Camelia, the Perl 6 bug

IRC log for #cdk, 2008-03-18

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All times shown according to UTC.

Time Nick Message
00:17 CIA-11 jmol: hansonr * r9145 /branches/v11_4/Jmol/src/org/jmol/viewer/ (Jmol.properties Viewer.java): version=11.4.1_dev # bug fix: minor missing ; in calculate surface state script
00:17 CIA-11 jmol: hansonr * r9146 /branches/v11_4/Jmol/src/org/​jmol/viewer/Jmol.properties: version=11.4.1_dev # bug fix: minor missing ; in calculate surface state script
02:28 CIA-11 jmol: hansonr * r9147 /trunk/Jmol/src/org/jmol/ (9 files in 4 dirs): version=11.5.18_dev # bug fix: zap x.y additional work -- connections, isosurfaces
02:30 CIA-11 jmol: hansonr * r9148 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: 11.5.18 VERSION
02:33 CIA-11 jmol: hansonr * r9149 /trunk/Jmol/src/org/jmol/sh​apespecial/Isosurface.java: 11.5.18 VERSION
04:06 CIA-11 jmol: hansonr * r9150 /trunk/Jmol/src/org/jmol/ (5 files in 2 dirs): 11.5.18 VERSION (+ some JVXL work for JR)
05:00 CIA-11 jmol: hansonr * r9151 /trunk/Jmol/src/org/jmol/modelset/ (AtomCollection.java ModelSet.java): 11.5.18 VERSION (+ a bug fix for zap x.y)
05:07 CIA-11 jmol: hansonr * r9152 /trunk/Jmol/src/org/jmol/modelset/ModelSet.java: 11.5.18 VERSION (coding)
05:28 CIA-11 jmol: hansonr * r9153 /trunk/Jmol/src/org/jmol/viewer/Eval.java: 11.5.18 VERSION (+ a bug fix for zap x.y) -- please release
05:30 masak joined #cdk
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07:39 jpansanel moin
07:43 jpansanel carsten : did you change your gpg key ?
07:43 carsten no!
07:43 carsten ah, you mean the invalid mail on OB-devel?
07:43 carsten that is a sourceforge but
07:43 jpansanel yes
07:43 carsten bug
07:43 carsten one more reason to hate sf
07:47 tjeerd joined #cdk
07:47 tjeerd god morgon
07:48 jpansanel guten Morgen
07:55 egonw joined #cdk
07:55 egonw moin
07:59 jpansanel moin
08:41 rojasm joined #cdk
08:42 egonw hi rojasm
08:51 rojasm hi egonw
08:52 rojasm how is the preparation for the defense
08:52 egonw nothing much done yet
08:52 egonw he, it's still two weeks :)
08:52 rojasm by the way!
08:52 rojasm how I should do to convert cdk-gpl into java project
08:53 egonw add a .classpath and a .project
08:53 rojasm ok
08:53 egonw and possible build.properties
08:53 egonw check cdk/
08:53 egonw check cdk/trunk/
08:53 rojasm yes
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09:03 rojasm one question. Now cdk-gpl depends of cdk
09:04 egonw sure
09:04 rojasm each one should do the dependency or we should fix for trunks
09:04 egonw not sure what you mean?
09:04 rojasm cdk-gpl.trunk depends cdk.trunk
09:04 egonw right
09:07 rojasm cdk-gpl needs the junit jar
09:07 rojasm what exactly 4.4 or 4.3.1
09:08 egonw see cdk/trunk/develjar/
09:08 rojasm there you have both
09:09 egonw oh... hahahaha
09:09 egonw thought only 3.8 and 4.x
09:09 egonw ok, see src/META-INF/test.libdepends
09:09 egonw in cdk/trunk
09:10 rojasm I see but there you don't have any of both
09:12 egonw http://cdk.svn.sourceforge.net/viewvc/c​dk/cdk/trunk/src/META-INF/test.devellib​depends?revision=10370&view=markup
09:12 egonw it was .devellibdepends
09:12 egonw .libdepends -> jar/
09:12 egonw .devellibdepends -> develjar/
09:12 rojasm ups ok
09:12 rojasm I see now
09:12 rojasm perfect thanks
09:14 egonw bbl
09:15 CIA-11 cdk: miguelrojasch * r10423 /cdk-gpl/trunk/develjar/junit-4.3.1.jar: added missed junit jar
09:20 CIA-11 bioclipse: ospjuth * r5113 /bioclipse2/trunk/plugins/net.bioclipse.core/s​rc/net/bioclipse/core/domain/IBioObject.java: Deprecated getParsedResource() from IBioObject. Not used and no obvious use in sight either.
