Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-02-25

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All times shown according to UTC.

Time Nick Message
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09:41 olas joined #bioclipse
09:41 olas hi all
09:41 * olas is at EBI in Hinxton, UK
09:42 jonalv cool
09:43 olas was up at 03.45
09:43 olas a bit tired
09:43 olas hopefully it'll be a good workshop
09:54 egonw ha, nice
09:54 Dahlo joined #bioclipse
09:54 egonw olas: you'll meet christoph I guess?
09:58 laszlo joined #bioclipse
10:01 olas hi egonw
10:01 olas yes, tomorrow
10:02 olas he's not at EBI today
10:02 egonw :)
10:02 olas but the DAS WS will be interesting
10:02 egonw yeah, looking forward to your blog items about the meeting
10:02 olas oh
10:03 olas :-)
10:08 thomas_ku_ joined #bioclipse
10:11 olas egonw: around?
10:11 olas in the bc2 branch, net.bioclipse.cdk does not compile
10:11 olas it's externalized from cdk svn
10:11 olas any idea why?
10:12 egonw not at this moment
10:12 egonw but will look at it asap
10:12 olas all cdk classes are lost in net.bc.cdk
10:12 olas very strange
10:12 jonalv it's missing Jama for me
10:13 olas I updated and lost all CDK classes
10:13 jonalv someone might have removed them...
10:13 olas all classes?
10:14 jonalv The CDK people said that they where very old when I was talking to them trying to fix em
10:14 olas all classes?
10:14 jonalv They might theink that they should be rewritten but the easistest way would be to check the logs...
10:14 olas what are you talking about?
10:14 jonalv nothing
10:14 olas I miss ALL cdk classes
10:14 olas lack
10:14 jonalv forget all I said and check the logs
10:15 olas logs for what?
10:15 olas bioclipse?
10:15 olas cdk?
10:15 egonw much simpler...
10:15 egonw the code went into src/main
10:15 jonalv hang on what do you mean by "I miss ALL cdk classes"?
10:15 egonw so, yes, all classes have been deleted... and stored somewhere else
10:15 egonw yes, ALL
10:15 egonw mom..
10:15 egonw will fix that now...
10:16 olas great
10:17 * egonw is googling to find how to change svn:externals
10:20 jonalv egonw, did you put all the stuff back? I still have the org.openscience.cdk package in net.bioclipse.cdk in my bc2...
10:20 egonw what do you mean?
10:20 * jonalv is confused
10:20 jonalv which classes should I lack+
10:20 olas all
10:21 CIA-22 bioclipse: egonw * r4910 /branches/bioclipse2/chemoinfor​matics/net.bioclipse.cdk/src/: Updated svn:externals for change in CDK SVN
10:21 olas have you updated?
10:21 olas thanks, egonw
10:21 * olas is updating
10:21 olas jonalv: are you at r4910?
10:22 jonalv I don't even know how to see that... :/
10:22 olas RC on project
10:22 jonalv yes I am
10:23 olas properties
10:23 olas Subversion tab
10:23 jonalv I never lost any classes though...
10:23 jonalv oh well never mind
10:23 olas :-)
10:23 olas does it compile?
10:24 jonalv no
10:24 jonalv I miss Jama
10:24 olas then we might need egonw's help...
10:24 egonw Jama jar got renamed...
10:25 * egonw is booting eclipse
10:26 CIA-22 bioclipse: ospjuth * r4911 /branches/bioclipse2/chemoinformatics/n​et.bioclipse.cdk/META-INF/MANIFEST.MF: removed weka from manifest exports
10:26 egonw oh wait...
10:26 olas yes, seems like jama is missing
10:26 * egonw still needs to finish that wiki page about setting up a BC2 devel environment
10:26 jonalv huh?
10:26 egonw you know
10:27 egonw which those circular deps
10:27 egonw remember?
10:27 jonalv I thought that was solved...
