Camelia, the Perl 6 bug

IRC log for #cdk, 2008-05-30

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All times shown according to UTC.

Time Nick Message
00:30 CIA-31 jmol: hansonr * r9442 /trunk/Jmol/src/org/jmol/viewer/ (Eval.java Jmol.properties): version=11.5.39_dev # bug fix: select _Xx; select unknown
02:49 CIA-31 jmol: hansonr * r9443 /trunk/Jmol/src/org/jmol/ (4 files in 3 dirs): version=11.5.39_dev
04:22 bag joined #cdk
05:30 jbrefort joined #cdk
06:26 rojasm joined #cdk
06:36 carsten joined #cdk
06:38 egonw joined #cdk
06:40 egonw hi rojasm
06:45 rojasm moin egonw
06:50 rojasm going to the uni. See you in 10 min
06:51 malick joined #cdk
07:17 thomas_ku joined #cdk
07:18 thomas_ku moin
07:21 egonw hi thomas_ku
07:22 thomas_ku egonw: I will try to get a new CDK-Taverna release out today
07:22 egonw oh, great!
07:22 CIA-31 cdk: egonw * r11196 /cdk/branches/cdk-1.0.x/src/org/openscie​nce/cdk/test/AtomContainerSetTest.java: Added unit test for IAtomContainer duplication upon IAtomContainerSet cloning
07:22 egonw mind this ugly bug...
07:22 egonw reported by Aleksey yesterday...
07:22 egonw working on unit tests to see the scope, will then apply his patch to fix the issue
07:23 egonw applies to trunk and 1.0.x/
07:24 thomas_ku thats great it is really weird that nobody recognized it before...
07:28 rojasm joined #cdk
07:28 rojasm moin
07:28 egonw yes, indeed
07:28 rojasm egonw I try now to reproduce the error compiling
07:29 egonw rojasm: ok, thanx!
07:41 CIA-31 cdk: egonw * r11197 /cdk/branches/cdk-1.0.x/src/org/openscie​nce/cdk/test/AtomContainerSetTest.java: Added unit test for IAtomContainerSet multiplier cloning
07:46 CIA-31 cdk: egonw * r11198 /cdk/branches/cdk-1.0.x/src/org/openscie​nce/cdk/test/AtomContainerSetTest.java: Use doubles, otherwise it still fails
07:48 CIA-31 cdk: thomaskuhn * r11199 /cdk-taverna/trunk/src/main/java/org​/openscience/cdk/applications/tavern​a/database/pgchem/DBConnector.java: Add some checks to prevent null pointer exceptions
07:49 CIA-31 cdk: thomaskuhn * r11200 /cdk-taverna/trunk/src/main/resources/META-​INF/services/org.openscience.cdk.applicatio​ns.taverna.scuflworkers.cdk.CDKLocalWorker: Change a wrong package name for two classes
07:50 CIA-31 cdk: thomaskuhn * r11201 /cdk-taverna/trunk/src/test/java/org/open​science/cdk/applications/taverna/database​/pgchem/InsertQSARResultsIntoDBTest.java: Add the header
07:51 CIA-31 cdk: thomaskuhn * r11202 /cdk-taverna/trunk/src/test/java/o​rg/openscience/cdk/applications/ta​verna/qsar/CSVGeneratorTest.java: Change test to use only a subset of the available qsar descriptors. This is used to speed up the unit tests.
07:51 CIA-31 cdk: thomaskuhn * r11203 /cdk-taverna/trunk/src/test/java/or​g/openscience/cdk/applications/tave​rna/qsar/QSARDescriptorTest.java: Change test to use only a subset of the available qsar descriptors. This is used to speed up the unit tests.
07:52 CIA-31 cdk: thomaskuhn * r11204 /cdk-taverna/trunk/src/test/java/or​g/openscience/cdk/applications/tave​rna/qsar/VectorGenerationTest.java: Change test to use only a subset of the available qsar descriptors. This is used to speed up the unit tests.
07:56 jonalv joined #cdk
08:01 CIA-31 cdk: egonw * r11205 /cdk/branches/cdk-1.0.x/src/org/openscie​nce/cdk/test/AtomContainerSetTest.java: Grpmh... now also compiles with just JUnit3
08:01 * egonw is now running all unit tests for cdk 1.0.x with Aleksey's two patches
08:02 egonw bbl
08:07 CIA-31 cdk: thomaskuhn * r11206 /cdk-taverna/trunk/src/main/java/org/op​enscience/cdk/applications/taverna/data​base/pgchem/GetQSARVectorFromDB.java: Changed the code to reduce the database loading and to minimize the memory consumption.
