Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-10-22

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All times shown according to UTC.

Time Nick Message
05:05 thomas_ku joined #bioclipse
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06:31 egonw joined #bioclipse
07:43 egonw joined #bioclipse
07:43 egonw hi stain!
07:43 zarah egonw: You have new messages. Write '@messages' to read them.
07:43 egonw @msg
07:43 zarah egonw: 15 h 51 m 40 s ago, jonalv said is our bugzilla totally open or do I have to get a log in?
07:44 egonw @tell jonalv you need a log in, but you can create one from the website
07:44 zarah Consider it noted.
07:44 egonw zarah: tack
07:44 zarah you're welcome, egonw :)
08:00 olaz joined #bioclipse
08:02 egonw http://git.or.cz/gitwiki/EclipsePluginScreenshots
08:02 zarah egonw's link is also http://tinyurl.com/5obdea
08:03 jonalv joined #bioclipse
08:03 olass joined #bioclipse
08:04 egonw jonalv: http://git.or.cz/gitwiki/EclipsePluginScreenshots
08:04 zarah egonw's link is also http://tinyurl.com/5obdea
08:04 egonw you've just missed it by seconds :)
08:04 egonw the plugin is under active development... last commits yesterday
08:07 gilleain joined #bioclipse
08:15 jonalv egonw: missed what with seconds?
08:17 egonw that URL
08:17 egonw I'll look into the email problem for bugzilla
08:18 jonalv egonw: HAve you tried it?
08:19 egonw nej
08:23 olass how is CIA?
08:23 egonw dead again, I think
08:24 egonw umm... Ubuntu intrepid has Bugzilla 3.0.4
08:24 olass it's dead a lot
08:24 egonw where we now use 2.22
08:24 olass oh!?
08:24 egonw should we upgrade pele along we go?
08:24 olass why not?
08:24 egonw is it physically accessible?
08:24 egonw in case the reboot fails...
08:25 egonw (kernel upgrade)
08:25 olass well, not really today
08:25 olass (for me at least)
08:25 egonw same here
08:25 egonw but Thu would be ok?
08:25 olass let's do it tomorrow then when we are in uppsala
08:25 egonw right
08:25 olass about cdk.debug
08:25 olass should that go in release?
08:26 jonalv olass: when are you planning to release?
08:26 egonw maybe not
08:26 egonw let's leave it out for now
08:26 olass now
08:26 olass ok
08:26 olass jonalv: about usermanager feature
08:26 olass should we release that too?
08:26 jonalv olass: no news. Still license trouble on that one...
08:26 olass or wait?
08:27 olass ok
08:27 olass no release then
08:27 jonalv olass: besides Idon't think we have anything that needs it...
08:27 olass true
08:27 olass and speclipse?
08:27 olass egonw: did you try it?
08:27 olass is it stable?
08:27 olass are there use cases?
08:27 olass no shk3 here
08:28 gilleain he's here, but not here here.
08:29 olass can you ask him to come here here soon soon?
08:29 edrin joined #bioclipse
08:30 edrin hi
08:30 zarah hi edrin
08:30 shk3 joined #bioclipse
08:30 jonalv hi edrin
08:30 jonalv hi shk3
08:30 edrin hi jonalv
08:30 shk3 hi jonalv
08:30 olass shk3: is speclipse feature stable?
08:31 olass enough for a release?
08:31 shk3 I think so, yes
08:31 olass sample data exists?
08:31 olass use cases?
08:31 shk3 I would say yes
08:31 olass good
08:31 shk3 sample data in sample data
08:31 shk3 not yet in the xml
08:31 shk3 use cases in wiki
08:33 egonw shk3: I'd say EBI should host the Speclipse feature
08:33 egonw shk3: I'd say EBI should host the Speclipse feature update site
08:34 shk3 hm, what does that mean?
08:35 edrin shk3: what does speclipse do?
08:35 shk3 what do we need to do for the update site?
08:35 shk3 edrin: see use cases on wiki
08:36 jonalv google speclipse bioclipse use cases
08:36 zarah jonalv: No hits.
08:36 shk3 http://wiki.bioclipse.net/index.php​?title=Use_Cases_for_Bioclipse_2.0
08:37 zarah shk3's link is also http://tinyurl.com/6ew7tl
08:42 gilleain Hmmm. There are quite a few (32) pages on the wiki that are orphans.
08:45 olass wiki needs a serious update
08:45 olass egonw: why?
08:45 olass why not bioclipse.net?
08:45 olass it IS in our svn...
08:46 olass shk3: basically just a web server
08:47 egonw world conquest
08:47 olass shk3: maybe it's better if you hosted anyway...
