Camelia, the Perl 6 bug

IRC log for #cdk, 2008-03-04

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All times shown according to UTC.

Time Nick Message
06:12 jbrefort joined #cdk
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08:40 egonw moin
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09:19 egonw rojasm: ping
09:22 rojasm hi egonw
09:22 egonw I uploaded a patch to trunk to see if a tested atom type is defined in the cdk_atomtypes.xml
09:22 egonw what was the other thing I would do again?
09:23 rojasm the isomorphism between aromatic rings
09:23 egonw oh... right
09:23 egonw thanx :)
09:24 egonw rojasm: http://www.chemspider.com/blog/how-many-structure​s-can-you-generate-from-a-molecular-formula.html
09:24 egonw maybe you like to add a comment to that thread?
09:26 rojasm interessant
09:27 egonw ja, vond ik ook :)
09:48 egonw man-di: ping... did you upload libcdk-java 1.0.2 to NEW, or are you waiting for me to apply that patch upstream?
09:52 CIA-18 bioclipse: carl_masak * r4951 /branches/bioclipse2/core/plugins/n​et.bioclipse.scripting/src/net/bioc​lipse/scripting/JsEnvironment.java:
09:52 CIA-18 bioclipse: [JsEnvironment.java]
09:52 CIA-18 bioclipse: * method returns immediately if Eclipse
09:52 CIA-18 bioclipse:  platform not running
09:52 CIA-18 bioclipse: * test no longer fails
09:52 steinbeck joined #cdk
09:54 man-di egonw: uploaded to NEW and ACCEPTED already
09:54 man-di so its in the archive now
09:54 egonw oh, brilliant :)
09:54 egonw I checked last night and this morning
09:54 egonw but could not find it in the queue nor in the archives...
09:54 egonw so, it's just in the middle now, then :)
09:56 egonw_ joined #cdk
09:56 egonw_ temporarily moving to the laptop, so that my desktop can boot into a more recent Linux kernel
09:57 man-di egonw_: you are always checking at the wrong time :-)
09:57 egonw_ yeah, it seems :)
09:58 egonw_ what about hardy?
09:58 egonw_ any chances on that?
09:58 egonw_ or am I pushing too much now :)
10:00 man-di egonw_: file a sync request
10:01 egonw_ where?
10:01 man-di egonw_: but you need a FeatureFreezeException for Ubuntu
10:01 man-di egonw_: launchpad
10:01 egonw_ ok, then I'll aim for hardy+1
10:01 man-di egonw_: there is a defined procedure for sync request
10:02 man-di it will be automcatically in hardy+1 if you do nothing
10:03 egonw_ ok, perfect :)
10:13 steinbeck joined #cdk
10:30 CIA-18 bioclipse: carl_masak * r4952 /branches/bioclipse2/core/plugins/net.bioclip​se.core.tests/net.bioclipse.recording/net/bio​clipse/recording/ScriptGenerationTests.java:
10:30 CIA-18 bioclipse: [ScriptGenerationTests.java]
10:30 CIA-18 bioclipse: * corrected test
10:31 CIA-18 bioclipse: carl_masak * r4953 /branches/bioclipse2/core/plugins/n​et.bioclipse.core/src/net/bioclipse​/recording/JsScriptGenerator.java:
10:31 CIA-18 bioclipse: [JsScriptGenerator.java]
10:31 CIA-18 bioclipse: * implemented tests
10:31 CIA-18 bioclipse: * all tests now pass
11:01 egonw joined #cdk
11:07 CIA-18 cdk: miguelrojasch * r10288 /branches/miguelrojasch/reaction/src/ (5 files in 3 dirs): added new dictionary for reactions
11:37 egonw rojasm: comparing trunk/ with reaction, I see 1 fixed fail, and 7 fixed errors
11:37 egonw cheers!
