Camelia, the Perl 6 bug

IRC log for #cdk, 2007-11-08

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All times shown according to UTC.

Time Nick Message
03:18 CIA-16 cdk: rajarshi * r9408 /trunk/cdk/tools/nightly.py: Updated the script to show the rev number against which the fixed test count and new test count were obtained
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05:29 CIA-16 cdk: egonw * r9409 /branches/egonw/ibondorder​/src/org/openscience/cdk/ (24 files in 8 dirs): More updates
05:36 CIA-16 cdk: rajarshi * r9410 /trunk/cdk/tools/nightly.py: Fixed a typo in nightly
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09:19 jpansanel moin
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10:20 CIA-16 jmol: hansonr * r8579 /trunk/Jmol/src/org/jmol/ (9 files in 5 dirs): 11.3.42 prerelease bug fixe -- select by itself not working; privatizing selectionManager
10:32 CIA-16 bioclipse: jonalv * r4185 /trunk/playground/plugins/ (2 files in 2 dirs): added remove variable functionality to calculator
10:43 CIA-16 bioclipse: jonalv * r4186 /trunk/playground/plugins/net.bioclipse.expressi​on/src/net/bioclipse/expression/Calculator.java: The Calculator now accepts '_' in variable names and function names
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11:51 CIA-16 jmol: hansonr * r8580 /trunk/Jmol/src/org/jmol/ (6 files in 2 dirs): 11.3.42/11.3.43 new feature: set echo [echoID] MODEL [model number]
11:56 CIA-16 jmol: hansonr * r8581 /trunk/Jmol/src/org/jmol/shape/Text.java:
12:04 CIA-16 jmol: hansonr * r8582 /trunk/Jmol/src/org/jmol/modelset/ModelSet.java:
12:05 CIA-16 jmol: hansonr * r8583 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: 11.3.42 VERSION
12:13 CIA-16 jmol: hansonr * r8584 /trunk/Jmol/src/org/jmol/ (shape/EchoRenderer.java shapespecial/Isosurface.java): debug comments out
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13:34 CIA-16 cdk: egonw * r9411 /branches/egonw/ibondorder/src/org/​openscience/cdk/tools/manipulator/ (AtomContainerManipulator.java BondManipulator.java): Added a few (often used) convenience methods
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13:34 egonw_cytoscape oh, OK only one channel :)
13:35 CIA-16 cdk: egonw * r9412 /branches/egonw/ibondorder​/src/org/openscience/cdk/ (11 files in 8 dirs): More IBond.Order compile fixes
13:35 egonw_cytoscape ha, lovely...
13:35 CIA-16 cdk: egonw * r9413 /branches/egonw/ibondorder/src/org/openscience/cd​k/tools/manipulator/AtomContainerComparator.java: Removed a method which I just added to AtomContainerManipulator
13:35 egonw_cytoscape the patches I wrote this morning on the train, brought to you by git-svn
13:36 thomas_ku oh great
13:36 thomas_ku did you saw the message on #bioclipse?
13:36 egonw_cytoscape no, sorry
13:36 thomas_ku ok mom
13:36 thomas_ku [14:33] <thomas_ku> do you have any idea why I have errors within the cdk-101 branch within eclipse? the ant script works perfectly but I get errors within the smartparser.java file
13:37 thomas_ku but only in eclipse
13:37 egonw_cytoscape run the javacc ant target
13:37 egonw_cytoscape then do a 'refresh' on the project
13:40 thomas_ku done but changed nothing
13:41 thomas_ku the smarts parser need a many classes which are not there like:
13:41 thomas_ku ASTAliphatic
13:41 thomas_ku ASTAromatic
13:41 thomas_ku etc
13:44 egonw_cytoscape umm... right... the SMARTScode has been removed...
13:44 egonw_cytoscape forgot that...
13:45 egonw_cytoscape can you check that the SmartsParser you have, also is in SVN?
