Camelia, the Perl 6 bug

IRC log for #cdk, 2007-12-06

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All times shown according to UTC.

Time Nick Message
04:24 CIA-16 jmol: hansonr * r8740 /trunk/Jmol/src/org/jmol/adapter​/smarter/AtomSetCollection.java:
05:13 CIA-16 jmol: hansonr * r8741 /trunk/Jmol/src/org/jmol/adapter​/smarter/AtomSetCollection.java: 11.3.53 VERSION (finally!)
05:22 CIA-16 jmol: hansonr * r8742 /trunk/Jmol/src/org/jmol/symm​etry/SymmetryOperation.java:
06:29 rojasm joined #cdk
07:23 CIA-16 jmol: hansonr * r8743 /trunk/Jmol/src/org/jmol/jvxl/readers/ (SurfaceGenerator.java VolumeFileReader.java XplorReader.java): preliminary Xplor reader
07:43 masak joined #cdk
08:12 steinbeck joined #cdk
08:13 egonw joined #cdk
08:15 CIA-16 jmol: hansonr * r8744 /trunk/Jmol/src/org/jmol/jvxl/readers/ (VolumeFileReader.java XplorReader.java):
08:20 egonw moin
08:34 CIA-16 bioclipse: ospjuth * r4400 /trunk/plugins/net.bioclipse.compute/ (icons/icon_wand.gif plugin.xml): New icon for compute wizard
08:53 CIA-16 bioclipse: ospjuth * r4401 /trunk/features/net.bioclipse.​spectrum-feature/feature.xml: Added bibtex to spectrum feature
09:08 jonalv joined #cdk
09:12 CIA-16 bioclipse: ospjuth * r4402 /trunk/bioclipsUpdateSite/site.xml: Updated update-site
09:12 CIA-16 bioclipse: ospjuth * r4403 /trunk/plugins/net.bioclipse/s​rc/net/bioclipse/preferences/ (3 files): Updated preference pages to select first line and updated Text size in dialogs
09:16 CIA-16 bioclipse: ospjuth * r4404 /trunk/ (33 files in 33 dirs): Update for release 1.1.6: Version, provider, dependencies, removed unused views, updated icons
09:20 CIA-16 bioclipse: ospjuth * r4405 /trunk/plugins/net.bioclip​se.biojava.ui/plugin.xml: Removed unused view
09:21 CIA-16 bioclipse: ospjuth * r4406 /trunk/plugins/net.bioclipse.biojava.ui/ (META-INF/MANIFEST.MF plugin.xml): Removed duplicate progress view and updated version
09:22 CIA-16 bioclipse: ospjuth * r4407 /trunk/plugins/net.bioclipse.chart/ (icons/chart.jpg plugin.xml): New icon and name for chart view
09:23 CIA-16 bioclipse: ospjuth * r4408 /trunk/features/ (4 files in 4 dirs): Updated version and set features to depend on 1.1.6
09:24 CIA-16 bioclipse: ospjuth * r4409 /trunk/plugins/net.bioclipse.​cdk.ui/META-INF/MANIFEST.MF: Set version to 1.1.6
09:33 CIA-16 bioclipse: ospjuth * r4410 /trunk/plugins/net.bioclipse/ (about.mappings plugin.properties): Updated plugin version and main contributors in about text
09:41 jpansanel moin
09:42 CIA-16 blueobelisk: pansanel * r222 /structures/trunk/src/ (8 files in 8 dirs): Fix xml issues
09:43 CIA-16 blueobelisk: pansanel * r223 /structures/trunk/xml/index.dtd: Add abbrev tag
09:44 CIA-16 blueobelisk: pansanel * r224 /structures/trunk/tools/ (7 files):
09:44 CIA-16 blueobelisk: Fix building issues
09:44 CIA-16 blueobelisk: Add doc to Python modules
09:50 CIA-16 bioclipse: ospjuth * r4411 /trunk/plugins/net.bioclipse/build.properties: Updated build for 1.1.6
09:58 CIA-16 bioclipse: ospjuth * r4412 /trunk/plugins/de.ipbhalle.msbi.mz​data.editor/META-INF/MANIFEST.MF: Removed org.eclipse.ui.editor as it depends on IDE. Don't know how many times I've done this, people keep adding it all the time...