12:21 masak joined #cdk
12:32 CIA-18 cdk: egonw * r10289 /trunk/cdknews/ (21 files in 3 dirs): Added a upcoming CDK News paper
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13:18 de_maas egonw: Hi Egon, can you give me a hand with the CDKHydrogenAdder?
13:19 de_maas I'm getting "IAtom is not typed! C"
13:20 egonw you first need to run CDKAtomTypeMatcher
13:20 de_maas OK thanks
13:21 egonw should be in the JavaDoc
13:21 egonw if not, it's a bug
13:23 de_maas Yes it is in, I missed that one.
13:31 CIA-18 cdk: miguelrojasch * r10290 /branches/miguelrojasch/reaction/src/main/org/op​enscience/cdk/dict/data/reaction-processes.owl: added the rest of reaction ID into the dictionary
13:44 rojasm egown: what do you mean with
13:44 rojasm comparing trunk/ with reaction, I see 1 fixed fail, and 7 fixed errors
13:44 egonw JUnit results
13:44 rojasm in reaction module?
13:44 rojasm or in general
13:44 egonw no, overall
13:44 egonw right
13:44 rojasm ok
13:44 egonw 7 fixes are actually in the reaction module :)
13:45 egonw you need to sync with trunk/ for that patch I mentioned this morning
13:45 rojasm I am doing now :)
13:49 CIA-18 cdk: miguelrojasch * r10291 /branches/miguelrojasch/reaction/src/ (71 files in 9 dirs): added new engine for ReactionProcess's which takes the parameters from the Dictionary.
13:55 CIA-18 bioclipse: jonalv * r4954 /branches/bioclipse2/core/plugins/net.bioclip​se.core.tests/net.bioclipse.recording/net/bio​clipse/recording/ScriptGenerationTests.java: Fixed error in test (now it fails as it should)
13:56 CIA-18 cdk: miguelrojasch * r10292 /branches/miguelrojasch/reaction/src/ (4 files in 3 dirs): Synchronized with trunk; merged 10272:10291
14:01 de_maas egonw: when reading molecules using MDLreader, would one not expect the atomtypes to be detected already?
14:01 rojasm left #cdk
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14:02 egonw why?
14:02 egonw MDL molfiles do not have atom type information?
14:02 egonw CDK concept include, only do the minimal that can be done
14:03 egonw and let the user aggregate functionality
14:03 * egonw is getting some coffee
14:03 de_maas OK, have a nice cup
14:11 rojasm egonw: in what module are the dictionaries?
14:11 rojasm or should be?
14:19 CIA-18 bioclipse: ospjuth * r4955 /branches/bioclipse2/ (core/plugins/net.bioclipse.core/ plugins/net.bioclipse.core/): Moved in SVN refactoring.
14:20 CIA-18 bioclipse: ospjuth * r4956 /branches/bioclipse2/ (2 files in 2 dirs): Moved in SVN refactoring.
14:20 rojasm found
14:20 CIA-18 bioclipse: ospjuth * r4957 /branches/bioclipse2/ (2 files in 2 dirs): Moved in SVN refactoring.
14:21 CIA-18 bioclipse: ospjuth * r4958 /branches/bioclipse2/ (2 files in 2 dirs): Moved in SVN refactoring.
14:21 CIA-18 bioclipse: ospjuth * r4959 /branches/bioclipse2/ (core/plugins/net.bioclipse.r/ plugins/net.bioclipse.r/):
14:22 CIA-18 bioclipse: ospjuth * r4960 /branches/bioclipse2/ (2 files in 2 dirs): Moved in SVN refactoring.
14:22 CIA-18 bioclipse: ospjuth * r4961 /branches/bioclipse2/ (2 files in 2 dirs): Moved in SVN refactoring.
14:22 CIA-18 bioclipse: ospjuth * r4962 /branches/bioclipse2/ (core/plugins/net.bioclipse.ui/ plugins/net.bioclipse.ui/): Moved in SVN refactoring.