10:27 egonw yes, but I never finished it fully
10:27 jonalv there is another problem with cdk in bc2 as well. but in cdk.ui
10:28 olas jonalv: I want us to create an sample plugin for bioclipse2 with dummy menus, actions, etc
10:28 jonalv it is that problem with org.openscience.cdk.tools.HydrogenAdder
10:28 * egonw is at step 4
10:29 jonalv egonw: please say that it is working :)
10:29 egonw hang on...
10:29 egonw doing three other thngs at the same time...
10:29 jonalv hehe
10:32 olas egonw is an octopus
10:39 egonw CDK has hit Debian GNU/Linux :)
10:39 jonalv cool
10:40 jonalv Wonder if we are gonna get Bioclipse in there
10:58 de_maas joined #bioclipse
11:05 olas joined #bioclipse
11:05 olas hi again
11:09 egonw [11:36] <-- olas has left this server ("User disconnected").
11:09 egonw [11:39] <egonw> CDK has hit Debian GNU/Linux :)
11:09 egonw olas: always important things happen when yuo're away :)
11:10 egonw so, one can soon do 'aptitude install libcdk-java'
11:13 egonw lunch
11:13 olas cool
12:09 CIA-22 bioclipse: egonw * r4912 /branches/bioclipse2/chemoinform​atics/net.bioclipse.cdk.ui/src/ (4 files in 2 dirs): Fixedcompile errors; removed class that is difficult to rewrite and of which the mechanism is going to change soon in CDK SVN soon anyway
12:11 CIA-22 bioclipse: egonw * r4913 /branches/bioclipse2/chemoinformatics/net.b​ioclipse.cdk.ui.tests/META-INF/MANIFEST.MF: Removed dep, as the source does not really depend on any biojava class
12:11 egonw jonalv: things are compiling again
12:11 viklund hurray
12:11 jonalv good
12:16 egonw no problems about broken functionality... but it compiles
12:18 jonalv I am not sure about how much functionality there is using CDK in bioclipse 2 yet
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13:29 olas joined #bioclipse
13:29 olas hi
13:36 egonw hi olas
13:36 egonw how is the meeting?
13:40 olas pretty good
13:41 olas I have sen many DAS clients in action
13:41 olas now it's more DAS architecture
13:41 olas and tomorrow hands-on coding DAS clients
13:41 egonw ha, net.bioclipse.das is just arond the corner :)
13:41 olas right :-)
13:42 olas but for that we need an alignment viewer
13:42 jonalv so in a few words: What id DAS?
13:42 olas decentralized annotations
13:42 jonalv hm sounds cool
13:42 egonw annotation of sequence?
13:42 olas DAS client can request info from many DAS servers and integrate the info in a single view or analysis.
13:43 olas let people annotate on their own
13:43 olas let client choose what annotations to display
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15:51 olas joined #bioclipse
15:51 olas egonw: jama is missing from net.bioclipse.cdk
15:51 olas or does it compile with you?
15:52 egonw yeah, it compile for me...
15:52 olas hmm
15:53 * egonw issued a 'clean'
15:54 olas egonw: rebuild classpath
15:54 olas still works?
15:54 olas my CP differ from the one on the repo
15:54 olas but I can't rebuild it
15:54 egonw rebuilding...
15:54 egonw 66%
15:55 egonw 77%
15:55 egonw done
15:55 egonw seems to work
15:55 egonw I do get a problem in cdk.ui now
15:55 olas hmm
15:55 olas seems to be non-updated jama in amnifest
15:55 olas replaced 1.0.1 with 1.0.1
15:55 olas 1.0.2 I mean
15:56 egonw 1.0.1 is listed here too...
15:56 olas committing
15:56 CIA-22 bioclipse: ospjuth * r4914 /branches/bioclipse2/chemoin​formatics/net.bioclipse.cdk/ (.classpath META-INF/MANIFEST.MF build.properties): Updated manifest to include jama 1.0.2
15:56 egonw ah...
15:56 egonw I'm sure I did a svn update this morning...
15:57 egonw but it's pulling more updates now...
