Camelia, the Perl 6 bug

IRC log for #cdk, 2007-12-17

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Time Nick Message
02:14 CIA-17 jmol: hansonr * r8795 /trunk/Jmol/src/org/jmol/ (11 files in 5 dirs):
02:14 CIA-17 jmol: version=11.3.59_dev draw DIAMETER fixes
02:14 CIA-17 jmol: # bug fix: draw DIAMETER N not properly functioning for curves or arrows
02:14 CIA-17 jmol: # new feature: draw DIAMETER X.Y allows setting diameter of points, lines, curves, and arrows to Angstroms
02:14 CIA-17 jmol: # bug fix: 11.3.58 can't set bond diameters
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03:54 CIA-17 jmol: hansonr * r8796 /trunk/Jmol/src/org/jmol/ (4 files in 3 dirs): version=11.3.59_dev # bug fix: draw ... nofill mesh properties not processed
03:55 CIA-17 jmol: hansonr * r8797 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: version=11.3.59 CRITICAL VERSION FIX
04:53 CIA-17 jmol: hansonr * r8798 /trunk/Jmol/src/org/jmol/viewer/ (Compiler.java Eval.java Jmol.properties Token.java):
04:53 CIA-17 jmol: version=11.3.59 VERSION
04:53 CIA-17 jmol: # bug fix: load append not saved in state properly
04:53 CIA-17 jmol: # code: trajectory command (never documented) removed
04:56 CIA-17 jmol: hansonr * r8799 /trunk/Jmol/src/org/jmol/viewer/Eval.java:
05:38 CIA-17 jmol: hansonr * r8800 /trunk/Jmol/src/org/jmol/ (3 files in 2 dirs):
06:28 CIA-17 jmol: hansonr * r8801 /trunk/Jmol/src/org/jmol/ (3 files in 2 dirs): toward trajectories in a multimodel context...
06:29 CIA-17 jmol: hansonr * r8802 /trunk/Jmol/src/org/jmol/modelset/ModelSet.java:
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07:48 rojasm Morning
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08:20 CIA-17 jmol: nicove * r8803 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
08:30 egonw joined #cdk
08:31 egonw moin
08:43 rojasm moin egonw
08:43 egonw hi rojasm
08:43 egonw just started reading my email...
08:43 egonw Cologne was fun
08:43 egonw we had a great hotel
08:43 rojasm what was?
08:44 rojasm the name of the hotel?
08:44 egonw park consul
08:44 egonw in muelheim
08:44 egonw which had a good deal for a executive room this weekend...
08:47 rojasm I am also looking some thing for Berlin now. What was the preis that you paid for that? If I can know
08:56 egonw 113 euro
08:56 egonw we found that via some hotel booking website
08:57 rojasm 113 both dopelroom
08:57 rojasm Other question about jcp
08:58 rojasm wenn I try to build the ethylene and then I remove the protons
08:59 rojasm they will appaer agein
08:59 egonw explicit or implicit?
09:01 rojasm first I make them explicit
09:01 egonw no idea
09:01 egonw would have to debug that...
09:01 egonw but not going to do that...
09:02 egonw before starting the new JCP
09:02 rojasm is that he controls has the correct saturation
09:03 rojasm other question I can not change the carbon symbol for X for example?
09:03 egonw right click on it...
09:03 egonw then there should be 'R' somewhere
09:03 egonw which you can give a different label, like 'X'
09:06 rojasm I receive a error when I changed direct in the cml file
09:06 rojasm from C to X
09:10 egonw oi...
09:11 egonw no idea
09:11 egonw file a bug report
09:11 egonw or bring it up on the list...
09:13 rojasm mmm
09:14 rojasm because the idea was to create examples for reactions agein
09:14 rojasm but only with the acitve bonds and atoms taking part in the reaction
09:14 rojasm other question about onthology
09:14 rojasm the important file is *.owl
09:15 rojasm right
09:36 jpansanel moin
09:38 CIA-17 bioclipse: ospjuth * r4501 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.qsar/: Initial import.
09:39 CIA-17 bioclipse: ospjuth * r4502 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.qsar/ (16 files in 7 dirs): Initial import. Plugin that should contain an MPE and Builder for QSAR.
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09:47 _thomas_k moin
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10:35 egonw olas: cdk-1.0.x has 75 failing unit tests...
10:35 egonw of which some 15 in cdk-standard...
10:37 egonw not sure if I want to put this in BC...