14:22 egonw rojasm: good question
14:22 egonw not sure
14:23 CIA-18 bioclipse: ospjuth * r4963 /branches/bioclipse2/ (2 files in 2 dirs): Moved in SVN refactoring.
14:23 CIA-18 bioclipse: ospjuth * r4964 /branches/bioclipse2/core/: Deleted in SVN refactoring.
14:26 rojasm cdk-extra
14:26 egonw the reaction onto should end up in the reaction module, I'd say
14:28 CIA-18 cdk: miguelrojasch * r10293 /branches/miguelrojasch/reaction/src/main/org/op​enscience/cdk/dict/data/reaction-processes.owl: added empty schemas necessaries for the dictionary.
14:32 CIA-18 bioclipse: egonw * r4965 / (12 files in 12 dirs): Created basic setup
14:36 rojasm egonw: report of reaction module> Tests run: 511, Failures: 1, Errors: 1, Time elapsed: 11.67 se
14:36 egonw right
14:36 egonw I had that too
14:36 rojasm one is the isomorphism and the other one the coverage
14:36 egonw that includes the arom problem..
14:36 egonw right :)
14:37 egonw ok, very good!
14:38 rojasm Using the dictionary is all more clean. e.g. with the parameters!
14:38 egonw yeah, really looks good!
14:38 rojasm I may be this weekend I make for constraints in atomcontainer
14:40 CIA-18 bioclipse: egonw * r4966 /bioclipse2/trunk/ (features/ plugins/): Set up features/ and plugins/, so that I can copy in, well, plugins and features...
14:43 carsten joined #cdk
14:43 rojasm egonw: did you find some solution to be able to distinguish between aromatic ring with double bonds in different positions.
14:44 egonw have not had time to look at that today...
14:44 egonw will do that on the train home
14:44 rojasm not problem!
14:47 CIA-18 bioclipse: egonw * r4967 / (2 files in 2 dirs): Moving into new hierarchy.
14:48 CIA-18 bioclipse: egonw * r4968 / (2 files in 2 dirs): Moving into new hierarchy.
14:48 CIA-18 bioclipse: egonw * r4969 / (2 files in 2 dirs): Moving into new hierarchy.
14:49 CIA-18 bioclipse: egonw * r4970 / (2 files in 2 dirs): Moving into new hierarchy.
14:49 CIA-18 bioclipse: egonw * r4971 / (2 files in 2 dirs): Moving into new hierarchy.
14:50 CIA-18 bioclipse: egonw * r4972 / (2 files in 2 dirs): Moving into new hierarchy.
14:53 CIA-18 bioclipse: egonw * r4973 / (2 files in 2 dirs): Moving into new hierarchy.
14:53 CIA-18 bioclipse: egonw * r4974 / (2 files in 2 dirs): Moving into new hierarchy.
14:54 CIA-18 bioclipse: egonw * r4975 / (2 files in 2 dirs): Moving into new hierarchy.
14:54 CIA-18 bioclipse: egonw * r4976 / (2 files in 2 dirs): Moving into new hierarchy.
14:55 CIA-18 bioclipse: egonw * r4977 / (2 files in 2 dirs): Moving into new hierarchy.
14:56 CIA-18 bioclipse: egonw * r4978 / (2 files in 2 dirs): Moving into new hierarchy.
14:56 CIA-18 bioclipse: egonw * r4979 / (2 files in 2 dirs): Moving into new hierarchy.
14:57 CIA-18 bioclipse: egonw * r4980 / (2 files in 2 dirs): Moving into new hierarchy.
14:58 CIA-18 bioclipse: egonw * r4981 / (2 files in 2 dirs): Moving into new hierarchy.
15:00 CIA-18 cdk: miguelrojasch * r10294 /branches/miguelrojasch/reaction/src/main/org/op​enscience/cdk/dict/data/reaction-processes.owl: complemented the mechanism onto Dictionary
15:00 CIA-18 bioclipse: egonw * r4982 / (2 files in 2 dirs): Moving into new hierarchy.