15:57 egonw among which java 1.0.2
15:57 olas jama
15:57 egonw right
15:57 olas java 1.0.2 is old
15:57 olas very old
15:57 egonw :)
15:57 olas :-)
15:57 olas yes, JCP does not compile now
15:57 olas I guess it was expected
15:57 egonw ok, so when is the orbit install planned?
15:57 egonw this week?
15:58 olas I am too busy to do it
15:58 olas on WS here mon-tus
15:58 olas and on WS in UA on thur-fri
15:58 olas only wed
15:58 olas and a lot to do then
15:58 olas is it a lot of work?
15:58 olas What needs to be done?
15:59 olas we want to use log4j in orbit instead of jar, right?
15:59 olas anything else?
15:59 olas how should we import orbit?
15:59 olas svn:externals?
15:59 egonw log4j is just one of the orbit plugins we need...
16:00 egonw let's import
16:00 egonw not svn:externals...
16:00 olas hmm
16:00 olas how do we do that?
16:00 egonw sounds nice, but would require too much maintainance...
16:00 egonw copy/paste ?
16:00 olas you mean copy to our svn repo?
16:02 olas which ones do we need to copy more?
16:05 * olas id downloading latest orbit
16:05 egonw the full thing?
16:06 egonw sorry... meanwhile arranging a hotel for meeting in March in COlogne
16:06 olas cologne!
16:06 olas that old place
16:07 olas 63 megs
16:07 olas ok, which ones do we need?
16:07 olas http://download.eclipse.org/tools/or​bit/downloads/drops/S20080209163815/
16:07 egonw mom
16:08 egonw quite a few
16:08 egonw org.apache.batik.*
16:08 egonw not all, but several at least...
16:09 olas why not have these as jars?
16:09 egonw org.antlr.runtime, I think...
16:09 egonw as plugin is better...
16:09 olas in what way?
16:09 egonw org.apache.commons.cli
16:09 egonw ummm...
16:09 olas many plugins make it hard
16:09 egonw because some are shared with other plugins
16:09 egonw better versioning
16:10 egonw smaller download sizes
16:10 olas I think we should have jars and plugins mixed
16:10 egonw easier to keep up with newer lib versions
16:10 egonw org.apache.log4j
16:10 olas how about update jar?
16:10 olas I am not convinced
16:11 olas log4j is needed by everyone
16:11 olas why not have a jar?
16:11 egonw yes, so one plugin on which the rest depends
16:11 olas why is a plugin better than a jar for log4j?
16:11 egonw much better than 10 copies of the log4j jar
16:11 olas why copis?
16:12 olas net.bc.logging contains it
16:12 olas all can import it from that plugin
16:12 egonw yeah, and several other plugins
16:12 olas that's wrong
16:12 egonw yes
16:12 olas but it's still not solved by a log4j oplugin
16:12 egonw I really think reusing what Eclipse is providing is better
16:12 olas but what is the benefit?
16:13 egonw no worries about exports?
16:13 egonw standard versions?
16:13 egonw packaging?
16:13 egonw clearer license issues?
16:13 egonw yeah, run ...
16:13 egonw :)
16:13 * egonw is away for some dinner shopping
16:13 egonw bbl
16:19 olas joined #bioclipse
16:19 olas hi again
16:19 olas we had a fire alarm
16:19 jonalv oh
16:19 olas again
16:20 olas we've had 3 so far today...
16:20 jonalv oh
16:20 olas I guess that means no fire but a very sensitive system
16:20 olas egonw: a proposal
16:21 olas we add plugins for projects that we think are important for many other plugins
16:21 olas log4j etc
16:21 olas and plgins that are only relevant to some Bioclispe plugins we keep as jars
16:21 olas or do you want all in orbit that we use?
16:22 olas that would really clutter my workspace
16:22 jonalv are you talking about log4j?
16:22 masak joined #bioclipse
16:22 olas hi masak
16:22 masak hello olas
16:23 olas egonw: what do you think?
16:24 olas jonalv: what do you think regarding log4j?