10:37 egonw might break more than it fixes...
10:37 egonw please advice on what'd you prefer...
10:38 egonw steinbeck: they're all AllringsFinger timeouts...
10:38 egonw steinbeck: might you run the tests for the standard module too, please...
10:38 egonw to make sure it is not something local...
10:41 olas egonw: what is the implication?
10:41 olas I cannot recommend here
10:41 olas I rely on your decision
10:42 egonw well... it's a stable branch...
10:42 egonw so, it should have improved...
10:42 egonw but 75 failing tests is much more than the around 40 CDK releases had in the past...
10:42 CIA-17 bioclipse: ospjuth * r4503 /branches/bioclipse2/chemoinformatics/ne​t.bioclipse.jmol/src/net/bioclipse/jmol/ (17 files in 6 dirs): Code cleanup, license and javadoc addition where missing
10:42 egonw there is no release manager for the CDK 1.0.x who monitors these things...
10:43 steinbeck egonw: mom
10:45 steinbeck egonw: will have to wait until about 1 pm
10:47 CIA-17 bioclipse: ospjuth * r4505 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.qsar/ (6 files in 4 dirs): Updated javadoc
10:55 CIA-17 bioclipse: biocoder * r4506 /trunk/plugins/net.bioclipse.statistics/src/​net/bioclipse/editors/MatrixGridEditor.java: Fixed plotting of non-continous selections
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12:02 olas egonw: Let me know when you have decided about CDK in BC1
12:02 olas could we not just apply stefans patch to bc1 branch of cdk?
12:02 olas anyway, let me know
12:02 olas I'll be around today
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12:25 egonw olas: no, because the branch has jars...
12:25 egonw so, we'd have to put in new jars...
12:25 egonw but not idea which revision the prev jars were build from...
12:25 egonw anyway, it contains several other bug fixes...
12:25 egonw will await steinbeck recompile and test results...
12:26 egonw maybe those timeouts are something with my system...
12:35 CIA-17 cdk: steinbeck * r9621 /trunk/paper/cdk-taverna/ (6 files): Initial import of article skeleton
12:37 steinbeck _thomas_k: article imported
12:45 CIA-17 bioclipse: biocoder * r4507 /trunk/plugins/net.bioclipse.chart/src/​net/bioclipse/dialogs/ChartDialog.java: Created a check that disables the user from trying to plot columns of different length against each other.
12:51 _thomas_k steinbeck: thanks
12:57 egonw http://blogs.talis.com/nodalities/2007​/12/licensing_open_data_creative_c.php
13:13 steinbeck egonw: I count 52 failures and 12 errors for my cdk-1.0.x test run (test-all)
13:13 steinbeck full report underway by email
13:14 egonw ok, no need
13:14 egonw I know enough...
13:14 egonw what d'you think?
13:14 egonw that's a lot of failures...
13:14 steinbeck yes
13:14 egonw good enough for Bioclipse 1.2.0 ?
13:15 steinbeck :-) dunno what to say here
13:15 egonw same here...
13:15 egonw ola needs an answer :(
13:15 steinbeck this is a bloody awful lot of failures
13:16 steinbeck what's in bioclipse at the moment?
13:16 steinbeck which cdk version?
13:16 egonw cdk 1.0.x
13:16 egonw not sure which version
13:17 egonw not sure if that version has less bugs, but would guess so...
13:17 egonw and no idea where all these bugs come from...
13:17 egonw I think I/someone needs to make a plot revision/bugCount for the cdk-1.0.x/ branch...
13:17 steinbeck "extra", "valency check" and "qsaratomic" ...
13:17 steinbeck which of course does not say much detail
13:17 egonw I'm sure cdk 1.0.0 had fewer bugs...
13:18 egonw but maybe also fewer junit tests...
13:18 steinbeck but one could guess that the important stuff for bioclipse basic functionality should work with 1.0.x
13:18 steinbeck ack
13:18 egonw yeah, one *could* say that :)
13:18 egonw I'm tempted to say that too :)
13:19 steinbeck ok, let's look at the log file of the test and see what fails...
13:19 steinbeck um, where was the test output again?
13:21 egonw reports/
13:26 egonw steinbeck: I will start a long running analysis for the revision/bugCount for the branch
13:26 egonw olas: around?
13:30 olas yes
13:30 CIA-17 bioclipse: ospjuth * r4508 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.qsar/ (7 files in 3 dirs): Updated builders and natures to use qsar.xml.
