Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-11-03

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All times shown according to UTC.

Time Nick Message
06:14 egonw_ joined #bioclipse
06:31 Gpox joined #bioclipse
06:32 egonw_ hi Gpox
06:32 egonw_ I applied your patches
06:32 egonw_ and ported the jcp ones into bioclipse-2.1.x of jchempaint-primary
06:33 egonw_ I noted one glitch...
06:33 egonw_ in the use of the parameter you were using .getDefault()
06:33 egonw_ which should be textColor.getValue()
06:39 Gpox I am pretty sure it should not
06:39 egonw_ how so?
06:39 Gpox where do you define the default value, when no value is set?
06:39 egonw_ what's a parameter if you cannot change the value?
06:40 egonw_ ah... indeed...
06:40 egonw_ getValue() must return the default if no other value is given...
06:40 egonw_ but isn't that taken care of by the Abstract impl then?
06:40 egonw_ did not check that...
06:40 Gpox the AbstractGeneratorParameter should implement getVAlue as if(parameterSetting == null) return getDefault()
06:41 egonw indeed
06:41 egonw I assumed that was the case
06:41 egonw ok, can you file me a bug report ?
06:41 egonw please?
06:41 egonw btw... sushi today?
06:41 Gpox I thought so too, but it dose not
06:41 Gpox yeah
06:41 egonw I will fix that
06:43 Gpox I is good to get an implementation using the GeneratorParamter to se if it work as expected.
06:43 Gpox dunno if i did it right, but it works :)
06:44 Gpox Thats the hard part of designing APIs
06:49 Gpox I was gonna update the jcp manager to use IEdits but it returns the created atom in the addAtom() method :/
07:24 egonw bbl
08:05 sneumann__ joined #bioclipse
08:09 samuell joined #bioclipse
08:17 olass joined #bioclipse
08:24 CIA-63 bioclipse.ds: Ola Spjuth master * r2662786 / plugins/net.bioclipse.ds/src/net/bi​oclipse/ds/impl/BaseSDFMatcher.java : Adapted for refactored SDFileIndexModel. - http://bit.ly/2F2P2L
09:00 egonw joined #bioclipse
09:03 egonw samuell: http://bio2rdf.org/page/nmrshiftdb_molecule:234
09:03 zarah egonw's link is also http://tinyurl.com/yf5xzk9
10:11 egonw samuell: http://www.biomedcentral.com/1471-2105/8/487
10:11 zarah egonw's link is also http://tinyurl.com/laxs6z
10:23 edrin joined #bioclipse
10:25 edrin hi
10:25 zarah privet edrin
10:43 egonw samuell: have you seen this page: http://www.semanticoverflow.com/
10:43 zarah egonw's link is also http://tinyurl.com/ygbbf4a
10:44 samuell egonw: No, not before now. Thx, will check.
10:44 egonw good place to ask questions :)
10:44 samuell Ok, good to know! :)
12:39 masak joined #bioclipse
13:04 sneumann__ joined #bioclipse
14:03 olass Ok, see these two blog posts by me: http://bioclipse.blogspot.com/2009/1​1/download-pdbs-with-bioclipse.html and http://bioclipse.blogspot.com/2009/11/ali​gn-sequences-with-kalign-web-service.html
14:03 zarah olass's link is also http://tinyurl.com/ycybur2
14:15 egonw olass++
14:15 olass :)
14:25 CIA-63 bioclipse.core: Ola Spjuth 2.2.x * rc459cfc / (19 files in 19 dirs): Updated version to 2.2.0.RC1 for release. - http://bit.ly/4Eccjf
14:25 olass egonw, masak: please set version to 2.2.0.RC1 for plugins and features in bioclipse.bioinformatics and bioclipse.cheminformatics
14:26 masak olass: will do.
14:40 CIA-63 bioclipse.balloon: Ola Spjuth master * r54aaa4b / (8 files in 8 dirs): Updated version to 2.2.0.RC1 for release. - http://bit.ly/1M0ipj
14:41 * egonw is close to the calc tanimoto matrix pop up menu
14:45 CIA-63 bioclipse.core: Ola Spjuth 2.2.x * r4b54891 / (3 files in 3 dirs): Set core and birt feature versions to 2.2.0.RC1. - http://bit.ly/r1CUU
14:48 masak I made a simple script that updates all the plugins' version for me at once: http://github.com/masak/bioclipse.bio​informatics/blob/master/bump-version
14:48 zarah masak's link is also http://tinyurl.com/yewenp7
14:53 egonw olass: ping...
