Camelia, the Perl 6 bug

IRC log for #cdk, 2008-01-21

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All times shown according to UTC.

Time Nick Message
00:46 CIA-18 jmol: hansonr * r8922 /trunk/Jmol/src/org/jmol/ (8 files in 3 dirs): (log message trimmed)
00:46 CIA-18 jmol: version=11.5.3_dev
00:46 CIA-18 jmol: # bug fix: color hbonds translucent
00:46 CIA-18 jmol: # bug fix: state: calculate hbonds not saved
00:46 CIA-18 jmol: # bug fix: state: calculate surfaceDistance WITHIN (({....}))
00:46 CIA-18 jmol: # missing outermost parentheses
00:47 CIA-18 jmol: # bug fix: state: selection state "end function" missing semicolon
00:58 CIA-18 jmol: hansonr * r8923 /branches/v11_4/Jmol/src/org/jmol/ (8 files in 3 dirs): (log message trimmed)
00:58 CIA-18 jmol: version=11.4.0_RC2
00:58 CIA-18 jmol: # bug fix: color hbonds translucent
00:58 CIA-18 jmol: # bug fix: state: calculate hbonds not saved
00:58 CIA-18 jmol: # bug fix: state: calculate surfaceDistance WITHIN (({....}))
00:58 CIA-18 jmol: # missing outermost parentheses
00:58 CIA-18 jmol: # bug fix: state: selection state "end function" missing semicolon
01:38 CIA-18 jmol: hansonr * r8924 /trunk/Jmol/src/org/jmol/ (4 files in 3 dirs): 11.5.3_dev # bug fix: color isosurface when isosurface is an lcaoCartoon only colors one lobe
01:44 CIA-18 jmol: hansonr * r8925 /branches/v11_4/Jmol/src/org/jmol/ (4 files in 3 dirs): 11.4.RC2_dev # bug fix: color isosurface when isosurface is an lcaoCartoon only colors one lobe
01:53 CIA-18 jmol: hansonr * r8926 /branches/v11_4/Jmol/src/org/​jmol/viewer/Jmol.properties: (log message trimmed)
01:53 CIA-18 jmol: 11.4.RC2 VERSION
01:53 CIA-18 jmol: # bug fix: color hbonds translucent
01:53 CIA-18 jmol: # bug fix: state: calculate hbonds not saved
01:53 CIA-18 jmol: # bug fix: state: calculate surfaceDistance WITHIN (({....}))
01:53 CIA-18 jmol: # missing outermost parentheses
01:53 CIA-18 jmol: # bug fix: state: selection state "end function" missing semicolon
01:53 CIA-18 jmol: hansonr * r8927 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: (log message trimmed)
01:53 CIA-18 jmol: 11.5.3 VERSION
01:53 CIA-18 jmol: # bug fix: color hbonds translucent
01:53 CIA-18 jmol: # bug fix: state: calculate hbonds not saved
01:53 CIA-18 jmol: # bug fix: state: calculate surfaceDistance WITHIN (({....}))
01:53 CIA-18 jmol: # missing outermost parentheses
01:54 CIA-18 jmol: # bug fix: state: selection state "end function" missing semicolon
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08:09 _thomas_k moin
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09:17 steinbeck moin
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09:30 kai_h hi all
09:31 kai_h someone here to help me with a cdk-related question?
09:32 kai_h steinbeck, rojasm?
09:35 steinbeck Hi Kai
09:35 steinbeck nice to see you here
09:37 kai_h hi christoph
09:38 kai_h still involved with the CDK? ;)
09:41 steinbeck Hope so. :-)
09:41 steinbeck Are you really in Braunschweig?
09:42 kai_h yes, I sit next to Susanna and try to get the Gibbspredictor fixed
09:42 steinbeck did you recognized that I moved to EBI?
