Camelia, the Perl 6 bug

IRC log for #bioclipse, 2007-11-05

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All times shown according to UTC.

Time Nick Message
00:11 nop76567 joined #bioclipse
05:42 masak joined #bioclipse
05:55 bjarni morrn carl
06:00 masak morrn bjarni
06:02 CIA-18 bioclipse: carl_masak * r4123 /trunk/playground/plugins/net.bioclip​se.expression.tests/src/net/bioclipse​/expression/tests/FunctionsTest.java:
06:02 CIA-18 bioclipse: [FunctionsTest.java]
06:02 CIA-18 bioclipse: * corrected misspelled function name
06:03 CIA-18 bioclipse: carl_masak * r4124 /trunk/playground/plugins/net.bioclipse.expressi​on/src/net/bioclipse/expression/Calculator.java:
06:03 CIA-18 bioclipse: [Calculator.java]
06:03 CIA-18 bioclipse: * implemented point notation for functions
06:03 masak ...though goodness knows if it's a good idea :/
06:04 masak it's sexy, yes, but is it sane?
06:10 bjarni what's exjobb in english?
06:10 masak bjarni: degree project
06:10 bjarni in that case, I'm looking at my degree project, reading about JRI, eating lunch and doing Update work
06:11 masak how multitasking of you
06:11 bjarni I am very proud
06:11 masak how's your lunch?
06:11 bjarni too hot
06:12 bjarni and it contains .24% lobster apparently
06:12 masak so you'd have to eat more than 400 lunches of that kind just to get one lobster
06:13 masak easier to just get a lobster, if you ask me
06:13 masak no, that's not it
06:13 bjarni what's the point
06:13 masak it probably doesn't contain a 400th of a lobster
06:14 masak more likely, .24% of it is lobster
06:14 bjarni yes that's what I meant
06:14 masak bjarni: if you had to guess, which weighs more, your lunch or a lobster?
06:14 bjarni it doesn't say how big the original lobster was
06:14 masak no, that's a problem
06:14 bjarni and I don't know how big a lobster is, but I'd say bigger than 350g
06:14 masak me too
06:15 masak up around 1 kg, I'd guess
06:15 bjarni not all of it is considered for inclusion in these meals though
06:15 masak shame. the shell is probably very nutritious
06:15 bjarni you'd never collect a complete lobster from the parts found in the food
06:15 bjarni I hope
06:16 masak in that sens, wonder how many percents lobster a lobster contains
06:16 bjarni it was a disturbing experience when I realised lions eat poop
06:16 masak well, pigs do too
06:17 masak and they're even closer to us, geographically and biologically
06:17 bjarni well yes, but lions eat poop in the form of freshly killed animals containing poop
06:17 bjarni they don't discriminate when they eat the animal
06:17 bjarni they just gobble it down, faeces and all
06:17 masak they're probably very hungry
06:17 bjarni still, I'd save it for hard times if I was them
06:18 bjarni I'm not sure poop goes bad
06:18 masak probably goes stale, though
06:18 bjarni I think I'd prefer that
06:18 masak what I meant was, they might be too hungry to have time to discriminate
06:18 bjarni ooh, I think I found the lobster bit
06:19 masak the .24%?
06:19 masak cool
06:19 bjarni I think so because it was red
06:19 masak what color is lion meat?
06:19 bjarni well red unless you remove all the blood I guess
06:19 bjarni otherwise flesh colour
06:20 masak there's no universal flesh color, is there?
06:20 bjarni more or less
06:20 bjarni when talking about mammals at least
06:21 masak ok
06:21 bjarni the paint hue which is called "flesh" is the colour that you and I are on the outside
06:22 masak oh, so we're flesh-colored?
06:22 bjarni yes
06:22 masak human: the other white meat
06:22 bjarni and most meat looks something like that doesn't it, except it can be a little whiter or browner or grayer
06:23 masak true
06:23 bjarni or maybe not whiter, but grayer anyway
06:23 masak there's some kind of color-space volume in which flesh exists
06:24 bjarni strange otherwise
06:24 masak no, I mean a strict subspace of the full color space
06:24 bjarni as in there is at least one colour which flesh can't be?
