Camelia, the Perl 6 bug

IRC log for #cdk, 2008-03-11

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All times shown according to UTC.

Time Nick Message
02:14 CIA-18 jmol: hansonr * r9080 /trunk/Jmol/src/org/jmol/ (modelset/ModelCollection.java viewer/Jmol.properties): 11.5.15_dev # bug fix getproperty("chaininfo") for non-biological model causes null pointer exception
02:14 CIA-18 jmol: hansonr * r9081 /branches/v11_4/Jmol/src/org/jmol/ (modelset/ModelCollection.java viewer/Jmol.properties): 11.4.RC11_dev # bug fix getproperty("chaininfo") for non-biological model causes null pointer exception
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04:07 s2a any1 here can help me wit grade 10 physical science?
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06:47 thomas_ku moin
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09:16 steinbeck moin
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12:15 thomas_ku egonw:
12:16 thomas_ku sorry we had some problems with the energy for your pc's
12:33 thomas_ku egonw: The isomorphism module is defenetly missing in the dist-large tag!
12:33 thomas_ku I will try to find out how to add it...
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12:54 egonw thomas_ku: check the build.xml
12:54 egonw there are likely other modules missing too...
12:54 egonw go to the dist-large module..
12:54 egonw and look for the Ant code to extract the jar contents for the cdk-*.jar's...
12:55 thomas_ku will commit a patch
12:55 * egonw has a bad flu and not continuesly online today (or the next days for that matter...)
12:55 thomas_ku that's not nice
12:55 thomas_ku I hope it will get better!!
12:57 egonw well... my wife and son just had it, and are recovering now... but the five days of feeling bad seems the standard for this DNA sequence...
12:58 thomas_ku I had it last week!
12:58 thomas_ku it was really no fun...
12:59 thomas_ku why do the commit messiges do not appear hear anymore?
12:59 egonw happens now and then
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13:21 tjeerd hi
13:23 egonw hi tjeerd
13:23 egonw welcome
13:24 tjeerd thanks
13:25 tjeerd perhaps it's good to introduce myself a little bit here
13:25 egonw one sentence would do
13:25 egonw but it's not necessary...
13:25 egonw people will ask here
13:26 thomas_ku egonw: what do I need to do to get the weka cdk stuff compiled?
13:26 tjeerd for anyone scrolling back: metabolomics, software developing, mass spectrometry
13:26 tjeerd :)
13:26 egonw thomas_ku: check out the cdk-gpl/ module
13:26 thomas_ku done
13:26 thomas_ku but I can't compile it....
13:27 egonw thomas_ku: did I not set up a build.xml yet?
13:27 thomas_ku there is a build xml but it do not work for me...
13:27 egonw tjeerd: did I send you the code of the XCMS2CMLSpect convertor code?
13:28 egonw there is a FAAH data set, which you can convert to CMLSpect...
13:28 tjeerd nope, not yet, if you could do that
13:28 tjeerd (thought there some minor fixes you had to do first)
13:28 egonw sorry, been too busy
13:28 egonw it convert the consensus spectrum... the aligned spectra, so to say
13:29 tjeerd I have the FAAH dataset here
13:29 egonw but not yet the individual spectra...
13:29 egonw http://metware.svn.sourceforge.net/vi​ewvc/metware/trunk/playground/CML/R/
13:29 egonw thomas_ku: ack
13:29 egonw thomas_ku: I guess I did not set up svn:externals, or did I?
13:30 thomas_ku I couldn't find them...
13:30 tjeerd egonw: thanks, i'll give it a try here
13:30 egonw ack... well, maybe better to copy in the cdk-large.jar anyway
13:30 thomas_ku and i have no idea how to setup them up
13:31 egonw thomas_ku: working on a new CDK-Taverna release?
13:31 egonw (I'll look at building cdk-gpl now...)
13:32 thomas_ku thank you, yes I am prepare some stuff for it, but will not get out a new release this month
13:32 thomas_ku :-(
13:33 egonw I still haven't gotten around to get Maven2 to install it locally...
13:33 egonw that is...
13:33 egonw have not fixed the CMLObject problem I had...
13:33 thomas_ku I remember...
13:33 thomas_ku That was really a strange thing...
13:34 thomas_ku And I am not sure if I should release the next cdk-taverna version for the "old" taverna or if I should release it already for the new T2, but this would take more time...
13:34 egonw go for the old for now...
13:35 egonw the T2 enactor is in flux
13:35 egonw and you should be able to run any T1 workflow with T2 too...
