Camelia, the Perl 6 bug

IRC log for #cdk, 2007-12-14

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All times shown according to UTC.

Time Nick Message
00:04 CIA-32 jmol: aherraez * r8785 /trunk/Jmol-web/build.xml: Update version nr to 11.2.14
00:15 dleidert joined #cdk
06:13 CIA-32 jmol: hansonr * r8786 /trunk/Jmol/src/org/jmol/viewer/ (Jmol.properties TransformManager.java Viewer.java): version=11.3.58_dev # bug fix: spin on missing in final state function.
06:19 CIA-32 jmol: hansonr * r8787 /trunk/Jmol/src/org/jmol/viewer/ (StateManager.java Viewer.java): version=11.3.58_dev # bug fix: spin on missing in final state function.
07:09 jonalv joined #cdk
07:55 steinbeck joined #cdk
08:55 egonw miguel has arrived here at PRI
08:55 egonw we're going to discuss CDK code...
09:24 rojasm joined #cdk
09:24 rojasm steinbeck congratulations
09:24 steinbeck thanks Miguel
09:25 egonw rojasm: http://www.steinbeck-molecular.de/steinblog/inde​x.php/2007/12/06/steinbeck-group-moves-to-europe​an-bioinformatics-institute-ebi-in-january-2008/
09:25 rojasm I am now with egon in wageningen and he expleined about the new good news
09:25 rojasm when is it the move just?
09:28 steinbeck At the beginning of January
09:59 jpansanel steinbeck: congratulations !
10:00 steinbeck jpansanel: thanks
10:01 jbrefort joined #cdk
10:15 steinbeck egonw: around?
10:16 rojasm steinbeck: yes
10:16 rojasm steinbeck: is it urgent?
10:16 steinbeck egonw: please check your gmail account for an invitation to join the grant mailing list
10:16 egonw_ in a meeting right now
10:16 steinbeck and join
10:16 steinbeck yes, sure
10:16 steinbeck take your time
10:16 egonw_ will do in some 15-30 mins
10:16 egonw_ bbl
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11:31 thomas_ku joined #cdk
11:31 thomas_ku moin
11:49 egonw hi thomas_ku
12:15 thomas_ku hi egonw
12:16 CIA-32 cdk: egonw * r9595 /trunk/cdk/src/org/openscience/cdk/​test/qsar/descriptors/bond/Resonanc​ePositiveChargeDescriptorTest.java: Removed obsolete assertion
12:17 CIA-32 cdk: egonw * r9596 /trunk/cdk/src/org/openscience/cdk/rea​ction/type/BreakingBondReaction.java: Use the new valency checker
12:18 CIA-32 cdk: egonw * r9597 /trunk/cdk/src/org/openscience/cdk/ (2 files in 2 dirs): Some minor clean up: spell check, see fix and copyright
12:19 CIA-32 cdk: egonw * r9598 /branches/egonw/lpchecker/ (237 files in 78 dirs): Synched with trunk version 9594
12:21 CIA-32 cdk: egonw * r9599 /trunk/cdk/src/org/openscience/cdk/test/ (ReactionCoverageTest.java modulesuites/MreactionTests.java): Added coverage testing for the reaction module
12:22 CIA-32 cdk: egonw * r9600 /trunk/cdk/src/org/openscience/cd​k/test/ReactionCoverageTest.java: Corrected module (stupid me)
12:22 egonw ha, only 400 commits from the big 10k !!!
12:25 steinbeck egonw: did you sign up for the group?
12:26 egonw yes
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12:43 CIA-32 cdk: egonw * r9601 /trunk/cdk/src/ (3 files in 3 dirs): Moved the StructureResonanceGeneratorTest to the reaction module (where is belongs); add missing dep for cdk-nonotify
12:51 CIA-32 cdk: egonw * r9602 /branches/egonw/lpchecker/sr​c/org/openscience/cdk/test/ (3 files in 3 dirs): Synched with trunk version 9601
13:03 CIA-32 cdk: egonw * r9603 /branches/egonw/lpchecker/src/org/openscience/cdk/ (3 files in 3 dirs): Merged 9595:9598 which I overlooked earlier
13:16 CIA-32 bioclipse: carl_masak * r4494 /trunk/playground/plugins/net.bioclipse.base2​/src/net/bioclipse/base2/views/TreeView.java:
13:16 CIA-32 bioclipse: [TreeView.java]
13:16 CIA-32 bioclipse: * various whitespace fixes
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18:59 rojasm joined #cdk
