Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-08-04

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
06:06 rojasm joined #bioclipse
06:07 Gpox joined #bioclipse
06:07 olas joined #bioclipse
06:08 olas hi all
06:08 zarah hi olas
06:20 CIA-49 bioclipse: ospjuth * r6433 /bioclipse2/trunk/features/ (2 files in 2 dirs): Updated feature info. Solves 2035794.
06:29 ilogger2 joined #bioclipse
06:29 CIA-49 bioclipse: ospjuth * r6434 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (tocdevelopers.xml toctutorials.xml): Close topic elements. Solves 2035802.
06:55 masak joined #bioclipse
07:06 olas hej masak
07:07 olas zarah: dog nyss
07:07 masak hej olas
07:07 masak yes, the downtime was planned at gatekeeper
07:07 olas right
07:08 masak I read about it a couple of minutes ago
07:08 olas what is gatekeeper anyway?
07:09 masak server of a friend
07:25 egonw joined #bioclipse
07:25 egonw moin
07:31 egonw did someone see zarah?
07:36 masak egonw: her server is down today...
07:39 masak I'm trying to install the required modules on pele, but with little luck so far
07:40 egonw yeah, no rush...
07:40 egonw I'm ill now and then too :)
08:04 jonalv joined #bioclipse
08:04 jonalv moin
08:04 jonalv zarah?
08:05 jonalv hm gatekeeper must already be down... :(
08:08 masak indeed
08:08 masak the gate is down
08:25 olas bad keeper for the gate
08:26 masak olas: not really, no
08:27 masak for a privately owned server, the uptime is quite outstanding
08:27 masak but we should be thinking about moving zarah to pele anyways
08:27 jonalv so is the backup service :)
08:27 masak indeed
08:28 masak olas: any news of ports/firewalls into and out of pele?
08:29 masak I'm having trouble getting an outbound FTP connection right now
08:31 olas masak: you need to use sftp
08:31 shk3 joined #bioclipse
08:31 masak hm. tell that to CPAN, the Perl module installer :/
08:31 olas hi shk3
08:31 shk3 hi olas
08:31 olas masak: I don't know otherwise
08:32 masak olas: though I agree on principle. ftp sucks, sftp is the way to go.
08:32 olas can you not download modules and install manually?
08:32 olas else maybe ITS can open it sin some way
08:32 olas but that could mean problems
08:32 olas and/or take time
08:33 olas but might be needed anyway for jabber/xmpp
08:33 olas which I will try this week (hopefully)
08:33 masak olas: I'll try to coax CPAN into using some other method of downloading
08:36 olas sounds good
08:37 olas we need a major wiki cleanup
08:37 masak who doesn't? :)
08:38 masak the wiki concept takes "under construction" and makes it an axiom
08:39 olas but bc wiki is mostly bc1, should be updated for bc2
08:39 olas would also be nice to get a mediawiki upgrade
08:40 masak 1.5.6 -- hm, yes
08:41 masak but for that you'd need a PHP upgrade, too
08:41 olas to?
08:41 masak (if memory serves me)
08:41 olas to what version?
08:41 masak 5
08:41 olas I think that's available
08:41 olas pretty sure
08:41 masak ok, goodie
08:41 olas will confirm
08:42 olas yup
08:42 olas php5 is available
08:42 olas should we start a new and populate it?
08:42 olas would that not give us the best updated info?
08:44 masak what info?
08:45 masak olas: if you start a new one, it will run a conversion script on the database, so the old one will probably stop working
08:49 olas exactly
08:49 olas so we need to extract the info we want from the old first
08:49 olas let's discuss this tomorrow
08:50 masak olas: one doesn't extract, one just upgrades using the same database, and hopes for the best
08:56 olas that's the point, if we start from scratch we will only have updated info
08:56 olas ok
08:56 olas let's talk tomorrow
08:56 masak oki
08:56 jonalv olas: you want to throw away everything in our wiki_
08:56 jonalv ?
08:58 olas jonalv: see my note at 11:00:07
08:58 masak "I use the time saved in not watching television to tell tales and sing songs to my children." -- someone on http://www.c2.com/cgi/wiki?GaveUpOnTelevision
08:58 olas and 10:53:31
08:58 * masak misses zarah too
08:59 jonalv olas: time is 10:58 what are you going to say in the future?