14:59 olass egonw: pong
14:59 egonw wanted to ask about ui.open(File, editorName)
15:00 egonw if I give the matrix editor there, it fails when that editor does not exist
15:00 egonw instead of taking the default as back up
15:00 olass sounds reasonable
15:00 olass ok
15:00 egonw I guess that makes sense
15:00 egonw it's as specified in the API...
15:01 egonw so intended...
15:01 egonw so, nevermind
15:01 egonw pop up for tanimoto works now
15:01 egonw but does not open a matrix editor, as that is not part of the platform
15:02 CIA-63 bioclipse.ds: Ola Spjuth master * r295e322 / (9 files in 9 dirs): Set version to 2.2.0.RC1 for plugins and features. - http://bit.ly/3RtdeP
15:03 olass egonw: should we make matrix editor part of platform?
15:04 egonw yes, in 2.4
15:04 egonw then again...
15:05 olass is it not stable enough for 2.2.0.RC1?
15:05 olass considering teh stability of other features...
15:05 egonw other features are tested
15:05 egonw have unit tests...
15:05 olass well.. to some extent, yes
15:05 egonw and for the rest...
15:06 egonw it's a stupid matrix editor
15:06 egonw can't even color cells by value
15:06 olass yes
15:06 olass it's rather limited
15:06 egonw and I have no clue what deps it brings in...
15:06 olass jama
15:06 olass only jama
15:06 olass hmm, maybe some other too
15:07 olass but not good that the matrix does not show for tanimoto and RMSD
15:07 egonw it does show up
15:07 egonw but just in a text editor
15:07 egonw but not really ideal indeed
15:08 CIA-63 bioclipse.cheminformatics: Egon Willighagen 2.2.x * r89a8ad4 / (2 files in 2 dirs): Added GUI action for calculating the Tanimoto Similarity Matrix which opens in a separate editor (fixes #1663) - http://bit.ly/3qm1Tb
15:08 zarah bug #1663 | http://tinyurl.com/y9zg3do
15:08 olass we could put matrix editor in experimental and write that to referees
15:08 olass or.. write that in the blog post
15:08 olass probably better
15:11 egonw there is a Statistics Feature
15:11 egonw we should put that on the update site
15:11 olass yup
15:11 egonw have to catch the bus soon...
15:11 olass very bad naming however
15:12 olass it has nothing about statistics to do
15:13 egonw no, not yet
15:13 egonw well...
15:13 egonw it was to some extend...
15:13 egonw isn't that scatter plot widget not also there
15:13 egonw that's about as much statistics as many biologists do :)
15:13 olass what has that to do with statistics?
15:14 olass it's a plot
15:14 olass really
15:14 egonw we could have it calculate column means, if that makes you feel better :)
15:14 egonw and don't tell me those are not statistics :)
15:15 egonw and yes, we should have a Proteochemometrics Feature indeed...
15:15 * olass thinks that a t-test minimum should be available in order for statistics to be a suitable name
15:15 olass PCM feature is in teh future
15:15 olass been planned for 5 years :)
15:15 egonw must be very well designed then :)
15:19 egonw anyway... it's very much closing in...
15:20 olass it is pending mostly bioclipse.bioinformatics
15:21 * egonw is catching his bus...
15:21 CIA-63 bioclipse.qsar: Ola Spjuth master * r036fdc8 / plugins/net.bioclipse.qsar.model/src/net/​bioclipse/qsar/util/QsarXMLProcessor.java : Stay within 80 chars - http://bit.ly/7TVkU
15:21 CIA-63 bioclipse.qsar: Ola Spjuth master * rac826da / (16 files in 16 dirs): Set version to 2.2.0.RC1 - http://bit.ly/2p8JnK
15:46 CIA-63 bioclipse.core: Carl Masak master * rf8652c0 / plugins/net.bioclipse.scripting.ui/src/net/bi​oclipse/scripting/ui/views/JsConsoleView.java :
15:46 CIA-63 bioclipse.core: [JsConsoleView] only says 'not found' if not found
15:46 CIA-63 bioclipse.core: Fixes #1704. - http://bit.ly/yT0I
15:46 zarah bug #1704 | http://tinyurl.com/yf9qvs6
16:04 masak I'm getting this when trying to start Bioclipse:
16:04 masak java.lang.UnsatisfiedLinkError: Cannot load 32-bit SWT libraries on 64-bit JVM
16:06 masak olass: has that happened to you?
