Camelia, the Perl 6 bug

IRC log for #cdk, 2007-12-04

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All times shown according to UTC.

Time Nick Message
00:13 CIA-16 jmol: hansonr * r8724 /trunk/Jmol/src/org/jmol/ (6 files in 2 dirs): version=11.3.53_dev # bug fix: completion of set parameter clean up
02:55 CIA-16 jmol: hansonr * r8725 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: 11.3.53 VERSION
05:44 CIA-16 joined #cdk
05:46 CIA-16 jmol: egonw * r8726 /trunk/Jmol/src/org/jmol/translation/Jmol/nl.po: Updated NL translation
05:49 CIA-16 jmol: egonw * r8727 /trunk/Jmol/src/org/jmol/tr​anslation/JmolApplet/nl.po: Updated NL translation
06:28 thomas_ku joined #cdk
06:28 thomas_ku moin
06:38 jbrefort joined #cdk
07:40 egonw hi thomas_ku
07:40 egonw no, did not update that URL
07:40 egonw don't really have an installed apache right now
07:40 egonw will need to read the maven2 docs on how to get a local dir target...
07:40 egonw if possible at all
07:41 thomas_ku that is possible
07:42 thomas_ku I can sent you an example where it copies it to a local dir
07:42 thomas_ku mom
07:42 egonw ok, thanx
07:43 egonw anyway...
07:43 egonw how can I make sure the test runs?
07:43 egonw btw, many tests are failing for me...
07:44 thomas_ku the test will run everytime you use a maven command like mvn compile, mvn install or mvn deploy
07:44 thomas_ku how many test are failing for you?
07:46 egonw difficult to say...
07:46 egonw it does not give a summary...
07:47 thomas_ku thats really strange...
07:47 egonw 97
07:48 thomas_ku than try it on eclipse, just click on the test folder and say run as junit test
07:48 egonw java.lang.OutOfMemoryError: Java heap space
07:48 egonw that's a random pick
07:48 egonw on the folder?
07:48 thomas_ku ah ok so you have mem problems
07:48 thomas_ku yes on the folder of src/test/java
07:48 egonw 123 tests in total?
07:50 thomas_ku sounds good
07:50 egonw OK, halfway now...
07:50 egonw several NullPointerExceptiones in getCMLFile()
07:50 egonw 11 fails so far
07:51 egonw NPEs in getCMLChemFile() to be precise
07:51 egonw 33 fails now
07:51 egonw 24, with 42 tests to go
07:51 egonw s/24/34/
07:51 egonw OK, got to go to a meeting now...
07:51 egonw bbl
07:51 thomas_ku ok is it possibly also a mem issue?
07:52 thomas_ku at my machine only 4 tests fail
07:52 thomas_ku can you please try it with more mem within the junit options from within eclipse?
08:35 thomas_ku joined #cdk
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08:42 jpansanel moin
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09:40 egonw thomas_ku: that helped...
09:40 egonw only five fails in Eclipse now
10:01 CIA-16 bioclipse: jonalv * r4381 /trunk/plugins/net.bioclipse/bioclipse.product:
10:01 jonalv wow
10:01 jonalv what did I just do?
10:04 CIA-16 bioclipse: jonalv * r4382 /trunk/plugins/net.bioclipse/bioclipse.product: reverted commit I didn't intend to do
10:05 thomas_ku egonw: thats good...
10:10 egonw thomas_ku: OK, the unit test for the InChI works too
10:51 egonw thomas_ku: around?
10:51 thomas_ku yes
10:52 egonw ok, found a problem...
10:52 egonw was trying deploy with a scp:// url...
10:52 egonw that failed...
10:53 egonw but <repository> instead of <snapshotRepository> might do the trick
10:54 thomas_ku ah if you want to deploy (not a snapshot version) than you have to use the normal repository
10:58 egonw what's the difference?
10:58 egonw (it worked btw)
11:01 egonw I think
11:01 egonw and now I can point Taverna to this local dir?
11:02 thomas_ku yes that is possible within within the plugin conf file of you update site...
11:03 egonw I just realized I should have bumped the version number...
11:04 egonw that's in pom.xml ?
11:04 thomas_ku mom got a call
11:08 thomas_ku the version number is in the pom
11:08 thomas_ku correct
11:14 CIA-16 jmol: hansonr * r8728 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: 11.3.53 NOT READY -- NOT VERSION -- STILL WORKING
11:15 egonw thomas_ku: what's the mvn command I should use?
11:22 CIA-16 cdk: egonw * r9566 /branches/egonw/lpchecker/src/ME​TA-INF/test-reaction.cdkdepends: Added a missing dep
11:24 CIA-16 cdk: egonw * r9567 /branches/egonw/ibondorder/src/org/openscience​/cdk/reaction/type/BreakingBondReaction.java: Fixed a NPE
11:48 * egonw has to go for a while...