09:00 masak jonalv: that's what we're all excited to find out! :)
09:00 jonalv bah
09:00 masak allegedly, it explains everything
09:03 olas here it is
09:04 olas masak,jonalv: tell zarah to slap masak and jonalv
09:04 masak heh.
09:04 olas jonalv: does that answer your questions?
09:04 jonalv aouch what did "I do wrong now?
09:04 masak olas: you can tell yourself!
09:04 olas ha
09:05 olas believe me, I did before I told zarah
09:05 * olas misses zarah
09:05 olas even though she is hard on me sometimes
09:05 olas saying I'm the stupid one and such...
09:06 * olas has not recoverd from that yet
09:06 olas was a terrible day
09:06 olas :-)
09:06 masak olas: that was the funnies moment in all of IRC
09:06 masak s/ies/iest/
09:14 CIA-49 bioclipse: ospjuth * r6435 /bioclipse2/trunk/plugins/ne​t.bioclipse.data.sampledata/ (8 files in 2 dirs): Updated icons and branded sampledata feature.
09:15 CIA-49 bioclipse: ospjuth * r6436 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui/ (6 files in 3 dirs): Added feature icon and branding.
09:19 egonw olas: maybe an idea to split the wiki up into a dev wiki and a user wiki?
09:19 olas maybe later, yes
09:19 olas when we have regular users
09:20 egonw hahahaha
09:32 masak Mark Shuttleworth likes Launchpad: http://www.markshuttleworth.com/archives/135
09:41 egonw sure, he's the guy he ordered people to write it :)
09:49 masak ah. :)
09:49 masak (Mark Shuttleworth ordering people to do cool stuff)++
09:49 olas should we move to launchpad?
09:49 masak olas: possibly.
09:50 olas coudl someone write up a mail to the ML with pros and cons?
09:50 olas so that other may comment?
09:51 egonw olas: what bits do you want to move?
09:51 egonw BTS?
09:51 egonw or SVN too?
09:51 egonw please make that clear in the email to the ML
09:52 * egonw is away for lunch and then relocating to other desktop in Wageningen
09:53 * olas will not write that mail
09:53 CIA-49 bioclipse: ospjuth * r6437 /bioclipse2/trunk/plugins/net.bioclipse.j​mol/src/net/bioclipse/jmol/views/outline/ (JmolAtom.java JmolChain.java JmolGroup.java): Jmol now shows outline for molecules with only atoms and no biopolymers/monomers.
09:53 * olas CANNOT write that mail
09:54 olas anyone with an idea of an icon for: 1) monomer 2) polymer 3) atom 4) bond ?
09:57 shk3 for atom, a sort of orbital model would be an option
09:57 CIA-49 bioclipse: shk3 * r6438 /bioclipse2/trunk/plugins/net.bioclipse.spectrum​/src/spok/parser/CMLToJcampSpectrumMapper.java: small fixes in jcamp writing
10:01 CIA-49 bioclipse: shk3 * r6439 /bioclipse/trunk/plugins/net.bi​oclipse.spectrum/src/spok/gui/: messed up svn
10:03 olas shk3: can you come up with a 16x16 atom?
10:03 olas we need to color it by symbol
10:05 CIA-49 bioclipse: ospjuth * r6440 /bioclipse2/trunk/plugins/net.bioclipse.j​mol/src/net/bioclipse/jmol/views/outline/ (3 files): Added properties for JmolModel.
10:06 shk3 no, I can't
10:06 shk3 sorry
10:06 shk3 I have official proof for it
10:07 shk3 I recently read my certificates from first years of school
10:07 shk3 and one of them says:
10:07 shk3 "for painting and drawing, he lacks manual ability"
10:08 shk3 that was testified by a German schoolteacher
10:09 shk3 so I am forever discharged from painting and drawing
10:09 zarah joined #bioclipse
10:10 masak zarah: OH HAI
10:10 zarah masak: excuse me?
10:10 masak zarah++
10:12 masak lunch &
10:13 olas wb zarah
10:13 olas zarah: wb
10:13 zarah olas: I did not understand that
10:13 olas zarah: welcome back
10:13 zarah olas: excuse me?
10:13 olas zarah: you were gone, right?