08:07 CIA-31 cdk: thomaskuhn * r11207 /cdk-taverna/trunk/src/test/java/org/ope​nscience/cdk/applications/taverna/databa​se/pgchem/GetQSARVectorFromDBTest.java: Add a unit test for the GetQSARVectorFromDB
08:21 CIA-31 cdk: egonw * r11208 /cdk/branches/cdk-1.0.x/src/org/ope​nscience/cdk/AtomContainerSet.java: Applied Aleksey's patch to fix the cloning problems with IAtomContainerSet
08:56 CIA-31 cdk: egonw * r11209 /cdk/branches/cdk-1.0.x/src/org/openscience/cdk/ (MoleculeSet.java test/MoleculeSetTest.java): Applied Aleksey's patch to the IMoleculeSet too now (the multiplier cloning seemed to work already, so not applied that bit of the patch)
08:56 rojasm egonw; It compiles for me
08:57 thomas_ku_ joined #cdk
08:57 egonw rojasm: ok, than I need to ask Rajarshi why Nightly fails when he is back in his office
08:57 egonw rojasm: thanx for testing
09:33 CIA-31 cdk: egonw * r11210 /cdk/trunk/src/test/org/openscien​ce/cdk/AtomContainerSetTest.java: Added unit test for IAtomContainer duplication upon IAtomContainerSet cloning
09:33 CIA-31 cdk: egonw * r11211 /cdk/trunk/src/test/org/openscien​ce/cdk/AtomContainerSetTest.java: Added unit test for IAtomContainerSet multiplier cloning
09:33 CIA-31 cdk: egonw * r11212 /cdk/trunk/src/ (3 files in 2 dirs): Applied second half of Aleksey' patch to trunk
09:46 CIA-31 cdk: egonw * r11213 /cdk/trunk/build.xml: Fixed dist-large generation: diff does not have any libdepends
11:33 thomas_ku_ rojasm: around?
11:35 thomas_ku_ egonw: around?
11:36 egonw yes
11:37 thomas_ku_ do you have any idea why the ionpot module is missing in the dist large tag?
11:38 egonw forgot to add it, I assume...
11:38 egonw hang on...
11:40 CIA-31 cdk: egonw * r11214 /cdk/trunk/build.xml: Added missing ionpot to dist-large
11:41 CIA-31 cdk: egonw * r11215 /cdk/trunk/src/test/org/opens​cience/cdk/ElementTest.java: Added clone test using the new diff tools
11:41 thomas_ku_ thanks egonw
12:28 thomas_ku_ egonw: around?
12:28 thomas_ku_ can you tell me what your branch of cdk-taverna contains which should go into the new release?
12:30 CIA-31 cdk: thomaskuhn * r11216 /cdk-taverna/trunk/pom.xml: Change to a current cdk version. This is the cdk from trunk r11215
12:31 CIA-31 cdk: thomaskuhn * r11217 /cdk-taverna/trunk/src/main/java/org/openscie​nce/cdk/applications/taverna/database/pgchem/ (GetMoleculesFromDB.java IterativeGetMoleculeFromDB.java): Adapting the current cdk version.
12:31 CIA-31 cdk: thomaskuhn * r11218 /cdk-taverna/trunk/src/main/java/org/op​enscience/cdk/applications/taverna/io/ (4 files): Adapting the current cdk version.
12:32 CIA-31 cdk: thomaskuhn * r11219 /cdk-taverna/trunk/src/main/java/org/openscience/​cdk/applications/taverna/qsar/descriptors/atomic/ (IPAtomic.java IPAtomicHOSE.java IPAtomicLearning.java): Adapting the current cdk version.
12:32 CIA-31 cdk: thomaskuhn * r11220 /cdk-taverna/trunk/src/main/java/org/openscience​/cdk/applications/taverna/qsar/descriptors/bond/ (IPBond.java IPBondLearning.java ResonancePositiveCharge.java): Adapting the current cdk version.
12:32 CIA-31 cdk: thomaskuhn * r11221 /cdk-taverna/trunk/src/main/java/o​rg/openscience/cdk/applications/ta​verna/qsar/descriptors/molecular/ (IPMolecular.java IPMolecularLearning.java): Adapting the current cdk version.
12:32 CIA-31 cdk: thomaskuhn * r11222 /cdk-taverna/trunk/src/main/java/org/opens​cience/cdk/applications/taverna/renderers/ (CreateSVGWith2DStructures.java Draw2DStructure.java):
12:33 CIA-31 cdk: thomaskuhn * r11223 /cdk-taverna/trunk/src/main/resources/ (3 files in 2 dirs):
12:34 CIA-31 cdk: thomaskuhn * r11224 /cdk-taverna/trunk/src/test/java/org/openscie​nce/cdk/applications/taverna/database/pgchem/ (6 files): Add some try catch sections.