08:47 olass that way you can update
08:47 olass yourself
08:47 egonw we want to show that EBI is actively working with Bioclipse
08:47 egonw that makes more impact of people download/update from ebi.ac.uk
08:49 edrin egonw: I fully agree
08:49 olass shk3: it's very easy
08:49 olass create a new project "update site"
08:49 egonw (olass: we could still secretly host it too, of course :)
08:49 olass add your feature
08:49 olass build update site
08:50 olass FTP entire content from the update site project to a location on a web server
08:50 olass add update site in bc2 pointing to the server
08:50 olass done
08:50 olass let me know if you run into problems
08:51 egonw olass: jonalv was able to log in on bugzilla@pele now
08:51 egonw email problem fixes
08:51 egonw email problem fixed
08:51 olass hmm
08:51 olass I get no email...
08:51 olass i got it
08:52 egonw excellent :)
08:52 olass hmm, link is very broken
08:52 egonw what link?
08:52 olass but I think I understand how to use it
08:52 egonw in the email?
08:52 olass yes
08:52 egonw hahah... indeed
08:52 egonw yeah, just go to the website
08:56 olass egonw: why have you added 1.2?
08:56 olass to bugzilla?
08:56 shk3 olass: need to talk to christoph about webspace
08:56 olass it is totally abandoned
08:56 egonw for the old bugs?
08:56 olass hmm
08:56 olass is it necessary?
08:56 egonw olass: did you close all 1.2 bugs on SF?
08:57 olass no
08:57 olass I have closed none
08:57 egonw anyway, just needed more than on thingy...
08:57 olass but will not solve any of them
08:57 egonw to test things
08:57 olass ok
08:59 * jonalv is exploring bugzilla...
09:03 egonw cool
09:03 jonalv egonw: is voting turned off?
09:03 egonw I just received a popup window on my screen
09:03 egonw olass: something about P2 -> P1 ??
09:03 egonw :)
09:03 jonalv a popup window?
09:03 egonw mylyn in action :)
09:04 egonw yes, a cool OSD popup :)
09:04 olass how use mylyn with bugzilla?
09:04 * egonw feels a growing open source development grid...
09:04 egonw jonalv: listening too?
09:05 jonalv egonw: you lost me..
09:05 egonw jonalv: just follow these steps:
09:05 jonalv egonw: oki
09:05 egonw Eclipse -> WIndow -> Show View
09:06 egonw -> Other
09:06 egonw Mylyn -> Task List
09:06 egonw and Mylyn -> Task Repositories
09:06 olass egonw: wiki page?
09:06 egonw we'll use both
09:06 egonw yes, will copy paste later into the wiki
09:06 olass go on
09:07 egonw open the Task Repos view
09:07 egonw hit the add repos icon
09:07 egonw blue battery + '+' signe
09:07 egonw pick Bugzilla
09:07 egonw (well, assuming that you already have mylyn installed...)
09:08 jonalv (or right click choose add task reposistpry...)
09:08 egonw if not, read the Mylyn 2.0 papers in IBM developers network
09:08 egonw OK, that should give a window called:
09:08 egonw Props for Task Repos
09:08 egonw with "Bugzilla Repos Settings"
09:09 egonw Server: http://pele.farmbio.uu.se/bugs
09:09 zarah egonw's link is also http://tinyurl.com/57eu7e
09:09 egonw Label Pele
09:09 egonw No Anom Access
09:09 egonw enter your User ID
09:09 egonw and Password
09:09 egonw (likely you click Save Password too)
09:10 egonw I have Http Auth enabled too, but not sure if that is really needed
09:10 egonw in Additional Settings:
09:10 egonw pick repos Version 2.22
09:10 egonw for the rest, default did it for me
09:10 egonw make sure to hit the 'Validate Settings' button
09:11 egonw oh... did not notice the 'Create new account' link earlier :)
09:11 olass so how set up query?
09:11 olass using form or URL?
09:11 olass to see all/my bugs
09:12 jonalv wow the dialog for query paramaters looks so cool! :)
09:13 egonw OK, now the query
09:13 egonw open the Task List view
09:13 egonw right click on view -> New -> Query
09:13 egonw and set up your query
09:13 egonw I have:
09:14 egonw Email: egon.willighagen
09:14 egonw with owner, reported, cc, commenter
09:14 egonw to see all related to me
09:14 egonw as one query
09:14 egonw another useful one would be 'unassiged'
09:15 egonw that's it
09:17 jonalv uhm I created a query for pele but it's not showing up in the Task List... :(
09:17 jonalv ah it's becasue it was empty
09:18 olass nice
09:18 olass I se my comment on your bug, egonw
09:18 * olass likes this
09:18 jonalv wow this is so cool! >(
09:18 jonalv |lol
09:18 jonalv :)
09:19 jonalv and you can attach a mylyn context to the bug?
09:20 egonw dunno that yet
09:20 egonw actually, how did I only have the mylyn context show up in my navigator again?
09:21 egonw I guess I just have to do some account clean up :)
09:25 egonw ok, everyone is using there farmbio email? right?
09:25 egonw so I delete all @gmail accounts now
09:26 jonalv oki
09:27 gilleain wait, what? egon's deleting all gmail accounts?
09:28 egonw yeah: ssh root@gmail.com; \rm -Rf /home/*
09:28 gilleain Er, more seriously - is this mylyn thing only going to work for those with farmbio emails?
