Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-04-30

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All times shown according to UTC.

Time Nick Message
06:09 egonw joined #bioclipse
07:14 Gpox joined #bioclipse
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07:38 CIA-73 bioclipse: egonw * r10012 /bioclipse2/trunk/cdk-externals/tru​nk/org.openscience.cdk.data/src/org​/openscience/cdk/MoleculeSet.java: Possible dangourous workaround for CDK bug #2784182
07:38 zarah bug #2784182 | http://tinyurl.com/cwmv5y
07:38 egonw fuck, fuck, fuck
07:38 CIA-73 bioclipse: goglepox * r10013 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint.view/src/net/bioclipse/​cdk/jchempaint/view/SWTRenderer.java:
07:38 CIA-73 bioclipse: Only draw implicit hydrogen if that preference is set
07:38 CIA-73 bioclipse: Fixes bug #884
07:38 zarah bug #884 | http://tinyurl.com/db2k7z
07:39 CIA-73 bioclipse: goglepox * r10014 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java: Call add messages to JCP-widget on the UI thread
07:40 egonw Gpox: ping
07:41 Gpox egonw: pong
07:41 egonw Gpox: bioclipse SVN had enormously diverged (aka forked) from CDK SVN
07:41 egonw still finding all sorts of bugs after last update
07:41 egonw not 100% in BC2 SVN was applied upstream
07:41 egonw not even close
07:41 egonw I'm still encountering bugs
07:42 egonw and rather tempted to revert the 'upgrade'
07:42 egonw which leaves as with a buggy CDK, but more stable JCP?
07:42 egonw two evils
07:42 egonw it seems to be reasonable close now
07:43 egonw but adding an bond from scratch, the first atoms ends up in a different IAtomContainer it seems...
07:43 egonw causing exception upon save
07:44 egonw can you please double check if you have no local patches hanging around that fixed stuff earlier?
07:45 egonw anyway... myself going offline any time now for valborg
07:45 egonw and no need to look at it today...
07:45 egonw if you have other plans...
07:58 edrin1 left #bioclipse
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08:00 egonw Gpox: thanx for fixing the thread issue
08:00 egonw Ola's Gist works again...
08:03 Gpox well the getCDKMolecuel is a litle bit of a hack used, it is used when saving
08:03 egonw yes, and it seems broken right now
08:03 egonw I cannot draw from scratch right now...
08:04 egonw but not sure that was working before my patches...
08:04 egonw will look at the ControllerHub tomorrow...
08:09 Gpox it seams ConnectivityChecker.isConnected assumes the atomcontainer passed to it has atoms
08:10 egonw yes, it very will might be...
08:10 egonw you have trouble with that?
08:10 egonw that is, it throws an exception when not having any atoms or so?
08:11 egonw if so, please file a bug report on sf.net/projects/cdk
08:11 Gpox yes with cleanup
08:12 egonw ok, please also file a copy in PZ
08:12 egonw so that we do not forget about it
08:14 Gpox ok, it is verifiable without running the code
08:25 egonw replied
08:25 egonw will fix this tomorrow
08:26 egonw OK, going offline now for valborg
08:26 egonw bye
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09:01 CIA-73 bioclipse: goglepox * r10015 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java: Clear attom container before addin elements from chemodel when getting CDKMolecule
09:01 CIA-73 bioclipse: goglepox * r10016 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java:
09:01 CIA-73 bioclipse: set editor name to 'UNNAMED' when molecule is missing IResource
09:01 CIA-73 bioclipse: Fixes bug #882
09:01 zarah bug #882 | http://tinyurl.com/c83hbk
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09:42 CIA-73 bioclipse: goglepox * r10017 /bioclipse2/trunk/ (5 files in 3 dirs):
09:42 CIA-73 bioclipse: Changed from int[] to Integer[] array for hydrogencount
09:42 CIA-73 bioclipse: This enables it to store the null vales and avoids NPEs
09:42 CIA-73 bioclipse: [jchempaint-primary] r14578
09:42 CIA-73 bioclipse: Changed from int[] to Integer[] array for hydrogencount
09:42 CIA-73 bioclipse: This enables it to store the null vales and avoids NPEs
09:59 edrin left #bioclipse
10:18 * maclean promotes bioclipse from ~/Downloads to ~/Applications. :)
11:01 maclean can anyone tell me how to print from within a script?
11:01 maclean I did try "print()"...
11:10 Gpox js.print maby
11:12 maclean hmmm. I'll try.
11:13 maclean no, not that.
11:14 maclean oh, well, I'm just saving the molecule to a file instead (a particular molecule from an sdf file).
11:16 maclean heh. Note to self : don't declare variables with an 'int' type in javascript...
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15:13 edrin hi egonw
15:15 maclean joined #bioclipse
15:50 rajarshi joined #bioclipse
16:12 edrin hi rajarshi
16:18 rajarshi hi
16:18 zarah privet rajarshi
17:09 edrin left #bioclipse
18:27 edrin joined #bioclipse
19:13 egonw joined #bioclipse
20:51 CIA-73 bioclipse: edrin_t * r10018 /xws/trunk/xws4j/src/net/bioclipse/xws/compon​ent/adhoc/function/FunctionInformation.java: added variables for sync and async functions, according to egon's suggestion
21:17 CIA-73 bioclipse: edrin_t * r10019 /xws/trunk/xws4j/src/net/biocl​ipse/xws/xmpp/XmppTools.java: added Javadoc comments.
21:24 CIA-73 bioclipse: edrin_t * r10020 /xws/trunk/xws4j-coffee-machi​ne-sample/src/coffee/machine/ (GetCoffeeCanStatus.java MakeNewCoffee.java): adapted to current API
21:29 CIA-73 bioclipse: edrin_t * r10021 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/ (7 files in 3 dirs): updated to current xws4j

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