09:21 rojasm egonw: I copy cdk/trunk.../libio/weka into cdk-gpl/trunk.../.
09:22 rojasm I think it is erroneous in cdk/trunk
09:25 CIA-11 cdk: miguelrojasch * r10424 /cdk-gpl/trunk/src/test/or​g/openscience/cdk/libio/: create directory libio/ in test
09:25 CIA-11 cdk: miguelrojasch * r10425 /cdk-gpl/trunk/src/test/org/​openscience/cdk/libio/weka/: create directory libio/weka in test
09:26 CIA-11 cdk: miguelrojasch * r10426 /cdk-gpl/trunk/src/test/org/ope​nscience/cdk/libio/weka/weka/: copy weka test into cdk-gpl project
09:28 CIA-11 cdk: miguelrojasch * r10427 /cdk-gpl/trunk/src/test/org/​openscience/cdk/libio/weka/: rm directory libio/weka/weka in test. Incorrect constracted
09:29 CIA-11 cdk: miguelrojasch * r10428 /cdk-gpl/trunk/src/test/org/​openscience/cdk/libio/weka/: copy weka test into cdk-gpl project
09:36 CIA-11 cdk: miguelrojasch * r10429 /cdk-gpl/trunk/src/main/org/opens​cience/cdk/libio/weka/Weka.java: some spelling and removed imports not necessaries.
09:37 CIA-11 cdk: miguelrojasch * r10430 /cdk-gpl/trunk/src/ (20 files in 3 dirs): Removed imports not used anymore.
09:38 rojasm egonw: net.sf.cdk.tools are necessary in cdk-gpl?
09:39 egonw yes
09:39 rojasm ok
09:39 egonw for Ant
09:39 rojasm ok
09:40 egonw also for the Annotation
09:40 egonw 's for test classes
09:44 CIA-11 cdk: miguelrojasch * r10431 /cdk-gpl/trunk/ (3 files in 2 dirs): added missed com-sun and xom jars for test's
09:48 CIA-11 cdk: miguelrojasch * r10432 /cdk/trunk/src/main/net/sf/cdk/tools/ (7 files in 2 dirs): added parameters to Maps and List
09:49 rojasm egonw: for ant compilation and test it should be only specific for qsar and right?
09:51 rojasm other question! now I make dependency for cdk-gpl/trunk with directory cdk/trunk. But should it not be better that cdk-gpl contains the cdk.jar
09:51 egonw rojasm: how so for qsar specific?
09:51 egonw no, I'd rather use svn:externals
09:52 egonw ah, right
09:52 egonw mom
09:52 egonw see cdk-gpl/trunk/README
09:52 egonw but please don't upload the CDK jar
09:52 egonw so, no svn:externals
09:53 rojasm ok :)
09:53 egonw a project dependency for Eclipse is a perfect idea
09:53 rojasm ok
09:54 CIA-11 cdk: miguelrojasch * r10433 /cdk-gpl/trunk/ (.classpath .project): modified .project and .classpath for java project
09:56 rojasm I mean that when I do in cdk-gpl a test-all it should not test smiles or some thing like that
09:56 egonw correct
09:56 egonw didn't I remove all but test-weka from build.xml ?
09:57 rojasm right?
09:57 rojasm I see now. Sorry
09:57 egonw no worries
10:01 rojasm the target in build.xml of javacc, dist-java3d are necessary?
10:02 egonw no, don't think so...
