Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-11-13

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All times shown according to UTC.

Time Nick Message
06:59 Gpox joined #bioclipse
08:45 egonw joined #bioclipse
08:59 egonw moin
08:59 zarah hi egonw
09:35 shk3 joined #bioclipse
09:35 egonw hi shk3!
09:35 egonw how was Goslar?
09:35 egonw hardly any social coverage :(
09:35 egonw was it really that busy?
09:36 egonw ~180 people?
09:38 shk3 hi egonw
09:38 shk3 197 people
09:39 shk3 but was good nevertheless
09:39 egonw 197!
09:39 egonw amazing...
09:39 shk3 200 is limit
09:39 shk3 so just space left for you next time
09:39 egonw :)
09:39 shk3 i can't go to bugzilla
09:39 shk3 http://pele.farmbio.uu.se/cgi-bin/bugzilla/
09:39 zarah shk3's link is also http://tinyurl.com/6pp42l
09:40 shk3 gives me an error
09:40 egonw yeah, next year I want to be there
09:40 shk3 403 forbidden
09:40 egonw http://pele.farmbio.uu.se/​cgi-bin/bugzilla/index.cgi
09:40 zarah egonw's link is also http://tinyurl.com/6c9nzh
09:40 egonw OR
09:40 egonw http://pele.farmbio.uu.se/bugzilla/
09:40 zarah egonw's link is also http://tinyurl.com/5duh93
09:40 egonw you just had a bad combination :)
09:40 shk3 ah thanks
09:40 egonw oh, left quite a few bug reports...
09:40 egonw played with Speclipse
09:40 shk3 this linke is from the reminder emails actually
09:41 shk3 good
09:41 egonw shk3: ok, please forward me a reminder email
09:41 egonw better:
09:41 shk3 did you try the problem with cdk plugin i reported
09:41 shk3 ?
09:41 egonw file a bug report
09:41 egonw with the content of the email
09:41 egonw not sure
09:41 egonw what problem was that again?
09:41 shk3 forwarded
09:41 shk3 the loadMolecule
09:42 shk3 and calculateSmiles
09:42 shk3 but I can do some investigation myself now
09:42 egonw did you file a bug report with details?
09:42 shk3 no
09:42 shk3 will do so
09:42 egonw thanx
09:43 shk3 but want to try first what's really wrong
09:43 shk3 without internet, it's hard to do that
09:43 shk3 and I will update before
09:44 egonw ok
09:49 shk3 ok, trying to catch up with my emails...
09:51 egonw shk3: fix email message URL
09:51 egonw fixed
09:53 shk3 just sent an email to the mailing list with some sensational news
09:53 shk3 watch out
09:59 shk3 egonw: does the bc2 alpha download contain any plugins or need these to be installed via update site?
10:00 egonw features, you mean?
10:00 egonw oh... which ML?
10:00 shk3 well, features are just collections of plugins, aren't they?
10:01 egonw yes
10:01 shk3 but yes, i mean: does the download contain any feature (chemoinformatics etc.) installed?
10:01 shk3 bioclipse ml
10:01 egonw no, those go via the update site
10:01 egonw interesting email
10:03 shk3 hm, ok
10:03 shk3 I must admit i am not sure if this is the right way
10:03 shk3 users who download something expect to get something
10:03 shk3 at least we should have a very prominent hint on welcome screen or so
10:04 egonw shk3: this is where branding comes in useful
10:04 egonw bioclipse should have (has) a welcome screen where they are invited to install functionality
10:05 thomasku joined #bioclipse
10:13 egonw shk3: I'm putting all my code snippets on Gist
10:13 egonw shk3: I see you have snippets on your slides...
10:13 egonw can you post those at Gist?
10:14 egonw or do you want to do that yourself?
10:14 egonw well, one snippet
10:26 shk3 what's gist?
10:26 egonw sort of pastebin with versioning
10:26 egonw gist.github.com
10:26 egonw http://delicious.com/tag/bioclipse+gist
10:26 zarah egonw's link is also http://tinyurl.com/5gqjet
10:26 egonw the latter is the tagging of them
10:27 egonw and sort of index of interesting code snippets for bioclipse
10:30 egonw shk3: something else
10:30 egonw please check http://wiki.bioclipse.net/index.php?title​=List_of_stable_managers_in_bioclipse_2.0
10:30 zarah egonw's link is also http://tinyurl.com/68dyxn
10:31 egonw we have been beefing up the managers
10:31 egonw the testing in particular
10:31 egonw please set up a XManagerTest and CoverageTest for the managers you have developed
10:32 egonw and please tell Gilleain too, when you see him
10:32 egonw shk3: ping
10:32 egonw one last thing...
