Camelia, the Perl 6 bug

IRC log for #cdk, 2008-08-08

| Channels | #cdk index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
05:07 masak joined #cdk
05:11 jbrefort joined #cdk
06:42 malick joined #cdk
07:25 thomas_ku joined #cdk
07:25 thomas_ku moin
07:25 zarah hi thomas_ku
07:42 egonw joined #cdk
08:05 jonalv joined #cdk
08:10 CIA-34 cdk: ospjuth * r11963 /cdk/trunk/META-INF/MANIFEST.MF: Updated Eclipse plugin versioning to 1.1.0.A20080808. A stands for Alpha.
08:15 zarah joined #cdk
08:30 zarah joined #cdk
08:32 shk3 joined #cdk
08:33 zarah joined #cdk
08:37 egonw shk3: ping
08:37 egonw shk3: not sure if you are still working on the builder3d
08:37 egonw but there are new failing tests...
08:37 egonw the used fingerprints are really sensitive to aromaticity detection, it seems...
08:38 egonw which is really bad...
08:38 egonw which makes the fingerprints change all the time, I think
08:39 CIA-34 cdk: ospjuth * r11964 /cdk/trunk/build.properties: Removed src/data from eclipse binary build.
08:41 shk3 hm, didn't look at it after spending half a day on it.
08:41 shk3 but i will try again
08:44 zarah joined #cdk
08:53 shk3 egonw: I found the smiles generator has 10 failing bugs in trunk, whereas in cdk10, all tests work
08:53 shk3 :-(
08:54 egonw shk3: I count 6
08:54 egonw less actually
08:55 egonw I count 2 failing unit test for the SmilesGenerator
08:55 egonw one which has to do with canonical numbers, I think
08:55 egonw one atom typing problem
08:56 egonw shk3: what other 8 do you see?
08:56 shk3 mom
08:56 shk3 just did it yesterday
08:57 shk3 everything from testAlaSmiles to testTest failes for me
08:57 shk3 in the order they show up in eclipse
09:01 egonw check Nightly
09:14 shk3 looks like file reading is a problem
09:14 shk3 does this no longer work in eclipse?
09:14 shk3 it used to, didn't it?
09:15 egonw did you update your build path?
09:15 egonw I moved the src/data into src/test/data
09:15 egonw as discussed on cdk-devel
09:30 shk3 hm, i updated. might be a problem with local setup. will not care right now.
09:55 carsten joined #cdk
10:00 shk3 is there a way to find out which methods lack unit tests?
10:00 shk3 looking at e. g. http://cheminfo.informatics.indiana.edu/~rguha/​code/java/nightly/test/result-fingerprint.html
10:00 zarah shk3's link is also http://tinyurl.com/58lcg8
10:00 shk3 it just tells me how many are missing
10:04 shk3 ah sorry, it's just on top of that...
10:04 shk3 should have read the whole file really
11:01 egonw_ joined #cdk
11:27 jpansanel moin
11:27 zarah hi jpansanel
11:47 malick left #cdk
11:52 zarah joined #cdk
13:13 egonw shk3: any plans for a mass spectroscopy version of the NMRShiftDB software?
13:14 shk3 just thinking about htis
13:14 shk3 christoph intends to apply for funding for this
13:14 shk3 btw: something a planned for nmrshiftdb for a while and should do is
13:14 shk3 to use cml/jumbo as internal data during the submit
13:15 shk3 this should make saving easier and avoid troubles like you had
13:15 shk3 it would also enable web service input to be handled directly
13:16 egonw sounds good
13:16 egonw ok, that's all I wanted to know
13:58 CIA-34 cdk: egonw * r11965 /cdk-qa/trunk/projects/080808-0001/ (. extractOBmol2AtomTypes.bsh zinc.ob.mol2): OK, extracted mol2 atom types that OB perceived
14:04 CIA-34 cdk: egonw * r11966 /cdk-qa/trunk/projects/080808-0001/ (4 files): First results: 37941 atom types perceived, with 9659 differences
14:04 CIA-34 cdk: egonw * r11967 /cdk-qa/trunk/projects/080808-0001/ (diff.ob2cdk.txt extractOBmol2AtomTypes.bsh mol2.ob.txt):
14:04 CIA-34 cdk: Rerun analysis: CDK does not do .ar types yet, as aromaticity detection is
14:04 CIA-34 cdk: currently not part of Sybyl atom type perception (should add that); now reset
14:05 CIA-34 cdk: C.ar (etc) in OB results to C.2 (etc). This results in 2715 differences
20:08 bag joined #cdk
22:48 zarah joined #cdk
22:48 thomas_ku joined #cdk
22:48 CIA-34 joined #cdk
22:48 jpansanel joined #cdk
22:48 azeem joined #cdk
22:48 Conrad joined #cdk
23:10 CIA-23 joined #cdk
23:13 edrin joined #cdk
23:37 CIA-35 joined #cdk

| Channels | #cdk index | Today | | Search | Google Search | Plain-Text | summary