10:02 egonw cdk-gpl/ does not have anythin JavaCC based
10:02 rojasm correct
10:02 egonw but I was too lazy to fix all the deps on the target
10:03 rojasm should I do it?
10:04 egonw yeah, please go ahaed
10:08 rojasm I have a problem with  QSARModelException because it is not in cdk-gpl!
10:08 rojasm how I can solve the problem?
10:08 egonw from the CL, or in Eclipse?
10:09 egonw make sure the cdk-svn-20080113.jar is in your classpath
10:09 rojasm ok
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10:23 rojasm egonw: but the compilation with ant can not access to cdk/trunk if I don't copy before into cdk-gpl/trunk/develjar
10:24 egonw see the README
10:24 rojasm ok
10:24 rojasm :)
10:56 CIA-11 cdk: miguelrojasch * r10434 /cdk-gpl/trunk/build.xml: removed target which not are into qsar descriptor
10:58 rojasm egonw: after to try a lot of times I don't find the solution. If I copy the cdk-svn*.jar in jar directory with Ant doesn't compile
10:58 egonw will try, hang on
11:01 CIA-11 cdk: miguelrojasch * r10435 /cdk/trunk/src/test/org/op​enscience/cdk/libio/weka/: removed weka test which is now situated in cdk-gpl project
11:03 CIA-11 cdk: miguelrojasch * r10436 /cdk/trunk/.classpath: removed the weka.jar from the path
11:15 egonw rojasm: OK, got it checked out now
11:15 egonw running ant works here
11:15 egonw creates me a dist/jar/cdk-qsarweka.jar
11:16 egonw and test-dist-all gives me the cdk-test-qsarweka.jar
11:16 egonw which is actually empty...
11:16 egonw is that the problem you mean?
11:43 rojasm not exactly
11:43 rojasm cannot find symbol
11:43 rojasm [javac] symbol  : class QSARModelException
11:43 rojasm [javac] location: class org.openscience.cdk.qsar.model.w​eka.SimpleLinearRegressionModel
11:43 rojasm [javac]     public void predict() throws QSARModelException {
11:43 egonw what's the output of: ls -al jar/
11:44 rojasm cdk-svn-20080221.jar
11:44 rojasm log4j.jar
11:44 rojasm vecmath1.2-1.14.jar
11:44 rojasm weka.jar
11:44 rojasm xom-1.1.jar
11:45 egonw rojasm: ok, rename that jar into cdk-svn-20080311.jar
11:45 egonw then you're fine
11:48 rojasm now is perfect :)
11:49 rojasm dist-all and test-all compiling again :)
11:50 egonw good :)
11:50 rojasm compailing
11:53 egonw http://www.amd.com/us-en/Corporate/Virtu​alPressRoom/0,,51_104_543~124325,00.html
11:54 rojasm egonw: there is a method in reactionSetManipulator that with getAllMolecules returns all molecules but it doesn't check if the same object is in more of one reactions
11:55 egonw yeah, possible
11:55 rojasm in short. getAllMolecuels should return only instance
11:55 egonw I think that was for a reason...
11:55 egonw not sure anymore...
11:55 egonw make sure to run all unit tests, and see that nothing fails...
11:56 rojasm ok
11:56 egonw if you make it only instances, and nothing fails, then I'm fine...
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11:56 rojasm you fine I fine every fine :)
11:57 egonw :)
11:57 egonw ok, will relocate now...
11:57 egonw bbl laer
11:57 egonw +t
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12:04 CIA-11 cdk: miguelrojasch * r10437 /cdk/trunk/src/main/org/openscience/cdk/too​ls/manipulator/ReactionSetManipulator.java: added parameters to the List objects
12:08 CIA-11 cdk: miguelrojasch * r10438 /cdk/trunk/src/main/org/openscience/cdk/too​ls/manipulator/ReactionSetManipulator.java: removed staff that I added erroneously.