10:33 egonw can you please review the cmlxom patch I have emailed about?
10:33 egonw Rajarshi already looked at it, but Miguel and Chris seem too busy to review...
10:44 egonw stain: ping
10:54 shk3 egonw: will look at the managers
10:55 shk3 have to work on them anyway (include more methods)
10:55 egonw and the cmlxom patch?
11:05 shk3 sorry, didn't come across that
11:05 shk3 what do I have to do?
11:05 egonw just review it
11:05 egonw mom
11:05 egonw will look up details
11:06 egonw https://sourceforge.net/tracker/ind​ex.php?func=detail&aid=2248050&​amp;group_id=20024&atid=320024
11:06 egonw and email:
11:07 egonw https://sourceforge.net/mailarchive/forum.php?th​read_name=6aeb064b0811090237j6fa08ba1lea952b972b​c3301d%40mail.gmail.com&forum_name=cdk-devel
11:21 shk3 reviewing
11:21 shk3 did not yet go through cdk mails
11:41 CIA-53 bioclipse: egonw * r7640 /bioclipse2/trunk/plugins/ (5 files in 4 dirs): Towards scripting JChemPaint
11:51 stain egonw: hey!
11:53 CIA-53 bioclipse: egonw * r7641 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.business.test/ (3 files in 2 dirs): Compile fix I overlooked: method moved the CDKDebugManager
12:05 CIA-53 bioclipse: goglepox * r7642 /bioclipse2/trunk/plugins/net.​bioclipse.cdk.jchempaint.view/ (18 files in 9 dirs): Initial commit, this plugin supplies a view useing new experimental rendering code.
12:05 CIA-53 bioclipse: goglepox * r7643 /bioclipse2/trunk/plugins/net.​bioclipse.cdk.jchempaint.view/ (7 files in 4 dirs): Added button for centering molecule and a icon.
12:05 CIA-53 bioclipse: goglepox * r7644 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint.view/src/net/bioclipse/cd​k/jchempaint/view/JChemPaintView.java: Updated renderer
12:06 CIA-53 bioclipse: goglepox * r7645 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jchem​paint.view/src/net/bioclipse/cdk/jchempaint/view/ (JChemPaintView.java SWTRenderer.java): Added bond generator to view
12:06 CIA-53 bioclipse: goglepox * r7646 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint.view/src/net/bioclipse/​cdk/jchempaint/view/SWTRenderer.java: Implemented visitWedge
12:07 CIA-53 bioclipse: goglepox * r7647 /bioclipse2/trunk/plugins/net.​bioclipse.cdk.jchempaint.view/ (3 files in 3 dirs): Updated Dependencis
12:08 CIA-53 bioclipse: goglepox * r7648 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jchem​paint.view/src/net/bioclipse/cdk/jchempaint/view/ (JChemPaintView.java SWTRenderer.java): Added ExtraBondGenerator to view and implemented wedge bond rendering
12:08 CIA-53 bioclipse: goglepox * r7649 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint.view/src/net/bioclipse/​cdk/jchempaint/view/SWTRenderer.java: Scale OvalElements radius
12:09 CIA-53 bioclipse: goglepox * r7650 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint.view/src/net/bioclipse/cd​k/jchempaint/view/JChemPaintView.java: showUmplicitHydrogen = true
12:09 CIA-53 bioclipse: goglepox * r7651 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint.view/src/net/bioclipse/​cdk/jchempaint/view/SWTRenderer.java: Reworked draw dashed wedge bond to use java.vecmath.Tupel2d.interpolate
12:10 CIA-53 bioclipse: goglepox * r7652 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint.view/src/net/bioclipse/​cdk/jchempaint/view/SWTRenderer.java: Stub implementation of visitBondSymbol()
12:10 CIA-53 bioclipse: goglepox * r7653 /bioclipse2/trunk/plugins/net.​bioclipse.cdk.jchempaint.view/ (2 files in 2 dirs): Chages to use JChemPaintView in editor pending refactoring
12:11 CIA-53 bioclipse: goglepox * r7654 /bioclipse2/trunk/plugins/net.​bioclipse.cdk.jchempaint.view/ (4 files in 2 dirs): Refactored out Canvas code in to JChemPaintWidget
12:15 CIA-53 bioclipse: goglepox * r7655 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk.jchempaint/ (3 files in 3 dirs): Changed to use new n.bc.cdk.jcp.view plugin
12:19 jonalv joined #bioclipse
12:19 jonalv hi
12:19 zarah hi jonalv
12:19 egonw hi
12:19 zarah hi egonw
12:21 CIA-53 bioclipse: egonw * r7656 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jche​mpaint.business.test/src/net/bioclipse/cdk/jchem​paint/business/test/JChemPaintManagerTest.java: Added test method to ensure all script methods are available from the manager
12:27 shk3 what is URL for in a bug report?
