Camelia, the Perl 6 bug

IRC log for #cdk, 2008-06-04

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All times shown according to UTC.

Time Nick Message
04:23 jbrefort joined #cdk
05:25 rojasm joined #cdk
06:28 CIA-31 jmol: hansonr * r9456 /trunk/Jmol/src/org/jmol/ (4 files in 2 dirs): (log message trimmed)
06:28 CIA-31 jmol: version=11.5.40_dev
06:28 CIA-31 jmol: # code: better handling of twin script manager threads
06:28 CIA-31 jmol: # new feature: /*SPLIT*/ in a command string allows it to be processed by
06:28 CIA-31 jmol: # the two independent processors. (just to isolate javascript from load commands
06:28 CIA-31 jmol: # for the signed applet
06:28 CIA-31 jmol: #
06:40 rojasm joined #cdk
06:43 jonalv joined #cdk
07:49 egonw joined #cdk
07:50 rojasm moin egonw
07:50 egonw hi rojasm
08:19 CIA-31 jmol: atrog * r9457 /branches/turner-dialogs/ (6 files in 3 dirs):
08:19 CIA-31 jmol: New dialog added to create Gaussian input. First attempt. New dialog is in
08:19 CIA-31 jmol: org/openscience/jmol/app/GaussianDialog.java; changed Write method in
08:19 CIA-31 jmol: org/jmol/viewer/Eval.java; added and modified getData methods in
08:19 CIA-31 jmol: org/jmol/viewer/Viewer.java. Minor changes to
08:19 CIA-31 jmol: org/openscience/jmol/app/GuiMap.java and org/openscience/jmol/app/Jmol.java to
08:19 CIA-31 jmol: make menu item.
08:49 shk3 joined #cdk
09:38 shk3 just checked out cdk
09:38 shk3 and can't find jcp
09:38 shk3 where did it go?
09:39 shk3 should be in applications package, shouldn't it?
09:39 rojasm I think not any more
09:40 rojasm it was moved to out side of the cdk project
09:40 rojasm again
09:40 shk3 :-(
09:40 shk3 why so?
09:40 rojasm cdk.svn.sourceforge.net/svnroot/cdk/jchempaint
09:41 shk3 right
09:41 shk3 how does the build process work?
09:41 shk3 any docs?
09:41 rojasm well I don't remember exactly the reasons
09:44 rojasm may be it is because not with eclipse you can point externally jcp direct to trunk/cdk like it is done in bioclipse.cdk10
09:44 shk3 hm, that project only contains the cdk src code,
09:44 jpansanel moin
09:44 shk3 no build.xml or whatever
09:45 rojasm it is not necessary to work with the jars
09:46 shk3 right, there is a dependency on org.openscience.cdk
09:46 shk3 yes, for running the standalone app not, but for applet build
09:46 CIA-31 cdk: miguelrojasch * r11274 /cdk/branches/cdk-1.0.x/src/org/ope​nscience/cdk/io/MDLRXNWriter.java: integrated in mdlrxnWriter the faculty to write a set of reactions and to set rdf map
09:48 shk3 looks like TestEditor class is the main class now.
09:48 shk3 no jcp class.
09:48 shk3 why?
09:48 rojasm Sorry I have no idea
09:49 shk3 where is egon?
09:49 shk3 the applet stuff disappeared
09:50 rojasm egow: why doesn't have cdk-1.0.x a test package?
09:50 shk3 altogether
09:50 rojasm some reasons?
09:50 shk3 there is a src/test, but that's empty
09:52 shk3 we will wait for egon
09:52 shk3 how is it going in leiden?
09:52 rojasm jeje I think that is the best that we can do
09:52 shk3 what's the weather like?
09:52 rojasm Nice! but too much work
09:52 shk3 pretty bad here
09:52 rojasm raining
09:53 rojasm like allways
09:53 rojasm and you in C
09:53 rojasm when did you starte?
09:53 shk3 on monday
09:53 rojasm Nice!