06:25 masak right
06:25 masak still sounds a bit tame when you put it like that
06:25 bjarni but it's probably true
06:25 masak bet it is
06:25 bjarni this is speaking of mammals though
06:25 masak sure
06:25 bjarni include fish, and you have to add an alpha channel
06:26 masak salmon are pink, for example
06:26 masak that's red + 50% alpha or something
06:26 masak no, that's not it
06:26 masak you really meant (semi-)transparent meat
06:26 bjarni no that's red + 50% turquoise
06:27 bjarni yes
06:27 masak ack
06:43 CIA-18 bioclipse: carl_masak * r4125 /trunk/playground/plugins/ (4 files in 2 dirs):
06:43 CIA-18 bioclipse: * implemented proof-of-concept where all variables are passed by value
06:43 CIA-18 bioclipse:  to the functions
06:43 CIA-18 bioclipse: * all tests now pass
06:46 CIA-18 bioclipse: carl_masak * r4126 /trunk/playground/plugins/ (4 files in 2 dirs):
06:46 CIA-18 bioclipse: * reverted last commit
06:46 CIA-18 bioclipse: * we're now undecided again
07:42 jonalv joined #bioclipse
07:43 masak mornin' jonalv
07:44 jonalv morning
07:51 thomas_ku joined #bioclipse
08:06 ilogger2 joined #bioclipse
08:26 egonw joined #bioclipse
08:35 CIA-18 bioclipse: carl_masak * r4127 /trunk/playground/plugins/ (4 files in 2 dirs):
08:35 CIA-18 bioclipse: [net.bioclipse.expression]
08:35 CIA-18 bioclipse: [net.bioclipse.expression.tests]
08:35 CIA-18 bioclipse: * merged in r4125 again
08:35 CIA-18 bioclipse: * deleted package net.bioclipse.expression.ast, no longer need
08:35 CIA-18 bioclipse:  symbolic expressions
08:38 CIA-18 bioclipse: carl_masak * r4128 /trunk/playground/plugins/net.biocli​pse.expression/META-INF/MANIFEST.MF:
08:38 CIA-18 bioclipse: [MANIFEST.MF]
08:38 CIA-18 bioclipse: * chased changes from last commit
09:06 CIA-18 bioclipse: jonalv * r4129 /trunk/playground/plugins/ (2 files in 2 dirs): Wrote test for exception being thrown when supressed variable is used in expressions
09:23 CIA-18 bioclipse: jonalv * r4130 /trunk/playground/plugins/net.bioclip​se.expression.tests/src/net/bioclipse​/expression/tests/FunctionsTest.java: Wrote functions tests for suppressed variables
09:30 EskilA joined #bioclipse
09:37 CIA-18 bioclipse: carl_masak * r4131 /trunk/playground/plugins/net.bioclip​se.expression.tests/src/net/bioclipse​/expression/tests/FunctionsTest.java:
09:37 CIA-18 bioclipse: [FunctionsTest.java]
09:37 CIA-18 bioclipse: * removed pesky annotations
09:41 CIA-18 bioclipse: carl_masak * r4132 /trunk/playground/plugins/net.bioclip​se.expression.tests/src/net/bioclipse​/expression/tests/FunctionsTest.java:
09:41 CIA-18 bioclipse: [FunctionsTest.java]
09:41 CIA-18 bioclipse: * fixed typo
09:49 CIA-18 bioclipse: carl_masak * r4133 /trunk/playground/plugins/ (3 files in 2 dirs):
09:49 CIA-18 bioclipse: [FunctionsTest.java]
09:49 CIA-18 bioclipse: [VariablesTest.java]
09:49 CIA-18 bioclipse: * further typo fixing
09:49 CIA-18 bioclipse: [Calculator.java]
09:49 CIA-18 bioclipse: * introduced suppressed variables
10:04 CIA-18 bioclipse: carl_masak * r4134 /trunk/playground/plugins/ (2 files in 2 dirs):
10:04 CIA-18 bioclipse: [VariablesTest.java]
10:04 CIA-18 bioclipse: * further typo fixing
10:04 CIA-18 bioclipse: [Calculator.java]
10:04 CIA-18 bioclipse: * first half of suppressed variables impl
10:14 CIA-18 bioclipse: carl_masak * r4135 /trunk/playground/plugins/net.bioclipse.​expression/src/net/bioclipse/expression/ (Calculator.java SuppressedVariableException.java):
10:14 CIA-18 bioclipse: [Calculator.java]
10:14 CIA-18 bioclipse: * implemented second half of suppressed vars
10:14 CIA-18 bioclipse: [SuppressedVariablesException.java]
10:14 CIA-18 bioclipse: * new exception to distinguish from other Calculator exceptions
10:24 olas joined #bioclipse
10:24 olas hi
10:28 bjarni hello
10:46 bjarni eclipse seems to have a very low good/bad ratio
10:47 bjarni I've started it twice today. first time it just hung and used up 1.3Gb of memory before I killed it.