09:59 CIA-16 bioclipse: ospjuth * r4413 /trunk/features/net.bioclipse.​spectrum-feature/feature.xml: Updated feature to not require ui.editor
10:04 jpansanel egonw : RDFa is only valid with XHTML1.1
10:05 jpansanel if I want to use semantic with structures, I need to use microformat
10:05 jpansanel (I'm using XHTML1.0 Strict)
10:12 adw good morning
10:12 steinbeck moin
10:23 egonw hi adw
10:23 CIA-16 bioclipse: biocoder * r4414 /trunk/plugins/net.bioclipse.statistics/src/​net/bioclipse/editors/MatrixGridEditor.java: Removed debug output
10:23 egonw jpansanel: ack
10:23 egonw jpansanel: why not use XHTML 1.1 then?
10:24 jpansanel some browser doesn't support XHTML1.1
10:24 jpansanel (IE series for example)
10:24 egonw ok
10:27 jpansanel I'll use your suggestions
10:27 jpansanel (span class="inchi" and class="smiles")
10:27 egonw ok, good
10:28 jpansanel do you know if some website is already using microformat for chemistry ?
10:31 jbrefort joined #cdk
10:46 CIA-16 bioclipse: biocoder * r4415 /trunk/plugins/net.bioclipse.chart/src​/net/bioclipse/chart/ChartUtils.java: Fixed a bug causing ClassCastException
10:47 steinbeck left #cdk
11:14 CIA-16 bioclipse: ospjuth * r4416 /trunk/plugins/net.bioclipse.descriptor/src/net​/bioclipse/jobs/DescriptorCalculationJob.java: Fixed a nasty bug that made editor open with unparsed input after close of first qsar_results.csv.
12:28 CIA-16 bioclipse: ospjuth * r4417 /trunk/plugins/ (3 files in 3 dirs): Resized icons to 16x16
13:00 CIA-16 bioclipse: ospjuth * r4419 /trunk/plugins/net.bioclipse.cdk.ui/src​/net/bioclipse/model/CDKResource.java: Removed question "would you like to switch to chemoinfo persp as it is in wrong place. Should be moved from parse to openEditor.
13:17 thomas_ku joined #cdk
13:17 thomas_ku moin
13:28 egonw hi thomas_ku
13:30 CIA-16 blueobelisk: pansanel * r225 /structures/trunk/tools/ (cmlwriter.py formulaindexwriter.py xhtmlwriter.py):
13:30 CIA-16 blueobelisk: formulaindexwriter: fix link and title
13:30 CIA-16 blueobelisk: cmlwriter, xhtmlwriter: switch from RDFa to MicroFormat
13:38 jbrefort joined #cdk
13:53 CIA-16 bioclipse: jonalv * r4420 /branches/bioclipse2/bioinformatics/pl​ugins/net.bioclipse.biojava.business/ (9 files in 4 dirs): Now the spring-osgi bundle can be started from console at least...
14:15 masak joined #cdk
15:05 CIA-16 bioclipse: ospjuth * r4422 /trunk/plugins/net.bioclipse/about.mappings: Updated about text to 1.2.0
15:05 CIA-16 bioclipse: ospjuth * r4423 /trunk/plugins/net.bioclipse.webservices/src​/net/bioclipse/plugins/bc_webservices/wizard​s/wizardpages/EBIWSDbfetchWizardPage.java: Fixed bug that broke download of PDB if uppercase ID in query
15:11 CIA-16 cdk: miguelrojasch * r9578 /branches/miguelrojasch/mf​/src/org/openscience/cdk/ (2 files in 2 dirs): added matrix for 7 elements
15:11 CIA-16 bioclipse: jonalv * r4424 /branches/bioclipse2/core/plugins/net.bioclips​e.core/src/net/bioclipse/core/Activator.java: Added the start() method to the Activator in core which someone removed in some commit just reasonly...