13:30 egonw olas: I think I second Stefan's suggestion to rip out SD file support...
13:30 olas yes, me too
13:31 olas I already have it working in bc2
13:31 egonw apparently no one knows who wrote the code, nor how it is supposed to work...
13:31 egonw what?
13:31 olas I agree
13:31 egonw what is 'it' ?
13:31 olas sdf file support
13:31 olas to support multiple children
13:31 egonw ok. there we go...
13:31 olas using the CNF
13:31 egonw cached?
13:31 egonw what's CNF?
13:31 olas can't be reused in bc1
13:31 egonw are the entries cached?
13:31 olas Common Navigator Framework
13:32 olas yes
13:32 egonw that is, can I open a 100MB SD file?
13:32 olas hmm, good question
13:32 egonw because that's why one has SD files...
13:32 olas no, donät think that would be wise with the current implementation
13:32 egonw not so much those 3 entry SD files we play with
13:32 olas hmm, ok
13:32 olas It needs some work then in bc2 as well
13:33 olas it is parsed with CDK now
13:33 egonw well, that's independent...
13:33 olas please explain
13:33 egonw sure you need to parse it...
13:33 egonw but that has nothing to do with how you represent it in BC1/2
13:33 egonw anyway...
13:33 egonw let's drop it then...
13:33 olas yes
13:33 olas about the cdk update in bc1?
13:33 egonw and then CDK has the time to work out what to do with those 64-75 failing junit tests...
13:34 egonw or was that for something else?
13:34 olas are you asking me?
13:34 egonw yes
13:34 olas ??
13:34 egonw :)
13:34 olas stefan and you updated cdk
13:34 olas I want it in bioclipse
13:34 egonw the CDK update was for the SD fix, not?
13:34 olas ask stefan
13:34 egonw mom
13:35 olas he filed a bug as he couldnät create new molecules
13:35 olas please test that it works in bioclipse1.2.0
13:35 olas after cdk update
13:35 olas I canät test it as I'm on mac
13:35 olas can't
13:36 olas but as soon as you confirm the bug is fixed I will make RC3 and then release tomorrow
13:36 olas (hopefully)
13:37 egonw olas: no, cdk update is not possible today
13:37 egonw too many junit test fails...
13:37 egonw no idea how much will break with the update
13:37 egonw I won't make that call
13:37 olas ok, then we'll have to postpone 1.2.0 again :-(
13:38 egonw better idea
13:38 olas yes?
13:38 egonw ... he asked hopefully... :)
13:38 olas :-)
13:38 egonw steinbeck: your comment too please...
13:39 egonw what about upon a JCP save call in BC1, to clean up the data model, and if IMoleculeSet remove all empty IAtomContainer...
13:39 egonw or maybe even just put all in one IAtomContainer...
13:39 steinbeck what the heck
13:39 egonw when saving MDL mol file that is...
13:39 egonw does that sound reasonable?
13:39 egonw that does not require a CDK lib update, but solve Stefan's report too
13:40 egonw not sure about the JCP bug report from Uppsala... did not see those details...
13:40 steinbeck what exactly am I supposed to comment on. There is an awful lot of stuff  written above
13:40 egonw the workaround I just suggested:
13:41 egonw [2007-12-17 14:43:39] <egonw> what about upon a JCP save call in BC1, to clean up the data model, and if IMoleculeSet remove all empty IAtomContainer...
13:41 egonw [2007-12-17 14:43:52] <egonw> or maybe even just put all in one IAtomContainer...
13:42 steinbeck is this still regarding SD file support?
13:42 egonw yes...
13:43 steinbeck I agree with you suggestion
13:43 egonw the molecule creation bug, according to Stefan, is that files created with JCP can't be opened afterwards
13:43 olas I am fine with dirty solutions as long as they work as intended
13:43 egonw because a SD files is created... which is broken, and should be removed...
13:43 egonw and that Bioclipse saves a SD file with empty molecules...
13:43 egonw which is due a JCP bug...
13:44 egonw olas: ha.... "as long as they work as intended" ... funny...
