Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-02-26

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All times shown according to UTC.

Time Nick Message
05:37 masak joined #bioclipse
07:45 Gpox joined #bioclipse
07:50 rojasm joined #bioclipse
08:02 egonw joined #bioclipse
08:12 Gpox joined #bioclipse
08:18 egonw joined #bioclipse
08:19 sneumann joined #bioclipse
08:30 * egonw is happy to see that his laptop can now use the full 4GB of memory, instead of just 3.5
08:30 egonw though I may actually recompile a custom kernel instead...
08:31 egonw ... of using the ubuntu server kernel
08:44 rojasm1 joined #bioclipse
08:44 edrin joined #bioclipse
08:44 edrin hi
08:44 zarah hello edrin, you fantastic person you
08:46 masak hiya edrin
08:49 grandm44 joined #bioclipse
08:49 egonw moin all
08:49 zarah privet egonw
08:50 masak morning, egonw
08:57 jonalv joined #bioclipse
09:02 sneumann moin all
09:02 zarah oh hai sneumann
09:02 egonw hi sneumann
09:02 sneumann ah, individual responses from zarah. She knows nationalities ?
09:02 masak oh hai sneumann
09:02 masak sneumann: nope.
09:03 sneumann ;-)
09:03 masak she just randomly says something.
09:07 jonalv We should wait with Bioclipse 2 RC until Eclipse 3.4.2
09:07 jonalv There is a very frustrating "Hoover" bug on macs...
09:08 egonw you do not have that one yet?
09:08 egonw I think I upgraded to 3.4.2 earlier this week
09:08 masak jonalv: a bug about vacuum cleaners?
09:08 jonalv egonw: uhm no, it's not released yet afaik
09:08 masak jonalv: or about American presidents?
09:09 jonalv masak-- //You know what I mean, no need to confuse people
09:09 egonw http://www.jroller.com/andyl/e​ntry/eclipse_3_4_2_maintenance
09:09 zarah egonw's link is also http://tinyurl.com/b5hw5m
09:09 egonw Fri 13 was the release
09:09 jonalv that's not the real one only a maintenance...
09:09 jonalv right?
09:09 egonw it's not 3.5, no
09:09 masak jonalv: fair enough.
09:10 masak I can be reasonable, no problem.
09:10 masak just watch me.
09:10 masak jonalv-- # for writing "Hoover" when he means something else.
09:10 jonalv masak-- // For not explaining what he exepects me to write instead
09:11 masak jonalv--: "hover"
09:11 masak :)
09:11 egonw btw, it seems that the robots.txt has worked
09:11 masak egonw++
09:11 jonalv egonw++
09:11 masak Google++
09:12 egonw or maybe the google bot is just down, like gmail earlier this week :)
09:12 egonw @karma
09:12 zarah egonw has a karma of 62
09:13 egonw btw, how can I see if which SE universities have access to a certain journal?
09:13 egonw say, Curr. Op. Drug Disc & Devel
09:13 egonw I know UU doesn't
09:14 shk3 joined #bioclipse
09:15 CIA-55 bioclipse: jonalv * r9069 /bioclipse2/trunk/plugins/​net.bioclipse.usermanager/ (2 files in 2 dirs): made the Usermanager work in Brunn
09:15 * jonalv wouldn't know...
09:20 rojasm joined #bioclipse
09:28 egonw @pz 600
09:28 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=600
09:30 CIA-55 bioclipse: carl_masak * r9070 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): [net.bioclipse.scripting] various minor cleanups
09:32 egonw Gpox: ping
09:32 Gpox egonw: pong
09:32 egonw ah, you're at UU...
09:32 CIA-55 bioclipse: egonw * r9071 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java: Temporarily commented out the undo/redo until it stops throwing exceptions all over the place...
09:35 jonalv egonw: http://icanhascheezburger.com/
09:35 zarah jonalv's link is also http://tinyurl.com/2kcq53
09:54 masak the precedence of 'instanceof' is just plain wrong.
