Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-11-18

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All times shown according to UTC.

Time Nick Message
07:16 thomas_ku joined #bioclipse
08:13 egonw joined #bioclipse
08:14 egonw my laptop/monitor decided to run on full resolution today...
08:14 egonw anyone needs some pixels...?
08:14 egonw I sell them for 1 krona per pixel
08:18 thomas_ku egonw: are you running linux on a mac?
08:19 egonw mac?
08:19 egonw no, rather not
08:20 thomas_ku I though you got a mac in sweden...
08:20 egonw who told you that??
08:21 egonw they wanted me too, but I did not
08:21 thomas_ku I remember an iirc chat where olas said something about a mac for you...
08:22 thomas_ku but not sure about that anymore...
08:23 thomas_ku what machine are you using now?
08:25 egonw still an old laptop
08:26 egonw yes, ola really wanted me to get a Mac
08:26 egonw but I don't like vendor hardware lockin
08:26 thomas_ku ok I just wanted to know if you have experience with running an other os on a mac...
08:27 egonw sorry
08:27 egonw jonalv does a bit
08:27 egonw I think he has had linux run on a mac
08:27 thomas_ku it is no problem I just thought you have problems because of [09:14:28] <egonw> my laptop/monitor decided to run on full resolution today...
08:27 Gpox joined #bioclipse
08:28 egonw moin Gpox
08:29 egonw yeah, my kubuntu is not so polished as earlier versions
08:29 egonw maybe to many dist-upgrades
08:29 egonw anyway... got an external monitor
08:29 egonw which runs at different resolution each time a recover my laptop from suspend
08:29 egonw and now the monitor is in 1600x1050 or so :)
08:29 egonw 24 inch
08:29 thomas_ku thats nice
08:31 egonw indeed
08:31 egonw I just don't know what to do with all those pixels....
08:32 thomas_ku I have a 24 inch monitor too with 1900x1200 pixel and i love those pixel...
08:35 egonw :)
08:55 jonalv joined #bioclipse
08:56 jonalv hi
08:56 zarah hi jonalv
08:59 egonw hi jonalv
08:59 Gpox hi jonalv
08:59 zarah hi jonalv
09:00 jonalv Gpox: working from home today?
09:00 Gpox yes
09:00 * jonalv is getting a tooth. He is in a foul mood... :(
09:00 jonalv It took me forever to eat some yughurt this morning...
09:01 egonw :(
09:04 CIA-53 bioclipse: jonalv * r7753 /bioclipse2/trunk/plugins/net.bioclipse.s​tructuredb/src/net/bioclipse/structuredb/ (AnnotationUIModel.java DBMoleculesEditorModel.java): [Structuredb] quick unoptimized code for opening labels for browsing
09:15 jonalv egonw: have you seen bug 134?
09:15 egonw yes, it is urgent?
09:16 egonw I'm going through the list of bugs
09:16 egonw and still closing 'fixed' bugs
09:16 jonalv egonw: Do you have any ideas?
09:16 egonw by verifying that the really have been fixed
09:16 egonw just found a new bug, whcih I am now fixing...
09:16 egonw yes, I have ideas...
09:16 egonw meet me here?
09:16 jonalv good :)
09:16 jonalv oki I will be right over... :)
09:56 edrin joined #bioclipse
09:56 edrin hi
09:56 zarah hi edrin
10:00 edrin egonw: available?
10:01 egonw yes
10:05 egonw jonalv: it will keep raining for the rest of the day :(
10:05 jonalv egonw: k
10:06 jonalv egonw: I wonder if we can speed up omports to structuredb somehow...
10:06 jonalv |imports
10:06 egonw yes, I think we should be able to do that
10:06 egonw but I don't have time for that now...
10:07 jonalv :)
10:11 jonalv egonw: so my great plkan to identify the entry that failed by it not having any SMILS wasn't that succesfull. 205 compounds from that file does not get SMILES...