11:48 egonw bbl
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12:20 thomas_ku egonw: what should the mvn command do?
12:23 egonw umm... create something I can use to install my local CDK-Taverna in Taverna
12:23 egonw the scp thingy did not work :(
12:24 CIA-16 cdk: egonw * r9568 /branches/egonw/lpchecker/src/org/op​enscience/cdk/test/CDKTestCase.java: Adding explicit hydrogens, requires atom types to be perceived for the new atoms too
12:51 egonw_ joined #cdk
12:56 thomas_ku egon than if you use the same!!! Version number as the last installed version of taverna-cdk (0.4.1.0) plugin
12:56 thomas_ku you can create the jar file with 'mvn package'
12:57 thomas_ku than you can copy this jar file into the .taverna1.6.2\repository\org... folder
12:58 thomas_ku so you would overwrite the "old" version of cdk-taverna with your version...
13:24 egonw_ thomas_ku: ok, good idea
13:40 egonw_ thomas_ku: how do I define a menu?
13:40 egonw_ like the CDK/SMILES menu?
13:41 egonw_ src/main/resources/META-INF/services/​org.openscience.cdk.applications.tave​rna.scuflworkers.cdk.CDKLocalWorker?
13:41 thomas_ku ah like what kind of a menu?
13:41 egonw_ like the SMILES menu
13:42 thomas_ku we have a SMILES menu?
13:42 egonw_ like the local worker SMILESParser
13:43 egonw_ Available Processors ->
13:43 egonw_ Local Services ->
13:43 egonw_ "CDK - Chemistry Development Kit" ->
13:43 thomas_ku Ah
13:43 egonw_ Basics
13:43 egonw_ SmilesTools
13:43 thomas_ku you want to have a folder like the one for smiles
13:43 thomas_ku correct
13:44 thomas_ku ?
13:44 egonw_ yeah, InChITools
13:44 thomas_ku thats really easy!
13:44 egonw_ ah, found it, I think
13:44 egonw_ cdk.properties?
13:45 thomas_ku correct
13:45 thomas_ku the structure there is:
13:45 * egonw_ issues 'mvn package'
13:45 thomas_ku package name.classname = FolerName:Name of worker
13:46 egonw_ right
13:46 egonw_ that was easy
13:54 egonw_ java.lang.ClassNotFoundException: org.openscience.cdk.applic​ations.taverna.CMLChemFile
13:54 egonw_ at net.sf.taverna.raven.repository.impl​.LocalArtifactClassLoader.findClass(​LocalArtifactClassLoader.java:195)
13:54 egonw_ at net.sf.taverna.raven.repository.impl​.LocalArtifactClassLoader.findClass(​LocalArtifactClassLoader.java:154)
13:54 egonw_ :(
13:54 egonw_ coffee time
13:55 thomas_ku is it possible that you changed the cdk-version within the pom file?
13:55 thomas_ku and that Taverna did not has this version of the cdk within its repository?
13:57 CIA-16 bioclipse: carl_masak * r4383 /branches/bioclipse2/core/plugins/net.bioclipse.u​i/src/net/bioclipse/ui/views/JsConsoleView.java:
13:57 CIA-16 bioclipse: [JsConsoleView.java]
13:57 CIA-16 bioclipse: * modified R support
14:06 CIA-16 bioclipse: carl_masak * r4384 /branches/bioclipse2/core/plugins/n​et.bioclipse.core/src/net/bioclipse​/core/scripting/JsEnvironment.java:
14:06 CIA-16 bioclipse: [JsEnvironment.java]
14:06 CIA-16 bioclipse: * removed old R{} support
14:18 egonw_ thomas_ku: yes
14:19 egonw_ but changed it back
14:19 egonw_ now checking if I forgot to change something back
14:20 egonw_ nothing found with grep... :(
14:29 thomas_ku thats strange
14:29 CIA-16 bioclipse: jonalv * r4385 /branches/bioclipse2/core/plugins/ (net.bioclipse.core.spring/ net.bioclipse.core.spring.osgi/): Deleted Spring plug-ins. These will be as an addition to target.platform instead
14:29 egonw_ thomas_ku: rerunning mvn package now... after I did mvn clean
14:29 thomas_ku try a 'mvn clean package'
14:30 thomas_ku that deletes everything before it recompiles it again!
14:30 thomas_ku have to go offline for an hour or so...
14:30 thomas_ku bbl
14:36 CIA-16 bioclipse: jonalv * r4386 /branches/bioclipse2/net.b​ioclipse.target.platform/: Initial import.