12:24 CIA-11 cdk: miguelrojasch * r10439 /cdk/trunk/src/test/org/openscience/cdk/tools​/manipulator/ReactionSetManipulatorTest.java: added parameters to the List objects
12:25 masak joined #cdk
12:34 CIA-11 cdk: miguelrojasch * r10440 /cdk/trunk/src/test/org/openscience/cdk/tools​/manipulator/ReactionSetManipulatorTest.java: added test testing the method getAllMolecules which returns Molecules objects
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12:47 CIA-11 cdk: miguelrojasch * r10441 /cdk/branches/miguelrojasch-CMLReact/: Made a branch for parsing correctly IReaction.. to CMLReact.
13:04 CIA-11 cdk: miguelrojasch * r10442 /cdk/branches/miguelrojasch-CMLReact/src/data/cml/ (5 files): added cml files with examples of cml reactions (Scheme, StepList, etc...)
13:06 CIA-11 cdk: miguelrojasch * r10443 /cdk/branches/miguelrojasch-CMLReact/src/m​ain/org/openscience/cdk/CDKConstants.java: A Molecular Formula Identifier for CDKConstants
13:12 CIA-11 cdk: miguelrojasch * r10444 /cdk/branches/miguelrojasch-CMLReact/s​rc/main/org/openscience/cdk/reaction/ (4 files): new ReactionSet extensions defining specific type of reaction (chain, scheme)
13:37 CIA-11 cdk: miguelrojasch * r10445 /cdk/branches/miguelrojasch-CMLReact/src/ (4 files in 3 dirs): test and method to parser scheme and stepList tags from CML
14:16 tjeerd anyone here known with xcms?
14:26 CIA-11 cdk: miguelrojasch * r10446 /cdk/branches/miguelrojasch-CMLReact/s​rc/main/org/openscience/cdk/tools/mani​pulator/ReactionSetManipulator.java: adapted the ReactionManipulator to new ReactionSet which can be ReactionScheme.
14:42 CIA-11 cdk: miguelrojasch * r10447 /cdk/branches/miguelrojasch-CMLReact/src/ (4 files in 4 dirs): adapted the conversion from ReactionScheme to CMLScheme
14:58 CIA-11 cdk: miguelrojasch * r10448 /cdk/branches/miguelrojasch-CMLReact/src/main/​org/openscience/cdk/io/cml/CMLCoreModule.java: added parameters to List
15:17 egonw joined #cdk
16:13 CIA-11 bioclipse: jonalv * r5114 /bioclipse2/trunk/plugins/net.bioclipse.u​sermanager/src/net/bioclipse/usermanager/ (4 files in 2 dirs): Working on bioclipse2ifying the usermanager. There is a good start on a usermanager interface now.
16:59 CIA-11 bioclipse: jonalv * r5115 /bioclipse2/trunk/plugins/net.bioclipse.bio​java.business/META-INF/spring/context.xml: wrote context.xml for usermanager plugin
17:00 CIA-11 bioclipse: jonalv * r5116 /bioclipse2/trunk/plugins/net.bioclipse.bioja​va.business/META-INF/spring/context-osgi.xml: deleted context-osgi.xml
17:10 CIA-11 bioclipse: jonalv * r5117 /bioclipse2/trunk/plugins/net.bioc​lipse.usermanager/META-INF/spring/ (. context.xml): added context.xml to usermanager
17:15 Annzi left #cdk
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17:45 CIA-11 bioclipse: jonalv * r5118 /bioclipse2/trunk/plugins/net.bioclipse.u​sermanager/src/net/bioclipse/usermanager/ (3 files in 2 dirs): Work primarily on the actual UserManager class. (yes this plugin doesn't even compile right now, (and looks strange) be patient...)
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18:50 CIA-11 jmol: nicove * r9154 /trunk/Jmol-FAH/projects/p4405.xyz.gz: Folding@Home
20:05 CIA-11 jmol: nicove * r9155 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
21:00 jbrefort joined #cdk
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23:20 CIA-11 jmol: aherraez * r9156 /trunk/Jmol/src/org/jmol/tr​anslation/JmolApplet/es.po: Spanish
23:22 CIA-11 jmol: aherraez * r9157 /branches/v11_4/Jmol/src/org/jmo​l/translation/JmolApplet/es.po: Spanish

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