10:47 bjarni second time I managed to create a project, but before I could edit it eclipse crashed...
10:47 EskilA joined #bioclipse
10:48 bjarni this would trouble me less if the program could be started in under a minute...
10:48 olas bjarni: that never happens on Mac OS X
10:48 bjarni that's not a very good excuse, is it?
10:48 olas Do you use Java 1.5?
10:49 bjarni I don't know, it's whatever the currently installed eclipse package uses in debian I suppose
10:50 olas you can see how you have staretd Eclipse by going to menu: About
10:50 bjarni a few moments then please...
10:50 olas and the nclick "configuration details"
10:50 bjarni I'm currently starting it, I'll be back when it's done :-)
10:51 olas Strange
10:51 olas Laszlo never complained about Eclipse on that laptop
10:51 olas You can try giving Eclipse more memory on startup
10:51 bjarni java.home=/usr/lib/jvm/java​-1.5.0-gcj-4.1-1.5.0.0/jre
10:52 bjarni that should answer the question
10:52 olas you should use Suns java 1.5
10:52 bjarni I'm not running it on the laptop
10:52 olas oh?
10:52 olas Your home computer?
10:52 bjarni update
10:52 olas ok
10:53 bjarni I imagine it's faster to run it in the same building than at bmc :-)
10:53 olas :-)
10:53 bjarni even though the local network in the terminal room is probably the bottleneck at 10MB/s
10:54 bjarni anyway, as you can see, it is running on java 1.5
10:54 olas is that Sun's java?
10:54 bjarni and there it crashed again
10:55 olas I don't think you should use gcj
10:55 bjarni argh
10:56 olas but maybe that's not the problem
10:56 bjarni that's how the debian package is configured...
10:56 olas http://www.klomp.org/mark/gij_eclipse/
10:57 bjarni ah
10:57 bjarni :-/
10:58 olas http://www.eclipsecon.org/2006/Sub.do?id=232
10:58 olas Seems like it is possible but might require a bit of tweaking
10:58 olas egonw: Have you used gcj with Eclipse?
10:59 * bjarni ssh:s to the laptop
10:59 olas One of egonw's interests is to run Eclipse/Bioclipse on open source VM's
10:59 bjarni that would be nice...
10:59 olas http://www.linuxjournal.com/article/7413
10:59 olas There are obviously many people who have succeeded
11:00 olas but I don't want to spend so much time on that
11:00 bjarni yes well I would prefer to spend as little time as possible tweaking packages
11:00 bjarni right
11:00 bjarni because I've already wasted plenty of time configuring that laptop
11:00 olas yup
11:00 bjarni not getting the external monitor to work, among other things
11:01 bjarni which is one of the reasons I would not have gotten a laptop for this if I had the choice
11:01 bjarni but that's policy I understand
11:01 olas not really
11:01 bjarni no?
11:01 olas you can use the other computer at BMC if you like
11:02 bjarni the one under the table?
11:02 olas see priv chat
11:03 bjarni I am replying there...
11:03 olas You have to register your nick
11:03 olas else I see nothing
11:03 bjarni er, how do I do that? :-S
11:03 olas hmmm don't remember
11:03 olas w8 a sec
11:03 bjarni and I guess that's why you never get my privs...