10:11 egonw :)
10:12 egonw well, let's start with the first...
10:12 egonw does it read PUBCHEM_COMPOUND_CIDs?
10:13 egonw that would be interesting annotation
10:14 jonalv egonw: I don't yet create annotations for those things but they are in the cml...
10:14 egonw ok, good
10:14 egonw then please give me the CID of the first structure without SMILES
10:14 jonalv 209
10:21 egonw grmph...
10:22 egonw 209?
10:22 egonw ...
10:22 egonw too many '209' strings in that file :(
10:22 jonalv yea I think so
10:23 egonw do you store CDKConstants.TITLE too?
10:23 egonw should be something like:
10:23 egonw -OEChem-10090810202D
10:23 egonw that's more unique :)
10:23 jonalv I don't think the moleculeseditor show that
10:23 jonalv hang on
10:23 egonw should be in the CML
10:24 egonw ok, found it
10:25 jonalv but It hink Bioclipse is configured to not calculate smiles on too big molecules...
10:25 egonw oh no
10:25 egonw they all have the same OEChem line :)
10:26 jonalv oh
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10:51 Julio joined #bioclipse
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10:57 gilleain joined #bioclipse
10:57 gilleain hallo.
10:57 edrin hello
10:57 zarah hi edrin
11:03 egonw hi gilleain
11:13 jonalv egonw: food?
11:13 egonw yes
11:19 gilleain huh. net.bioclipse.core has groovy on its bundle classpath.
12:03 egonw isn't that the javascript engine?
12:05 jonalv uhm wouldn't that be rhino?
12:06 egonw yes, i think you're right
12:09 egonw Gpox: will you be at UU tomorrow?
12:09 Gpox yes
12:13 gilleain yes, rhino is surely the javascript engine, I guess the groovy requirement was/is for some kind of groovy console? (I really hate the name 'groovy', but I'm reading a book about it at the moment).
12:21 jonalv gilleain: ah, yea we had a groovy console for a little while. I think it got removed duirng the first build because we didn't manage to make it work and didn't have the time to fiddle around with it...
12:22 gilleain oh well, the js works, so that's all good.
12:23 gilleain Seems that 'dynamic java' (as I call groovy) has some nifty features, though, like Range objects
12:23 gilleain like : "for (i in 1..10) print i"
12:24 gilleain or, ruby-like : 1..10.each(print i)
12:34 * egonw is taking some time to step away from debugging
12:34 egonw and do something new
12:36 gilleain something new?
12:36 egonw yes, like a new plugin for bioclipse
12:36 gilleain oooh.
12:37 jonalv which one are you gonnna do? :)
12:37 egonw net.bioclipse.rdf
12:37 jonalv rdf?
12:37 egonw right
12:37 jonalv what will it do?
12:37 gilleain rich data feeds?
12:38 egonw nah, that's CMLRSS
12:38 gilleain oh, right.
12:38 egonw @google rdf
12:38 zarah egonw: http://www.w3.org/RDF/
12:38 gilleain resouce description framework
12:39 gilleain huh "s/souce/source/"
12:39 jonalv so what are the use cases in Bioclipse?
12:40 egonw with a bit of luck, I can demo on Thu/Fri
12:40 egonw oh, btw, we have a *really* nice room for friday :)
12:40 egonw make sure to bring your tuxedo and sigar :)
12:41 egonw oh... an laptop
12:41 egonw but that's default, not?
12:41 gilleain ah good. will you be bringing some of the spare pixels from your screen :)
12:41 jonalv egonw: huh? What room have you gotten?
12:41 egonw Scheele
12:41 jonalv aha
12:41 jonalv that's nice :)
12:41 egonw nah, but will bring a beamer
12:41 egonw so, we'll have large pixels...
12:41 gilleain a BMW?
12:41 gilleain oh, a projector.
12:41 egonw :)
12:43 edrin the bc js console now crashs my bc instance btw...
12:44 jonalv :(
12:44 jonalv edrin: what system are you on?