09:28 egonw no
09:28 gilleain ah, ok.
09:28 egonw but the postfix got time outs from the gmail.com relay
09:29 gilleain hmm.
09:29 egonw [10:41] <egonw> Oct 22 09:33:49 pele postfix/smtp[19874]: connect to alt2.gmail-smtp-in.l.google.com[209.85.163.27]:25: Connection timed out
09:31 egonw ok, 4 registered users left
09:31 egonw olass, jonalv, egonw, Gpox
09:31 jonalv egonw: yea?
09:32 jonalv oh hehe sry
09:32 jonalv olass: what happend to olas?
09:39 olass dunni
09:39 olass early vac?
09:41 jonalv what does the last s stand for? :)
09:41 egonw sad
09:45 * jonalv <- lunch
09:45 egonw Gpox: so, how do I 'open' your context?
09:46 Julio joined #bioclipse
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09:46 egonw Gpox: never mind
09:46 egonw I now see the 'retrieve context'
09:48 egonw how did I 'search' for classes in Eclipse again?
09:49 olass ctrl shift T
09:50 olass egonw: have you set our permissions on bugzilla?
09:50 egonw I have not touched any permissions
09:50 olass I'd like to be admin
09:50 olass hmm
09:50 olass how do we assign bugs?
09:50 olass aah
09:50 olass scroll down :-)
09:51 egonw ola.spjuth now has supercow powers
09:52 olass hmm
09:52 olass we assign by email?
09:52 egonw hmm... indeed
09:53 olass no combobox?
09:53 egonw yes, by email
09:53 olass so you must remember everyones email!?
09:54 egonw hahahaha :)
09:54 egonw I hope not
09:54 egonw check the docs
09:54 egonw http://www.bugzilla.org/docs/2.22/html/
09:54 zarah egonw's link is also http://tinyurl.com/erkcq
09:55 egonw http://www.bugzilla.org/doc​s/2.22/html/lifecycle.html
09:55 zarah egonw's link is also http://tinyurl.com/fsua4
09:55 egonw sounds like one 'takes possesion' of a bug
09:55 egonw instead of getting a bug assigned
09:57 egonw Mylyn has a content assistent for the Assigned
09:57 egonw but it only shows me...
09:57 egonw not sure how that is filled
10:09 egonw how do I get a manager to output a message to the console?
10:09 egonw google Bioclipse Console message
10:09 zarah egonw: http://www.bioclipse.net/doc/1.0.1/​bioclipse/doc/tutorials_extApp.html
10:09 egonw google Bioclipse 2 Console message
10:09 zarah egonw: http://www.biomedcentral.com/1471-2105/8/59
10:09 egonw hahaha
10:19 olass egonw: you here?
10:20 egonw ja
10:20 olass priority p5 is most urgent or p1 ?
10:20 * egonw is working on the JChemPaintManager
10:20 egonw olass: no idea :)
10:20 olass P1 right?
10:21 egonw no clue
10:21 egonw trying to find it in the docs
10:22 egonw #
10:22 egonw Priority: The bug assignee uses this field to prioritize his or her bugs. It's a good idea not to change this on other people's bugs.
10:23 egonw really, no clue
10:23 Gpox i would say that mylyn thinks p1 is very high
10:24 egonw ok, good
10:27 egonw olass: ping
10:28 egonw Gpox: ping
10:28 egonw both for lunch?
10:28 Gpox no i am here
10:29 egonw Gpox: how do I open a MDL file in the new JChemPaint editor?
10:29 egonw is that possible already?
10:33 Gpox Open With -> Other...
10:33 egonw ok, that killed my BC2 :)
10:34 egonw and that's reproducable... :(
10:34 egonw and I don't get stacktraces or what
10:38 olass egonw: pong
10:39 olass egonw: I dare say that org.openscience.cdk.atomtype was not created 1.1.0.20080907
10:39 olass should it not be 1.2.0?
10:39 olass and why that date?
10:40 olass did you not create that plugin just a week ago?
10:40 egonw do you want to me copy in a new snapshot of CDK 1.2.x?
10:40 olass let's have disc over IRC and not via bug reports
10:40 olass hmm
10:40 egonw hope not
10:40 olass maybe not
10:40 egonw because this would not be good at this moment
10:40 olass ok
10:40 egonw better directly *after* a release
10:40 olass then let's stick to your version
10:40 olass thought you used lates for the plugins
10:42 egonw it's not horribly old...
10:42 egonw if you really want to change them...
10:43 egonw I can set the date to when I actually generated them
10:43 egonw whcih I should be able to recover from SVN logs
10:43 egonw tack
10:43 egonw I really like this OSD updates :)
10:44 egonw makes you feel to be in the same office :)
10:45 egonw OK, lunch time now
10:48 Gpox egonw: I think i solved the jchempainteditor crash
10:48 egonw great
11:03 olass egonw: OSD updates?
11:04 olass how are you informed?
11:04 olass egonw: please announce on devel our move to bugzilla
11:04 olass and that people should register there
11:04 olass and that SF will be phased out
11:06 olass hmm
11:06 olass anyone has any notion if I ever checked in a feature patch to SVN?
11:07 gilleain joined #bioclipse
11:10 olass should XOM go with bioclipse-feature? It sems central to many plugins...
11:10 * olass created a new feature patch anyways
11:10 egonw no, would not do that
11:10 egonw would just add it to those features that really need it
11:17 olass OK
11:17 olass egonw: chemoinfo feature requires org.op.cdk.jchempaint
11:17 olass but that is not in svn externals
11:17 olass why?
11:18 olass can I remove it from feature?
11:18 olass (this is for release)
11:18 egonw think so
11:18 olass ok
11:19 olass is that the one you are working on?
11:19 egonw no
11:19 egonw got things in a branch
11:19 egonw in net.bioclipse.cdk.jchempaint.business
11:20 olass ok
11:20 olass feature updated anyway
11:21 * jonalv just found much more work with structuredb business and gui layer...
11:25 olass egonw: chemoinfo feature does not export
11:25 olass can you look at it?
11:25 olass here's how to reproduce:
11:26 olass check out update-site (or create a new one, you just need one for testing purposes)
11:26 olass hmm
11:26 olass will do this in a bug report
11:26 egonw tack
11:30 olass egonw: did you get that?
11:30 egonw yes
11:30 egonw upon a sync
11:31 egonw it does not do that every second :)
11:31 egonw no context?!?!
11:38 olass no
11:38 olass since you can create your own update site
11:47 egonw OK, all trackers on SF are now no longer visible to users...
11:47 egonw bugs and feature requests still have items open (64+29(
11:47 jonalv so how do we do with the porting?
11:47 egonw which need to be closed and transfered to pele
11:48 egonw you port those assigned to you, or reported to you
11:48 jonalv but if I no longer can see them...
11:48 egonw mark them as:
11:48 egonw closed, duplicated
11:48 egonw closed, duplicate
11:48 egonw jonalv: both those two trackes are visible to project members
11:49 egonw but you might need to log in on SF first
11:49 jonalv egonw: oh okey
11:49 egonw I've added a default reply: "Moved to Bugzilla"
11:50 egonw and in Bugzilla I add the link to the SF bug report as URL
11:50 jonalv ah okey
11:52 egonw btw
11:52 egonw olass: 1.2.0 bugs which do not apply to 2.0 we just close with "Out of Date", correct?
11:52 olass yes
12:08 egonw OK, 58 open bugs remaining in SF
12:20 jonalv I will have a look once I have gotten through this readtrue of StrucutredbManagerTest.java :)
12:21 egonw ack
12:21 * egonw will get to this bug report on exporting the chemoinformatics feature
12:22 gilleain joined #bioclipse
12:30 edrin egonw: hi, and did you play with xws ?
12:30 egonw hi edrin, ah, no :(
12:30 egonw but I did play with Mylyn/Bugzilla
12:31 egonw and JChemPaintManager
12:31 egonw it's high on my todo list...
12:31 egonw but it's pretty crowded at the top
12:31 edrin hehe
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13:06 gilleain joined #bioclipse
13:10 egonw olass: ping
13:10 olass pong
13:10 egonw did you not have this problem last time?
13:10 egonw can you try this:
13:10 olass what prob?
13:10 egonw got to the cdk10 plugin
13:11 egonw and run the ant task javacc
13:12 olass I have no build.xml there
13:13 egonw ok
13:14 egonw hang on
13:14 egonw another exit svn:externals
13:15 olass exit?
13:16 olass did you fix the export problem of chemoinfo-feature??
13:16 egonw that's what we are talking about
13:16 olass ok
13:16 olass previously I have always removed all tests from cdk10
13:16 olass just deleted them
13:16 olass maybe not required anymore...
13:16 egonw the problem that the 'export' forgot to autogenerate some .java files with this 'javacc' ant target
13:17 egonw actually, these cannot even be imported with svn:externals
13:17 egonw it never showed up, because I think we had the dependent .java files removed from the build path
13:17 egonw apparently the export does not care about excludes from the build path
13:17 egonw :(
13:18 egonw so, this is what I shall do:
13:18 egonw uploade the CDK pure 1.0.4 jar
13:19 egonw and hope nothing breaks
13:20 egonw jonalv: you have two SF accounts??
13:20 jonalv egonw: uhm yea... It's not something I am proud about..
13:20 egonw :)
13:20 egonw miguel howard, of Jmol fame, switch account name too
13:20 egonw so,. you're in a good audience :)
13:21 egonw but, why???
13:21 olass egonw: eclipse export can NOT have classes not on th classpath
13:21 egonw olass: right
13:21 olass you need to remove all those
13:21 egonw which is why I asked, whether this has ever workde :)
13:21 egonw olass: whcih I can't, because they are in CDK SVN...
13:21 egonw hence, I'll upload the jar
13:21 egonw and be done with that
13:21 olass ok
13:21 jonalv I didn't want to mess up my "play" account with the one I used for Bioclipse + I wanted the same nich on both sourceforge and freenode
13:22 olass egonw: as long as it works I'm fine with it
13:22 egonw :)
13:22 egonw :)
13:22 olass ping me when done
13:22 olass REALLY want this solved today
13:22 egonw mmm... already 306 downloads for CDK 1.0.4
13:22 egonw not bad
13:23 egonw I had no idea so many people were still using the 1.0.x series
13:29 egonw olass: good news, and bad news
13:29 egonw what do you want first
13:29 olass bad
13:29 olass always bad first
13:29 egonw ok, it will take me another hour or so, to work things out...
13:29 egonw maybe more...
13:29 olass good?
13:29 egonw and things will need some new testing
13:30 edrin that is good?
13:30 egonw he, I'm not done with the bad news yet... :)
13:30 olass right...
13:30 olass go on
13:30 edrin long list
13:30 egonw the good news is, I can reuse the new 3rd party libs
13:30 egonw which will reduce the download size
13:30 olass :-)
13:31 egonw oh, sorry... that's not good news to you :)
13:31 olass working is most important
13:31 olass cdk10 is scheduled for removal anyway
13:32 olass how long?
13:32 olass one hour?
13:32 jonalv okey out of 223 tests in Bioclipse2 110 passes. If anyone is intrested... :)
13:32 olass how many are structuredb out of these 233?
13:33 olass 223
13:33 jonalv I am glad you asked. 122 of them are from structuredb
13:33 olass do you run as junit-plugin-tests or junit-tests?
13:33 jonalv oh right these where the junit-tests ones
13:33 jonalv there are a few more plugin tests
13:33 jonalv forgot about them :)
13:34 olass any crucial that fail?
13:34 shk3 guys, are we moving away from sf for bugtracking?
13:34 jonalv shk3: yup
13:34 shk3 why so?
13:34 jonalv olass: I don't know really. HArd to say...
13:34 olass shk3: there's a mail on devel ML from egon
13:34 olass shk3: REALLY nice with good integration of bugzilla in mylyn
13:35 olass egonw promised to write up a wiki page with screenshots how to set that up
13:35 olass actually not hard at all
13:35 shk3 they always say that
13:35 egonw no screenshot, but the wiki page is mentioned in the emila
13:35 shk3 how do we get accounts in bugzilla?
13:35 jonalv it was easy
13:35 shk3 sure it was easy...
13:35 gilleain I applied for one, but it never arrived.
13:36 gilleain It said to contact some "egon" guy, I dunno.
13:37 olass egon fixed it
13:37 olass try again
13:37 egonw (connect to pihlis.ebi.ac.uk[193.62.195.233]:25: Connection timed out)
13:37 egonw mmm...
13:37 egonw I fixed farmbio email...
13:37 egonw but it seems not just gmail is failing ...
13:38 egonw but ebi email too...
13:38 * jonalv has a bad feeling about this...
13:38 egonw I guess we need to ask permission for pele to use the 25 port?
13:38 olass problem with open ports on server?
13:38 olass right
13:38 egonw weird thing is...
13:38 egonw this is port 25 on the target
13:38 egonw not pele:25
13:38 olass that might be tricky but not impossible
13:38 olass so port 25 out?
13:39 egonw yes
13:39 jonalv egonw: are you taking over responibility for pele? (that would be awesome...)
13:39 egonw jonalv: nope
13:39 olass seems so :-)
13:39 egonw just making the admins life hell :)
13:39 olass jonalv was admin
13:39 olass is the new egonw?
13:40 egonw no
13:41 egonw but happy to maintain bugzilla
13:42 gilleain woah. I didn't realise the internals of GridLayout were so complex.
13:45 shk3 well, account creation didn't work for me
13:46 egonw gilleain, shk3: I'll email you your pwd
13:46 gilleain ta.
13:47 egonw please change it immediately
13:47 gilleain will do.
13:49 gilleain oh very funny.
13:49 egonw hahahaha
13:50 egonw please let me know if it works
13:50 egonw shk3: you too please
13:51 gilleain Eclipse just crashed.
13:51 egonw a custom ebi version?
13:51 shk3 no
13:51 shk3 i get
13:51 gilleain no
13:51 egonw disallowing certain passwords?
13:51 shk3 Not Found
13:51 shk3 The requested URL /cgi-bin/bugzilla/cgi-bin/bugzilla/index.cgi was not found on this server.
13:51 egonw sure
13:51 shk3 when hitting the login button
13:52 egonw using the webinterface?
13:52 shk3 yes
13:52 gilleain yup.
13:52 shk3 i go to http://pele.farmbio.uu.se/bugzilla/
13:53 zarah shk3's link is also http://tinyurl.com/5duh93
13:53 egonw works for me
13:53 shk3 not for me
13:53 egonw where do you log in?
13:53 gilleain not for me, neither.
13:53 shk3 the url it generates has /cgi-bin/bugzilla two times in it
13:53 egonw ah, indeed
13:53 egonw that one does not work for me either...
13:54 egonw try the Log In in the bottom right
13:54 egonw meanwhile, I'll fix that form
13:54 gilleain success.
13:54 gilleain for, me
13:54 egonw feels like I am the first Ubuntu user actually installing Bugzilla :(
13:55 shk3 username or password wrong
13:55 shk3 what is my username?
13:55 shk3 email?
13:55 egonw yes
13:55 gilleain changed pwd.
13:56 shk3 not working
13:56 shk3 username stefan.kuhn@ebi.uk.ac
13:56 shk3 password the funny one you sent
13:56 shk3 ok, wrong email
13:57 gilleain unless the uk has been taken over by the academic world! :)
13:57 egonw OK, front page login should work again
13:57 egonw dirty hack
13:57 egonw but works :)
13:58 egonw gilleain: hehehehe
13:58 gilleain :). Right, I'm trying mylyn again. better not crash, though *shakes fist*
13:59 gilleain Ok, cool, that seems to do more stuff now. Query form and all that jazz.
14:01 olass egonw: how's progress with cdk10?
14:02 egonw olass: working on it...
14:02 egonw it's compiling CDK
14:03 olass ok
14:06 egonw http://wiki.bioclipse.net/index.php?title=Mylyn
14:06 zarah egonw's link is also http://tinyurl.com/5qp5rl
14:06 egonw now improved, with screenshot
14:06 egonw per popular demand
14:09 jonalv ywy now even better :)
14:16 egonw grpmh...
14:26 jonalv grmph?
14:27 egonw you know... the sounds you make when you do not like something?
14:27 jonalv egonw: ah yea, but what made you do the sound? :)
14:28 egonw oh, sent a jar in the wrong direction
14:28 olass egonw: ETA for cdk10?
14:28 egonw tomorrow
14:28 olass sorry for buggering you but waiting for it...
14:28 olass NO
14:29 olass really?
14:29 olass :-(
14:29 olass :-(
14:29 olass :-(
14:29 egonw working on it...
14:29 zarah :-(
14:29 jonalv :(
14:29 olass was it that hard?
14:29 olass or much I guess
14:29 egonw well, it's back in the SVN world
14:29 * olass is always here
14:30 * olass just moved his car and bought a muskavadobulle
14:30 olass I wonder what it tastes like
14:30 jonalv sounds intresting
14:30 olass will make coffee first
14:31 * jonalv is gonna guy and buy something to eat too. That was a good idea :)
14:31 olass probably muskavado...
14:31 * jonalv afk
14:32 olass http://en.wikipedia.org/wiki/Muscavado
14:32 zarah olass's link is also http://tinyurl.com/6e6sz5
14:35 olass seriously, egonw, you will not make it today?
14:35 egonw trying...
14:35 olass egonw++ # good job
14:38 gilleain joined #bioclipse
14:39 egonw olass: is the rdfeditor and sdfeditor stuff in the feature too?
14:39 olass sdf, not rdf
14:40 olass cdk10.sdf, not cdk.sdf
14:40 egonw ok
14:40 egonw fixed cdk10 and cdk10.jchempaint
14:40 egonw as least no the compile level
14:40 egonw won't have time to test
14:40 egonw comitting now
14:40 olass thx
14:40 egonw and'd welcome if you cuold test
14:41 olass sure
14:41 olass will jump right on
14:41 egonw ok, that's commited
14:41 olass ok
14:41 olass see you tomorrow
14:42 olass or later :-)
14:42 egonw I'm not gone yet
14:43 olass should I do a fresh checkout?
14:43 egonw what do you mean with fresh?
14:44 egonw oh, you're in the SVN world :)
14:44 olass check out new?
14:44 egonw umm... not sure
14:44 egonw I had too...
14:44 olass update complains about already have a jar folder
14:44 egonw for cdk10
14:44 egonw that is
14:44 egonw the others should be fine without
14:44 egonw right
14:44 egonw \rm -Rf net.bioclipse.cdk
14:44 egonw oops
14:44 egonw \rm -Rf net.bioclipse.cdk10
14:44 egonw svn update net.bioclipse.cdk10
14:48 olass egonw: I get errors in cdk.jcp
14:48 olass import org.openscience.cdk.applicatio​ns.jchempaint.JChemPaintModel;
14:48 olass missing
14:48 egonw in cdk.jcp?
14:48 egonw or cdk10.jdp
14:48 olass cdk10.jcp
14:48 egonw did you update that one?
14:48 olass hmm
14:49 olass yes
14:49 olass confirmed
14:50 olass hmm that package is not in cdk1.0.jar
14:50 olass egonw?
14:50 olass how can that compile for you?
14:50 olass clean + upsate classpath
14:51 olass has jcp been refactored out of cdk1.0?
14:51 olass in that case we need taht jar too
14:51 olass oh
14:51 egonw yes, the classes for that are in cdk10.jchempaint/jars/cdk-jchempaint.jar
14:51 olass that jar is in cdk10,jcp
14:51 olass just not on CP
14:51 olass mom, fixing
14:51 egonw wait
14:52 egonw just commited some extra fixes
14:52 egonw please try that first
14:52 egonw otherwise we get svn conflicts
14:52 egonw it's almost done
14:52 olass too late :-(
14:52 olass ok
14:52 olass will undo my fixes
14:52 egonw check r7364
14:53 olass updating
14:53 olass ok, no compile errors
14:53 olass will try export now
14:54 olass building...
14:54 olass that that work with you?
14:54 olass update site -> build?
14:54 olass ah, no errors at least
14:54 egonw trying now
14:54 olass or maybe...
14:55 egonw and do note the download sizes ...
14:55 egonw mmm... I did not get any errors
14:56 olass me neither
14:56 olass good
14:56 olass will test now
14:56 olass wish me luck
14:59 jonalv olass: good luck
14:59 egonw olass: good luck
14:59 gilleain good test-luck.
15:00 egonw olass: you can stop now
15:00 egonw was too good to be true
15:00 egonw export is not good
15:00 egonw JCP does not work
15:00 egonw missing deps
15:00 egonw hang on
15:01 olass ok
15:03 olass I can confirm that jcp does not work :-)
15:04 egonw just learned something about rcp classloading :)
15:05 olass fixed?
15:06 egonw think so
15:07 olass committed?
15:07 olass only cdk10.jcp plugin?
15:07 olass to update I mean?
15:08 olass egonw: let me know
15:08 egonw you know
15:08 egonw just cdk10
15:08 olass ok
15:08 egonw not cdk10.jcp :)
15:08 egonw that's the thing about classloading
15:08 egonw cdk10.jcp was using something from cdk10 which was missing a class :)
15:09 egonw my first attempt was to add the missing class as depp to cdk10.jcp
15:09 egonw stupid me
15:09 egonw :)
15:09 egonw OK, that's enough for me today
15:09 egonw I even fixed InChI generation missing class on the fly
15:09 shk3 just one question
15:09 egonw that will have to do
15:09 olass DEBUG - java.lang.NoClassDefFoundError: org/xmlcml/cml/element/CMLMolecule
15:09 egonw have to catch the bus home
15:09 egonw hahahah
15:09 egonw oops
15:09 egonw ok, you know the drill
15:09 olass egonw: no
15:10 egonw go to nb.cdk10
15:10 shk3 i am sure there will be another bus
15:10 egonw add net.bioclipse.cml
15:10 olass ok
15:10 olass ok
15:10 egonw rest will ahve to be tomorrow
15:10 egonw otherwise my kids will beat me up
15:10 egonw (or tonite)
15:10 egonw after dinner
15:11 olass Caused by: org.openscience.cdk.excepti​on.NoSuchAtomTypeException: The AtomType C.3 could not be found
15:11 egonw ah, cool
15:11 olass what have you done?
15:11 egonw and not cool
15:11 egonw because that is not cdk10 stuff
15:11 olass I know
15:11 egonw so, sort of scary
15:12 olass m2d depends on cdk for atom typing
15:12 olass and cdk10 for JCP rendering
15:12 egonw ah, nasty...
15:12 olass but what is wrong?
15:12 egonw just rendering?
15:12 egonw then use cdk.jchempaint
15:12 egonw for now
15:12 egonw ok, bye!
15:12 egonw olass: no idea
15:12 egonw let's finish it tomorrow
15:12 olass but you have changed something
15:13 olass it worked before
15:13 olass ok
15:13 egonw yes, I fixed an export bug
15:13 olass I guess we have to...
15:13 olass fixed and fixed...
15:13 egonw yeah, we're bound to find other problems
15:13 olass ok
15:13 olass tomorrow then
15:13 egonw gone now
15:13 olass bye
15:15 olass egonw: I can still see you...
15:20 jonalv zarah: ping
15:20 zarah jonalv: pong
15:20 jonalv zarah: tell zarah hi
15:20 zarah jonalv: You are wasting your time, and mine.
15:20 jonalv zarah: tell me a joke
15:20 zarah jonalv: You have no new messages.
15:21 jonalv zarah: that wasn't funny...
15:21 zarah jonalv: excuse me?
15:21 jonalv zarah: no fun
15:21 zarah jonalv: I see.
15:21 jonalv zarah: good
15:21 zarah jonalv: please rephrase or stop trying to be witty :)
15:21 jonalv zarah: so basically...
15:21 zarah jonalv: excuse me?
15:22 jonalv zarah: okey...
15:22 zarah jonalv: are you making fun of me?
15:22 jonalv zarah: what if I am?
15:22 zarah jonalv: are you making fun of me?
15:23 jonalv zarah: what if I am?
15:23 zarah jonalv: excuse me?
15:23 jonalv zarah: you are excused...
15:23 zarah jonalv: well, yeah. you're excused too.
15:23 jonalv zarah: good
15:23 zarah jonalv: I did not understand that
15:38 olass zarah: tell ME a joke
15:38 zarah Consider it noted.
15:38 olass ?
15:39 olass zarah: tell me a joke
15:39 zarah olass: You have no new messages.