13:36 thomas_ku but only if you create a "Translater" for t2 as far as I understand it and as far as they solved it for the current 1.7 release...
13:36 egonw oh... I though I had run some CDK workflow...
13:36 egonw was interested on how it would scale...
13:36 thomas_ku yes but not with the new enactor...
13:36 egonw with proper data flow avaiable...
13:37 egonw yeah, *with* the new enactor
13:37 egonw but not sure which nodes I used...
13:37 egonw but it was molecules, so must have used one of the IteratingReaders ?
13:37 thomas_ku Ok... I haven't test this
13:37 thomas_ku Will try it later today...
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14:27 CIA-18 cdk: egonw * r10353 /trunk/cdk-gpl/src/main/org/openscience/cdk/libio/ (. weka/): Making room for another weka file
14:28 CIA-18 cdk: egonw * r10354 /trunk/ (2 files in 2 dirs): Moved another weka file
14:41 CIA-18 cdk: egonw * r10355 /trunk/cdk-gpl/ (10 files in 6 dirs): Compiles again...
14:42 egonw thomas_ku: here you go
14:43 * egonw is going offline
15:01 thomas_ku thank you egonw
15:02 CIA-18 jmol: hansonr * r9082 /branches/v11_4/Jmol/src/org/jmol/viewer/ (Jmol.properties TransformManager.java): version=11.4.RC11_dev # bug fix: state saving with rotateSelected spinning spins entire model
15:03 CIA-18 jmol: hansonr * r9083 /trunk/Jmol/src/org/jmol/viewer/ (Jmol.properties TransformManager.java): version=11.5.15_dev # bug fix: state saving with rotateSelected spinning spins entire model
15:09 CIA-18 jmol: hansonr * r9084 /trunk/Jmol/src/org/ (34 files in 3 dirs):
15:09 CIA-18 jmol: version=11.5.15_dev WebExport upgrade
15:09 CIA-18 jmol: # bug fix: WebExport with http:// files fails to save file
15:09 CIA-18 jmol: # bug fix: WebExport with local . directory fails to save JmolApplet.jar and Jmol.js
15:09 CIA-18 jmol: # code: refactoring of jmol.app.webexport: adding html subdirectory
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15:36 CIA-18 jmol: hansonr * r9085 /trunk/Jmol/src/org/openscience/j​mol/app/webexport/WebPanel.java:
15:36 CIA-18 jmol: version=11.5.15_dev WebExport upgrade
15:36 CIA-18 jmol: # bug fix: WebExport with http:// files fails to save file
15:36 CIA-18 jmol: # bug fix: WebExport with local . directory fails to save JmolApplet.jar and Jmol.js
15:36 CIA-18 jmol: # code: refactoring of jmol.app.webexport: adding html subdirectory
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16:32 CIA-18 jmol: hansonr * r9086 /trunk/Jmol/src/org/jmol/ (adapter/readers/more/CsfReader.java viewer/Jmol.properties): version=11.5.15_dev # bug fix: CAChe CSF reader not reading partial charges
16:33 CIA-18 jmol: hansonr * r9087 /branches/v11_4/Jmol/src/org/ (47 files in 3 dirs):
16:33 CIA-18 jmol: version=11.4.RC11_dev WebExport
16:33 CIA-18 jmol: # bug fix: WebExport with http:// files fails to save file
16:33 CIA-18 jmol: # bug fix: WebExport with local . directory fails to save JmolApplet.jar and Jmol.js
16:33 CIA-18 jmol: # code: refactoring of jmol.app.webexport: adding html subdirectory
16:36 CIA-18 jmol: hansonr * r9088 /branches/v11_4/Jmol/src/org/jmol/ (adapter/readers/more/CsfReader.java viewer/Jmol.properties): version=11.4.RC11_dev # bug fix: CAChe CSF reader not reading partial charges
17:06 CIA-18 bioclipse: jonalv * r5083 /bioclipse/trunk/plugins/net.​bioclipse/bioclipse.product: reverted commit version 5082. Those changes was only for Brunn. Dangerous to have commit rights when Eclipse doesn't make any differences from which repo plugins are situated in...
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19:15 CIA-18 jmol: nicove * r9089 /trunk/Jmol-FAH/projects/ (5 files): Folding@Home
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20:07 CIA-18 jmol: nicove * r9090 /trunk/Jmol/src/org/jmol/translation/ (Jmol/pt_BR.po JmolApplet/pt_BR.po): Translation: Brazilian Portuguese (pt_BR)
20:28 CIA-18 jmol: nicove * r9091 /branches/v11_4/Jmol/src/org/jmol/translation/ (Jmol/pt_BR.po JmolApplet/pt_BR.po): Translation: Brazilian Portuguese (pt_BR)
20:39 CIA-18 jmol: hansonr * r9092 /branches/v11_4/Jmol/src/org/​jmol/viewer/Jmol.properties: 11.4.RC11 VERSION
20:41 CIA-18 jmol: hansonr * r9093 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: 11.5.15 VERSION
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21:00 CIA-18 jmol: nicove * r9094 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
21:11 CIA-18 jmol: nicove * r9095 /branches/v11_4/Jmol/src/org/​jmol/viewer/Jmol.properties: Version
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