12:44 edrin windows
12:44 gilleain :( ** 10
12:44 edrin it freezes
12:44 gilleain ahhh. did that to me too.
12:44 gilleain I has bug reports.
12:44 edrin one cmd is ok, next cmd freez
12:45 edrin ok
12:45 gilleain @pele gilleain
12:45 gilleain hmm
12:45 zarah [Bug 77] paths in windows slash problems http://tinyurl.com/578aen
12:45 zarah [Bug 78] CR/LF problems on windows       http://tinyurl.com/6eznsa
12:45 zarah Entire list at http://tinyurl.com/674uaz
12:45 gilleain hooray!
12:46 jonalv hm
12:46 jonalv @pele jonalv
12:47 zarah [Bug 97] missing unit test for fromCm... http://tinyurl.com/5lxvyh
12:47 zarah [Bug 101] missing unit test for loadM... http://tinyurl.com/5s3c2p
12:47 zarah [Bug 108] missing manager unit test f... http://tinyurl.com/5ok8h9
12:47 zarah [Bug 109] missing manager unit test f... http://tinyurl.com/6crhlx
12:47 zarah [Bug 94] missing unit test for create... http://tinyurl.com/674rgn
12:47 zarah Entire list at http://tinyurl.com/6cpumc
12:47 jonalv @pele jonathan
12:47 zarah [Bug 77] paths in windows slash problems http://tinyurl.com/578aen
12:47 zarah [Bug 78] CR/LF problems on windows       http://tinyurl.com/6eznsa
12:47 zarah [Bug 1] There are people not using Bi... http://tinyurl.com/55k8wf
12:47 zarah Entire list at http://tinyurl.com/5zhsv8
12:48 gilleain ah.
12:48 jonalv strange...
12:48 gilleain hmm.
12:54 gilleain oh, I meant #123
12:55 gilleain or bug #123
12:55 egonw @pz #123
12:55 zarah http://tinyurl.com/67c3my
12:56 gilleain that's the fellow.
12:56 gilleain and @pz #124
12:56 gilleain @pz #124
12:56 zarah http://tinyurl.com/6lgvoh
12:56 gilleain riight.
13:00 CIA-53 bioclipse: egonw * r7754 /bioclipse2/branches/rdf/: Branch for some experimental RDF work.
13:28 CIA-53 bioclipse: jonalv * r7755 /bioclipse2/trunk/plugins/ (4 files in 3 dirs): [structuredb] wrote test + stub for attempt at retrieving molecules in a label one by one when needed.
13:28 egonw jonalv: coffee with cake
13:29 edrin egonw: i just sent you a mail
13:29 egonw ok
13:29 egonw bbl
13:30 edrin maybe you can read it, if you like it i will send it to the ws mailing list
13:30 egonw yeah, looks fine
13:30 egonw please send it
13:31 edrin :)
13:31 edrin will do so
13:33 edrin egonw: do you think i should also crosspost it to jdev ?
13:51 CIA-53 bioclipse: shk3 * r7756 /bioclipse2/trunk/plugins/net.bioclip​se.specmol/src/net/bioclipse/specmol/​wizards/AddSpectrumWizardPage.java: better layout
13:57 CIA-53 bioclipse: shk3 * r7757 /bioclipse2/trunk/plugins/net.bioclipse​.specmol/src/net/bioclipse/specmol/wiza​rds/MoleculeFileContentProvider.java: solves bug #137
13:57 zarah bug #137 | http://tinyurl.com/6ynbfj
13:58 egonw edrin: yes, why not
13:58 egonw not sure how fond they are of advertisement, but should be OK, I think
13:58 egonw it's not commercial
13:59 masak joined #bioclipse
14:01 edrin :)
14:02 edrin maybe will post when released
14:02 edrin i posted to ws now
14:02 egonw yes, saw it
14:02 egonw jonalv: setting target platform helped resolve the Require-Bundle not found
14:06 masak jonalv++
14:18 egonw bwahahahaha
14:19 egonw who wants to see some cool graphics?