10:13 zarah olas: I'm just a bot, you expect me to understand that?
10:14 olas zara: you are the same as always, arenät you?
10:14 olas zara: you are the same as always, aren't you?
10:14 olas zarah: you are the same as always, aren't you?
10:14 zarah olas: please rephrase or stop trying to be witty :)
10:14 olas hahaha
10:14 olas she's back, indeed
10:31 egonw joined #bioclipse
10:58 masak zarah: you're the welcome one!
10:58 zarah masak: no, YOU'RE the welcome one!
10:59 masak :)
10:59 jonalv zarah: you are the binary one!
10:59 zarah jonalv: oh, shut up :)
10:59 zarah jonalv: no, YOU are the binary one! :)
10:59 jonalv zarah: no
10:59 zarah jonalv: I see.
11:02 masak @update
11:03 CIA-49 bioclipse: carl_masak * r6441 /bot/trunk/zarah.pl: [zarah] now returns after saying "oh shut up"
11:03 zarah joined #bioclipse
11:03 masak zarah: you're the cute one!
11:03 zarah masak: no, YOU are the cute one! :)
11:04 masak zarah: no, YOU'RE the cure one!
11:04 zarah masak: no, YOU are the cure one!
11:04 masak zarah: no, YOU'RE the cure one!
11:04 zarah masak: no, YOU'RE the cure one!
11:04 masak zarah: no, YOU'RE the cure one!
11:04 zarah masak: no, YOU'RE the cure one!
11:04 masak zarah: no, YOU'RE the cure one!
11:04 zarah masak: no, YOU'RE the cure one! :)
11:04 masak zarah: no, YOU'RE the cure one!
11:04 zarah masak: no, YOU are the cure one! :)
11:04 masak zarah: no, YOU'RE the cure one! :)
11:04 zarah masak: no, YOU'RE the cure one! :)
11:04 masak zarah: no, YOU'RE the cure one! :)
11:04 zarah masak: oh, shut up :)
11:04 masak :)
11:04 masak s/cure/cute/ # lots of times
11:04 jonalv zarah, masak having fun?
11:04 zarah jonalv: excuse me?
11:05 masak jonalv: excuse me? :)
11:05 jonalv zarah: you are excused
11:05 zarah jonalv: please rephrase or stop trying to be witty :)
11:05 masak jonalv: please stop trying to be witty :)
11:20 CIA-49 bioclipse: carl_masak * r6442 /bot/trunk/zarah.pl: [zarah] now handles meklund backticks correctly
11:21 CIA-49 bioclipse: carl_masak * r6443 /bot/trunk/zarah.pl: [zarah] improvement handling an arbritary amount of meklund backticks
11:22 zarah joined #bioclipse
11:26 jonalv olas: ping
11:30 edrin joined #bioclipse
11:30 jonalv hi edrin
11:30 masak hi edrin
11:33 edrin hi
11:33 zarah hi edrin
12:02 CIA-49 bioclipse: carl_masak * r6444 /bioclipse2/trunk/plugins/net.bioc​lipse.biojava.ui/src/net/bioclipse​/biojava/ui/editors/Aligner.java: [Aligner] made the color scale tone correctly
12:06 malic1 joined #bioclipse
12:09 masak speaking of project handling systems and bug trackers, I really like RT
12:11 masak http://bestpractical.com/rt/
12:12 jonalv we need a java solution not more Perl ;)
12:23 masak jonalv: I find that reasoning hard to understand.
12:25 olas masak: that was an answer worthy of zarah
12:25 olas jonalv: please rephrase or stop trying to be witty :-)
12:25 masak :)
12:26 jonalv huh
12:26 masak no really, I don't see why someone would prefer a Java bugtracker just because "we need a java solution not more Perl"
12:26 masak jonalv was probably trying to be funny, but I thought the joke was strange, too
12:27 olas I'd prefer something that's more tightly integrated with Eclipse and mylyn
12:27 olas like bugzilla or JIRA
12:27 olas or Trac
12:28 jonalv masak: my point was that you always suggest things made in Perl...
12:28 olas :-)
12:29 masak jonalv: I don't. my overriding rule is to suggest things I like.
12:29 masak jonalv: many, _many_ webapps are written in Perl
12:29 masak more than in Java
12:33 egonw I agree that a BTS with an open API would be really nice
12:33 egonw SF does not have that...