12:28 jonalv we have used for referenceing old sourcedforge bugs in migrated bugs...
12:28 shk3 ah
12:28 shk3 ok
12:28 shk3 egonw: I filed a bug report on the loadMolecule problem
12:28 jonalv so things like that I guess.. :)
12:28 shk3 I think this is a major problem
12:28 shk3 I would consider my bug report usefull
12:29 jonalv @pelezilla loadMolecule problem
12:29 shk3 please ask if anything is unclear
12:29 zarah [Bug 78] CR/LF problems on windows       http://tinyurl.com/6eznsa
12:29 zarah [Bug 120] loadMolecule not working       http://tinyurl.com/69qo3f
12:29 zarah [Bug 76] Bioclipse crashes when text ... http://tinyurl.com/5eaofv
12:29 zarah [Bug 63] CDKManager.loadMolecule uses... http://tinyurl.com/5sltxw
12:29 zarah [Bug 1] There are people not using Bi... http://tinyurl.com/55k8wf
12:29 zarah Entire list at http://tinyurl.com/6nvj5v
12:29 shk3 bug 120
12:29 charlgren joined #bioclipse
12:33 egonw Gpox: http://cdk.svn.sourceforge.net/viewvc/cd​k/cdk/branches/goglepox-jchempaint/src/m​ain/org/openscience/cdk/renderer/IRender​er2D.java?revision=12521&view=markup
12:33 zarah egonw's link is also http://tinyurl.com/6n6vop
12:34 egonw shk3: thanx
12:34 egonw will look at it...
12:52 Gpox egonw: done adding @cdk.module  render
12:52 egonw ack
12:58 jonalv Gpox, egonw: is net.bioclipse.cdk.ui.sdfeditor supposed to build without troubles?
12:58 jonalv If so, what could I be doing wrong?
12:59 egonw no, it's pending an update...
12:59 egonw I'm a bit slow
12:59 jonalv Gpox, egonw: Or actually the real problem seems to be net.bioclipse.cdk.jchempaint.wi​dgets.JChemPaintEditorWidget...
12:59 egonw right
12:59 egonw cdk.render needs an update
13:00 egonw and I'm working on that
13:00 jonalv oki
13:00 jonalv good :)
13:00 * jonalv shouldn't be so eager to update.. :)
13:01 egonw crap....
13:01 jonalv uhm?
13:01 egonw bumb in the road
13:05 egonw Gpox: renderer/modules should not be exported?
13:06 Gpox no
13:06 egonw perfect
13:06 egonw bc2 patch pending
13:07 CIA-53 bioclipse: egonw * r7657 /bioclipse2/trunk/cdk-externals/t​runk/org.openscience.cdk.render/ (20 files in 4 dirs): Updated from the gpox-jchempaint branch
13:14 CIA-53 bioclipse: egonw * r7658 /bioclipse2/trunk/cdk-externals/trunk​/org.openscience.cdk.render/src/org/o​penscience/cdk/renderer/generators/ (BasicBondGenerator.java ExtraGenerator.java): Use the CDK logger, to solve dependency issues
13:15 egonw Gpox: can you come for a second?
13:16 egonw gettin access restriction issues..
13:17 jonalv charlgren: http://www.java-tips.org/java-se-tips/java​.io/how-to-generate-a-temporary-file.html
13:17 zarah jonalv's link is also http://tinyurl.com/6huz39
13:17 charlgren jonalv: thanks
13:18 CIA-53 bioclipse: goglepox * r7659 /bioclipse2/trunk/plugins/net.​bioclipse.cdk.jchempaint.view/ (2 files in 2 dirs): Fixed dependency error
13:22 CIA-53 bioclipse: egonw * r7660 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.ui.sdfeditor/META-INF/MANIFEST.MF: Added missing (new) dep
13:30 egonw going to relocate to my home desktop
14:22 CIA-53 bioclipse: shk3 * r7661 /bioclipse2/trunk/features/net.biocl​ipse.speclipse_feature/feature.xml: had to move update site
14:26 CIA-53 bioclipse: shk3 * r7662 /bioclipse2/trunk/plugins/net.bioclipse.sp​ectrum/src/net/bioclipse/spectrum/editor/ (GeneralMetadataFormPage.java SpectrumEditor.java): avoids npes
14:27 shk3 does anybody know what a org.eclipse.jdt.core.prefs file is for?