11:04 olas http://freenode.net/faq.shtml
11:04 bjarni yes, I noticed now that I got a message from the server about that
11:04 bjarni not in reply to the priv itself though, which is why I didn't see it
11:04 olas I know
11:04 olas I think it's confusing as well
11:05 bjarni anyway, I'll register, but about the computer: did you mean the one under my table at bmc?
11:06 olas yes
11:06 bjarni I think it has 256Mb of memory
11:06 bjarni it will need to swap to even start eclipse
11:06 olas really?
11:06 olas not the one with the broken front
11:06 olas the big tower
11:07 bjarni I think that's the one
11:07 olas It might need more memory, but it should have at least 1 Gb
11:07 bjarni we turned it on and checked it since I figured I'd much rather have a full computer to work on
11:07 olas We'll talk about that tomorrow
11:07 bjarni that sounds great
11:07 olas Let's meet at 10 and check out things
11:08 bjarni ok
11:08 * olas will have lunch now
11:12 viklund joined #bioclipse
11:15 bjarni so, I need to register a nick but bjarni is already taken
11:15 bjarni can't think of one
11:15 bjarni ... that would be acceptable here
11:28 kaskelot ok then, registered :-P
11:40 jonalv hi olas, kaskelot
11:44 olas hi kaskelot
11:44 olas kaskelot: why not bjarni?
11:45 kaskelot because it was taken :-P
11:46 jonalv kaskelot: join #farmbio! :)
11:53 egonw kaskelot: using 64bit?
11:53 egonw if so, reset to 32bit, and your Eclipse mem problems are solved
11:53 * egonw is away for a meeting
11:54 kaskelot it's a 32 bit system
12:13 olas http://bioclipse.blogspot.com/
12:15 jonalv nice olas that is a great thing!
12:18 olas I like it
12:18 olas let's talk about that tomorrow
12:18 jonalv yep that is more or less all we need right?
12:18 olas It goes a long way anyways
12:18 jonalv yep
12:18 olas and was really easy to implement
12:18 olas Extension points are great
12:19 jonalv nice
12:21 CIA-18 bioclipse: ospjuth * r4136 /trunk/plugins/net.bioclipse.rhino/ (5 files in 3 dirs): Added an extension point and interface for adding scripting commands to Rhino.
12:21 CIA-18 bioclipse: ospjuth * r4137 /trunk/plugins/net.bioclipse.rhino/​src/net/bioclipse/plugins/bc_rhino/ (2 files in 2 dirs): Adapted plugin to use new extension point
12:23 CIA-18 bioclipse: ospjuth * r4138 /trunk/playground/plugins/​net.bioclipse.biomoby.ui/ (3 files in 2 dirs): Added an extension to provide BioMoby scripting commands for Rhino
12:30 edrin joined #bioclipse
12:31 edrin hi
12:31 olas hi edrin
12:31 edrin hi olas
12:31 olas did yo usee my post?
12:31 olas http://bioclipse.blogspot.com/
12:31 olas created that EP we talked about
12:31 olas also wrote on: http://wiki.bioclipse.net/index.php?title=Bc_r​hino#Adding_a_simple_namespace_for_your_plugin
12:32 olas Noted that no need for dependency in bc_rhino
12:32 olas som removed that from the wiki
12:32 olas scripting in Bioclipse is comming along nicely!
12:34 olas With the console that masak is working on, it will be an even more interesting experience
12:34 edrin yes, indeed
12:35 edrin a console? greate... i can really use this for my xmpp thing...
12:35 * jonalv doesn't understand HSQLDB... :(
12:35 edrin and the extension point is greate for other developers, so they can hook in
12:36 olas yup
12:37 jonalv yep that's sounds great. I wanna try and hook in Spring AOP beans into that real soon now :)
12:37 olas yes!
12:37 CIA-18 bioclipse: ospjuth * r4139 /trunk/plugins/net.bioclipse.biojava.ui/ (5 files in 4 dirs): Use new scripting extension point in net.bioclipse.rhino to add scripting commands for BioJava
12:37 * olas is looking forward to that
13:05 egonw olas: might you kill the "Links" section in the blog...
13:05 egonw or fill them with something other than "Edit-Me" ?