12:33 masak sf.net--
12:33 egonw and I just love to be able to have a few (Java, Perl, Pyton, whatever) scripts to list me all bugs given a group, and match that with source code mark up
12:33 egonw in the CDK we use @cdk.bug
12:34 egonw to enrich the JavaDoc with links to open bugs for classes
12:34 egonw being a library that is really important for users
12:34 egonw but the current system doesn't function optiomally with two main branches
12:35 egonw being able to close a bug by having "closes #bla" in your commit message is just great
12:35 egonw but impossible with SF technology
12:35 masak egonw: that would indeed be wonderful.
12:35 egonw Debian uses such set up
12:35 egonw I think even using ChangeLog's, not even commits
12:35 masak egonw: RT works via many channels. I've seen it used with great ease over www and mail
12:35 egonw but that's just a matter of changing script
12:36 egonw yeah, Debian uses an email interface too, IIRC
12:36 olas I have no objections to abandonong SF, other than it gives us legitimity
12:36 olas it's slow
12:36 olas unpredictable
12:36 olas and lacks features
12:37 olas the speed is the worst part IMO
12:37 olas a faster SVN would be nice
12:37 olas a better bug tracking would be nice too
12:43 edrin do you have an alternative in mind?
12:44 masak question is legitimity for whose sake?
12:45 masak if we find a better bug tracker and are happy there, who's gonna complain about legitimity?
12:45 olas well
12:45 olas not just that
12:46 olas moving SVN from SF
12:46 jonalv what would we do about the df project then? Just leave it?
12:46 olas people really like that BC is on SF
12:46 olas df?
12:46 egonw file releases
12:46 egonw that can certainly remain there
12:46 jonalv *sf
12:46 egonw SF has a good track record with mirrors etc
12:46 egonw sf++
12:47 olas right
12:47 olas so we're talking just a new bug tracker
12:47 masak aye
12:47 olas like launchpad?
12:48 jonalv well it sounds like you wanan emmigrate svn too....
12:48 masak migrate.
12:48 masak yes, maybe.
12:48 jonalv masak: yea...
12:52 * egonw would be interesting in LP for the BTS
12:52 egonw and see how that works out
12:52 egonw at least it would not have the trouble of setting up and maintaining a BTS oneselves
12:52 egonw which is why sf++
12:53 masak indeed.
12:53 jonalv LP? BTS?
12:54 egonw LaunchPad
12:54 masak jonalv: Launchpad. Bug Tracking System.
12:54 egonw Bug Track System
12:54 olas @zarah: tell jonalv BTS=Bug Track system
12:54 olas damn
12:54 olas whaeve
12:54 jonalv zarah: tell me...
12:54 zarah Consider it noted.
12:54 jonalv huh?
12:54 masak haha
12:55 jonalv I fixed that
12:55 masak apparently not
12:55 jonalv it worked the other week...
12:55 olas zarah: tell jonalv
12:55 zarah Consider it noted.
12:55 masak zarah: tell jonalv
12:55 zarah Consider it noted.
12:55 olas "what do you want me to tell?"
12:55 jonalv zarah: tell me
12:55 zarah jonalv: olas said jonalv
12:55 zarah jonalv: masak said jonalv
12:56 masak that's a bit strange too
12:56 masak zarah soon needs her own BTS...
12:56 zarah masak: excuse me?
12:56 masak zarah: you soon need your own BTS!
12:56 zarah masak: excuse me?
12:56 masak zarah: aw, shut up
12:56 zarah masak: :)
12:56 olas zarah: dz
12:56 zarah you're welcome, olas :)
12:56 masak zarah: dz
12:56 zarah no, YOU'RE the cute one! :)
12:56 masak :)
12:59 olas jonalv: why is logging not working?
13:00 CIA-49 bioclipse: jonalv * r6445 /bot/trunk/zarah.pl: I thought I already ade this commit...
13:00 jonalv zarah: boo!
13:00 jonalv olas: I don't know
13:00 zarah joined #bioclipse
13:01 jonalv zarah: tell me...
13:01 zarah jonalv: You have no new messages.
13:05 olas jonalv: I need help with the logging
13:05 olas :-(
13:05 jonalv olas: I am working on Brunn user documentation today...
