Camelia, the Perl 6 bug

IRC log for #cdk, 2008-03-26

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Time Nick Message
00:12 rojasm left #cdk
00:21 CIA-11 jmol: hansonr * r9203 /trunk/Jmol/src/org/jmol/viewer/ (Eval.java Viewer.java): version=11.5.21_dev # minimize
05:21 jbrefort joined #cdk
06:26 CIA-11 bioclipse: Annzi * r5179 /bioclipse2/trunk/plugins/net.bioclipse.moss/ (2 files in 2 dirs): Corrected the parameters that exclude atoms and molecules as seed and from mining since they seemed to set same parameter.
07:26 rojasm joined #cdk
07:34 Annzi joined #cdk
08:47 thomas_ku moin
08:54 jonalv joined #cdk
08:57 masak joined #cdk
09:27 egonw joined #cdk
09:35 carsten joined #cdk
09:58 CIA-11 bioclipse: jonalv * r5180 /bioclipse2/trunk/plugins/net.bioclipse.usermanag​er/src/net/bioclipse/dialogs/EditUserDialog.java: Fixed GUI problem. Still can't log in though...
09:59 jpansanel moin
10:01 carsten Moin Jerome!
10:02 steinbeck joined #cdk
10:04 jpansanel moin carsten !
10:06 egonw hi all
10:47 masak joined #cdk
10:49 thomas_ku egonw: do you have success in compiling cdk-gpl?
10:50 egonw I did, yes
10:50 egonw but I copied in some files later...
10:50 egonw did you read the README?
10:50 egonw did you correctly named the CDK jar?
10:51 jpansanel gonw : what is cdk-gpl ?
10:51 jpansanel s/gonw/egonw/
10:51 thomas_ku_ joined #cdk
10:51 thomas_ku_ my other irc client crashed
10:52 egonw [11:50] <egonw> I did, yes
10:52 egonw [11:50] <egonw> but I copied in some files later...
10:52 egonw [11:50] <egonw> did you read the README?
10:52 egonw [11:50] <egonw> did you correctly named the CDK jar?
10:52 thomas_ku_ how is the corret name?
10:55 egonw check the README
10:55 thomas_ku_ ok I found the problem
10:57 thomas_ku_ my cdk produces a cdk-svn-20080221.jar but the cdk-gpl wants to have a cdk-svn-20080311.jar
10:58 egonw just rename it
10:58 thomas_ku_ yeah i have done this
10:58 thomas_ku_ and it works
10:59 thomas_ku_ but where do the date for the cdk-svn-xxxxxx.jar came from? are theiy hard coded?
10:59 egonw no, added by the build.xml
10:59 egonw but in cdk-gpl it's hardcoded
10:59 egonw in src/META-INF/*.libdepends
11:01 thomas_ku_ ah ok thanks for the information
11:03 thomas_ku_ are you sure the this information is not hard coded in the cdk? because in the build.props file is the version number of the cdk which was build on my system! It is not the current date!
11:03 steinbeck_ joined #cdk
11:04 thomas_ku_ Is this the expected behaviour
11:05 steinbeck__ joined #cdk
11:05 egonw thomas_ku_: would have to check...
11:05 egonw I do indeed remember Rajarshi changing something...
11:05 egonw for Nightly...
11:05 thomas_ku joined #cdk
11:06 thomas_ku_ ok I was just wondering
11:06 thomas_ku_ because I can remember that I got it with the current date some time ago
11:06 steinbeck__ egonw: nice quote from the hotel reservation email:
11:07 steinbeck__ "Wireless internet is available in the entire hotel and costs EUR 17.00 per hour."
11:07 steinbeck__ is it always so cheap in NL?
11:07 steinbeck__ :-)
11:07 egonw what?
11:07 egonw that's rudiculous
11:07 egonw on the other hand...