09:54 egonw rojasm, shk3: ping
09:55 egonw shk3: please read the mailing list archives
09:55 egonw which has info on my JCP is missing from trunk
09:55 egonw rojasm: cdk1.0.x/src/org/openscience/cdk/test
09:55 egonw cdk1.0.x does not have the src/main|test split up
09:55 rojasm ach so
09:55 rojasm now
09:55 malick joined #cdk
09:56 shk3 sorry for not following the list
09:56 egonw no worries, that what the archives are for :)
09:56 rojasm If I try to debug from bioclipse2 some cdk code what is the best way to do it
09:56 egonw shk3: there are also bits in my blog
09:57 egonw shk3: next week I'm done with a few deadline, can explain more then
09:57 rojasm because afterwords it will be more complicated to merge again to cdk
09:57 rojasm or not?
09:57 egonw rojasm: bc2 is using CDK SVN directly
09:57 shk3 i just wanted to fix the bug reported yesterday
09:57 shk3 can I do this?
09:58 rojasm egonw yes but not trunk/cdk but branches/cdk-1.0.x
09:58 rojasm or at least my
09:58 rojasm mm
09:58 egonw shk3: which JCP version?
09:59 shk3 I thought doing it in the current one
09:59 shk3 the bug should be everywhere, i think
09:59 egonw shk3: ok, so 2.3.x
10:01 rojasm mm I don't what I have incorrectly!
10:01 egonw that should be based on cdk1.0.x
10:02 egonw rojasm: bc2 is using both
10:02 shk3 cdk 1.0.x is trunk?
10:02 egonw no
10:02 rojasm no
10:02 shk3 no
10:02 egonw cdk1.0.x is in cdk/cdk/branches/cdk1.0.x
10:02 shk3 right
10:03 shk3 so there is not yet (plans for) a jcp from trunk?
10:03 rojasm Than now the question if I implement some thing I should add both
10:03 egonw shk3: yes, there are plans...
10:03 rojasm cdk1.0.x and trunk
10:03 shk3 sorry, I am not in the development process right now
10:03 egonw shk3: but also little effort so far
10:03 egonw rojasm: depends
10:03 shk3 ok, so 1.0.x is current production
10:03 egonw yes
10:03 shk3 so I will look at that
10:04 egonw JCP 2.3.x is based on that
10:04 shk3 the new renderer is in ...?
10:04 egonw JCP 3 is based on trunk
10:04 rojasm writer reader of a set of rxn reactions
10:04 egonw that's what's in cdk/jchempaint
10:04 egonw rojasm: check the MACiE reader
10:04 egonw that's a RXN reader too
10:04 egonw RDF really...
10:10 rojasm ok
10:11 rojasm you propose that the rdfEditor based on MACiE format
10:12 rojasm strange because the MACiE format doesn't have a writer
10:13 rojasm neither tests
10:13 rojasm for reader
10:13 rojasm mmm
10:23 egonw RDF is a rather free format...
10:23 egonw regarding the meta data
10:23 egonw but the molecules (products, reactants) are always using RXN
10:23 rojasm ok! I am downloading both papers of MECiE
10:23 rojasm MACiE
10:25 rojasm but what now I just committed  putting a list of rxn reactions into the rdf file like mdl writer, is it not correct?
10:32 egonw no idea
10:33 egonw that's not what I have seen
11:37 thomas_ku joined #cdk
11:39 thomas_ku moin
11:54 egonw joined #cdk
12:49 shk3 i am having problems building the jcp applet
12:50 shk3 getting
12:50 shk3 Problem creating jar: Negative seek offset
12:50 shk3 I remember that, but don't remember what to do about it :-(
12:50 shk3 anybody an idea
12:50 shk3 ?
12:53 rojasm joined #cdk
12:53 egonw I have that question too, but no clue
12:53 egonw never had that myself
12:54 thomas_ku I never build the applet before sorry
12:56 shk3 i remember I had it...
12:56 shk3 I think i remember (but not sure) it always worked when repeating the dist a second time
12:56 shk3 it was some sort of dirty trick
12:58 jonalv joined #cdk
13:56 shk3 btw, I found a use of generics in cdk 1.0.x
13:56 shk3 shall I remove this?