15:01 CIA-18 bioclipse: egonw * r4983 / (2 files in 2 dirs): Moving into new hierarchy.
15:01 CIA-18 bioclipse: egonw * r4984 / (2 files in 2 dirs): Moving into new hierarchy.
15:02 CIA-18 bioclipse: egonw * r4985 / (2 files in 2 dirs): Moving into new hierarchy.
15:03 CIA-18 bioclipse: egonw * r4986 / (2 files in 2 dirs): Moving into new hierarchy.
15:04 CIA-18 bioclipse: egonw * r4987 / (2 files in 2 dirs): Moving into new hierarchy.
15:05 CIA-18 bioclipse: egonw * r4988 / (2 files in 2 dirs): Moving into new hierarchy.
15:06 CIA-18 bioclipse: egonw * r4989 / (2 files in 2 dirs): Moving into new hierarchy.
15:06 CIA-18 bioclipse: egonw * r4990 / (2 files in 2 dirs): Moving into new hierarchy.
15:08 CIA-18 bioclipse: egonw * r4991 / (2 files in 2 dirs): Moving into new hierarchy.
15:09 CIA-18 bioclipse: egonw * r4992 / (2 files in 2 dirs): Moving into new hierarchy.
15:10 CIA-18 bioclipse: egonw * r4993 /bioclipse2/trunk/ (_playground_/net.bioclipse.pkpd/ plugins/net.bioclipse.pkpd/): Moving into new hierarchy.
15:11 CIA-18 bioclipse: egonw * r4994 / (2 files in 2 dirs): Moving into new hierarchy.
15:12 CIA-18 bioclipse: egonw * r4995 / (2 files in 2 dirs): Moving into new hierarchy.
15:13 CIA-18 bioclipse: egonw * r4996 / (bioclipse2/trunk/pmd/ branches/bioclipse2/pmd/): Moving into new hierarchy.
15:14 CIA-18 bioclipse: egonw * r4997 / (bioclipse2/trunk/pmd.xml branches/bioclipse2/pmd.xml): Moving into new hierarchy.
15:15 CIA-18 bioclipse: egonw * r4998 / (2 files in 2 dirs): Moving into new hierarchy.
15:18 carsten egonw: Do you want some kind of new record?
15:22 CIA-18 bioclipse: egonw * r4999 /branches/bioclipse2/ (bioinformatics/ chemoinformatics/ features/ plugins/): Clean up
15:22 CIA-18 bioclipse: egonw * r5000 / (bioclipse2/trunk/test/ branches/bioclipse2/test/): Moving into new hierarchy.
15:24 CIA-18 bioclipse: egonw * r5001 /branches/bioclipse2/: Last traces
15:24 egonw carsten: :)
15:25 egonw yeah, ola is now going to send me a toffifee :)
15:41 CIA-18 bioclipse: jonalv * r5002 /bioclipse2/trunk/test/: removed "test"
15:55 dleidert egonw: ping
15:55 egonw dleidert: pong
15:56 dleidert Short and dumb question: cdk also depends on common-cli (and several other) that are under an Apache license, which is not compatible to the GPL (and I guess this means LGPL too) - doesn't this create a license issue?
15:56 dleidert do you know that?
15:57 egonw I think you might be right
15:57 egonw please file a bug report
15:58 CIA-18 bioclipse: shk3 * r5003 /trunk/plugins/net.bioclipse.​nmrshiftdb/speclipse.product: export for all systems
15:58 man-di dleidert: ASL and LGPL together is okay
15:58 dleidert LGPL 2.x?
15:58 man-di yes
15:58 dleidert The FAQ says, that ASL and GPL 3 are compatible
15:59 man-di only GPL is the problem
15:59 man-di ASL2 and GPL3 are
15:59 dleidert ah ok, so only Jmol has a problem then
15:59 man-di the other not
15:59 egonw dleidert: which is why Nico sent that email
15:59 dleidert Yes I know (1.1 and 1.0 are generalyly incompatible)
15:59 egonw 1.1 and 1.0 ?