11:08 egonw you'll have WLAN in the pool now :)
11:08 egonw and the sauna, of course
11:08 steinbeck__ hehe
11:09 jpansanel :)
11:28 jbrefort joined #cdk
11:47 CIA-11 jmol: hansonr * r9204 /trunk/Jmol/src/org/jmol/viewer/ (Eval.java Jmol.properties StateManager.java): (log message trimmed)
11:47 CIA-11 jmol: version=11.5.21 VERSION -- MINIMIZATION
11:47 CIA-11 jmol: # new feature: minimize command -- mostly untested
11:47 CIA-11 jmol: #
11:47 CIA-11 jmol: # set minimizationSteps 100
11:47 CIA-11 jmol: # set minimizationRefresh true
11:47 CIA-11 jmol: # set minimizationCriterion 0.001
11:53 masak joined #cdk
11:57 CIA-11 jmol: hansonr * r9205 /branches/bob-minimize/Jmol/src/org/jmol/minimize/ (Minimizer.java forcefield/CalculationsUFF.java): (log message trimmed)
11:57 CIA-11 jmol: version=11.5.21 VERSION -- MINIMIZATION
11:57 CIA-11 jmol: # new feature: minimize command -- mostly untested
11:57 CIA-11 jmol: #
11:57 CIA-11 jmol: # set minimizationSteps 100
11:57 CIA-11 jmol: # set minimizationRefresh true
11:57 CIA-11 jmol: # set minimizationCriterion 0.001
13:21 CIA-11 bioclipse: jonalv * r5181 /bioclipse2/trunk/ (2 files in 2 dirs): CAn log in and log out now. Events are fired. I have a feeling the serialisation to file isn't working perfect though...
14:14 CIA-11 bioclipse: carl_masak * r5182 /bioclipse/trunk/plugins/net.bioclipse.base2/src/​net/bioclipse/base2/model/Base2ModelObject.java:
14:14 CIA-11 bioclipse: [Base2ModelObject.java]
14:14 CIA-11 bioclipse: * typo
14:39 CIA-11 bioclipse: jonalv * r5183 /bioclipse2/trunk/plugins/ (4 files in 4 dirs): fixed some progress monitor stuff
14:56 egonw joined #cdk
15:02 Annzi left #cdk
15:03 CIA-11 cdk: thomaskuhn * r10512 /cdk-taverna/trunk/src/main/java/org/op​enscience/cdk/applications/taverna/arom​aticity/DetectHueckelAromaticity.java: Update this worker to use the current cdk svn from trunk
15:06 CIA-11 cdk: thomaskuhn * r10513 /cdk-taverna/trunk/src/main/java/org/​openscience/cdk/applications/taverna/​basicutilities/CDKAlternatives.java: Update this worker to use the current cdk svn from trunk
15:07 CIA-11 cdk: thomaskuhn * r10514 /cdk-taverna/trunk/src/main/java/org/o​penscience/cdk/applications/taverna/ba​sicutilities/CMLChemFileWrapper.java: Add a method which casts a DataThing object to a List<CMLChemfile>
15:07 CIA-11 cdk: thomaskuhn * r10515 /cdk-taverna/trunk/src/main/java/org/openscience/c​dk/applications/taverna/qsar/VectorGenerator.java: Update this worker to use the current cdk svn from trunk
15:07 CIA-11 cdk: thomaskuhn * r10516 /cdk-taverna/trunk/src/main/java/o​rg/openscience/cdk/applications/ta​verna/qsar/descriptors/molecular/ (3 files): Update this worker to use the current cdk svn from trunk
15:08 CIA-11 cdk: thomaskuhn * r10517 /cdk-taverna/trunk/src/main/java/org/openscience/c​dk/applications/taverna/qsar/descriptors/protein/ (. TaeAminoAcid.java): Update this worker to use the current cdk svn from trunk
15:08 CIA-11 cdk: thomaskuhn * r10518 /cdk-taverna/trunk/src/main/java/or​g/openscience/cdk/applications/tave​rna/qsar/model/weka/Selection.java: Update this worker to use the current cdk svn from trunk
15:08 CIA-11 cdk: thomaskuhn * r10519 /cdk-taverna/trunk/src/main/java/or​g/openscience/cdk/applications/tave​rna/renderers/Draw2DStructure.java: Update this worker to use the current cdk svn from trunk
15:09 CIA-11 cdk: thomaskuhn * r10520 /cdk-taverna/trunk/src/main/java/org/openscience/c​dk/applications/taverna/tools/HydrogenTools.java: Update this worker to use the current cdk svn from trunk
15:09 CIA-11 cdk: thomaskuhn * r10521 /cdk-taverna/trunk/src/test/java/org/openscience/c​dk/applications/taverna/qsar/descriptors/protein/ (. TaeAminoAcidTest.java): Update this worker to use the current cdk svn from trunk
15:10 CIA-11 cdk: thomaskuhn * r10522 /cdk-taverna/trunk/src/main/resources/ (2 files in 2 dirs): Update this worker to use the current cdk svn from trunk
15:10 CIA-11 cdk: thomaskuhn * r10523 /cdk-taverna/trunk/pom.xml: Update this worker to use the current cdk svn from trunk
15:11 CIA-11 cdk: thomaskuhn * r10524 /cdk-taverna/trunk/src/test/java/o​rg/openscience/cdk/applications/ta​verna/qsar/descriptors/molecular/ (3 files): Update this worker to use the current cdk svn from trunk
15:31 Annzi joined #cdk
16:01 CIA-11 bioclipse: Annzi * r5184 /bioclipse2/trunk/plugins/net.bioclipse.moss/ (10 files in 5 dirs): Poking here and there: added help, documentation and worked with file paths but no actual(working)change were done.
