Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-02-16

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All times shown according to UTC.

Time Nick Message
06:12 sneumann joined #bioclipse
07:36 annzi joined #bioclipse
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07:49 egonw joined #bioclipse
08:28 egonw Gpox: have you seen jonalv yet?
08:28 Gpox no
08:28 masak he's probably knocked-ish out after yesterday's swimming.
08:28 s_wolf joined #bioclipse
08:30 egonw Gpox: please do file me bug reports, if you run into problems... the PT table code in the CDK has quite changed, I made the updates, but did not really test it yet...
08:30 egonw bye for now
08:59 jonalv joined #bioclipse
09:04 jonalv egping
09:04 jonalv zarah: seen egonw
09:04 zarah egonw was last seen 33 m 42 s ago in #bioclipse saying 'bye for now'
09:04 jonalv where did he go?
09:07 masak` joined #bioclipse
09:10 sneumann jonalv: how should zarah know *that* ?!
09:10 jonalv sneumann: oh that question wasn't for zarah but for anyone in here
09:11 sneumann :-)
09:11 masak zarah: where did egonw go?
09:11 zarah masak: eh... wha'?
09:23 olass joined #bioclipse
09:23 olass hi
09:23 zarah oh hai olass
09:30 egonw joined #bioclipse
09:33 jonalv hi egonw, you are not gonna make it to Uppsala tomorrow I take it?
09:33 jonalv olass: hi, how are you?
09:33 egonw don't know yet...
09:33 * olass neither
09:33 * olass hopes so
09:34 * olass is also feeling a bit ill
09:34 * olass has taken a few pills and is feeling a bit better
09:34 jonalv egonw: okey you said somethign about missing the Jmol thing, (which is tomorrow) so I thougth you were not going to make it
09:34 egonw jonalv: oh, indeed
09:34 egonw I had it booked for both days...
09:34 egonw not sure why
09:34 jonalv right, so maybe we should reschedule that meeting?
09:35 egonw let's see about that tomorrow
09:35 olass +1
09:35 egonw rescheduling might be premature
09:35 jonalv I will be at a meeting from 9
09:36 jonalv So I would like to know whether I should leave that meeting early (if it goes on) to run to our meeting or if I can sit calmly...
09:44 egonw we also have the UUCJC meeting after yours, and I have to leave at 12:15... so (if it goes on), yes
09:46 jonalv egonw: but if you are sick you should probably stay home?
09:46 egonw I'm recovering
09:46 egonw worst was Sunday
09:46 egonw slept bad last night, but think I'll be tired but fine tomorrow
09:46 egonw that's how I think about it right now
09:47 jonalv aight so I should probably try to read the article... :)
09:50 egonw yes, and make sure you understand it to some extend, at least to be able to tell us what you think are strong and weak points of the article, and why
10:03 annzi joined #bioclipse
10:14 CIA-71 chembl.rdf: Egon Willighagen master * r6a4b8f9 / compounds.php : Fixed Bio2RDF for ChEBI entries (fixes #3) - http://bit.ly/dsK4jC
10:14 zarah bug #0003 | http://tinyurl.com/y8duc4y
10:16 edrin joined #bioclipse
10:29 egonw Gpox: ping...
10:29 Gpox egonw: pong
10:29 egonw Gpox: with your recent patching for transparency...
10:29 egonw would a transparent background work too now, instead of a white-filled one?
10:30 olass egonw: ping
10:30 Gpox it might
10:30 olass egonw: I'd really really appreciate if you looked at bug 1870
10:30 olass it is quite serious
10:31 olass since core chemical functionality might have a fluke
10:32 egonw ack. looks serious indeed
10:32 egonw won't have time to look at it before Fri earliest
10:33 egonw VR grant app deadline on Thu
10:45 egonw annzi: not sure how to delete the bad bio2rdf owl:sameAs triples, but the correct ones are loaded now: http://rdf.farmbio.uu.se/chembl/snorql/?describe=​http://rdf.farmbio.uu.se/chembl/molecule/m545827
10:45 zarah egonw's link is also http://tinyurl.com/ylzfqum
10:46 annzi great, thanx
11:30 samuell joined #bioclipse
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13:45 CIA-71 bioclipse.cheminformatics: Arvid Berg master * rb29e7de / plugins/net.bioclipse.cdk.ui/src/net/bioc​lipse/cdk/ui/views/PeriodicTableView.java : Generate list of symols when control is created. - http://bit.ly/ctmOrC
13:45 hithere joined #bioclipse
13:45 hithere hi
13:45 zarah ni hao hithere
13:46 egonw hi hithere, are you a bot?
13:46 hithere no
13:46 hithere sorry
14:11 CIA-71 org.openscience.cdk: Egon Willighagen cdk-jchempaint * rd568d5c / (62 files in 57 dirs): Uploaded CDK-JChemPaint 6 - http://bit.ly/a1xyJc
14:28 olass egonw: hoe do I compile CDK with support for inchi?
14:28 olass is it out of the box in dist-all?
14:28 egonw yes
14:28 egonw why would you want to do that?
14:28 egonw got a jni-inchi 6-std patch lined up, have you?
14:28 olass calculate inchi?
14:29 olass you wish ;)
14:29 egonw indeed :)
14:29 olass anyone working on that?
14:29 olass Sam is not I am certain
14:30 olass egonw: I get an error
14:30 olass InChIGeneratorFactory.getInst​ance().getInChIGenerator(ac);