13:06 olas ok
13:06 olas that is important, I know
13:06 jonalv olas:  Are you looking at the logging now?
13:06 olas no
13:06 olas don't know where to start
13:06 olas hence I will not start now
13:06 jonalv Richard probably can fix it quick....
13:09 olas I'll email him
13:10 masak is it a bird? is it a plane? no, it's rklancer!
13:13 gilleain joined #bioclipse
13:15 egonw hi gilleain
13:15 gilleain hi everybody, I have just started as a postdoc in Dr Steinbeck's group.
13:15 jonalv hi gilleain
13:16 egonw welcome!
13:16 gilleain I will be working on some parts of nmr spectrum stuff.
13:16 gilleain could I have an account on the wiki, please?
13:17 shk3 Gilleain will bring the CASE stuff in Bioclipse to production stage
13:18 edrin hello gilleain
13:19 edrin olas: i personally like having project at sf. This looks somehow "professional" although I agree that svn is really slow.
13:19 olas edrin: that is my opinion too
13:20 olas hi gilleain
13:20 olas gilleain: I'll set you up with a wiki account
13:20 gilleain thanks, olas.
13:20 olas please give me desired email, username and full name
13:21 gilleain "gilleain.torrance@gmail.com", "gilleain", and "gilleain torrance"
13:21 olas mom
13:21 egonw gilleain: and your SF account?
13:22 gilleain I do have a sf account, yes, by the same name.
13:22 egonw gilleain, that is, I assume?
13:22 egonw I'll add that
13:22 gilleain thanks.
13:23 olas you should have gotten an email about wiki access now
13:23 olas welcome to the Bioclispe project!
13:23 egonw gilleain: you should have SVN write access now
13:23 gilleain great.
13:24 shk3 olas: can you also make gilleain a developer in Bioclipse project on sf?
13:24 shk3 I will do so in cdk.
13:24 olas It would be great if you could send an email to bioclipse-devel mailing list and introduce yourself and what your plans with Bioclipse are
13:24 egonw shk3: already did that
13:24 shk3 thanks
13:24 gilleain Sure, I will do that.
13:24 olas great
13:24 olas Welcome!
13:24 egonw gilleain: I'm the guy who wrote the current seneca code for Bioclipse
13:25 egonw the main stopper was the performance of the determinstic structure generator
13:25 gilleain Ah, right, I guess I'll see you in the @author tags.
13:25 egonw gilleain: you'll be at the EBI when I visit on Sept 1, I hope.. ?
13:25 gilleain I will, yes.
13:25 egonw good
13:26 egonw looking forward to discussing with you the state of the code I wrote...
13:26 shk3 gilleain: you are a member of cdk project now
13:26 shk3 so you can hack on the structure generator if you like
13:26 egonw 1 year postdoc with Christoph was too short to fully get SENECA working...
13:26 gilleain Ah good, I've logged in to the wiki.
13:26 egonw shk3: you are aware that the deterministic structure generator has been removed?
13:28 shk3 yes
13:28 shk3 but it could still be a starting point, I guess?
13:28 shk3 and it's not the thing for gilleain right now, obviously
13:28 shk3 first he needs to get into bioclipse
13:29 gilleain bioclipse2 (core) seems to build without errors, at least.
13:29 CIA-49 bioclipse: shk3 * r6446 /bioclipse/trunk/plugins/net.bi​oclipse.spectrum/src/spok/gui/ (9 files): the last change should be in bc2 but went to bc1 since I had copied the .svn over
13:31 shk3 great. can you run?
13:32 gilleain no, it has an error, I'll follow the extra steps on the wiki.
13:33 shk3 ok
13:33 masak gilleain: since about a month back, one has to set the target platform on Eclipse startup
13:33 masak we don't know why.
13:35 gilleain success!
13:35 masak gilleain++
13:35 gilleain Hmm. Many things in Eclipse seem to be a bit magic.
13:35 masak gilleain: such as?
13:36 masak oh, you mean the target platform thing.
13:36 masak well, in this case it's not magic _enough_ :)
13:36 masak or at least the wrong kind of magic
13:36 gilleain Heh.