14:40 CIA-16 bioclipse: jonalv * r4387 /branches/bioclipse2/net.b​ioclipse.target.platform/ (151 files in 36 dirs): target platform including Spring and Spring OSGI stuff
14:49 CIA-16 bioclipse: carl_masak * r4388 /branches/bioclipse2/core/plugins/n​et.bioclipse.ui/src/net/bioclipse/u​i/views/ScriptingConsoleView.java:
14:49 CIA-16 bioclipse: [ScriptingConsoleView.java]
14:49 CIA-16 bioclipse: * new method recieveOutputEvent(String) to receive async output to console
15:01 CIA-16 bioclipse: carl_masak * r4389 /branches/bioclipse2/core/plugins/n​et.bioclipse.ui/src/net/bioclipse/u​i/views/ScriptingConsoleView.java:
15:01 CIA-16 bioclipse: [ScripringConsoleView.java]
15:01 CIA-16 bioclipse: * better change the method name to 'receive' before anyone starts calling it
15:21 CIA-16 bioclipse: Updatebjarni * r4390 /branches/bioclipse2/core/plugins/net​.bioclipse.core/META-INF/MANIFEST.MF: No dependency on r anymore.
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15:36 CIA-16 cdk: egonw * r9569 /branches/egonw/lpchecker/src/org/openscience/cdk/ (46 files in 31 dirs): Synched with trunk version 9568
15:54 egonw_ Developers : 53
16:10 steinbeck_ left #cdk
16:10 carsten joined #cdk
16:12 egonw_ hi carsten
16:12 egonw_ still in france?
16:12 egonw_ or back home?
16:12 carsten home
16:12 carsten was there for just 2 days
16:14 CIA-16 jmol: hansonr * r8729 /trunk/Jmol/src/org/jmol/modelset/Model.java: for Ola
16:23 CIA-16 bioclipse: ospjuth * r4391 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.jmol/ (META-INF/MANIFEST.MF jars/Jmol.jar): Updated to Jmol.jar as of 20071204 with getChains() support.
16:55 carsten jpansanel: here?
16:56 carsten egonw_: my mail was about density in bodr
16:56 egonw_ still haven't seen that email
17:22 CIA-16 bioclipse: jonalv * r4392 /branches/bioclipse2/core/plugins/net.​bioclipse.core/src/net/bioclipse/core/ (Activator.java business/): REmoved old junk which I was responsible for
17:24 CIA-16 cdk: egonw * r9570 /branches/drzz/: Added a place for Dan's branch
17:24 CIA-16 bioclipse: jonalv * r4393 /branches/bioclipse2/core/plugins/net​.bioclipse.core/META-INF/MANIFEST.MF: removed unnecessary dependency
17:24 CIA-16 cdk: egonw * r9571 /branches/drzz/cdk/: Created a branch for Dan (drzz).
17:26 CIA-16 bioclipse: jonalv * r4394 /branches/bioclipse2/core/plugins/ne​t.bioclipse.ui/META-INF/MANIFEST.MF: removed a strange Spring dependency
17:30 CIA-16 cdk: egonw * r9572 /branches/drzz/cdk/.project: Customized project name for branch
17:32 CIA-16 bioclipse: jonalv * r4395 /branches/bioclipse2/core/plugins/n​et.bioclipse.ui/bioclipse.product: removed spring plugin from product and added -consolelog as a standard for bioclipse 2. (I got tiered of having to write it all the time, remove it again if you feel that you must...)
18:00 CIA-16 bioclipse: jonalv * r4396 /branches/bioclipse2/net.bioclipse.ta​rget.platform/target-platform.target: changed evil spelling errors
18:04 CIA-16 cdk: miguelrojasch * r9573 /branches/miguelrojasch/mf​/src/org/openscience/cdk/ (8 files in 2 dirs): Some update which some cases was incorrect.
18:06 CIA-16 cdk: miguelrojasch * r9574 /trunk/cdk/src/org/openscience/cdk/t​est/debug/DebugChemObjectTest.java: Error to compile
18:25 carsten joined #cdk
19:00 CIA-16 jmol: nicove * r8730 /trunk/Jmol-FAH/projects/ (p4113.xyz.gz p4116.xyz.gz p4117.xyz.gz): Folding@Home
19:13 CIA-16 cdk: drzz * r9575 /branches/drzz/cdk/ (4 files in 3 dirs): updated Jumbo to 5.4.1
21:16 jbrefort joined #cdk
21:52 CIA-16 jmol: hansonr * r8731 /trunk/Jmol-datafiles/tests/scr​ipts/check/monster_script.spt:
22:46 CIA-16 jmol: hansonr * r8733 /trunk/Jmol/src/org/opensc​ience/jmol/app/Jmol.java: typo
22:57 CIA-16 jmol: hansonr * r8734 /trunk/Jmol/src/org/jmol/ (shape/MeasuresRenderer.java viewer/Jmol.properties):
22:57 CIA-16 jmol: version=11.3.53 VERSION
22:57 CIA-16 jmol: # bug fix: set measures 0.1 --- solid line does not move.

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