CIA-61 bioclipse.core: Egon Willighagen 2.4.x * r314be8e / plugins/net.bioclipse.scripting/src/net​/bioclipse/scripting/JsEnvironment.java : Removed an unused import which caused a compile fail here - http://bit.ly/d04rRQ
13:51 egonw olas: I get a compile error in cdk.smartsmatching
13:51 egonw olas: do you have a pending commit for that?
14:26 CIA-61 bioclipse.cheminformatics: Egon Willighagen 2.4.x * r830759d / plugins/net.bioclipse.cdk.smart​smatching/META-INF/MANIFEST.MF : Added missing dependency on vecmath - http://bit.ly/dzS6SU
14:37 CIA-61 bioclipse.joelib: Egon Willighagen 2.4.x * r7044cc0 / externals/net.sourceforge.joelib/.classpath : Excluded two files that depended on Log4J itself, and are not used anyway - http://bit.ly/at1yC5
14:39 s_wolf joined #bioclipse
16:22 CIA-61 bioclipse.balloon: Arvid Berg master * r618e710 / (3 files in 3 dirs): Removed log4j version - http://bit.ly/d1Fno2
16:23 CIA-61 bioclipse.balloon: Arvid Berg master * r8bc974d / (3 files in 3 dirs): Removed bundle and package versions - http://bit.ly/9D4udI
16:23 CIA-61 bioclipse.balloon: Arvid Berg master * rd856c92 / (3 files): Added update site feature - http://bit.ly/atXuao
16:51 samuell joined #bioclipse
20:22 egonw joined #bioclipse
20:43 olass joined #bioclipse
20:43 olass egonw: ping
20:43 olass org.openscience.cdk.log4j does not compile for me
20:43 egonw pong
20:43 olass seems like a logging issue
20:43 olass am I using wrong branch?
20:43 egonw olass: that's because someone removed org.apache.log4j from the classpath
20:44 olass bioclipse2.4
20:44 olass yes
20:44 egonw indeed
20:44 olass I thought arvid had fixed that
20:44 olass did he not send you a patch?
20:44 egonw yes, that's why you get the error :)
20:44 egonw ok, here's the story
20:44 egonw org.openscience.cdk.log4j requires log4j
20:44 egonw it's the LoggingTool impl for the CDK using log4j
20:45 egonw hence the dependency
20:45 egonw now, Bioclipse does not use log4j
20:45 egonw but which does not expose everything
20:45 egonw hence the error
20:45 egonw but
20:45 egonw bioclipse2.4 is not using cdk.log4j
20:45 egonw so, the answer is to just remove that plugin
20:45 egonw so, the answer is to just remove that bundle
20:45 egonw so, the answer is to just remove that thing
20:45 olass ok
20:46 olass hmm, is it in the feature too?
20:46 olass yes
20:46 olass so will remove it from there too
20:47 egonw yes, that remains to be fixed
20:47 egonw talked with Gpox about that
20:47 egonw we need more CDK features
20:47 egonw more finetuned
20:52 olass how do I turn off the OSGI logging?
20:53 olass egonw?
20:56 egonw was wondering about that too
20:56 egonw I have no clue
20:58 olass ok, let's ask gpox tomorrow
20:58 olass goodnight
20:58 egonw will have course day tomorrow

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