13:46 thomas_ku I have done an update to get the lastest branch
13:46 egonw_cytoscape I would guess not... did you check if CDK Nightly for 1.0.x reported trouble?
13:46 thomas_ku the ant target worked
13:46 egonw_cytoscape thomas_ku: sure, but the file is autogenerated...
13:46 thomas_ku also with my version
13:46 egonw_cytoscape seems a clean forgot to remvoe it
13:47 thomas_ku ?
13:49 thomas_ku do you mean that the generated files will not be removed after a clean from the ant target so that I can easily delete them
13:49 thomas_ku ?
13:50 egonw_cytoscape check: http://cdk.svn.sourceforge.net/viewvc/cdk/bran​ches/cdk-1.0.x/src/org/openscience/cdk/smiles/
13:50 egonw_cytoscape no smiles dir
13:50 egonw_cytoscape that is... just remove it...
13:50 egonw_cytoscape the SmartsParser no longer exists in the branch
13:51 thomas_ku ah ok
13:51 thomas_ku so it is a relict of my old checkout
13:54 egonw_cytoscape right
14:03 CIA-16 bioclipse: carl_masak * r4187 /trunk/plugins/net.bioclipse.rhino/src/net/biocli​pse/plugins/bc_rhino/views/RhinoConsoleView.java:
14:03 CIA-16 bioclipse: [RhinoConsoleView.java]
14:03 CIA-16 bioclipse: * added "// verbose" and "// quiet" meta-commands
14:42 CIA-16 bioclipse: jonalv * r4188 /trunk/playground/plugins/net.bioclipse.exp​ression/src/net/bioclipse/expression/ast/: removed ast
15:15 jonalv egonw_cytoscape: olas said that you are intreseted in an expressionparaser for the Grideditor. Maybe we should adopt our new net.bioclipse.expression? Do you have a more concrete example of what you would want? Sort of a wishlist? :)
15:34 egonw_cytoscape jonalv: oi...
15:34 egonw_cytoscape expression parser for the grideditor?
15:34 egonw_cytoscape you mean that I can use the content of the editor to start a R modeling?
15:34 egonw_cytoscape that would be very useful indeed
15:35 masak egonw_cytoscape: not sure what you mean
15:35 jonalv eh what? Not sure we are talking about the same thing here...
15:35 masak maybe best to describe what exists today
15:36 masak there's an expression parser which interacts with the contents of the plates in different ways
15:36 masak the so called Plate Functions and Well Functions are convenient ways to interact between the plate and the expression parser
15:37 jonalv that is it is an expression parser for some sort of mathematical expressions wich supports variables and functions
15:38 egonw_cytoscape guess so...
15:38 jonalv But maybee that wasn't what you where looking for?
15:38 egonw_cytoscape no idea how the code is currently working...
15:38 egonw_cytoscape no change of just passing the code to the R engine?
15:38 jonalv which code?
15:38 masak egonw_cytoscape: doubful
15:38 egonw_cytoscape not sure what Ola was talking about...
15:38 * jonalv neither
15:38 masak in any case, it's no more easy now than it was yesterday
15:39 masak egonw_cytoscape: do you have a use case?
15:39 masak when would one want to interact with R this way?
15:42 egonw_cytoscape what I would like to do is something like this:
15:42 egonw_cytoscape matrixX = BioclipseResource("bla")
15:42 egonw_cytoscape matrixY = BioclipseResource("bla2")
15:42 egonw_cytoscape model = pls(matrixX, matrixY, options..)
15:42 masak egonw_cytoscape: working on that :) hold on a couple of weeks
15:42 egonw_cytoscape loadingMatrix = model.loadings
15:43 egonw_cytoscape scoresMatrix = model.scores
15:43 egonw_cytoscape masak: ack :)
15:43 masak more exactly, kaskelot++ is hacking on R integration
15:43 jonalv In what way would this be realted to the Calculator in the expression package?
15:43 masak jonalv: in no way, most likely
15:44 egonw_cytoscape jonalv: no idea...