16:25 olas would using the orbit plugin solve any problems?
16:25 jonalv that we should have the latest version and only one version. That's all I think. If you want some more fancy solution feel free
16:26 olas well
16:26 olas if some plugin want an old version?
16:26 jonalv then they should take care of that themself
16:27 jonalv (with a jar file in their plugin) And I can not emphasize this enough: NOT EXPORT that other version
16:28 olas I agree
16:32 egonw sorry... got to play mario first...
16:32 olas haha
16:33 olas egonw: I want to reach some sort of consensus regarding orbit
16:33 egonw well, i'd prefer orbit...
16:33 olas what do you say regarding workspace clutering with 20 more projects?
16:33 olas I like new users to simply check out a few "core" plugins and then go
16:34 olas that is a major thing IMO
16:34 egonw but if you and jonalv are more happy with jars...
16:34 egonw well...
16:34 olas I am not happy with jars
16:34 egonw is it possible to have it install from the orbit update site?
16:34 olas but I am scared that many plugins is trouble as well
16:34 olas no
16:34 jonalv I dont' care too much
16:35 egonw I have no problem with 20 projects in my eclipse workspace
16:35 jonalv I think we could place it in the target.plattform
16:35 olas that would be something
16:35 olas Then I'd like it
16:35 olas we have a target platfiorm for bioclipse
16:35 olas I vote for that
16:35 olas egonw?
16:36 olas jonalv: you'll have to set it up. You are resposnible
16:36 olas for the target platform :-)
16:36 egonw you vote for what exactly?
16:36 olas put orbit plugins in target.platform
16:36 jonalv I am responsible for what?
16:36 olas target platform :-)
16:36 olas you added it
16:36 egonw target.platform is not one plugin?
16:37 olas it's a project with a lot of plugins
16:37 jonalv it's a collection of plugins
16:37 jonalv And it already contains log4j....
16:37 olas if it works then it sounds lke just what we need
16:37 egonw like chemoinformatics/ ?
16:37 olas no
16:37 olas it's an eclipse structure
16:37 jonalv brb
16:38 olas you can define the core set of plugins to run on
16:38 olas and if you want another core set of plugins you can provide your own target platform
16:38 olas we do that already
16:38 olas as we add spring plugins to eclipse
16:39 egonw ok,
16:39 * olas is watching a presentation of biomart
16:39 egonw so we can add the orbit plugins as deps there too?
16:39 olas sounds likely
16:39 egonw olas: ok, pay attention
16:39 egonw I'd love to have biomart support in Bioclipse2
16:39 olas I want biomart in BC2
16:39 egonw we use it here locally...
16:39 olas :-)
16:39 egonw me too
16:39 egonw ok, got to go now...
16:39 olas ok cu
16:40 egonw but having those orbit as depsn in target.platform sounds the best solution
16:40 egonw jonalv: please make it so
16:40 olas jonalv: can we just copy them there?
16:40 * olas is downloading them
16:42 rklancer joined #bioclipse
16:43 rklancer hi all ... I've been trying to compile bioclipse2 (with some successes)...
16:43 jonalv I am waiting for the "but"
16:43 rklancer ...and I noticed logging is causing mass confusion?
16:43 jonalv yes...
16:44 rklancer that's the "but" :)
16:44 masak logging _is_ causing mass confusion
16:44 jonalv logging is causing massive confusion
16:44 masak :)
16:44 olas I thought we solved that for now...
16:44 rklancer So I did some surgery on the bioclipse distribution & maybe even have some suggestions
16:45 masak cool.
16:45 olas nice!