13:15 olas egonw: done
13:15 * olas is not an experienced blogger
13:15 egonw I think you are doing an excellent job :)
13:19 egonw edrin: you don't got a blog, right?
13:19 jonalv seems popular with blogging...
13:19 CIA-18 bioclipse: ospjuth * r4140 /trunk/plugins/net.bioclipse.rhino/ (2 files in 2 dirs): Added 'console' as namespace when scripting, and command available is now: 'console.write("hello world");'
13:19 olas edrin: would you like to blog on bioclipseblog?
13:28 egonw olas: too bad the example code does not show how the fasta can be opened as BioJavaResource
13:31 egonw OK, pluggin it a bit in the blogosphere: http://chem-bla-ics.blogspot.com/2007/11/g​lueing-biomoby-services-together-with.html
13:33 olas :-)
13:34 jonalv By the way I wrote my first blog post last week: <http://loveorm.blogspot.com/> I am not at all an experienced blogger and that post was maybe not that great but the next one will be full of wisdom :)
13:35 olas I'll try to make a script create a resource and open it in an editor.
13:37 CIA-18 bioclipse: jonalv * r4141 /trunk/playground/plugins/ (3 files in 3 dirs): The test database now uses the database aliases so the connection url for it is on localhost/testServer. This technique will be necessary in order to work with multiple databases later on.
13:46 olas wooops
13:46 olas why did the logger leave?
13:47 jonalv ooh bother....
13:47 ilogger2 joined #bioclipse
13:47 jonalv ah there it is again :)
13:49 CIA-18 bioclipse: ospjuth * r4142 /trunk/plugins/net.bioclipse.biojava.ui/ (2 files in 2 dirs): Fix BioJava scripting commands
13:49 kaskelot ah here we go
13:49 kaskelot now I have a hello world plugin working in eclipse :-)
13:49 kaskelot sun java 1.5 and eclipse 3.3
13:50 jonalv kaskelot: good
13:50 egonw kaskelot: happy to hear that
13:50 kaskelot :-)
13:50 jonalv kaskelot: thought you would be here today...?
13:51 kaskelot isn't it tuesday and wednesday?
13:51 jonalv oh thougt it was monday - tuesday - wednesday now..
13:51 kaskelot oh ok, I wasn't sure we decided that
13:52 kaskelot but fine, I'll be there next monday :-)
13:52 jonalv me neither really but masak made me think it was...
13:52 jonalv or rather that we did
13:52 kaskelot mm, it's so nice to see a hello world program use nine hundred megabytes of memory
13:53 jonalv nine hunded meg? What are you doing?
13:53 kaskelot the hello world example in eclipse
13:53 kaskelot I mean this eclipse is the most memory-hungry program I've seen ever I think
13:53 jonalv hm my eclipse is using 232 meg and I am doing more advenced stuff than hello world
13:53 olas kaskelot: please work on JRI from within Eclipse. Martin needs that badly.
13:54 kaskelot olas: that's what I'm working on, trying to figure out eclipse here
13:54 olas If you can get the example to run, you can tell him what you did to achieve that.
13:54 kaskelot I've never used it before you know
13:54 olas good
13:54 olas I know
13:54 kaskelot I'll get right on doing the same things with some jri example code
13:54 kaskelot but jri looks like it's kind of hairy
13:55 kaskelot they have an entry in their faq about running jri programs where they answer "just use the provided shells cript to start you java code, it saves you the headache of setting everything up"
13:56 olas you got to be kidding
13:56 olas well, good luck :-)
13:56 kaskelot nope :-)
13:56 kaskelot it needs a lot of environment variables apparently
13:56 kaskelot paths to everything and so on, but I'll look into it
13:58 jonalv Have a nice swim in the environment-variables-ocean then kaskelot! :)
13:59 kaskelot \o/
14:42 CIA-18 bioclipse: jonalv * r4144 /trunk/playground/plugins/​net.bioclipse.structuredb/ (5 files in 3 dirs): renamed StructuredbDataBaseType -> Structuredb and added map for applicationcontexts. Right now the pedulum is swinging in the one-separate-applicationcontext-for-each-database direction...
15:08 CIA-18 bioclipse: jonalv * r4145 /trunk/playground/plugins/n​et.bioclipse.structuredb/: svn:ignore...