14:21 * masak is a bit busy right now
14:25 gilleain locally?
14:26 egonw yeah... sorry
14:26 egonw you'll have to wait until wednesday
14:26 masak egonw: make a screenshot!
14:26 egonw umm... tomorrow
14:26 gilleain :c
14:26 egonw masak: yes, will do :)
14:30 gilleain oh, egonw: talking of graphics, I forgot to mention that I was trying out tumblr:
14:30 gilleain gilleain.tumblr.com
14:31 gilleain (I am always spamming things here, sorry :)
14:31 egonw nice
14:31 masak indeed. gilleain++
14:31 gilleain it was only because I was pleased to have made the inner-ring stuff work 'right'.
14:32 egonw :)
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15:04 Julio joined #bioclipse
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15:08 Julio joined #bioclipse
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15:20 CIA-53 bioclipse: carl_masak * r7758 /bioclipse2/trunk/plugins/net.biocl​ipse.encryption.tests/src/net/biocl​ipse/encryption/EncrypterTest.java: [encryption] fixed some whitespace
15:20 CIA-53 bioclipse: carl_masak * r7759 /bioclipse2/trunk/plugins/net.bioclipse.encrypti​on/src/net/bioclipse/encryption/Encrypter.java: [encryption] implemented key-based encryption. all tests now pass.
15:22 CIA-53 bioclipse: carl_masak * r7760 /bioclipse2/trunk/plugins/net.bioclipse.encrypti​on/src/net/bioclipse/encryption/Encrypter.java: [encryption] added URL to page with usage examples
15:25 CIA-53 bioclipse: shk3 * r7761 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/​business/test/CDKManagerPluginTest.java: bug #98 (looks like this was not committed)
15:25 zarah bug #098 | http://tinyurl.com/5by2yn
15:25 CIA-53 bioclipse: egonw * r7762 /bioclipse2/branches/rdf/p​lugins/net.bioclipse.rdf/ (14 files in 7 dirs): Added RDF plugin, which will show knowledge about a molecule
15:25 shk3 was #100, actually
15:26 CIA-53 bioclipse: egonw * r7763 /bioclipse2/branches/rdf/featu​res/net.bioclipse.rdf_feature/ (. .project build.properties feature.xml): Added Bioclipse RDF feature
15:27 CIA-53 bioclipse: egonw * r7764 /bioclipse2/branches/rdf/plugin​s/net.bioclipse.rdf/plugin.xml: Better category name
15:28 CIA-53 bioclipse: egonw * r7765 /bioclipse2/branches/rdf/plugins/net.bio​clipse.rdf/src/net/bioclipse/rdf/views/ (RDFContentProvider.java RDFLabelProvider.java RDFView.java): Now uses data providers, so that the data shown updates on IStructuredSelection events
15:30 CIA-53 bioclipse: shk3 * r7766 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business.test/src/net/bioclipse/​cdk/business/test/CDKManagerTest.java: solves bug #98
15:30 zarah bug #098 | http://tinyurl.com/5by2yn
15:33 * masak likes that people suddenly write bug id numbers in their commit comments a lot
15:33 masak shk3++ egonw++
15:34 gilleain karma all round! map(operator.increment, everyone)
15:34 zarah all round! map(operator.increment, everyone) has a karma of 0
15:34 gilleain er...
15:34 masak she's very literal sometimes.
15:35 egonw gilleain: http://chem-bla-ics.blogspot.com/2008/​11/solubility-data-in-bioclipse-1.html
15:35 zarah egonw's link is also http://tinyurl.com/5zcv9x
15:35 egonw bottom right
15:35 egonw shk3: please add to the commit message what is actually fixes...
15:35 egonw so that one does not have to go off to pele to understand what the patch is supposed to do
15:36 gilleain hmmm. yes, egonw, that sure is an example of one of those! :) I've never seen a better example of that sort of thing.