12:34 CIA-31 cdk: thomaskuhn * r11225 /cdk-taverna/trunk/src/main/java/org/open​science/cdk/applications/taverna/qsar/des​criptors/bond/MassNumberDifference.java: Adapting the current cdk version.
12:34 CIA-31 cdk: thomaskuhn * r11226 /cdk-taverna/trunk/src/test/java/org/​openscience/cdk/applications/taverna/​jchempaint/JChemPaintEditorTest.java: Add some try catch sections. JCP will not be supported currently.
12:35 CIA-31 cdk: thomaskuhn * r11227 /cdk-taverna/trunk/src/test/java/org/openscience/​cdk/applications/taverna/qsar/descriptors/atomic/ (3 files): Adapting the current cdk version.
12:35 CIA-31 cdk: thomaskuhn * r11228 /cdk-taverna/trunk/src/test/java/org/openscience​/cdk/applications/taverna/qsar/descriptors/bond/ (4 files): Adapting the current cdk version.
12:36 CIA-31 cdk: thomaskuhn * r11229 /cdk-taverna/trunk/src/test/java/o​rg/openscience/cdk/applications/ta​verna/qsar/descriptors/molecular/ (IPMolecularLearningTest.java IPMolecularTest.java):
12:36 CIA-31 cdk: thomaskuhn * r11230 /cdk-taverna/trunk/src/test/java/org/open​science/cdk/applications/taverna/reaction​enumerator/ReactionEnumeratorTest.java:
12:36 CIA-31 cdk: thomaskuhn * r11231 /cdk-taverna/trunk/src/test/java/or​g/openscience/cdk/applications/tave​rna/renderers/SVGCreationTest.java: Adapting the current cdk version.
12:36 CIA-31 cdk: thomaskuhn * r11232 /cdk-taverna/trunk/src/test/resources/data/sdf/ (2 files): Small modification on the data. Remove some mdl mol functions which caused problems.
12:38 egonw thomas_ku_: mom
12:39 egonw thomas_ku_: what's the svn URL?
12:43 thomas_ku_ http://cdk.svn.sourceforge.net/viewvc/cdk​/cdk-taverna/branches/egonw-metabolomics/
12:44 egonw ah, thanx
12:46 egonw ok, checking it out on my laptop, and will then inspect the changes...
12:47 thomas_ku_ ok thanks, as far as I remember did you create some worker for inchi handling...
12:47 egonw yes, but that was already applied to your version earlier, not?
12:48 thomas_ku_ no it is not in trunk currently and there is no release out there with this functionallity
12:49 CIA-31 cdk: thomaskuhn * r11233 /cdk-taverna/trunk/src/test/java/org/ope​nscience/cdk/applications/taverna/qsar/ (CSVGeneratorTest.java VectorGenerationTest.java): Change the name and path of testfiles
12:49 egonw not sure the InChI patch is in the above branch...
12:49 egonw will check
12:49 CIA-31 cdk: thomaskuhn * r11234 /cdk-taverna/trunk/src/test/java/org/open​science/cdk/applications/taverna/reaction​enumerator/ReactionEnumeratorTest.java: Comment out some code which is good to find bugs but which do not test something
12:50 thomas_ku_ yes it is
12:50 thomas_ku_ as far as I can see
12:50 egonw yes, seems so
12:50 egonw commit 9648
12:50 egonw and more
12:50 egonw and that's all, it seems
12:51 jonalv joined #cdk
12:52 thomas_ku_ ok would it be ok if I copy these file directly to trunk without using some svn sophisticate stuff?
12:52 thomas_ku_ or could you ally this as patch?
12:53 thomas_ku_ ally = apply
12:53 egonw copy is fine
12:53 egonw actually...
12:53 egonw just use svn copy
12:53 egonw you have trunk/ and the branch chekced out?
12:53 egonw then do:
12:54 thomas_ku_ yes I have
12:54 egonw svn copy branches/egonw-metabolomics/path/to/Bla.java trunk/path/to/Bla.java
12:54 thomas_ku_ but as separate projects within eclipse
12:54 egonw you'd have to got to the command line...
12:54 egonw shall I do it?
12:54 egonw just the copy
12:54 egonw so that you can clean it up?
