Camelia, the Perl 6 bug

IRC log for #cdk, 2008-03-10

| Channels | #cdk index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
02:23 CIA-18 bioclipse: rklancer * r5061 /bioclipse2/trunk/ (27 files in 21 dirs): Logging fixup: fixed manifests to strictly use import-package to get logging packages; removed redundant export of logging packages; removed redundant logging jars
02:24 CIA-18 bioclipse: rklancer * r5062 /bioclipse2/trunk/net.bioclipse​.target.platform/required-libs/ (8 files): logging fixup: updating to SLF4J version 1.5.0
02:31 CIA-18 bioclipse: rklancer * r5063 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (3 files in 2 dirs): logging fixup: changes needed to configure logging on startup
03:07 CIA-18 bioclipse: rklancer * r5064 /bioclipse2/trunk/net.bioclipse.targ​et.platform/target-platform.target: general/logging fixup: fixed target-platform.target to specify exactly which plugins can contribute to Bioclipse. See http://wiki.bioclipse.net/ind​ex.php?title=Target_Platform
03:11 CIA-18 bioclipse: rklancer * r5065 /bioclipse2/trunk/plugins/net.b​ioclipse.ui/bioclipse.product: logging fixup: Made product configuration list of plugins conform to fixed-up list of plugins in the target platform. Linked SLF4J's commons-logging implementation to Log4J.
04:37 Conrad joined #cdk
06:16 jbrefort joined #cdk
07:04 rojasm joined #cdk
07:12 rojasm moin
08:20 egonw joined #cdk
08:21 egonw moin
08:32 rojas1 joined #cdk
08:45 thomas_ku moin
08:51 jonalv joined #cdk
09:15 CIA-18 bioclipse: miguelrojasch * r5066 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): update from CDK the MFAnalyser to MolecularFormulaManipulator to extract the elemental composition. MFAnalyser does't exist anymore.
09:18 CIA-18 bioclipse: ospjuth * r5067 /bioclipse2/trunk/plugins/net.bioclipse​.biojava.ui/src/net/bioclipse/biojava/u​i/views/SequenceContentProvider.java: Working on viewer updates when resources changes.
09:24 masak joined #cdk
09:31 CIA-18 bioclipse: ospjuth * r5068 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: cdk.business compiles again.
09:38 carsten joined #cdk
09:54 rojasm egonw: cdk is able to create cml file from IReactionSet objects right?
10:04 egonw yes, I think so
10:17 carsten egonw: I got a patch for bodr
10:17 carsten well, for the copy in Kalzium
10:17 carsten will check if needed in bodrs elements.xml
10:17 carsten element 118 has an issue
10:18 steinbeck joined #cdk
10:18 egonw ok
10:18 egonw check the BODR 7 and 8 changelog
10:18 egonw some patch has been applied to 188
10:18 egonw 118
10:18 egonw hi steinbeck
10:19 jpansanel moin
10:19 steinbeck moin everybody
10:21 jpansanel egonw : did you asking me something about FOAF ?
10:21 * egonw will visit Heiko Schoof tomorrow at MPI in Cologne who hosts a BioMoby/Metabolomics meeting
10:21 egonw hi jpansanel
10:21 egonw yeah, do you have a FOAF?
10:22 jpansanel no, but I can fill a card
10:22 egonw no worries
10:23 egonw see members page in Blue Obelisk wiki
10:23 egonw steinbeck: please read my blog about putting refs in your FOAF
10:29 rojasm egonw but not to handeln reactionScheme cml?
10:30 egonw no, likely not
10:30 egonw did you already add that to SVN?
10:30 egonw missed that, I guess
10:31 rojasm not!
10:32 rojasm We didn't finish the discussion about other IReactionSet extensions
10:33 egonw ok, let's discuss that over the mailing list?
10:34 rojasm ok
10:48 jpansanel egonw : http://www.pansanel.net/resources/foaf.xml
10:48 egonw please add it to the BO wiki too, if youv'e not done that yet
10:49 jpansanel ok
10:49 jpansanel I'll add it to the BO wiki
11:02 jpansanel egonw : it's interesting: you can sign your FOAF with PGP
11:02 egonw yeah, saw something about that...
11:17 CIA-18 bioclipse: jonalv * r5069 /bioclipse2/trunk/plugins/net.bioclipse.core​/src/net/bioclipse/core/domain/BioList.java: Fixes concurrent modification exception problem which was due to wrong use of iterators and maps
11:32 carsten_ joined #cdk
11:47 jpansanel hi carsten