16:45 * jonalv is going to be semionline for a few minutes
16:45 olas we thought of orbit
16:45 rklancer I think that makes sense
16:45 olas and maybe put it in target.platform
16:45 rklancer there is a log4j in the target platform now, actually - org.springframework.osgi.log4j.osgi
16:46 rklancer and three different (obsolete) log4j jars in the various net.bioclipse.* plugins
16:46 olas yes
16:46 olas they should be removed
16:46 rklancer one problem is the log4j jar in the net.bioclipse plugins is an obsolete version (1.2.8) ... the spring-provided log4j, at least, is 1.2.13
16:47 olas jonalv said the same thing
16:47 rklancer spring is expecting to have access to 1.2.13 ... 1.2.8 doesn't have a TRACE level, for example, and spring writes to that level
16:47 rklancer right.
16:47 olas aah
16:47 olas that's where that dreaded TRACE error comes from
16:47 CIA-22 bioclipse: Annzi * r4915 /branches/bioclipse2/chemoinformatics/ne​t.bioclipse.moss/src/net/bioclipse/moss/ (7 files in 2 dirs): Added more parameters (not all works)
16:48 jonalv yes I know and I thought I fixed it
16:48 masak jonalv: you did
16:48 masak but people un-fixed it last week because they didn't understand your fix
16:48 rklancer and in my environment, at least, the spring libraries get wired to the log4j jar from net.bioclipse.core, not from the external org.springframework.osgi.log4j.osgi plugin...
16:49 rklancer masak: not without reason
16:49 rklancer there's some other complications
16:49 jonalv yes that's a bit of a stochastic process...
16:49 masak rklancer: the plot thickens...
16:50 rklancer there are *some* rules to package resolution in osgi but yeah it often appears to be stochastic
16:50 masak I think jonalv was referring to our development process, bu
16:50 masak but I'm not sure
16:50 rklancer haha :)
16:51 jonalv no I was reffereing to the package resolution actually
16:51 masak I sit corrected. :)
16:51 Annzi left #bioclipse
16:51 rklancer oh boy I have an audience I'd better check my notes :)
16:51 masak you do that :)
16:51 rklancer okay ...
16:52 rklancer there's several providers of org.apache.commons.logging in bioclipse as it stands ...
16:52 rklancer there probably should be just one, the jcl104_over_slf4j jar from the target platform
16:53 jonalv yes
16:53 rklancer springframework provides slf4j, which people like, but there's a bug (http://bugzilla.slf4j.org/show_bug.cgi?id=73) that causes a problem with PDE export (you get a classpath cycle)
16:53 jonalv you are absolutely right
16:53 rklancer so you have to fix the manifest.mf in slf4j...
16:53 jonalv I am really bad at logging.
16:54 jonalv wow
16:54 jonalv I think you lost me...
16:55 rklancer well I'm kind of info dumping so maybe I should write up a wiki page with what I've been able to figure out & what still eludes me?
16:55 * masak already loves rklancer
16:55 rklancer then we could wok it out together
16:55 rklancer wok=work
16:55 olas sounds excellent
16:55 jonalv yup
16:55 rklancer cool, will do...
16:56 olas rklancer: will you write on bioclispe wiki or on another wiki?
16:56 rklancer bc wiki, if i can get permissions
16:56 olas sure
16:56 olas I need your email
16:56 rklancer just register & log in?
16:56 rklancer oh okay
16:57 olas and full name please :-)
16:57 rklancer rpk@pobox.com
16:57 rklancer RIchard Klancer
16:57 olas It's all due to spammers...
16:57 olas ok, 2 secs
16:57 rklancer oh spammers how I love thee
16:58 olas email sent
16:59 masak rklancer: are you the same Richard Klancer as the one who works on nematodes?
17:00 rklancer masak, yeah, that was me
17:01 rklancer (got the email)
17:02 masak cool
17:02 rklancer i learned to like the little guys :)
17:02 rklancer but i still prefer coding
17:03 rklancer and open science stuff
17:04 jonalv cool
17:04 rklancer jonalv, I really like the macro recording idea
17:05 rklancer and providing scripting support generally ... it would be cool if bioclipse could provide a stable platform for lots of user-generated scripts and plugins and--maybe some kind of scripting-language based plugins?
17:06 masak yep
17:06 masak aiming there
17:06 jonalv scripting-language based plugins? hm sounds cool
17:06 jonalv how would you envision that?