15:16 CIA-16 bioclipse: ospjuth * r4425 /trunk/plugins/net.bioclipse.biojava.ui/src/net/​bioclipse/extensions/PDBSequenceExtractor.java: Replaced sysout with logger.debug
15:21 CIA-16 bioclipse: ospjuth * r4426 /trunk/bioclipsUpdateSite/site.xml: Updated for 1.2.0 features
15:31 CIA-16 bioclipse: ospjuth * r4427 /trunk/plugins/net.bioclipse/bioclipse.product: Updated product for 1.2.0
15:33 CIA-16 bioclipse: ospjuth * r4428 /trunk/features/net.bioclipse.data.d​rugbank-feature/feature.properties: Updated drugbank feature to be named drugbank feature and not BODR
15:46 CIA-16 bioclipse: carl_masak * r4429 /branches/bioclipse2/core/plug​ins/net.bioclipse.scripting/: Initial import.
15:46 CIA-16 bioclipse: carl_masak * r4430 /branches/bioclipse2/core/plu​gins/net.bioclipse.scripting/ (23 files in 8 dirs): Initial import.
15:48 CIA-16 bioclipse: carl_masak * r4431 /branches/bioclipse2/core/plugins​/net.bioclipse.scripting.tests/: Initial import.
15:48 CIA-16 bioclipse: carl_masak * r4432 /branches/bioclipse2/core/plugin​s/net.bioclipse.scripting.tests/ (10 files in 6 dirs): Initial import.
15:49 CIA-16 bioclipse: carl_masak * r4433 /branches/bioclipse2/core/plugins/ (11 files in 9 dirs):
15:49 CIA-16 bioclipse: * moved scripting out of net.bioclipse.core
15:49 CIA-16 bioclipse: * jonalv++
16:01 CIA-16 bioclipse: jonalv * r4434 /branches/bioclipse2/ (4 files in 3 dirs):
16:01 CIA-16 bioclipse: [net.bioclipse.ui]
16:01 CIA-16 bioclipse: Added config.ini which starts the spring osgi bundle
16:01 CIA-16 bioclipse: [net.bioclipse.biojava.business]
16:01 CIA-16 bioclipse: Changed to work with the movement of the scripting parts
16:01 CIA-16 bioclipse: In general the fact that scripting is a separate plugin means that the deadlock occuring when starting bioclipse with spring osgi is no more and things are now working
16:06 rojasm left #cdk
16:15 carsten joined #cdk
17:06 CIA-16 bioclipse: jonalv * r4435 /branches/bioclipse2/core/plugins/ (2 files in 2 dirs): Removed special config.ini from net.bioclipse.ui. The activator in net.bioclipse.core now starts the org.springframework.osgi.bundle.extender bundle if it finds it
18:17 test joined #cdk
18:17 Topic for #cdkis now The Chemistry Development Kit (http://cdk.sf.net) | JUnit: 3597 test, 43 fails + 68 errors (3.09%) | CDK 1.0.x TODO: see http://cdk.sf.net/wiki/ | Logs at http://moritz.faui2k3.org/​irclog/out.pl?channel=cdk
18:17 Topic for #cdkis now The Chemistry Development Kit (http://cdk.sf.net) | JUnit: 3597 test, 43 fails + 68 errors (3.09%) | CDK 1.0.x TODO: see http://cdk.sf.net/wiki/ | Logs at http://moritz.faui2k3.org/​irclog/out.pl?channel=cdk
19:06 edrin joined #cdk
19:27 CIA-31 joined #cdk
20:06 jbrefort joined #cdk
20:17 CIA-31 jmol: nicove * r8745 /trunk/Jmol/src/org/jmol/translation/ (22 files in 2 dirs): Update of .po files
20:23 CIA-31 jmol: nicove * r8746 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version

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