16:00 dleidert I wsa confused by the FAQ - it just tells about the GPL but not if that means GPL *and* LGPL - I mean there is no FAQ for the LGPL
16:00 dleidert egonw: ASL1.1 and 1.0
16:00 egonw ah, ok
16:25 CIA-18 cdk: miguelrojasch * r10295 /branches/miguelrojasch/reaction/src/ (6 files in 4 dirs): added two new reactions for radical site ionization with it is charged
16:52 CIA-18 bioclipse: ospjuth * r5004 /bioclipse2/trunk/_playground_/ (net.bioclipse.template/ net.bioclipse.templateUI/):
16:58 CIA-18 bioclipse: Annzi * r5005 /bioclipse2/trunk/plugins/net.bioclips​e.moss/src/net/bioclipse/moss/wizards/ (5 files): Handling errors and help
17:02 Annzi left #cdk
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17:24 CIA-18 bioclipse: ospjuth * r5006 /bioclipse2/trunk/plugins/net.bioclipse.services/ (5 files in 3 dirs): Added handlers and menus for bogus services in bioinformatics.
17:38 CIA-18 bioclipse: ospjuth * r5007 /bioclipse2/trunk/plugins/net.bioclipse.services/ (META-INF/MANIFEST.MF plugin.xml): Removed decorator and adde dep for core and ui.
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21:57 CIA-18 cdk: egonw * r10296 /trunk/cdk/src/main/org/openscience/cdk/isomor​phism/matchers/QueryAtomContainerCreator.java: Added a convenience method to look for substructures
21:58 CIA-18 cdk: egonw * r10297 /trunk/cdk/src/main/org/openscience/cdk/isomo​rphism/matchers/OrderQueryBondOrderOnly.java: Added Bond matcher that does not care about aromaticity, but focuses on the bond order only
21:58 CIA-18 cdk: egonw * r10298 /trunk/cdk/src/test/org/openscience/cdk/isomorph​ism/matchers/QueryAtomContainerCreatorTest.java: Added a missing test class
22:00 CIA-18 cdk: egonw * r10299 /trunk/cdk/ (30 files in 4 dirs): Set up a new module to get this code well tested
22:01 CIA-18 cdk: egonw * r10300 /trunk/cdk/ (6 files in 4 dirs): Set up a test module for 'isomorphism'
22:15 man-di dleidert: I have problems with spnsoring you...dget: curl cvsweb_3.0.6-3.dsc http://debian.wgdd.de/debian/inco​ming/packages/cvsweb_3.0.6-3.dsc failed
22:15 dleidert oh, Michael uploaded all of them yesterday
22:16 dleidert But you could be so kind to sponsor http://debian.wgdd.de/debian/incoming/p​ackages/debichem/openbabel_2.1.1-4.dsc
22:16 man-di GRRRRR, thanks for telling
22:17 man-di dleidert: Please, never ask multiple people to sponsor you.
22:18 dleidert I told you that Michael is normally sponsoring me, but that he was too busy. Yesterday he found the time to upload them.
22:18 dleidert I'm sorry that I forgot the mail to tell you.
22:20 man-di dleidert: I read that you ask me because he has no time, not that maybe has time to do it..
22:22 dleidert then I'm sorry for the misunderstanding .. we are almost daily in the same IRC channlel and yesterday he made an upload session and I reminded him to upload my packages, which he did ... I'm sorry then
22:22 man-di no problem
22:23 man-di dleidert: but please keep that in mind to not cause duplicated work
22:23 dleidert of course
22:24 dleidert I'm DM for some time now, so with every upload I get the permission to upload the package myself in the future ... unfortunately Michaels sbuild used dpkg 1.14.15, which stripped the field from the .dsc files :(
23:24 CIA-18 bioclipse: Annzi * r5008 /bioclipse2/trunk/plugins/net.bioclipse.moss/ (6 files in 2 dirs): Added help buttons

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