15:39 olass @msg
15:39 zarah olass: You have no new messages.
15:55 hello____ joined #bioclipse
15:56 hello____ hii anybody there?
15:57 gilleain hello, hello___
15:57 hello____ hii gilleain
15:57 hello____ how are u ?
15:57 jonalv hi hello____ who are you_
15:58 gilleain I am fine, I don't know about this "u" fellow.
15:58 hello____ well i am new in this chat room
15:58 jonalv hello____: yup... :)
15:58 hello____ i am a coputer graduate and started some reacher in bioinformatics
15:59 hello____ research*
15:59 hello____ what abt u ?
16:00 gilleain mostly the same. currently swearing at layout managers.
16:00 jonalv I am a new phd-student in Uppsala. I haven't worked much with Bioclispe 1 but I have been a central part of the development of Bioclispe 2 :)
16:00 charlgren joined #bioclipse
16:00 jonalv charlgren: hi
16:01 charlgren jonalv: hi
16:01 hello____ thts nice
16:02 hello____ well i am basically programmer so trying to do some computation thigns in gene motifs analysis and promoter prediction
16:02 jonalv hello____: ohh bioinformatics :)
16:03 hello____ yes
16:03 hello____ jonalv
16:03 jonalv (much chemoinformatics around here normally...) :)
16:03 hello____ i see jonalv
16:04 hello____ then am i the first person of bioinformatics here ? jonalv
16:04 jonalv but it is _bio_clipse after all :)
16:04 hello____ ya thts true jonalv
16:04 jonalv well since my master program was in Bioinfomatics I am not sure I would go that far... :)
16:04 hello____ basically i search using bioinformatics jonalv
16:08 hello____ so wht do u do jonalv
16:09 jonalv for the moment I am working on a integrated database for storing molecules with annotation in Bioclipse. Spring, iBatis, HSQLDB...
16:09 jonalv hello____: I am also in deep in the core parts of Bioclipse... :)
16:10 jonalv Bioclispe 2 that is...
16:10 hello____ the development of bioclioes ? jonalv or any project dvelopment using bioclipse?
16:11 gilleain heh. whenever I see "bioclispe" I think of some sort of BioLisp (like BioJava, or so :)
16:12 hello____ well yes i also guess so
16:12 stain (((gene 'GATTACCATA)))))))))
16:12 hello____ i generally use c#.net to program for bioinformatics
16:13 hello____ currently i am working on promoter prediction algorithm development
16:13 jonalv hello____: I am sort of responsible for the "manager architecture" as it looks in Bioclipse 2 and then I am doing the structure database and I am also doing the Brunn project. Which is a database for screening data from microtiter plates.
16:15 hello____ tht is good
16:16 hello____ my research is in core level tht is developing algorithm and also testing performance of those
16:16 jonalv hello____: so if you have any Bioclipse 2 related questions I should be able to answer or at least direct you to someone who can answer :)
16:17 hello____ thanks actually i didnt use Bioclipse before but yes i will try it jonalv
16:19 gilleain left #bioclipse
16:20 hello____ well... jonalv can u give me some hints about research funds on bioinformatics ?
16:21 jonalv hello____: uhm no I don't think so...
16:21 hello____ jonalv ok thx
16:25 hello____ ok jonalv nice to chat with u
16:25 hello____ now i am leaving this room
16:25 jonalv hello____: bye
16:25 hello____ left #bioclipse
16:35 jonalv did someone know mister hello____?
16:35 egonw nope
16:35 egonw where is .bd ?!?!
16:37 jonalv bangladesh?
16:37 egonw http://plindenbaum.blogspot.com/2008/1​0/javadoc-is-not-enough-java2dia.html
16:37 zarah egonw's link is also http://tinyurl.com/6navjk
16:39 jonalv since javadoc isn't enough we have an annotation that does soet of the same thing. example: http://bioclipse.svn.sourceforge.net/viewvc/b​ioclipse/bioclipse2/trunk/plugins/net.bioclip​se.structuredb/src/net/bioclipse/structuredb/​business/IStructuredbManager.java?view=markup
16:39 jonalv :)
16:39 zarah jonalv's link is also http://tinyurl.com/5n9tlb
16:54 edrin egonw: nice tool. I am curious how xws4j would look like...
16:55 edrin going home, cu later if you still around
16:55 charlgren_ joined #bioclipse
16:55 edrin left #bioclipse
19:14 edrin joined #bioclipse
19:38 masak joined #bioclipse
20:27 edrin hi masak
20:27 masak hello edrin
20:28 masak I'm only semi-here tonight
20:28 edrin sure, me, too
20:41 masak @reload
20:42 zarah joined #bioclipse
20:42 masak @fnord
20:57 masak zarah: restart, dear
20:59 zarah joined #bioclipse
21:14 m4r1in joined #bioclipse
21:17 masak zarah: restart again dear. thanks.
21:17 zarah joined #bioclipse
21:40 masak @restart
21:41 zarah joined #bioclipse

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