11:48 carsten moin
11:56 CIA-18 bioclipse: ospjuth * r5070 /bioclipse2/trunk/plugins/ne​t.bioclipse.biojava.ui.test/ (2 files in 2 dirs): Proper setup of tests.
11:58 CIA-18 bioclipse: ospjuth * r5071 /bioclipse2/trunk/plugins/net.bioclipse​.biojava.ui/src/net/bioclipse/biojava/u​i/views/SequenceContentProvider.java: Updates to resources regarding sequences propagate to viewer.
12:02 CIA-18 bioclipse: ospjuth * r5072 /bioclipse2/trunk/plugins/net.bioclipse.services/ (9 files in 6 dirs): Implemented run on services according to command "service.run("clustalw@EBI");
14:45 carsten egonw: pinog
14:45 carsten egonw: you migrated bugs from sourceforge to LaunchPad, right?
14:45 carsten cdk?
14:45 carsten egonw: would you do that again? I am thinking about suggesting that to Avogadro
14:46 tjeerd joined #cdk
15:09 CIA-18 bioclipse: ospjuth * r5073 /bioclipse2/trunk/plugins/net.bioclipse.services/ (20 files in 7 dirs): Added a ServiceView with its own model.
15:11 egonw carsten: no, I did not do that
15:11 egonw for no project at all
15:12 egonw carsten: we use launchpad only for development management
15:13 carsten ah, ok
16:05 dleidert joined #cdk
16:13 dleidert carsten: ping
16:13 carsten mion
16:13 dleidert moin
16:13 dleidert you have access to the bodr svn so you can commit yourself
16:14 dleidert ... if you want
16:14 dleidert :)
16:15 carsten well, review is always good :-)
16:15 carsten dleidert: also svn didn't work for me today
16:15 carsten then I figured out my password on SF was expired
16:15 dleidert yes, they made an password expiration round
16:15 egonw yeah, they found some scary code
16:16 dleidert about the review: there is ono reference for eka-eka-emanation
16:16 dleidert s/ono/no
16:24 carsten dleidert: right, the eka is wrong
16:26 dleidert I think your patch is correct.
16:32 rojasm joined #cdk
16:53 rojasm joined #cdk
17:00 rojasm joined #cdk
17:07 rojasm joined #cdk
17:08 CIA-18 cdk: cniehaus * r27 /trunk/bodr/ (ChangeLog elements/elements.xml elements/nameorigin.txt): fixing nameOrigin of element 118 as discussed with daniel leidert
18:13 CIA-18 bioclipse: ospjuth * r5074 /bioclipse2/trunk/plugins/net.bioclipse.services/ (24 files in 6 dirs): A lot of work on the ServiceView. See wiki page http://wiki.bioclipse.net/index.​php?title=Service_infrastructure for screenshot.
18:13 CIA-18 bioclipse: ospjuth * r5075 /bioclipse2/trunk/plugins/net.bioclipse.core/ (3 files in 2 dirs): Added a convenience class to cache images.
18:14 CIA-18 bioclipse: ospjuth * r5076 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (3 files in 2 dirs): Updated icon and category for Bioclipse Navigator.
18:57 CIA-18 bioclipse: ospjuth * r5077 /bioclipse2/trunk/plugins/net.bioclipse.s​ervices/src/net/bioclipse/services/model/ (ServiceImpl.java ServiceImplementation.java ServiceType.java): New model for ServiceTypes and ServiceImplementations that initializes from Extension Points.
18:58 CIA-18 bioclipse: ospjuth * r5078 /bioclipse2/trunk/plugins/net.biocl​ipse.services/src/net/bioclipse/ser​vices/business/ServiceManager.java: Updated ServiceManager to work on new model objects.
19:44 CIA-18 cdk: dleidert * r28 /trunk/bodr/ (COPYING ChangeLog): * COPYING: Updated copyright. Reformatting to textwidth of 80 characters.
20:33 jbrefort joined #cdk
22:13 CIA-18 joined #cdk
23:09 CIA-18 bioclipse: rklancer * r5079 /bioclipse2/trunk/plugins/net.bioclipse.​ui/src/net/bioclipse/ui/Activator.java: fixed race condition between logging configuration and Spring bundle extender startup
23:19 CIA-18 bioclipse: rklancer * r5080 /bioclipse2/trunk/net.bioclipse.targ​et.platform/target-platform.target: Removed slf4j.simple from target. Having both slf4j.simple and slf4j.log4j12 seemed to confuse PDE too much.
23:33 CIA-18 bioclipse: rklancer * r5081 /bioclipse2/trunk/plugins/net.bioclipse.​ui/src/net/bioclipse/ui/Activator.java: trivial formatting cleanup

| Channels | #cdk index | Today | | Search | Google Search | Plain-Text | summary