15:10 CIA-18 bioclipse: jonalv * r4146 /trunk/playground/plugins/net.​bioclipse.structuredb.tests/: svn:ignore...
15:11 CIA-18 bioclipse: jonalv * r4147 /trunk/playground/plugins/net.bioclip​se.usermanager/META-INF/MANIFEST.MF: manifest configs...
16:04 CIA-18 bioclipse: jonalv * r4148 /trunk/playground/plugins/ (2 files in 2 dirs): added method for getting a list of account ids for an accounttype name
16:06 CIA-18 bioclipse: jonalv * r4149 /trunk/playground/plugins/net.bioclipse.structured​b/src/net/bioclipse/structuredb/Structuredb.java: Made Structuredb a UsermanagerEventListener since it should respond to login / logout events. Not entirely sure what it will do though...
16:29 * egonw just reinstall bioclipse 1.1.3
16:30 olas egonw: why?
16:30 egonw to display some CDK test files
16:31 olas :-)
16:31 egonw he, that's why we developed BC, not?
16:32 CIA-18 bioclipse: ospjuth * r4150 /trunk/plugins/net.bioclipse.biojava.ui/ (2 files in 2 dirs): Tried to get visualization working from scripts. Seems Eclipse has changed selections in 3.3... we should not rely on this method in Bioclipse2! Problem unresolved.
16:36 CIA-18 bioclipse: ospjuth * r4151 /trunk/plugins/net.bioclipse.rhino/ (4 files in 3 dirs):
16:36 CIA-18 bioclipse: Added BioResource scripting tools and Editor scripting tools. Example features:
16:36 CIA-18 bioclipse: myres=bioresource.create(content);
16:36 CIA-18 bioclipse: myres=bioresource.create("myseq.seq", content);
16:36 CIA-18 bioclipse: editor.open(myres);
16:36 CIA-18 bioclipse: Note: Selections are not triggered and hence no views are able to display created resources. They are however opened in correct editor. Unresolved problem (appeared in Eclipse 3.3). Should be resolved in Bioclipse2.
16:36 egonw olas: cool, thanx!
16:37 CIA-18 bioclipse: ospjuth * r4152 /trunk/playground/plugins/net.biocli​pse.biomoby.ui/META-INF/MANIFEST.MF: Exported packages to get scripting to work.
16:37 olas egonw: it is really not nice att all currently
16:37 olas been struggling to get Bioclipse push selections, but it just doesn't respond to it
16:37 olas (and it used to)
16:37 olas Don't know how to fix it :-(
16:38 olas will update the rhino scripts page with sample script
16:38 egonw ack
16:38 egonw I don't know either :)
16:39 CIA-18 bioclipse: ospjuth * r4153 /trunk/plugins/net.bioclipse/src/net/​bioclipse/views/BioResourceView.java: Tried to adapt for IStructuredSelection but unable to resolve selection problem from a script.
16:59 egonw bye all
16:59 CIA-18 bioclipse: ospjuth * r4154 /trunk/plugins/net.bioclipse/src/net/​bioclipse/views/BioResourceView.java: Created a RefreshRunnable to update TreeViewer from GUI thread. Still doesn't work...
16:59 CIA-18 bioclipse: ospjuth * r4155 /trunk/plugins/net.bioclipse.rhino/src/net/b​ioclipse/plugins/bc_rhino/EditorTools.java: Tried to refresh using new runnable. No, doesn't do the trick.
17:39 CIA-18 bioclipse: ospjuth * r4156 /trunk/plugins/net.bioclipse.biojava.ui/src/n​et/bioclipse/plugins/views/SequenceView.java: Removed debug outs
17:41 CIA-18 bioclipse: ospjuth * r4157 /trunk/plugins/net.bioclipse.webservices/ (4 files in 3 dirs): Added scripting namespace for webservices plugin. Only method available now: 'mypdb=ws.downloadPDB("1ale");'
18:08 edrin joined #bioclipse
18:09 edrin no, i currently have no blog
18:26 edrin good night
18:26 edrin left #bioclipse
19:39 egonw joined #bioclipse
22:32 olas left #bioclipse

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