15:36 egonw that was in reply to?
15:37 CIA-53 bioclipse: egonw * r7767 /bioclipse2/trunk/plugins/net.bioclipse.cdk10/ (.classpath build.properties jar/jumbo52.jar): Added old CML library, which cdk1.0.4 depends on, and no longer available from another plugin
15:37 CIA-53 bioclipse: carl_masak * r7768 /bot/trunk/zarah.pl: [zarah] now really doesn't accept task times longer than 16h
15:37 shk3 I like the sdf editor, btw
15:37 zarah joined #bioclipse
15:37 gilleain Oh, I just mean that I'm not sure what that is a picture of, but it looks good.
15:38 egonw gilleain: ah, ok
15:38 gilleain Is it a topic map?
15:38 egonw gilleain: and when you see it live, it is actually animated
15:38 egonw yes, like that
15:38 gilleain ahh.
15:38 CIA-53 bioclipse: egonw * r7769 /bioclipse2/trunk/plugins/net.bioclipse.cdk10/doc/ (cdk_home.html lgpl.html): Added missing CDK info for TOC (fixes #136)
15:38 zarah bug #136 | http://tinyurl.com/62zl6m
15:38 gilleain spring-layout type thing?
15:38 gilleain er, force-directed layout, rather.
15:38 egonw not currently...
15:39 egonw but I guess that is possible
15:39 gilleain no, I don't know, whatever works.
15:39 gilleain for arbitrary networks, force-directed is often used.
15:41 CIA-53 bioclipse: carl_masak * r7770 /bot/trunk/zarah.pl: [zarah] now accepts the filter word 'new' in @plan task listings
15:42 zarah joined #bioclipse
15:44 CIA-53 bioclipse: carl_masak * r7771 /bot/trunk/zarah.pl: [zarah] refined 'new' filter
15:44 zarah joined #bioclipse
15:46 egonw ok, going home
15:46 egonw cu tomorrow!
15:46 edrin bye
15:46 egonw shk3: are you coming to BMC in the afternoon?
15:46 egonw shk3, gilleain: you will have a laptop with you, I hope?
15:46 gilleain one, each, no doubt.
15:47 gilleain er. "one each,..."
15:49 egonw ok, have a safe trip, cu tommorow, at least at 18:00!
15:49 egonw bye!
15:51 shk3 uppsala: tell egon egonw I will hopefully be at BMC in the afternoon
15:52 shk3 will be in uppsala aroun 3 pm, I think
15:53 masak @tell egonw shk3 says he will hopefully be at BMC in the afternoon. will be in uppsala aroun 3 pm, he thinks.
15:53 zarah Consider it noted.
15:54 shk3 @messages
15:54 zarah shk3: You have no new messages.
15:55 CIA-53 bioclipse: carl_masak * r7772 /bot/trunk/zarah.pl: [zarah] slight refactor of plan directives
15:55 zarah joined #bioclipse
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16:15 CIA-53 bioclipse: carl_masak * r7773 /bot/trunk/zarah.pl: [zarah] surgically removes the "Bug" in "[Bug NN]" to save precious space
16:20 CIA-53 bioclipse: jonalv * r7774 /bioclipse2/trunk/plugins/net.bioclipse.u​sermanager.tests/tests/log4j.properties: added a log4j.properties to get logging when running tests
17:44 edrin left #bioclipse
17:56 CIA-53 bioclipse: shk3 * r7775 /bioclipse2/trunk/plugins/ne​t.bioclipse.spectrum.test/: Initial import.
17:57 CIA-53 bioclipse: shk3 * r7776 /bioclipse2/trunk/plugins/n​et.bioclipse.spectrum.test/ (16 files in 10 dirs): Initial import.
19:45 CIA-53 bioclipse: edrin_t * r7777 /xws/trunk/xws4j-sample-client/src​/sample/client/SampleClient.java:
19:46 edrin joined #bioclipse

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