09:42 kai_h oops, no
09:42 steinbeck cool
09:42 kai_h right, do you work with Asad? :)
09:43 steinbeck for him :-)
09:43 steinbeck no, not really
09:43 steinbeck Dr. Christoph Steinbeck
09:43 steinbeck Team Leader Chemoinformatics and Metabolism
09:43 steinbeck European Bioinformatics Institute (EBI)
09:43 steinbeck Wellcome Trust Genome Campus
09:43 steinbeck Hinxton, Cambridge CB10 1SD UK
09:43 steinbeck Phone: +44 1223 49 2640
09:43 steinbeck Email: steinbeck@ebi.ac.uk
09:43 steinbeck Web: http://www.ebi.ac.uk/steinbeck
09:43 steinbeck I have to go
09:43 kai_h Sounds great
09:43 steinbeck It is :-)
09:43 steinbeck What is your current email address?
09:44 kai_h Kai.Hartmann at gmx.de
09:44 kai_h that's my private one ...
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11:44 CIA-18 bioclipse: ospjuth * r4732 /branches/bioclipse2/bioinformatic​s/plugins/net.bioclipse.jalview/: Initial import.
11:47 CIA-18 bioclipse: ospjuth * r4733 /branches/bioclipse2/bioinformati​cs/plugins/net.bioclipse.jalview/ (33 files in 9 dirs): Initial import. This plugin is for visualizing and editing multiple sequence alignments by wrapping Jalview (http://www.jalview.org).
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13:26 CIA-18 bioclipse: ospjuth * r4734 /branches/bioclipse2/bioinformati​cs/plugins/net.bioclipse.jalview/ (4 files in 3 dirs): Cleaned up code, icon, and set editor name set to filename.
13:29 CIA-18 bioclipse: jonalv * r4735 /trunk/playground/plugins/net.biocli​pse.expression/META-INF/MANIFEST.MF: new version number on expression
13:46 sus joined #CDK
13:46 kai_h hi all
13:46 kai_h second try: someone here to help me with a cdk-related question?
13:46 kai_h :)
13:47 kai_h ahh, egonw is here ...
13:47 egonw he, kai_h
13:47 egonw did not see you... how are you?
13:47 kai_h fine, how are you?
13:47 egonw ha, you just arrived :)
13:47 egonw good
13:47 egonw very happy in my current position
13:47 egonw metabolomics
13:48 kai_h right ... chatted with steinbeck earlier on
13:48 kai_h everyone is moving into this direction it seems
13:48 kai_h I am in Braunschweig blocking someone else's pc at the moment
13:49 egonw yeah, that's where the fun is :)
13:49 kai_h do you have time for a quick (*hope*) question?
13:49 egonw ah... visiting Schomburg's group?
13:49 kai_h right
13:49 egonw sure go ahead
13:49 egonw I hope the answer is quick too :)
13:49 kai_h I have a problem with the inchi library within cdk jar on 64 bit systems
13:50 kai_h it seems to be compiled for 32 bit systems only
13:50 kai_h did someone else mention the problem?
13:51 egonw yes
13:51 egonw your analysis is correct
13:51 egonw it's 32 bit only
13:51 kai_h any workaround?
13:51 egonw at least the .so
13:51 egonw set up a 32 bit chroot
13:51 kai_h can I provide a 64 bit version?
13:52 kai_h it's for the gibbspredictor, a java program that uses cdk
13:52 egonw provide? sure, most welcome
13:52 egonw I have no idea how to compile a 64 bit .so myself
13:52 kai_h I already tried to compile the jniinchi project, but ran into problems
13:53 kai_h maybe I have to ask there
13:53 kai_h just wanted to make sure my analysis was correct
13:53 kai_h thx
13:54 egonw ping Sam Adams
13:54 egonw and send your compile problems to the mailing list
13:54 kai_h ok
13:54 egonw http://jni-inchi.sourceforge.net/
13:54 kai_h one other thing, I tried to register to the devel mailing list of cdk again, but it doesn't seem to work
13:55 egonw ML at: http://sourceforge.net/mail/?group_id=173262
13:55 kai_h maybe sf doesn't like my gmx address
13:55 egonw oh...