18:59 egonw hi rojasm :)
18:59 rojasm hi egonw: just at home
19:00 rojasm Outsite it is really cool. I hope it will not be worse
19:05 egonw yeah, winter is really cool indeed :)
19:05 egonw yeah, it will be colder this weekend
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20:50 rguha joined #cdk
20:51 rguha hi
20:52 rguha egonw: was the IBond.Order patch process fully completed?
20:53 egonw yes
20:53 egonw and so is the lpchecker/ patch
20:53 rguha ok
20:56 egonw rguha: yes, it was likely just marketing...
20:56 egonw it's an american thing...
20:56 rguha :)
20:56 egonw did you see:
20:57 rguha ?
20:57 egonw http://bioclipse.blogspot.com/2007/12/r-matey.html
20:57 rguha oh yes, very cool stuff
20:57 egonw indeed :)
20:57 rguha will it be able to access directly from Bioclipse? So, generate the descriptor matrix and then fire up R and use that marix?
20:57 egonw oh, I just love the idea of creating some resource in bioclipse, sending it of to some taverna workflow, and run some R script on the results... :)
20:57 egonw yes, that's the goal
20:58 rguha impressive
20:58 egonw yeah, Ola's group is doing a great job there in Uppsala...
20:59 rguha is it using JGR? How are graphics handled? I know that traditionally R + Java graphics is tricky
20:59 egonw you should try to visit the next Bioclipse workshop!
20:59 rguha damn $#%@#^ visa's
20:59 egonw no idea... see my question in the comments...
20:59 rguha oh right
20:59 egonw ah, visa's... indeed...
21:00 rguha are you going to be in new orleans? Or Philadelphia?
21:00 rguha ACS that is
21:00 egonw no, don't think so...
21:00 egonw I'll go for Christoph's original goal...
21:00 egonw once every two years
21:00 rguha aah
21:01 egonw until he got that CIC-president position :)
21:01 rguha that would certainly help :)
21:01 egonw indeed :)
21:01 egonw Miguel was in Wageningen today...
21:01 egonw and we had a nice long hack session on his CDK code for reactions
21:01 rguha ccol
21:01 egonw I'm starting to get grip on his code...
21:02 rguha btw, I was thinking of looking into Marksuh structure handling
21:02 rguha strting with file reading and storage
21:02 egonw and things in trunk are now broken, because it fully moved to cdk atom types...
21:02 rguha aah
21:02 egonw but, the new code will be much cleaner...
21:02 rguha great
21:02 egonw as with everything that moves to CDK atom types :)
21:03 rguha do you know who's playing with the reaction code? Is it just Christoph/Miguel?
21:03 egonw the key thing here is that atom type perception is factored out...
21:03 egonw just Miguel
21:03 rguha I'd like to know who is using what featuresw
21:03 egonw it's part of his thesis
21:03 rguha would be a good way to prioritize stuff
21:03 rguha aah
21:03 egonw it's used for IP calculation, fragmentation reactions, so MS spectrum prediction
21:03 egonw but you'll see when Miguel finished his thesis...
21:04 rguha ok
21:05 egonw OK, going to shut down the laptop...
21:05 egonw will be away for the weekend...
21:05 rguha ok, ttyl
21:05 egonw we should think about a CDK bug squash week/IRC meeting...
21:06 rguha march may be good
21:06 egonw because the number of open bugs is higher than ever...
21:06 rguha yes
21:06 egonw too late, I think...
21:06 egonw seems that a lot of people are using trunk/ ...
21:06 rguha I'm not going to be able to do much before Jan 23
21:06 egonw from the bug reports...
21:06 rguha hmm
21:07 egonw ack
21:07 egonw ok, we'll see...
21:07 rguha i'll look over stuff in th next few days till my wife comes down
21:07 rguha then I'm off line :)
21:07 egonw ok, cu next week
21:07 rguha byw

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