16:04 Annzi left #cdk
16:28 CIA-11 bioclipse: jonalv * r5185 /bioclipse2/trunk/plugins/ (6 files in 6 dirs): The sandbox testt for the usermanager now passes
16:47 CIA-11 bioclipse: ospjuth * r5186 /bioclipse2/trunk/plugins/net.bioclipse.core/s​rc/net/bioclipse/core/domain/IBioObject.java: removede deprecated getParsedResource()
16:48 CIA-11 bioclipse: ospjuth * r5187 /bioclipse2/trunk/plugins/net.bioclipse.qsar/ (4 files in 2 dirs): Some small updates for forms in QSAR plugin. Nothing useful yet.
16:48 CIA-11 bioclipse: ospjuth * r5188 /bioclipse2/trunk/plugins/net.bioclipse.services/ (5 files in 4 dirs): Renamed extension point and adapted all uses for this.
16:51 CIA-11 bioclipse: ospjuth * r5189 /bioclipse2/trunk/plugins/net.bio​clipse.cdk/META-INF/MANIFEST.MF: Removed JCP from export in manifest as it obviously is not included in the current net.bioclipse.cdk version.
16:53 CIA-11 bioclipse: ospjuth * r5190 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui/ (.classpath plugin.xml): Excluded all JCP-related stuff from build and commented out JCPEditor from plugin.xml. cdk.ui now compiles.
17:17 CIA-11 bioclipse: ospjuth * r5191 /bioclipse2/trunk/plugins/net.bioclipse.biomoby/: Initial import from 1.2.0.
17:18 CIA-11 bioclipse: jonalv * r5192 /bioclipse2/trunk/plugins/net.bioclipse.us​ermanager/src/net/bioclipse/usermanager/pr​eferences/UserManagerPreferencePage.java: added a persist command when properties have been edited
17:20 CIA-11 bioclipse: ospjuth * r5193 /bioclipse2/trunk/plugins/net.bioclipse.biomoby/ (72 files in 9 dirs): Initial import from 1.2.0.
17:22 CIA-11 bioclipse: jonalv * r5194 /bioclipse2/trunk/plugins/net.bioc​lipse.usermanager/src/net/bioclips​e/usermanager/UserContainer.java: removed getParsedResource method
17:42 CIA-11 jmol: nicove * r9206 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
17:43 CIA-11 bioclipse: jonalv * r5195 /bioclipse2/trunk/plugins/ (4 files in 4 dirs): Now there is a test failing corresponding to the problems I see in the gui
17:52 CIA-11 bioclipse: jonalv * r5196 /bioclipse2/trunk/plugins/net.​bioclipse.usermanager.tests/: added data file to ignore
17:54 CIA-11 bioclipse: ospjuth * r5197 /bioclipse2/trunk/plugins/​net.bioclipse.biomoby.ui/: Initial import from 1.2.0 with a lot of changes to make it compile.
17:55 CIA-11 bioclipse: ospjuth * r5198 /bioclipse2/trunk/plugins/​net.bioclipse.biomoby.ui/ (67 files in 15 dirs): Initial import from 1.2.0 with a lot of changes to make it compile.
18:30 Annzi joined #cdk
18:30 Annzi left #cdk
18:37 CIA-11 jmol: nicove * r9207 /trunk/Jmol-FAH/projects/p2619.xyz.gz: Folding@Home
19:10 CIA-11 bioclipse: ospjuth * r5199 /bioclipse2/trunk/plugins/ (25 files in 13 dirs): Major refactoring for biomoby in Bioclipse2.
19:13 CIA-11 bioclipse: ospjuth * r5200 /bioclipse2/trunk/plugins/ (8 files in 6 dirs): Finished refactoring of model from ui plugin.
19:16 CIA-11 bioclipse: ospjuth * r5201 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Added import of log4j in maniifest.
19:18 CIA-11 bioclipse: ospjuth * r5202 /bioclipse2/trunk/plugins/ne​t.bioclipse.biomoby.tests/: Initial import of tests plugin for biomoby.