14:30 olass gives me xception in thread "main" java.lang.NullPointerException
14:30 olass at net.sf.jnati.deploy.NativeArtefactLocator.g​etArtefact(NativeArtefactLocator.java:129)
14:30 olass at net.sf.jnati.deploy.NativeLibraryLoader.​loadLibrary(NativeLibraryLoader.java:37)
14:31 olass at net.sf.jniinchi.JniInchiWrapper.lo​adLibrary(JniInchiWrapper.java:92)
14:31 olass hmmm
14:31 olass might be a known problem?
14:32 olass nvm, will look into it
14:33 egonw ah, you too...
14:33 egonw jonalv had that problem too, if not mistaken
14:33 egonw but, I have no clue
14:33 egonw I guess your platform does not have a binary?
14:33 egonw you're running OS/X right?
14:33 egonw 32 or 64 bit?
14:34 egonw I'd need to check if both are supported by JNI-InChI
14:34 egonw at least one of the two is...
14:34 egonw jonalv's case is even worse, as it only sometimes failed...
14:34 olass damn that inchi
14:35 egonw I think we should opt for the NestedVM route
14:35 olass what is that?
14:35 egonw it's an opensource library that implements a VM for a particular special architecture
14:35 egonw then, you compile the InChI at just this architecture
14:35 egonw and run it in that VM, which itself is implemented in Java
14:36 olass sounds like it might decrease performance?
14:36 egonw making the code running on any platform
14:36 egonw yes, possibly
14:36 annzi egonw: I want one of my methods to communicate with the javascript console while it runs, is that possible? or should I rethink?
14:36 olass then again, better than now
14:36 egonw and the size is pretty large, and we would need to write a command line wrapper, IIRC
14:36 egonw annzi: rethink
14:36 annzi damn it :)
14:36 egonw annzi: what d'you want to do...
14:37 * egonw is feeling he will never make it to bed
14:37 olass annzi: we don't use the console for echoing messages
14:37 olass it might be hidden
14:37 olass or doing something else
14:37 annzi I can't figure out a safe way to set all parameters for a moss run
14:38 annzi Well there are ways, but not safe or really complicated for an enduser
14:41 sneumann I guess we'll have the same question for MetFrag,
14:42 sneumann because I naively placed (some of) the parameters in getter/setter methods
14:42 sneumann violating the stateless property of the managers
14:42 egonw eclipse-- (for not getting the classpath deps analysis right for once)
14:42 sneumann eclipse--
14:43 sneumann So either we'll place zillions of parameters into the method,
14:43 egonw annzi, sneumann: I suggest to use a parameter helper class
14:43 sneumann any examples to look into ?
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14:43 egonw olass: did you receive arvid's patches for metaprint2d?
14:44 egonw no, but I suggest:
14:44 egonw params = metfrag.createParameters()
14:44 olass metfrag?
14:44 egonw metfrag.setFoo(params, fooValue)
14:44 egonw annzi: for you, to answer olass question, it would be:
14:45 egonw params = moss.createParameters()
14:45 egonw moss.setFoo(params, fooValue)
14:45 egonw @gg metfrag bioclipse
14:45 zarah egonw: http://pastebin.com/m2e363070
14:45 olass egonw: no, did not receive any patches
14:45 egonw but you know how to fix it?
14:45 olass have not looked into it yet but at least I have a clue
14:45 sneumann olass: msbi.ipb-halle.de/MetFrag/
14:46 olass will give it a try
14:46 sneumann please feed back ;-)
14:46 egonw olass: good, then I'm to bed now
14:46 olass sleep well
14:47 sneumann get well
14:47 annzi egonw: thanx I will figure something out, sleep well
14:48 egonw annzi, sneumann: use a simple Bean-class parameters class
14:48 egonw @msg jonalv the JS recording should recognize Bean classes, and serialize following the bean patterns
14:48 zarah egonw: You have no new messages.
14:48 egonw @tell masak the JS recording should recognize Bean classes, and serialize following the bean patterns
14:48 zarah Consider it noted.
14:48 egonw @tell jonalv the JS recording should recognize Bean classes, and serialize following the bean patterns
14:48 zarah Consider it noted.
14:49 egonw why, oh, why, did I not realize that earlier?!?!
14:49 egonw so bloody obvious
14:49 egonw a down right minimal requirement!
14:49 edrin http://news.bbc.co.uk/2/hi/in_depth/8517716.stm
14:49 zarah edrin's link is also http://tinyurl.com/y8syhwe
14:50 edrin do you know one of them?
14:50 edrin i wonder why german news do not show these images... they do not even link to them
14:51 egonw that Gail one is brilliant... it's a guy!
14:57 edrin heh :)
14:57 edrin you know him?
14:57 edrin if they show these images..
14:57 edrin they should find them
14:57 edrin most likely the names are not true
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21:30 CIA-71 bioclipse.cheminformatics: Egon Willighagen master * rbce441a / (7 files in 5 dirs): Updates for API changes for getting and setting rendering parameters in CDK-JChemPaint 6 - http://bit.ly/cfdH8R

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