Camelia, the Perl 6 bug

IRC log for #bioclipse, 2012-11-15

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All times shown according to UTC.

Time Nick Message
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08:05 egonw konditorn: wanna test a patch?
08:05 egonw jonalv: or you?
08:05 egonw I file a bug report...
08:06 egonw it fixes the last unit test fail on Hudson for .cheminfo
08:07 konditorn I'm not sure I know enough chemistry….
08:09 egonw np
08:09 egonw konditorn: can you make sure the patch gets looked at today?
08:10 egonw http://pele.farmbio.uu.se/bug​zilla36/show_bug.cgi?id=3436
08:10 konditorn yes, I should be able to do that.
08:11 egonw thanx
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08:28 commitbot [bioclipse.ds] goglepox pushed 1 new commit to 2.5.x: http://git.io/nJYv5Q
08:28 commitbot bioclipse.ds/2.5.x 87b309f Arvid Berg: Only reset parameters that are registered in the renderer model...
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08:49 commitbot [bioclipse.cheminformatics] goglepox pushed 1 new commit to 2.5.x: http://git.io/kpMYxg
08:49 commitbot bioclipse.cheminformatics/2.5.x 235463f Egon Willighagen: Simplified the code, fixing JavaCDKManagerPluginTest.testPerceiveAromaticity() regression....
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10:04 jonalv oh hai olass
10:05 olass o/
10:07 jonalv olass: I have been thinking, I think we should try to get 2.6.1 out sooner rather than later and provide bug fixes
10:07 jonalv I think we will have plenty of bugs
10:07 olass ok
10:07 jonalv Good to get 2.6.0 out soon and then quickly follow up with a bug fix
10:08 jonalv because that makes people see that we are doing stuff and it tests the update system
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11:09 commitbot [bioclipse.cheminformatics] goglepox pushed 1 new commit to 2.5.x: http://git.io/BVoZIA
11:09 commitbot bioclipse.cheminformatics/2.5.x ae9f79e Arvid Berg: Only refresh outline if it exist...
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12:32 commitbot [bioclipse.statistics] valyo pushed 1 new commit to 2.5.x: http://git.io/abTH-A
12:32 commitbot bioclipse.statistics/2.5.x 2a66fab Valentin Georgiev: Fix Bug 3435
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12:32 zarah bug #3435 | http://pele.farmbio.uu.se/bug​zilla36/show_bug.cgi?id=3435
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12:35 commitbot [bioclipse.core] valyo pushed 2 new commits to 2.5.x: http://git.io/BhM8AQ
12:35 commitbot bioclipse.core/2.5.x 8f1f29d Valentin Georgiev: Fix Bug 3435
12:35 commitbot bioclipse.core/2.5.x a7e238e Valentin Georgiev: Merge remote-tracking branch 'upstream/2.5.x' into 2.5.x
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12:35 zarah bug #3435 | http://pele.farmbio.uu.se/bug​zilla36/show_bug.cgi?id=3435
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14:54 commitbot [bioclipse.opentox] KlasJoenssson pushed 1 new commit to master: http://git.io/F9fe6Q
14:54 commitbot bioclipse.opentox/master 27b982f Klas Jönsson: Made OpenTox server prefs persisted when changed in preferences
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15:08 konditorn egonw: ping
15:08 egonw pong
15:09 konditorn did you pushed the commits in patch you wanted me to test?
15:09 egonw no, that was not me...
15:09 egonw but they have been commited indeed
15:09 egonw well, it...
15:10 egonw huh?
15:10 egonw I'm sure I saw it in my inbox...
15:10 egonw but don't see it here...
15:11 egonw https://github.com/bioclipse/biocl​ipse.cheminformatics/commit/235463​f52ffae4181ff5474914fcda3e860d4ef6
15:11 egonw Gpox commited it
15:12 konditorn can you give me som example of how to test it?
15:13 konditorn i.e. something I can do in BC to see if its working...
15:13 egonw in the test suite you'll find a file called aromatic.mol
15:14 egonw http://pele.farmbio.uu.se/jenkins/job/Bioclipse​.test.chemoinformatics/489/testReport/net.biocl​ipse.chemoinformatics.test.feature.AllFeaturePl​uginTest$net.bioclipse.cdk.AllCDKBusinessPlugin​TestSuite$net.bioclipse.cdk.business.test/JavaC​DKManagerPluginTest/testPerceiveAromaticity/
15:14 zarah egonw's link is also http://tinyurl.com/ad58goy
15:14 egonw used in that method
15:15 egonw but basically what needs testing, is that is properly detects aromaticity and double bond positions...
15:15 egonw e.g. by testing SMILES you find in the bug tracker with:
15:15 egonw ui.open(cdk.fromSMILES("c1ccccc1"))
15:17 konditorn oki
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16:47 konditorn egonw: the only test method that concerns aromaticity and fails is testPerceiveAromaticity()...
16:47 egonw that *used* to fail
16:48 egonw but should no longer
16:48 konditorn it did for me...
16:48 konditorn :(
16:49 egonw it works for me and for Jenkins too
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16:58 konditorn egonw: now it works here to, guess that it wasn't up to date when I run it before…=)
16:59 egonw yeah, that happens to me only too often :)
16:59 konditorn =)
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17:26 * egonw is heading home...
17:26 egonw and will see what he can do about Conclusion sections...
17:26 egonw I really need to install Mylyn again, so that he can work on Bioclipse bugs on the way home too...
17:27 * egonw will write a Dutch article on Bioclipse-OpenTox tomorrow...
17:27 egonw and tons of things more I do not even want to think about ... :(
17:27 egonw bye all
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