Camelia, the Perl 6 bug

IRC log for #cdk, 2007-12-11

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All times shown according to UTC.

Time Nick Message
05:13 CIA-31 jmol: hansonr * r8764 /trunk/Jmol/src/ (16 files in 7 dirs):
05:13 CIA-31 jmol: version=11.3.55_dev
05:13 CIA-31 jmol: # bug fix: slab/depth planes not properly constructed
05:13 CIA-31 jmol: # new feature: _slabPlane, _depthPlane variables
05:13 CIA-31 jmol: # code: MUCH simpler slab plane code
05:20 CIA-31 jmol: hansonr * r8765 /trunk/Jmol/src/org/ (64 files in 19 dirs): version=11.3.55_dev # code: simplified Logger.debugging flag
05:34 egonw joined #cdk
05:47 CIA-31 jmol: hansonr * r8766 /trunk/Jmol/src/org/jmol/ (5 files in 2 dirs): version=11.3.55_dev # new feature: set wireframeRotation
06:09 CIA-31 cdk: egonw * r9584 /branches/egonw/ibondorder/ (52 files in 34 dirs): Synched with trunk/ 9505:9583
06:42 jbrefort joined #cdk
07:06 rojasm joined #cdk
07:06 rojasm morning
07:07 rojasm egonw around?
07:10 egonw hi rojasm
07:10 egonw yes I am
07:10 egonw brilliant
07:10 egonw that is:
07:10 egonw the ibondorder patch is >650kB :)
07:12 egonw here it comes...
07:12 rojasm that is as say nothing
07:13 rojasm I mean not a lot size
07:13 rojasm :(
07:13 rojasm I mean a lot size
07:13 egonw :)
07:13 rojasm I was checking the checkerLP
07:13 rojasm and for me run all test
07:14 rojasm only the test resonance I think
07:14 rojasm fails
07:14 rojasm But it is brillant all run very good
07:14 egonw yes
07:14 egonw yeah, would very much like to discuss the resonance issue...
07:14 rojasm Apropo. for this Freiday
07:15 rojasm We cam right
07:15 egonw yes
07:15 rojasm perfect
07:15 egonw I'm at home right now... ill... but think I will have recovered by friday
07:15 egonw so, yes, I expect you on friday
07:15 rojasm perfect
07:17 rojasm one remark about the exactMass of atoms type. Is there some method in cdk for extract the molecular weight?
07:17 egonw AtomContainer.getTotalMass()
07:17 egonw or so...
07:17 egonw umm... in AtomContainerManipulator, I mean
07:17 rojasm but that is not the MajorIsotope of each Atomtype
07:18 egonw there is no accurate mass version?
07:18 egonw aka monoisotopic mass
07:19 egonw brb
07:20 rojasm I discuber (I bit late) we can define the atomcontainer as monoisotopic mass, molecular weight and HRMS weight
07:22 egonw what's the difference between HRMS and monoisotopic mass?
07:22 egonw HRMS != high resolutin mass spec weight?
07:23 rojasm I think so
07:23 rojasm http://www.ch.cam.ac.uk/magnus/MolWeight.html
07:26 egonw right...
07:26 egonw nothing special, or ?
07:32 rojasm nothing especial right. But may be interesant to distinguish between monoisotopic mass and molecular weight, right?
07:36 egonw but we do...
07:37 egonw well, sort of...
07:37 egonw we can, at least
07:37 egonw and we do...
07:37 egonw but semantics are not that accurate
07:37 egonw on cdk.interfaces level they are not...
07:37 egonw but they are on method API level
07:38 egonw crap...
07:38 egonw SF's svn seems to have gone down or so...
07:47 CIA-31 cdk: miguelrojasch * r9585 /branches/miguelrojasch/mf/src/org/opensc​ience/cdk/formula/MassToFormulaTool.java: added matrix for 8 and 9 elements
08:01 egonw argh...
08:01 egonw maybe the commit is too large :)
08:03 CIA-31 cdk: egonw * r9586 /trunk/cdk/src/org/openscience/cdk/applications/ (3 files in 3 dirs): Applied the IBond.Order patch
08:04 egonw ok, maybe in a few batches
08:05 egonw ok, two more to come
08:07 carsten joined #cdk
08:08 CIA-31 cdk: egonw * r9588 /trunk/cdk/src/org/openscience/cdk/test/ (73 files in 28 dirs): Applied the IBond.Order patch
08:11 CIA-31 cdk: egonw * r9589 /trunk/cdk/src/org/openscience/cdk/ (38 files in 5 dirs): Applied the IBond.Order patch
08:12 egonw OK, that seems to work
08:12 CIA-31 cdk: egonw * r9590 /trunk/cdk/src/org/openscience/cdk/ (38 files in 4 dirs): Applied the IBond.Order patch
08:15 egonw ok, and the final one
08:15 CIA-31 cdk: egonw * r9591 /trunk/cdk/src/ (63 files in 30 dirs): Applied the IBond.Order patch
08:17 CIA-31 cdk: egonw * r9592 /branches/egonw/ibondorder/: Applied to trunk/; closing branch.
08:22 jpansanel moin
09:52 CIA-31 cdk: egonw * r9593 /branches/speleo3/: Added a place for Thomas H. to work on his Iterable patch