17:07 masak sounds a bit like what Firefox is doing
17:07 olas joined #bioclipse
17:07 jonalv wb oals
17:07 olas thx
17:07 jonalv *olas
17:07 rklancer olas, got the email, thx
17:07 olas good
17:07 rojasm left #bioclipse
17:07 rklancer jonalv, dunno yet, I figure you guys are the experts
17:09 rklancer but, yeah, something like that ... because lots of labs will have people comfortable writing scripts
17:09 jonalv you seem to be quite an expert yourself
17:09 rklancer and if there was a stable platform to integrate all that stuff
17:10 jonalv yea that sounds like a good idea
17:10 masak I have a hard time figuring out what it would require, though
17:10 rklancer eh i spent the weekend+ figuring the logging stuff out ... I'm no really no java or eclipse expert
17:11 jonalv I think edrin++ has been somewhat along these paths as well
17:11 rklancer dumb question...
17:11 jonalv Are you familiar with Spring?
17:11 rklancer "++" is an honorific?
17:11 jonalv yup it's from the Perl world (maybee even just Perl 6, masak?)
17:11 rklancer no although the aop and di stuff looks interesting
17:12 masak jonalv: no, it's just IRC slang
17:12 masak but prevalent on #perl6, yes
17:12 masak jonalv: originally the syntax is from C or even B
17:13 jonalv it is, but complex. The recording is far from done and I am not even sure we can do all the recording we will want to. But I am staying hopeful
17:13 rklancer i do have a spring book, at least, so maybe I'll be able to help a little
17:14 rklancer <-- hopeful too
17:14 jonalv sounds great
17:16 rklancer oh another thought:
17:17 rklancer we should probably make an explicit list of the target platform plugins required, rather than importing all plugins from ${eclipse_home}/plugins
17:18 jonalv okey
17:18 rklancer would help transition to a stable set of target platform plugins to do automated builds against
17:20 rklancer for example I'm using http://paste2.org/p/14311
17:23 masak sounds like a sane idea
17:23 jonalv it sounds very sane indead
17:24 jonalv rklancer, have you got commit rights to Bioclipse?
17:24 rklancer no
17:26 jonalv oh, well I can't give you
17:27 rklancer no worries - I'll write stuff up for the wiki and then people can decide what to commit
17:27 rklancer (or not to commit!)
17:33 rklancer ok lunch is calling :)
17:37 olas joined #bioclipse
17:39 olas http://bioclipse.blogspot.com/
17:39 olas egonw: a long blog item...
17:40 olas just for you
17:40 * olas doesn't expect many others to read it :-)
17:40 masak permalink: http://bioclipse.blogspot.com/200​8/02/das-workshop-2008-day-1.html
17:41 olas sant
17:41 masak for people reading the logs :)
17:41 olas sorry 'bout that
17:41 masak np ;)
17:41 olas >100 on the workshop in Uppsala on thurs-fri
17:42 olas impressive!
17:42 olas Should probably work on my presentation...
17:42 olas and you on the poster :-)
17:43 * olas is talking to the Uppsala team
17:43 rklancer hey i spent enough time copying and pasting between ncbi, pfam, blast, and wormbase to be happy to see things are moving along
17:43 rklancer :)
17:43 olas rklancer: glad you're helping out
17:43 rklancer btw, is lincoln stein there?
17:44 olas don't know him
17:44 olas what does he do?
17:44 olas recognize the name
17:44 rklancer i had the impression he was the grandaddy of das but i don't know
17:44 rklancer pi of wormbase
17:44 rklancer and father of bioperl i think
17:45 olas don't think he's here
17:45 olas only his followers :-)
17:45 rklancer haha
17:45 olas DAS is becomming really big...
17:46 rklancer nice
17:46 rklancer okay, lunch isn't just calling anymore, it's yelling (!)
17:46 rklancer au revoir
17:47 rklancer left #bioclipse
17:56 thomas_ku_ joined #bioclipse

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