13:55 egonw possibly...
13:55 egonw email me your address, and I will add it manually...
13:55 kai_h but I can fill out the online forms, too
13:56 kai_h ok, I'll do that
13:56 kai_h so, I free this pc
13:56 kai_h thanks a lot
13:56 kai_h and good luck for you in metabolomics
13:56 egonw ok, bye
13:56 egonw join in online some more...
13:57 kai_h yes, will do
13:57 egonw love to hear what you're currently doing
13:57 CIA-18 bioclipse: ospjuth * r4736 /branches/bioclipse2/misc/net​.bioclipse.data.sampledata/: Initial import of plugin to install sample data using a NewProjectWizard.
13:57 kai_h I just gave a talk here ... should have set up an online session :)
13:57 kai_h Cheers
14:36 CIA-18 bioclipse: carl_masak * r4737 /trunk/playground/plugins/net.bioclipse.base2/ (10 files in 6 dirs):
14:36 CIA-18 bioclipse: [net.bioclipse.base2]
14:36 CIA-18 bioclipse: * now connects to database and pulls down things
14:36 CIA-18 bioclipse: * so, no more mocking here
14:36 CIA-18 bioclipse: [net.bioclipse.base2.model]
14:36 CIA-18 bioclipse: * mostly API interaction code to accomplish the above
14:40 CIA-18 bioclipse: carl_masak * r4738 /trunk/playground/plugins/net.bioclipse.base2​/src/net/bioclipse/base2/views/TreeView.java:
14:40 CIA-18 bioclipse: [TreeView.java]
14:40 CIA-18 bioclipse: * whitespace
14:40 CIA-18 bioclipse: * removed unused imports
14:46 CIA-18 bioclipse: ospjuth * r4739 /branches/bioclipse2/misc/ne​t.bioclipse.data.sampledata/ (56 files in 14 dirs): Added wizard and data to be installed. No installation yet.
14:49 egonw oi, things are going really fast...
14:49 egonw cheers Ola!
14:55 CIA-18 bioclipse: ospjuth * r4740 /branches/bioclipse2/misc/net.b​ioclipse.data.sampledata/data/: Updated installable data.
14:59 CIA-18 bioclipse: ospjuth * r4741 /branches/bioclipse2/misc/net.b​ioclipse.data.sampledata/data/ (285 files in 26 dirs): Updated installable data.
15:24 CIA-18 bioclipse: carl_masak * r4742 /trunk/playground/plugins/net.bioclip​se.expression.tests/src/net/bioclipse​/expression/tests/FunctionsTest.java:
15:24 CIA-18 bioclipse: [FunctionsTest.java]
15:24 CIA-18 bioclipse: * character '%' now allowed in function names
15:24 CIA-18 bioclipse: * 1 failing test
15:25 rojasm egonw: I sent you a mail. Check it please!
16:03 CIA-18 bioclipse: jonalv * r4743 /trunk/playground/plugins/net.bioclipse.expressi​on/src/net/bioclipse/expression/Calculator.java: % is now a legal character in functions in the expression parser
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19:34 CIA-18 cdk: egonw * r9939 /branches/miguelrojasch/reaction/sr​c/org/openscience/cdk/test/tools/St​ructureResonanceGeneratorTest.java: Added a few basic unit tests, to get a feeling of how it works. Some work, some don't: missing radical atom types one cause. The phenyl ring example seems a genuine fail...
19:51 CIA-18 cdk: egonw * r9940 /branches/miguelrojasch/reaction/src/org/open​science/cdk/atomtype/CDKAtomTypeMatcher.java: Fail on radicals
19:54 CIA-18 cdk: egonw * r9941 /branches/miguelrojasch/reaction/sr​c/org/openscience/cdk/test/tools/St​ructureResonanceGeneratorTest.java: Check atom type perception of structures
20:31 CIA-18 cdk: egonw * r9942 /branches/miguelrojasch/reaction/ (81 files in 30 dirs): Synched with trunk; merged 9869:9941
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