19:18 CIA-11 bioclipse: ospjuth * r5203 /bioclipse2/trunk/plugins/n​et.bioclipse.biomoby.tests/ (12 files in 8 dirs): Initial import of tests plugin for biomoby.
19:20 CIA-11 bioclipse: ospjuth * r5204 /bioclipse2/trunk/plugins/ (14 files in 4 dirs): Refactored existing tests to test plugin.
19:23 CIA-11 bioclipse: ospjuth * r5205 /bioclipse2/trunk/plugins/n​et.bioclipse.biomoby.tests/ (2 files in 2 dirs): Added stub for testing biomoby central.
19:41 CIA-11 cdk: thomaskuhn * r10525 /cdk-taverna/trunk/src/main/java/org/​openscience/cdk/applications/taverna/​atomtype/PerceiveMM2AtomTypes.java: Some clean up and upgrade to Java 5 standards
19:41 CIA-11 cdk: thomaskuhn * r10526 /cdk-taverna/trunk/src/main/java/org/o​penscience/cdk/applications/taverna/at​omtype/PerceiveMMFF94AtomTypes.java: Some clean up and upgrade to Java 5 standards
19:41 CIA-11 cdk: thomaskuhn * r10527 /cdk-taverna/trunk/src/main/java/org/o​penscience/cdk/applications/taverna/ch​arges/PartialChargesCalculator.java: Remove unused old class
19:42 CIA-11 cdk: thomaskuhn * r10528 /cdk-taverna/trunk/src/main/java/or​g/openscience/cdk/applications/tave​rna/filters/Has2DCoordinates.java: Some clean up and upgrade to Java 5 standards
19:42 CIA-11 cdk: thomaskuhn * r10529 /cdk-taverna/trunk/src/main/java/or​g/openscience/cdk/applications/tave​rna/filters/Has3DCoordinates.java: Some clean up and upgrade to Java 5 standards
19:42 CIA-11 cdk: thomaskuhn * r10530 /cdk-taverna/trunk/src/main/java/o​rg/openscience/cdk/applications/ta​verna/io/ConvertToCMLString.java: Some clean up and upgrade to Java 5 standards
19:42 CIA-11 cdk: thomaskuhn * r10531 /cdk-taverna/trunk/src/main/java/org/openscience/​cdk/applications/taverna/io/ReadMDLMolFile.java: Some clean up and upgrade to Java 5 standards
19:43 CIA-11 cdk: thomaskuhn * r10532 /cdk-taverna/trunk/src/main/java/org/openscience/​cdk/applications/taverna/io/WriteToCMLFile.java: Some clean up and upgrade to Java 5 standards
19:43 CIA-11 cdk: thomaskuhn * r10533 /cdk-taverna/trunk/src/main​/resources/cdk.properties: Removed old class entries
19:43 CIA-11 cdk: thomaskuhn * r10534 /cdk-taverna/trunk/src/main/resources/META-​INF/services/org.openscience.cdk.applicatio​ns.taverna.scuflworkers.cdk.CDKLocalWorker: Removed old class entries
19:46 CIA-11 bioclipse: ospjuth * r5206 /bioclipse2/trunk/plugins/net.bioclipse.biomoby​.tests/src/net/bioclipse/biomoby/tests/central/ (3 files): Started on tests for Biomoby central.
21:26 rojasm joined #cdk
21:28 CIA-11 cdk: thomaskuhn * r10535 /cdk-taverna/trunk/src/main/java/org/openscience/c​dk/applications/taverna/io/WriteToMDLMolFile.java: Some clean up and upgrade to Java 5 standards
21:28 CIA-11 cdk: thomaskuhn * r10536 /cdk-taverna/trunk/src/main/java/org/​openscience/cdk/applications/taverna/​isomorphism/SubstructureFilter.java: Some clean up and upgrade to Java 5 standards
21:29 CIA-11 cdk: thomaskuhn * r10537 /cdk-taverna/trunk/src/main/java/org​/openscience/cdk/applications/tavern​a/jchempaint/JChemPaintEditor.java: Some clean up and upgrade to Java 5 standards
21:50 edrin joined #cdk
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23:02 CIA-11 jmol: hansonr * r9208 /trunk/Jmol/src/org/jmol/viewer/ (Jmol.properties Token.java Viewer.java): 11.5.22_dev # bug fix: minimizer for compounds containing isotopes D and T
23:43 CIA-11 jmol: hansonr * r9209 /trunk/Jmol/src/org/jmol/viewer/StateManager.java: minimization variables should not be part of the defined state

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