09:58 egonw rojasm: around?
09:59 CIA-31 cdk: egonw * r9594 /branches/speleo3/iterable/: Created a branch for Thomas H. for his Iterable patch.
10:15 rojasm yes egonw!
10:16 egonw ah...
10:16 egonw did you have a look at the lpchecker branch?
10:16 egonw as reported, it did not introduce new failing tests...
10:22 steinbeck joined #cdk
11:58 thomas_ku joined #cdk
11:58 thomas_ku moin
11:59 thomas_ku egonw: do you have any idea who submited the class not found bug of cdk-taverna?
12:01 egonw I did
12:01 thomas_ku ok
12:01 egonw was the problem I was talking about...
12:01 thomas_ku a question: do you have other installed version of taverna like 1.6.1?
12:01 egonw that was with a fresh install... not sure what happened...
12:02 egonw I removed all ~/.taverna* dirs
12:02 thomas_ku the problem is that if you have "older" taverna installation the new freshly installed version will also look at the old installed version for the libraries...
12:02 thomas_ku ok so all old libs are deleted?
12:02 egonw guess so...
12:03 thomas_ku ok
12:03 thomas_ku can you verify that the cdk and cdk-taverna.jar files are within the fresh installed taverna repository?
12:03 egonw mom
12:04 egonw I'm booting my workplace desktop
12:06 egonw ok, confirmed to have really only one .taverna dir
12:06 egonw -1.6.2
12:06 egonw so, which jars should I look for?
12:06 thomas_ku mom
12:06 egonw $ find . -name "*cdk*jar"
12:06 egonw ./repository/org/openscien​ce/cdk/1.0.1/cdk-1.0.1.jar
12:06 egonw ./repository/org/openscience/cdk/applications/tav​erna/cdk-taverna/0.4.1.0/cdk-taverna-0.4.1.0.jar
12:06 egonw ./repository/org/openscien​ce/cdk/1.0.2/cdk-1.0.2.jar
12:06 egonw that's what I have
12:07 egonw ah, note the 1.0.1.jar too
12:07 thomas_ku ok that could be a problem....
12:07 thomas_ku but no idea why this is there...
12:07 egonw neither do I...
12:07 thomas_ku i will check my installation...
12:07 egonw I did see it getting downloaded...
12:07 egonw it's certainly of the fresh install I made last time
12:09 thomas_ku mom
12:14 thomas_ku I found why it downloaded both version and changed it...
12:15 thomas_ku so could you please try again a fresh installation of taverna and cdk-taverna
12:15 thomas_ku I forgot to update the pom file for jchempaint
12:16 thomas_ku to cdk version 1.0.2 which is in fact an current snapshot of the cdk-1.0.x branch
12:16 egonw will do
12:16 egonw and email you the outcome
12:16 thomas_ku thanks
12:16 egonw will report later
12:16 thomas_ku I am sorry but this caused no problem on my machines up to now!!
12:52 CIA-31 jmol: hansonr * r8767 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: 11.3.55 VERSION
12:55 CIA-31 bioclipse: biocoder * r4461 /trunk/plugins/net.bioclipse.chart/src/ne​t/bioclipse/plugins/views/ChartView.java: changed method of getting the display so that it's returned from the workbench instead of shell as according to convention.
13:47 CIA-31 jmol: hansonr * r8768 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: 11.3.55 HOLD
15:06 steinbeck left #cdk
15:07 CIA-31 jmol: hansonr * r8769 /trunk/Jmol/src/org/jmol/viewer/ (Eval.java Jmol.properties TransformManager.java Viewer.java):
15:07 CIA-31 jmol: version=11.3.55
15:07 CIA-31 jmol: # bug fix: XOR returning OR when not a bitset
15:07 CIA-31 jmol: # bug fix: unary minus for planes and points
15:35 CIA-31 jmol: hansonr * r8770 /trunk/Jmol/src/org/jmol/ (5 files in 2 dirs):
15:35 CIA-31 jmol: version=11.3.55 VERSION
15:35 CIA-31 jmol: # bug fix: axes/unitcell improperly slabbing on internal slab
15:39 CIA-31 jmol: hansonr * r8771 /trunk/Jmol/src/org/jmol/viewer/Eval.java:
15:39 CIA-31 jmol: version=11.3.55 VERSION
15:39 CIA-31 jmol: # bug fix: axes/unitcell improperly slabbing on internal slab
15:47 thomas_ku joined #cdk
16:01 dleidert joined #cdk
16:05 carsten joined #cdk
17:39 jbrefort joined #cdk
18:31 egonw joined #cdk
21:10 jbrefort joined #cdk
21:16 CIA-31 jmol: nicove * r8772 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
21:41 CIA-31 jmol: nicove * r8773 /trunk/Jmol-extensions/wiki/​MediaWiki/JmolMediaWiki.js: MediaWiki extension: fix for Popup window

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