13:38 CIA-49 bioclipse: ospjuth * r6447 /bioclipse2/trunk/plugins/net.bioclipse.jmol/s​rc/net/bioclipse/jmol/editors/JmolEditor.java: JmolOutline is now activated if clicked on an element, even if outline is not active part.
13:38 olas IMO we have gotten bc2 to be much more stable in the last 2 weeks
13:39 olas we now rarely experience many problems
13:39 olas and running seem to be ok
13:40 CIA-49 bioclipse: ospjuth * r6448 /bioclipse2/trunk/plugins/net.bioclipse.j​mol/src/net/bioclipse/jmol/views/outline/ (4 files): Implemented properties for JmolMonomers.
13:45 jonalv karma
13:45 zarah jonalv has a karma of 0
13:45 jonalv :(
13:45 shk3 jonalv++
13:46 jonalv :)
13:46 jonalv karma
13:46 zarah jonalv has a karma of 1
13:46 masak jonalv--
13:46 masak :>
13:46 jonalv masak--
13:46 masak :)
13:47 masak @restart
13:47 CIA-49 bioclipse: carl_masak * r6449 /bot/trunk/zarah.pl: [zarah] replies sarcastically to people who say she is excused
13:47 zarah joined #bioclipse
13:47 masak zarah: you're excused.
13:47 zarah masak: you've just exceeded my capabilities :/
13:47 masak dang.
13:48 jonalv zarah: you are excused
13:48 zarah jonalv: I'm just a bot, you expect me to understand that?
13:49 masak @restart
13:49 CIA-49 bioclipse: carl_masak * r6450 /bot/trunk/zarah.pl: [zarah] added missing m//x modifier
13:49 zarah joined #bioclipse
13:50 masak zarah: you are excused.
13:50 zarah masak: oh, thank you, thank you!
13:50 masak :)
13:52 steinbeck joined #bioclipse
13:57 masak zarah: you're the excused one!
13:57 zarah masak: no, YOU'RE the excused one!
14:10 jonalv zarah?
14:10 zarah jonalv: yes?
14:11 jonalv zarah: just checking that you where there...
14:11 zarah jonalv: I did not understand that
14:11 jonalv zarah: oh well now you know :)
14:11 zarah jonalv: I'm just a bot, you expect me to understand that?
14:11 masak zarah: he says he was _checking_... that you were _there_...
14:11 zarah masak: I'm just a bot, you expect me to understand that?
14:11 masak no
14:23 edrin hi steinbeck
14:23 steinbeck cheers
14:42 gilleain joined #bioclipse
15:03 malick joined #bioclipse
15:09 olas edrin: got a minute?
15:09 CIA-49 bioclipse: shk3 * r6451 /bioclipse2/trunk/plugins/net.bioclipse.sp​ectrum/src/net/bioclipse/spectrum/editor/ (ChartPage.java SpectrumEditor.java): added charts to spectrum editor
15:09 olas I need some starters to set up XMPP Web services
15:10 olas can't find the links you gave me last time
15:10 olas edrin: ping me when back
15:10 * olas is away for 5 mins
15:10 CIA-49 bioclipse: shk3 * r6452 /bioclipse2/trunk/plugins/n​et.bioclipse.spectrum/lib/ (jcommon-1.0.0.jar jfreechart-1.0.1.jar): added charts to spectrum editor
15:10 CIA-49 bioclipse: shk3 * r6453 /bioclipse2/trunk/plugins/net.bioclipse.sp​ectrum/src/spok/utils/SpectrumUtils.java: added charts to spectrum editor
15:16 olas edrin: still here? :-)
15:22 olas zarah: tell edrin to ping me
15:22 zarah Consider it noted.
15:28 edrin hi
15:28 edrin back
15:28 zarah hi edrin
15:28 zarah edrin: You have new messages. Write '@messages' to read them.
15:28 edrin l@messages
15:28 edrin @messages
15:28 zarah edrin: olas said to ping me
15:28 edrin hi olas
15:29 olas hi edrin
15:29 olas got a minute to start me on xmpp?
15:29 olas and server setup/config?
15:29 edrin yes
15:32 olas did you have links for the process?
15:32 olas any wiki pages?
15:32 edrin to setup a jabber daemon?