10:03 CIA-55 bioclipse: egonw * r9072 /bioclipse2/trunk/cdk-externals/trunk/org.o​penscience.cdk.control/src/org/openscience/​cdk/controller/ControllerParameters.java: Removed hydrogen (solving the atom to 'disappear' when explicit hydrogen are supressed) and added halogens
10:21 olass joined #bioclipse
10:21 CIA-55 bioclipse: ospjuth * r9073 /bioclipse2/trunk/plugins/s​e.uu.farmbio.hivpred.model/ (.classpath META-INF/MANIFEST.MF build.properties jar/ jars/): Relies on xom bundle, not jar. Solves #557.
10:30 olass shk3: After you have marked RESOLVED FIXED and you are reporter, please close the bug. See bug #295 for example. Please update your queries to catch these occasions.
10:41 CIA-55 bioclipse: ospjuth * r9074 /bioclipse2/trunk/plugins/net.bio​clipse.qsar/META-INF/MANIFEST.MF: Removed version dependencies in manifest
10:41 CIA-55 bioclipse: ospjuth * r9075 /bioclipse2/trunk/plugins/net.bioclipse​.qsar/src/net/bioclipse/qsar/business/ (IQsarManager.java QsarManager.java): Renamed manager methods to be easily understandable.
10:41 CIA-55 bioclipse: ospjuth * r9076 /bioclipse2/trunk/plugins/net.biocl​ipse.qsar/src/net/bioclipse/qsar/pr​efs/QSARPreferenceInitializer.java: More extensible logging on preference initialization.
10:42 CIA-55 bioclipse: ospjuth * r9077 /bioclipse2/trunk/features/net.bi​oclipse.qsar_feature/feature.xml: Added missing deps to feature.
10:42 ChanServ joined #bioclipse
10:42 CIA-55 bioclipse: ospjuth * r9078 /bioclipse2/trunk/plugins/net.biocli​pse.qsar.test/META-INF/MANIFEST.MF: Added missing deps to feature.
10:42 CIA-55 bioclipse: ospjuth * r9079 /bioclipse2/trunk/plugins/net.biocli​pse.qsar.test/src/net/bioclipse/qsar​/test/business/TestQsarManager.java: Updated test to API changes.
10:43 CIA-55 bioclipse: ospjuth * r9080 /bioclipse2/trunk/plugins/net.biocl​ipse.qsar.ui/META-INF/MANIFEST.MF: Removed version dependencies in manifest
10:43 CIA-55 bioclipse: ospjuth * r9081 /bioclipse2/trunk/plugins/net.bioclipse​.statistics.jama/META-INF/MANIFEST.MF: Cleaned up manifest for 3.4+.
10:44 CIA-55 bioclipse: ospjuth * r9082 /bioclipse2/trunk/plugins/net.biocl​ipse.cdk.qsar.test/src/net/bioclips​e/cdk/qsar/test/TestCDKQsar.java: Fails if not all CDK descriptors are present in BO descr ontology.
10:46 CIA-55 bioclipse: ospjuth * r9083 /bioclipse2/trunk/features/net.bioclipse_feature/ (.project feature.xml): Renamed Bioclipse core feature to net.bioclipse.core_feature.
10:47 CIA-55 bioclipse: ospjuth * r9084 /bioclipse2/trunk/features/net.bi​oclipse.qsar_feature/feature.xml: Bundle cdk descriptors with qsar_feature.
10:49 egonw olass: going to put the QSAR feature online too?
10:50 olass experimental
10:50 olass I hope
10:50 olass if not too much work...
10:50 egonw :)
10:50 olass will at least investigate it
10:50 egonw looking forward to it
10:51 CIA-55 bioclipse: ospjuth * r9085 /bioclipse2/trunk/features/ (9 files in 8 dirs): Updated dependency to renamed net.bioclipse.core_feature.
10:52 CIA-55 bioclipse: ospjuth * r9086 /bioclipse2/trunk/features/net.​bioclipse.blueobelisk_feature/: Initial import.
11:17 CIA-55 bioclipse: ospjuth * r9087 /bioclipse2/trunk/features/net.​bioclipse.blueobelisk_feature/ (.project build.properties feature.xml): A missing feature commit.
11:23 edrin ok, i'm gone
11:23 edrin available over email
11:23 edrin left #bioclipse
12:02 charlgren joined #bioclipse
12:24 masak joined #bioclipse
12:25 CIA-55 bioclipse: egonw * r9088 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.business/src/net/bioclip​se/cdk/business/ICDKManager.java: Fixed inline API (fixes #586)
12:25 zarah bug #586 | http://tinyurl.com/cj7n9m
12:25 CIA-55 bioclipse: egonw * r9089 /bioclipse2/trunk/plugins/n​et.bioclipse.ui/.gitignore: Ignore additional .products files
12:48 CIA-55 bioclipse: egonw * r9090 /bioclipse2/trunk/ (2 files in 2 dirs): Updated for core feature name change
13:06 masak olass: will there be one of those status meetings next week?
13:08 olass yes
13:08 olass that would indeed be good
13:08 olass tuesday sounds fine with me
13:08 olass you?
13:08 egonw sounds good
13:09 masak tuesday's fine.
13:09 olass dependeing on beta3 tomorrow (and status of things in general) I was hoping for RC1 next friday
13:09 masak olass: I've just found something about the exception-in-console issue.
13:09 olass good
13:09 olass or bad?
13:09 masak good and bad.
13:09 masak good: I can echo something to the console.
13:10 masak bad: I can't echo the actual error.
13:10 olass why not?
13:10 masak it might be that I misunderstood something...
13:10 masak (need to talk to edrin about it)
13:10 masak ...but it seems that I never get an exception from Rhino.
13:10 masak just a string.
13:10 olass send him an email
13:11 olass say it's urgent
13:11 CIA-55 bioclipse: egonw * r9091 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java:
13:11 CIA-55 bioclipse: Fixed saving of files created from an empty canvas: synchronize the CDKMolecule model with the ControllerHub model.
13:11 CIA-55 bioclipse: Again, but now no longer breaks saveAs(). (fixes #597)
13:11 masak oki
13:11 zarah bug #597 | http://tinyurl.com/b8rd5s
13:11 masak olass: I'll make the best of what I have in the meantime.
13:11 olass great
13:11 masak echoing out a general error message.
13:11 olass maybe edrin can take it from there?
13:11 masak "Something went wrong. See the logs."
13:11 olass hmm, yes
13:11 olass ok for beta3 but not RC1
13:11 masak olass: well, if what I'm seeing is right, there's no way to solve this. :(
13:12 masak so I hope I'm wrong.
13:12 olass then we need another mechanism
13:12 masak aye.
13:12 olass we had one before...
13:12 masak Python, maybe :)
13:12 egonw Perl6 perhaps?
13:12 olass masak: it used to work before. What has changed?
13:12 masak Ruby, I hear Ruby's good.
13:12 masak olass: Rhino has changed, I think.
13:12 masak but I'm not sure.
13:13 * masak emails edrin
13:16 egonw shk3: did you manage to do the perspective? if you need help, I have some experience...
13:16 egonw would save me a few clicks for each step when testing speclipse
13:17 shk3 not yet worked on that
13:41 * jonalv is trying to use jmopl in Bioclipse for soem real work
13:42 jonalv a frustrating thing just turned up
13:43 jonalv the menu alternatives perfoprms there actions on all atoms and not just on the selected ones... :(
13:56 CIA-55 bioclipse: shk3 * r9092 /bioclipse2/trunk/plugins/net.bioclipse.specmol/ (2 files in 2 dirs): file opens after creation (bug #602)
13:56 zarah bug #602 | http://tinyurl.com/ba4zd4
14:02 masak egonw: found a possible bug in org.openscience.cdk.smiles​.SmilesParser.parseString
14:03 masak @tell egonw found a possible bug in org.openscience.cdk.smiles.​SmilesParser.parseString(). it throws a StringIndexOutOfBoundsException when given the empty string.
14:03 zarah Consider it noted.
14:03 masak zarah++
14:04 shk3 was there a decision if there should be default names in new file wizards or not?
14:06 masak default names?
14:06 shk3 like unnamed.cml or so
14:06 shk3 in the name text field
14:10 CIA-55 bioclipse: goglepox * r9093 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.ui.sdfeditor/nattable-core-1.6.5.jar: Added nattable jar
14:11 CIA-55 bioclipse: goglepox * r9094 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui.sdfeditor/ (5 files in 3 dirs): Try with NatTable
14:11 CIA-55 bioclipse: goglepox * r9095 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MoleculesEditorLabelProvider.java: Refactored for better overview and limited object creation
14:11 shk3 you had a discussion about that recently, if I remember correctly
14:11 CIA-55 bioclipse: goglepox * r9096 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui.sdf​editor/src/net/bioclipse/cdk/ui/sdfeditor/editor/ (MoleculeTableContentProvider.java MoleculesEditor.java): Added coulumn resize
14:12 CIA-55 bioclipse: goglepox * r9097 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.ui.sdfeditor/src/net/bioclipse/cdk/u​i/sdfeditor/editor/JCPCellPainter.java: Class for painting 2D-structures in MolecleTable
14:13 CIA-55 bioclipse: goglepox * r9098 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui.sdf​editor/src/net/bioclipse/cdk/ui/sdfeditor/editor/ (4 files): Changed MoleculeTableViewer to use NatTable
14:13 CIA-55 bioclipse: goglepox * r9099 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui.sdfeditor/ (4 files in 3 dirs): Added extension point for generators
14:14 CIA-55 bioclipse: goglepox * r9100 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui.sdfeditor/ (2 files in 2 dirs):
14:14 CIA-55 bioclipse: Removed trailing spaces
14:14 CIA-55 bioclipse: Added comment with popupmenu code
14:15 shk3 olass?
14:16 CIA-55 bioclipse: goglepox * r9101 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui.sdf​editor/src/net/bioclipse/cdk/ui/sdfeditor/editor/ (JCPCellPainter.java MoleculesEditor.java): Added popup menu and fixed NPE
14:18 shk3 anybody listening?
14:18 shk3 guys, I need an answer
14:19 shk3 I want to get rid of this bug report
14:19 shk3 don't you feel like this yourself sometimes?
14:19 shk3 please say "no policy on that" if there is none.
14:22 de__maas joined #bioclipse
14:27 CIA-55 bioclipse: carl_masak * r9102 /bioclipse2/trunk/plugins/net.bioclipse​.scripting/src/net/bioclipse/scripting/ (JsEnvironment.java JsThread.java):
14:27 CIA-55 bioclipse: [scripting] "fixed" exception in js console
14:27 CIA-55 bioclipse: The current solution is an unsatisfactory workaround. For some reason, the
14:27 CIA-55 bioclipse: js context has stopped throwing exceptions back at us, it just returns Strings.
14:27 CIA-55 bioclipse: That's so bad it almost can't be right... but I can't seem to get it to
14:27 CIA-55 bioclipse: work in any other way either. Given all this, I take the String returned
14:27 CIA-55 bioclipse: when something goes wrong, and replace it with a slightly nicer error message.
14:51 jonalv "pz 189
14:51 jonalv @pz 189
14:51 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=189
14:51 jonalv masak: help!
14:51 masak jonalv: how may I serve you today, sir?
14:52 jonalv @pz 189
14:52 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=189
14:53 masak jonalv: how may I serve you today, sir?
14:53 jonalv masak: help me...
14:53 masak please state the nature of your medical emergency.
14:55 masak jonalv: what Stefan says makes sense to me.
14:55 jonalv masak: I want your oppinion on whther we should ahave default values in these dialogs so that the user can see from the example how to name the files (whether to add file endings or not) + so that you can easy click around and try the dialog without having to add stuff in them before you can click finish. Or whether we jsut should leave the dialog fielnds empty and leave our users out in the cold so to say...
14:55 masak jonalv: would it be possible to summarize your problem?
14:56 masak I fell asleep halfway through that paragraph...
14:56 jonalv masak: I want default values in all dialogs
14:56 masak jonalv: ok.
14:56 masak in what way?
14:56 jonalv masak: And I need some votes to back me up...
14:56 jonalv olass: help me Ö=
14:56 jonalv :)
14:56 masak jonalv: so, the folder is already preset, right?
14:56 masak jonalv: what more is it you want, exactly?
14:56 jonalv masak: I am not 100% sure but I think so yea
14:57 jonalv I want default values for all fields in all dialogs
14:57 jonalv there should be reasonable defaults
14:57 jonalv you should not have to guess what to write in one single dialog in Bioclipse
14:58 masak jonalv: I'm not sure I understand what you're getting at in this specifig case...
14:58 masak could you show me?
14:58 jonalv there should always be reasonable default values which you can try it out with and see what happends
15:00 masak jonalv: ok, after a demonstration, I agree with you.
15:12 jonalv masak++ //thankyou
15:12 masak no sweat.
16:18 CIA-55 bioclipse: shk3 * r9103 /bioclipse2/trunk/plugins/net.bioclipse.sp​ectrum/src/net/bioclipse/spectrum/wizards/ (NewSpectrumFileWizardPage.java NewSpectrumWizard.java): folder set (bug #599)
16:18 zarah bug #599 | http://tinyurl.com/aenvex
16:36 CIA-55 bioclipse: carl_masak * r9104 /bioclipse2/trunk/plugins/net.bioclipse​.scripting.ui/src/net/bioclipse/scripti​ng/ui/views/ScriptingConsoleView.java:
16:36 CIA-55 bioclipse: resolved #262
16:36 CIA-55 bioclipse: Keypresses are listened to in the output text widget, and inserted last in the
16:36 CIA-55 bioclipse: input widget, which is also given focus. Since we still want to be able to
16:36 CIA-55 bioclipse: copy text in the output widget, certain special keys are ignored.
16:47 Gpox joined #bioclipse
16:47 jonalv Gpox: oh hai!
16:48 olass hi
16:48 zarah ni hao olass
16:50 CIA-55 bioclipse: goglepox * r9105 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MoleculeTableContentProvider.java: Fixed double up of properties and some clean up.
16:51 olass Gpox++ //looking forward to testing new MolTable
16:55 Gpox you do that and file bug reports
17:08 de__maas left #bioclipse
18:34 CIA-55 bioclipse: ospjuth * r9106 /bioclipse2/trunk/plugins/net.bioc​lipse.qsar.ui/src/net/bioclipse/qs​ar/ui/editors/ResponsesPage.java: Handle case where arrayValue is "" and value !null.
18:47 CIA-55 bioclipse: ospjuth * r9107 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Added missing setResource(file) for molecules created in loadMolecules(..). Also added lines to test this in CDKManagerPluginTest.
19:16 egonw joined #bioclipse
20:07 olass joined #bioclipse
20:08 CIA-55 bioclipse: ospjuth * r9108 /bioclipse2/trunk/plugins/net.bioclipse.cdk.qsar/ (.settings/org.eclipse.jdt.core.prefs plugin.xml): Updated default value and description for BondCountDescriptor.
20:09 CIA-55 bioclipse: ospjuth * r9109 /bioclipse2/trunk/plugins/ (6 files in 4 dirs): Cleaned up manifest and classpath.
20:09 CIA-55 bioclipse: ospjuth * r9110 /bioclipse2/trunk/plugins/net.b​ioclipse.qsar/build.properties: Added missing stuff to build.props.
20:09 CIA-55 bioclipse: ospjuth * r9111 /bioclipse2/trunk/plugins/net.biocl​ipse.qsar.ui/src/net/bioclipse/qsar​/ui/editors/DescriptorsPage.java: Set minimum height on parameters component on descriptors page.
20:10 CIA-55 bioclipse: ospjuth * r9112 /bioclipse2/trunk/plugins/net.bioclipse.qsar.ui/sr​c/net/bioclipse/qsar/ui/builder/QSARBuilder.java: Updated Builder. Sorting is now same as molecules list. Removed processedMolecules trailing number.
20:11 CIA-55 bioclipse: ospjuth * r9113 /bioclipse2/trunk/plugins/net.biocli​pse.statistics/src/net/bioclipse/sta​tistics/model/MatrixResource.java: Caught error on parsing double to return NaN and log this.
20:12 CIA-55 bioclipse: ospjuth * r9114 /bioclipse2/trunk/plugins/ (9 files in 6 dirs): Updated settings and classpath.
20:19 CIA-55 bioclipse: ospjuth * r9115 /bioclipse2/trunk/ (9 files in 9 dirs): Set version to 2.0.0.B20090227
20:20 rojasm joined #bioclipse
20:45 olass @tell egonw: can you confirm cdk plugins (org.openscience.*) have updated IDs for beta3?
20:45 zarah Consider it noted.

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