14:27 CIA-53 bioclipse: shk3 * r7663 /bioclipse2/trunk/plugins/net.biocli​pse.nmrshiftdb/src/net/bioclipse/nmr​shiftdb/wizards/PredictWizard.java: missing . in file name
14:27 shk3 i get these created in bioclipse from time to time accidentially
14:50 egonw joined #bioclipse
14:51 shk3 hi egonw
14:52 shk3 do you know what a org.eclipse.jdt.core.prefs file is for?
14:53 egonw no
14:53 shk3 ok
14:53 shk3 do you know where I can set the speclipse update site as included in the update sites by default?
14:54 shk3 looks a bit like the UIPreferenceInitializer class is handling that,
14:54 egonw no
14:54 shk3 but I don't know how to set multiple sites
14:55 egonw brb
14:55 shk3 when will ola be back
14:55 shk3 ?
15:18 CIA-53 bioclipse: shk3 * r7664 /bioclipse2/trunk/plugins/net.bi​oclipse.ui/src/net/bioclipse/ui/ (BioclipseConstants.java prefs/UIPreferenceInitializer.java): added the speclipse update site to default update sites
15:22 egonw joined #bioclipse
16:01 shk3 egonw: just trying to solve bug 119, but don't really understand what you did
16:01 shk3 could you explain
16:01 shk3 ?
16:02 egonw zarah: bug #119
16:02 zarah egonw: you've just exceeded my capabilities :/
16:02 egonw que?
16:02 egonw @pelezilla 119
16:02 zarah egonw: I couldn't find anything on '119' in the database.
16:03 egonw shk3: it happens when you have a closed project in your workspace
16:03 shk3 i closed one project, but it still works for me
16:05 shk3 do you predict a spectrum for a molecule in a closed project?
16:07 egonw maybe it was fixed after the latest release..
16:07 egonw tried from the update site
16:07 egonw no
16:08 shk3 if I have a closed project in the workspace, it works for files in the open project
16:08 shk3 was that your setup?
16:11 egonw OK, please assign to me, and add a comment if I can reproduce it in trunk...
16:17 shk3 thanks
16:20 CIA-53 bioclipse: shk3 * r7665 /bioclipse2/trunk/plugins/net.​bioclipse.specmol/plugin.xml: fixes bug #116
16:20 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=116
16:20 CIA-53 bioclipse: shk3 * r7666 /bioclipse2/trunk/plugins/net.bioclipse.nm​rshiftdb/cheatsheets/SubmitCheatSheet.xml: fixes bug #116
16:20 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=116
16:41 CIA-53 bioclipse: shk3 * r7667 /bioclipse2/trunk/plugins/net.bioclipse.s​pecmol/src/net/bioclipse/specmol/wizards/ (AddMoleculeWizardPage.java FileContentProvider.java): avoids problems with closed projects
16:41 shk3 egonw: I found there were problems with closed projects when using the new specmol wizard.
16:41 shk3 might be this solves your problems as well.
16:41 egonw good :)
16:43 CIA-53 bioclipse: shk3 * r7668 /bioclipse2/trunk/plugins/net.biocli​pse.specmol/src/net/bioclipse/specmo​l/wizards/FileContentProvider.java: avoids problems with closed projects
16:43 shk3 btw, shall we close fixed bugs or reassign to the submitter?
16:45 egonw mark as fixed and reassign to submitter for confirmation
16:48 CIA-53 bioclipse: carl_masak * r7669 /bot/trunk/zarah.pl: [zarah] now goes directly do bug NN on @pelezilla NN call
16:48 zarah joined #bioclipse
16:50 egonw @pelezilla 119
16:50 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=119
16:50 egonw :)
16:51 CIA-53 bioclipse: carl_masak * r7670 /bot/trunk/zarah.pl: [zarah] returns tinyurl instead on @pelezilla NN request
16:51 zarah joined #bioclipse
16:53 CIA-53 bioclipse: carl_masak * r7671 /bot/trunk/zarah.pl: [zarah] fixed braino; reversed comparison
17:16 egonw greeting from Ola
17:23 egonw dinner
17:24 egonw bye all
19:47 charlgren joined #bioclipse
20:02 CIA-53 bioclipse: egonw * r7672 /bioclipse2/trunk/features/net.bioclips​e.chemoinformatics_feature/feature.xml: Added the new plugin to the feature
20:04 CIA-53 bioclipse: egonw * r7673 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Added stubs for script commands
20:06 CIA-53 bioclipse: egonw * r7674 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Started implementation of script methods, but ran into bugs (filed)
20:35 edrin joined #bioclipse

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