13:46 olas :-)
13:58 CIA-17 cdk: egonw * r9622 /trunk/cdk/src/org/openscience/cdk/ (40 files in 20 dirs): Fixed spelling error: configer -> configure
14:05 CIA-17 cdk: egonw * r9623 /trunk/cdk/src/org/openscience/cdk/tools/m​anipulator/AtomContainerManipulator.java: Do not try to configure an IAtom of no IAtomType has been perceived; added JavaDoc to explain the expected behavior
14:09 CIA-17 cdk: egonw * r9624 /trunk/cdk/src/org/openscience/cdk/test/tools/​manipulator/AtomContainerManipulatorTest.java: Added JUnit test: don't throw an exception when no atom type is perceived
14:16 CIA-17 cdk: egonw * r9626 /trunk/cdk/src/org/openscience/cdk/test/tool​s/manipulator/AtomTypeManipulatorTest.java: Added JUnit test: an IllegalArgumentException must be thrown if the given IAtomType was null
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14:41 CIA-17 bioclipse: ospjuth * r4509 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.qsar/ (6 files in 3 dirs): OK, can assign nature via action and builder kicks in when qsar.xml is change. No functionality yet though.
15:04 CIA-17 bioclipse: egonw * r4510 /trunk/plugins/net.bioclipse.cdk.jch​empaint/src/net/bioclipse/plugins/bc​_jchempaint/editors/JCPEditor.java: Use the builder to instantiate new classes: don't imply a certain data model impl
15:11 egonw _thomas_k: thomas... in cdk-taverna -> SMILE -> SMILES
15:11 egonw the 'S' is not for plural
15:12 egonw for stands for 'specification'
15:13 egonw olas: one down
15:17 olas great
15:23 CIA-17 bioclipse: ospjuth * r4512 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.qsar/ (7 files in 4 dirs): Started working on a QSAREditor as an MPE with molecules on first tab, descriptors on second, and XML-serialization on third.
15:26 steinbeck left #cdk
15:28 CIA-17 bioclipse: egonw * r4513 /trunk/plugins/net.bioclipse.cdk.ui/src​/net/bioclipse/model/CDKResource.java: Ensured unique model names (not a SdfResource problem at all) by adding a count
15:29 egonw olas: that'll have to do...
15:29 egonw addresses the two problems
15:29 * egonw is ready to see another RC
15:30 egonw and looking forward to BC2 with a proper resource handling...
15:30 egonw no crap about .mol, .sdf, .whatever all trying to map to CDKResource
15:32 olas yup
15:32 olas I agree
15:33 olas ok, will do RC3 now
15:34 CIA-17 jmol: hansonr * r8804 /trunk/Jmol/src/org/jmol/ (7 files in 2 dirs): (log message trimmed)
15:34 CIA-17 jmol: version=11.3.60_dev load trajectory work
15:34 CIA-17 jmol: # bug fix: load trajectory extended to multifile context
15:34 CIA-17 jmol: # in which case "select 1.3", if file 1 is a trajectory, not only
15:34 CIA-17 jmol: # selects that file, but also sets the trajectory to 1.3.
15:34 CIA-17 jmol: # So a "select" of a trajectory also affects the display.
15:34 CIA-17 jmol: # This makes "select" in a trajectory context similar to "display"
15:40 CIA-17 bioclipse: jonalv * r4514 /branches/bioclipse2/core/plugins/net.bioclipse.u​i/src/net/bioclipse/ui/views/JsConsoleView.java: Added stack trace printing when R is not working (and oh I get a IOException --"File not found" when trying to start R although I can run it from prompt...)
15:49 egonw OK, /me is running one 'ant test-all' on each and every revision made to the CDK 1.0.x branch...
15:49 egonw hope to report the outcome tommorow...
15:50 olas egonw: please test RC3 now from update/dev with a clean RC2
15:50 olas and verify that bugs are resolved
15:50 egonw will do that tonight at home
15:50 olas ok
15:50 egonw please send email to -devel
15:51 olas ok
15:51 olas please email me the outcome either way
15:51 egonw yes, will run some tutorials
15:53 egonw bye all
15:55 olas bye
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21:10 CIA-17 jmol: hansonr * r8808 /trunk/Jmol/appletweb/Jmol.js: web site comment update
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23:07 CIA-17 cdk: dleidert * r6 /trunk/bodr/ (ChangeLog Makefile.am):
23:07 CIA-17 cdk: 2007-12-18 Daniel Leidert <daniel.leidert@wgdd.de>
23:07 CIA-17 cdk:  * Makefile.am (docsdir): Use the docdir variable.
23:36 CIA-17 jmol: hansonr * r8809 /trunk/Jmol/src/org/jmol/ (5 files in 2 dirs): version=11.3.60 # bug fix: more work on trajectories in a multimodel context

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