13:57 shk3 (still java 1.3 there, isn't it?)
14:06 rojasm egonw I implemented in MDLXNR the possibility to add more of one reaction
14:07 jonalv java 1.3? May I wonder why? :)
14:07 egonw 1.4
14:07 shk3 because of the applet
14:07 shk3 no, it's 1.3
14:07 shk3 (in the build.xml)
14:07 egonw not for cdk1.0.x
14:07 egonw but it compiles to 1.3 classes, I think
14:08 shk3 then you need to change the build.xml
14:08 egonw anyway... generics should not be part of cdk1.0.x
14:08 egonw where did you find it?
14:08 shk3 right
14:08 shk3 here:
14:09 * shk3 expects the CIA message here
14:09 CIA-31 cdk: shk3 * r11275 /cdk/branches/cdk-1.0.x/src/org/ope​nscience/cdk/io/MDLRXNWriter.java: removed a generic from 1.0.x branch
14:09 shk3 if we say we do not want 1.5 there, there is no point in not having 1.3 instead of 1.4, btw
14:10 egonw rojasm: please set Eclipse to use Java1.4 for your cdk-1.0.x project
14:11 rojasm ups sorry
14:11 rojasm yes I will do it
14:13 rojasm thanks shk3
14:17 CIA-31 cdk: miguelrojasch * r11276 /cdk/trunk/src/ (5 files in 3 dirs): implementation picking a set of reaction in MDLRXNReader and writer! Added tests for both.
14:21 rojasm egonw I want to merge what I just committed to trunk to cdk1.0 branches, should I look one for one and than copy-paste for differences?
14:21 shk3 you are welcome
14:21 rojasm or is there some faster way?
14:22 egonw whatever is faster
14:26 CIA-31 cdk: miguelrojasch * r11277 /cdk/branches/cdk-1.0.x/src/org/ope​nscience/cdk/io/MDLRXNReader.java: The reader rdf is able to read a set of reactions
14:52 CIA-31 cdk: miguelrojasch * r11278 /cdk/trunk/src/ (2 files in 2 dirs): Implemented a method to get a list of all IReaction inside an IChemFile.
14:55 CIA-31 cdk: miguelrojasch * r11279 /cdk/branches/cdk-1.0.x/src/org/openscience/cd​k/tools/manipulator/ChemFileManipulator.java: method which Get a list of all IReaction inside an IChemFile.
15:03 carsten joined #cdk
15:25 malick left #cdk
15:32 jbrefort joined #cdk
17:01 CIA-31 jmol: hansonr * r9458 /trunk/Jmol/src/org/jmol/v​iewer/ScriptManager.java: coding error
17:22 CIA-31 jmol: hansonr * r9459 /trunk/Jmol/src/org/jmol/ (5 files in 3 dirs): version=11.5.40_dev # new feature: frank appears RED in signed applet, and popup about menu identifies the applet as signed.
17:24 CIA-31 jmol: hansonr * r9460 /trunk/Jmol/src/org/jmol/shape/FrankRenderer.java: version=11.5.40_dev # new feature: frank appears RED in signed applet, and popup about menu identifies the applet as signed.
17:25 CIA-31 jmol: hansonr * r9461 /trunk/Jmol/src/org/jmol/viewer/Viewer.java: version=11.5.40_dev # new feature: frank appears RED in signed applet, and popup about menu identifies the applet as signed.
18:57 CIA-31 jmol: nicove * r9462 /trunk/Jmol-FAH/projects/ (p782.xyz.gz p783.xyz.gz p786.xyz.gz): Folding@Home
19:17 thomas_ku joined #cdk
19:24 thomas_ku moin
19:41 rojasm joined #cdk
20:24 bag joined #cdk
22:04 CIA-31 cdk: rajarshi * r11280 /cdk/trunk/src/main/org/openscience/cdk/qsar​/descriptors/molecular/TPSADescriptor.java: Changed the name of the descriptor to remove clash with a CPSA descriptor

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