16:06 mgerlich_ joined #bioclipse
16:08 olass masak: no
16:09 olass masak: how did that happen?
16:09 masak olass: trying to get Bioclipse running.
16:09 masak got that when I tried.
16:16 masak I suspect I have the wrong Eclipse or something.
16:17 olass it just happened in the middle out of nothing???
16:17 olass masak: did it work yesterday with same Eclipse?
16:17 masak olass: this is the first time I try to get Bioclipse to run on this hard drive.
16:18 olass I see...
16:18 masak have been able to code without running Bioclispe yesterday and today.
16:18 masak but I felt like checking out http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1706
16:18 zarah masak's link is also http://tinyurl.com/ydauawk
16:18 masak and see if I could reproduce it.
16:18 masak that's when I ran into problems.
16:19 olass are you running with Java 1,6?
16:19 masak that might be.
16:19 masak checking.
16:19 olass try 1.5
16:20 masak good idea. how?
16:20 masak yup, running 1.6.0_15
16:20 olass in run config
16:20 olass select 1.5 JRE
16:20 olass or better, set Eclipse to use 1. by default
16:20 masak oki.
16:21 olass maybe you need to install 1.5?
16:21 masak seems not.
16:21 masak at least, it was an option among the Runtimes.
16:22 masak oh, and I also get a warning about an error in net.bioclipse.webservices.
16:22 olass oh?
16:22 olass what error?
16:23 masak I can check.
16:23 masak hm. still getting the 64-bit JVM error.
16:23 masak am I the first dev to run Snow Leopard?
16:24 olass probably
16:24 masak ah. webservices has cdk dependencies.
16:24 masak and I haven't installed cdk.
16:24 olass have you pulled?
16:24 olass that should not be
16:24 olass I fixed that
16:24 masak pulled what? core?
16:24 olass core
16:24 olass yes
16:24 * masak pulls
16:25 masak Already up-to-date.
16:25 olass 2.2.x branch?
16:25 masak admittedly not.
16:25 * masak tries that one
16:25 olass we have not merged master with 2.2.x in a while..
16:26 * olass suggests we do that after RC1 release
16:26 masak hm, that gave me more errors...
16:27 olass please report
16:27 olass (after a refresh)
16:27 olass (possible after 'clean')
16:28 olass and set target platform
16:28 * masak cleans
16:28 * masak sets target platform... again
16:29 masak wow. building is fast.
16:29 masak still lots of errors.
16:30 masak I think the original error is in MANIFEST.MF
16:30 masak line 8: Require-Bundle: org.eclipse.ui,
16:30 masak Unsatisfied version constraint: org.eclipse.ui: 0.0.0
16:31 masak same with lines 9-15.
16:37 olass sounds bad
16:38 masak I'm pretty sure I downloaded Eclipse RCP Mac Cocoa 32bit.
16:38 masak maybe I should try 64bit instead?
16:38 olass but you are running a 64 bit machine now!
16:38 olass SnowLeopard is 64 bit
16:38 masak \o/
16:38 masak have to get used to that.
16:38 olass :)
16:38 masak maybe that's why everything is so dang fast?
16:39 masak because it does everything 64 bits at a time instead of 32...
16:39 olass I suppose that is the intention...
16:40 * masak downloads the 64bit version
16:46 olass @tell egonw you talked about a Statistics Feature but there is none in bioclipse.statistics repo.
16:46 zarah Consider it noted.
16:47 masak heh, funny.
16:47 masak downloaded the 64bit Eclipse, opened it and kept working on the exact same workspace.
16:49 masak nope. still the exact same problem.
16:52 masak I think I'm stuck.
16:59 samuell joined #bioclipse
17:36 CIA-63 bioclipse.statistics: Ola Spjuth master * r468bc66 / (2 files in 2 dirs): Set version to 2.2.0.RC1. - http://bit.ly/uWNc2
17:48 masak olass: ping
17:49 olass masak: pong
17:49 masak olass: can I discuss the manuscript here, or is some other place better?
17:50 * masak goes privmsg
18:49 sneumann__ joined #bioclipse
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19:44 edrin left #bioclipse
21:13 egonw joined #bioclipse
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