15:44 egonw_cytoscape jonalv: you said ola suggested that
15:44 egonw_cytoscape but clearly I am clueless about what Ola actually did mean :)
15:44 * masak too
15:45 * jonalv too and olas says he doesn't have the time to explain right now...
15:50 egonw_cytoscape :)
15:50 egonw_cytoscape the current presentation is interesting...
15:51 egonw_cytoscape it's on visualization of networks...
15:51 egonw_cytoscape nice move...
15:51 egonw_cytoscape +i
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15:51 olas hi
15:51 olas what's up?
15:52 egonw_cytoscape <jonalv> egonw_cytoscape: olas said that you are intreseted in an expressionparaser for the Grideditor. Maybe we should adopt our new net.bioclipse.expression? Do you have a more concrete example of what you would want? Sort of a wishlist? :)
15:52 egonw_cytoscape what were you refering too?
15:52 olas if you don't know, then I don't
15:52 olas probably a mixup of things
15:52 olas nevermind
15:52 egonw_cytoscape ack
15:52 olas you mentioned something about concatenation in grid editor
15:53 * egonw_cytoscape is watching a demo of this program: http://hal.inria.fr/inria-00144496/en/
15:53 egonw_cytoscape olas... right
15:53 olas min(a+b)/log(c*d)
15:53 egonw_cytoscape but that was not directly related to scripting...
15:53 olas in a cell in grid editor as I understood
15:53 egonw_cytoscape but the scripting version is interesting...
15:53 olas no, nothing at all with scripting
15:53 egonw_cytoscape ah, that's not what I meant at all...
15:53 olas ok, let's leave scriupting
15:53 egonw_cytoscape but still interesting too :)
15:53 olas what did you mean?
15:54 olas I must have gotten things completely wrong
15:54 olas anyway, no time now
15:54 olas bye
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16:28 CIA-16 cdk: egonw * r9414 /branches/egonw/ibondorder​/src/org/openscience/cdk/ (34 files in 15 dirs): Ah finally compiles again. Now comes the bug fixing, and performance testing...
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16:41 rguha hi
16:41 rguha egonw_cytoscape, are you using cytoscape?
16:48 egonw_cytoscape no, not using it...
16:49 egonw_cytoscape but the conference day had a very exciting list of speakers...
16:49 egonw_cytoscape looks interesting tool though
16:50 egonw_cytoscape my IBond.Order branch finally compiles...
16:51 egonw_cytoscape but it currently has 248 new failing tests :)
16:51 egonw_cytoscape btw, Noel mentioned svnmerge.py...
16:51 egonw_cytoscape in my blog...
16:51 egonw_cytoscape have not tried it yet... but looks useful
16:53 egonw_cytoscape rguha, thanx for that Nightly update
16:55 egonw_cytoscape do you have experience with cytoscape?
16:55 rguha very impressive tool
16:55 rguha actually I just submitted a paper about SAR's and graphs
16:55 rguha and I'm trying to get uipto speed on Cytoscape
16:56 rguha I need to write a plugin where I can click on a node and bring up a 2D structure diagram
16:56 egonw_cytoscape cool
16:56 rguha of course 48 hour days would help :-/
16:56 egonw_cytoscape have a look at reactome.org
16:56 rguha yes, seen that. Very cool
16:57 egonw_cytoscape which is supposed to have a cytoscape java webstart thingy
16:57 rguha btw, how was the Hopkins talk? I met him at this years GRC
16:57 rguha polypharmacology is very interesting and he's a great speaker
16:57 egonw_cytoscape yeah, was a great talk
16:59 rguha anyway, back to paper writing :(
16:59 egonw_cytoscape ack, cu
17:05 egonw_cytoscape cu tomorrow
17:05 * egonw_cytoscape is preparing for the drink...
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18:36 egonw hi test
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23:15 CIA-16 cdk: miguelrojasch * r9415 /branches/miguelrojasch/mf​/src/org/openscience/cdk/ (12 files in 5 dirs): MolecularFormula add IAtom and not IElement.
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