12:55 thomas_ku_ yes could you do it please
12:56 egonw ok, but got to pick up son from school first
12:56 egonw will be back in ~25 minutes
12:56 thomas_ku_ no problem
12:57 CIA-31 cdk: egonw * r11235 /cdk/trunk/src/ (2 files in 2 dirs): Added comparison of two doubles
12:58 CIA-31 cdk: egonw * r11236 /cdk/trunk/src/ (3 files in 3 dirs): Added diff for IIsotope
12:58 CIA-31 cdk: egonw * r11237 /cdk/trunk/src/ (5 files in 3 dirs): Added diff for IAtomType
13:00 CIA-31 cdk: thomaskuhn * r11238 /cdk-taverna/trunk/pom.xml: Change the version number to 0.5.0 as this will be the next release
13:33 egonw thomas_ku_: ping
13:40 CIA-31 cdk: egonw * r11239 /cdk-taverna/trunk/src/ (8 files in 4 dirs): Added InChI nodes from branches/egonw-metabolomics
13:51 thomas_ku_ jep
13:52 egonw I've uploaded things...
13:52 egonw but I think only one inchi node is registered now...
13:53 egonw but I think there should be both as .java...
13:53 egonw please verify
13:53 egonw anyway...
13:53 egonw there was also the use of CDKAromaticityDetector...
13:53 egonw but that is something you already use, right?
13:55 thomas_ku_ yes that in use already
13:56 thomas_ku_ I will check this
13:57 CIA-31 jmol: hansonr * r9444 /trunk/Jmol/src/org/jmol/ (3 files in 2 dirs):
13:57 CIA-31 jmol: version=11.5.39_dev evalCallback
13:57 CIA-31 jmol: # new feature: jmolSetCallback("evalCallback", "someFunction")
13:57 CIA-31 jmol: # -- overrides _jmol.noEval
13:57 CIA-31 jmol: # -- canNOT be set using "set evalCallback"
13:57 CIA-31 jmol: # -- was necessary for Protein Explorer javascript callbacks
14:54 rojasm joined #cdk
14:58 CIA-31 cdk: thomaskuhn * r11240 /cdk-taverna/trunk/src/main/java/org/openscience/​cdk/applications/taverna/inchi/InChIParser.java: Adapting the current cdk version.
14:58 CIA-31 cdk: thomaskuhn * r11241 /cdk-taverna/trunk/src/main​/resources/cdk.properties: Adding the inchi generator as worker
14:59 CIA-31 cdk: thomaskuhn * r11242 /cdk-taverna/trunk/src/main/resources/META-​INF/services/org.openscience.cdk.applicatio​ns.taverna.scuflworkers.cdk.CDKLocalWorker: Adding the inchi generator as worker
15:10 thomas_ku_ egonw: arount?
15:11 thomas_ku_ around?
15:12 thomas_ku_ is it possible that the inchi worker will not work under a 64 bit os? the test work perfect on my WinXP 32 bit machine but on the opensuse 64 bit they fail!
15:19 egonw thomas_ku_: correct
15:19 egonw there is only a 32 bit .so for Linux and 32 bit .dll for windows
15:21 thomas_ku_ ok thanks
15:30 CIA-31 cdk: thomaskuhn * r11243 /cdk-taverna/trunk/ChangeLog: update the changelog
15:31 CIA-31 cdk: thomaskuhn * r11244 /cdk-taverna/trunk/pom.xml: remove old unused libraries from the pom file
15:31 CIA-31 cdk: thomaskuhn * r11245 /cdk-taverna/trunk/README: update the readme
15:31 CIA-31 cdk: thomaskuhn * r11246 /cdk-taverna/trunk/ReleaseNotes: update the release notes
15:46 CIA-31 cdk: egonw * r11247 /cdk/trunk/src/ (5 files in 3 dirs): More diff code
19:53 bag joined #cdk
20:08 egonw joined #cdk
20:17 CIA-31 cdk: egonw * r11248 /cdk/trunk/src/META-INF/test-data.cdkdepends: Added missing (new) dependency
20:27 bag hi
20:28 bag anyone familiar with smarts-pattern?
20:37 egonw a bit
20:41 bag hi egonw
20:41 egonw hi bag
20:41 bag i try to create a smarts-pattern for two or three 6-rings
20:41 bag do you know if that is possible?
20:42 egonw think so
20:42 egonw SMILES is a subset of SMARTS
20:42 bag or is the easiest way to use the smile
20:42 egonw assuming you know how those rings are connected
20:42 egonw yes, I'd start with the SMILES one...
20:43 bag ok thank you
20:43 egonw then you can replace specific elements by more general SMARTS queries, like [carbon or nitrogen] etc
20:44 bag i wasn't sure if it is possible to use rX or RX in any combination to specify three connected 6rings
20:44 bag thank you
20:47 egonw bag: I think it is...
20:47 egonw but don't have much SMARTS experience...
20:47 egonw theoretically, it should work...
20:47 egonw if it does not, email cdk-users... Rajarshi will surely be able to tell you
20:50 bag ah ok, thank you

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