15:32 olas I guess all steps
15:32 edrin or to write a xws
15:32 olas some sort of outline
15:33 edrin service
15:33 edrin ah
15:33 edrin i haven't created one yet
15:33 edrin I wanted to try this this evening
15:33 olas taht would be very useful to me
15:33 olas great
15:34 edrin lets hope this will work :)
15:53 CIA-49 bioclipse: shk3 * r6454 /bioclipse2/trunk/plugins/net.bioclipse.spectrum/ (META-INF/MANIFEST.MF build.properties): added charts to spectrum editor
16:03 CIA-49 bioclipse: shk3 * r6455 /bioclipse2/trunk/plugins/net.bi​oclipse.spectrum/src/spok/gui/: svn is corrupted, hope this helps
16:06 jonalv I have a feeling our alpha tag is broken. The externals link to the cdk repo probably goes to trunk...
16:10 olas jonalv: report that to masak
16:10 olas he made the tag
16:10 CIA-49 bioclipse: shk3 * r6456 /bioclipse2/trunk/plugins/net.biocli​pse.spectrum/src/spok/guicomponents/ (4 files): added charts to spectrum editor
16:14 CIA-49 bioclipse: shk3 * r6457 /bioclipse2/trunk/plugins/net.biocli​pse.spectrum/src/spok/guicomponents/ (SpectrumAxisListener.java SpokChartPanel.java): added charts to spectrum editor
16:15 jonalv zarah: tell masak I fear the Bioclipse alpha 01 tag you made is broken since the cdk svn:externals in it probably points to trunk. Or did you remember to change that to the current version at that time?
16:15 zarah Consider it noted.
16:16 CIA-49 bioclipse: shk3 * r6458 /bioclipse2/trunk/plugins/net.bioclipse.spectrum/ (.classpath src/net/bioclipse/spectrum/editor/ChartPage.java): added charts to spectrum editor
16:18 shk3 btw, I added help to two plugins the same way as it was done in bc1, but they don't show up.
16:18 shk3 anything changed with help?
16:18 shk3 ah, get an error when calling help:
16:18 shk3 java.lang.NoClassDefFoundError: org/eclipse/equinox/http/jetty/JettyConfigurator
16:19 shk3 does this ring a bell?
16:19 olas jetty should run
16:19 olas help shows for me
16:19 zarah olas: avaliable commands are clear-messages google help hi karma messages restart seen slap tell thanks
16:20 olas zarah: tell masak I'd like to be able to start my sentences with help, and propose @help to lead to zarah help
16:20 zarah Consider it noted.
16:24 rojasm joined #bioclipse
16:27 shk3 hm, where does jetty come from?
16:28 shk3 which plugin?
16:29 edrin left #bioclipse
16:32 olas shk3: I think org.apahe.jetty
16:34 shk3 hm, no such thing existing
16:34 jonalv what is jetty?
16:35 shk3 no idea
16:35 jonalv web server it seems
16:35 jonalv is that in Biolcipse?
16:36 shk3 don't know
16:36 shk3 it's just complaining about that
16:36 shk3 do you have an org.apache.jetty plugin?
16:36 jonalv I don\t think so
16:36 shk3 does help work for you?
16:37 jonalv don't know...
16:37 jonalv I fumbled and is currently downloading the tag...
16:38 jonalv Must remember to only check out trunk next time... :(
16:52 olas shk3: have you run Bioclipse from the product?
16:52 olas for me, it shows help
16:52 olas se the bioclipse.feature
16:52 olas it lists all plugins in product
16:52 olas jetty should be there
16:54 shk3 where is bioclipse.feature?
16:55 shk3 I run from product
17:04 olas product is based on features
17:04 olas it runs the bioclipse-feature
17:05 olas in SVN trunk/bioclipse2/features
17:07 shk3 hm, now works
17:07 shk3 don't really know why
17:07 shk3 but it does
17:19 CIA-49 bioclipse: shk3 * r6459 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui/ (5 files in 2 dirs): added help
17:23 CIA-49 bioclipse: ospjuth * r6460 /bioclipse2/trunk/plugins/net.bioc​lipse.jmol/src/net/bioclipse/jmol/ (8 files in 3 dirs): Selections in JmolEditor now propagates to JmolOutline for molecules with/without models/chains.
17:46 egonw joined #bioclipse
21:03 rojasm joined #bioclipse

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary