Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-10-02

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All times shown according to UTC.

Time Nick Message
05:22 Gpox joined #bioclipse
06:28 rojasm joined #bioclipse
07:02 egonw joined #bioclipse
07:12 olas joined #bioclipse
07:12 olas moin
07:12 zarah hi olas
07:18 egonw moin
07:18 zarah hi egonw
07:21 olas egonw: had an evening session yesterday with edrin about xws
07:24 egonw yes, saw the commits
07:25 egonw browsed the tutorial last nite, but forgot to download BC1 :)
07:25 egonw olas: you're at home?
07:27 olas yup
07:42 jonalv joined #bioclipse
07:48 jonalv -names
07:52 egonw olas: this is the CMLComp I talked about: http://209.85.135.104/search?q=cache:92​p6GyzgivgJ:www.lexical.org.uk/golem/+go​lem+cml&hl=en&ct=clnk&cd=1
07:52 egonw via google cache
07:54 olas Golem?
07:54 egonw yes
07:54 olas why from cache?
07:55 olas did they remove the webpage?
07:56 egonw no, but I can't connect to it right now
07:56 egonw already send message to Andrew
08:00 egonw Yes, finally SF-OpenID-Blogger.com works :)
08:17 olas YES! WOOHOOO!
08:17 * olas is SOOOO glad that server is online again
08:18 egonw of golem?
08:18 egonw what server?
08:18 jonalv huh? What are you up to? :)
08:18 olas SF-OpenID-Blogger.com
08:18 olas actually
08:18 olas never heard of it
08:18 egonw hahahahaha
08:19 egonw OpenID allows you to login anywhere when you are logged in on your OpenID provider
08:19 egonw blogger.com is an openID provider
08:19 egonw and SourceForge allows logging in via openID
08:19 egonw however, it did not work for me in the past
08:19 egonw now it does
08:19 egonw which is goes...
08:20 egonw because I was getting *really* tired of having to log in again and again with SF
08:20 * olas too
08:20 egonw now, SF seems to have restored 'Remember' as well as fixed the OpenID stuff
08:20 egonw the first would have been good enough though
08:20 olas Remember works for me
08:20 olas right
08:21 * olas is a caffeine addict
08:30 stain egonw: but why would you care about SF? :-)
08:30 stain Taverna is finally moving away, btw.. Googlecode is the new SF
08:30 egonw stain: not github?
08:30 egonw or launchpad.net?
08:30 egonw stain: I don't care about the one... I use whatever I need :)
08:30 stain I think git would scare away too many..
08:31 egonw stain: yes, it's a trade off...
08:31 stain we already scare people off with Raven and Maven :)
08:31 egonw does the git-performance-boost of your own development outperform the loss of part-time developers and patchers...
08:31 egonw yes, maven sucks
08:31 egonw :)
08:32 stain it would mean more time spent on support emails
08:32 stain I guess it's still possible to use git locally and push up to SVN
08:32 egonw that's what I currently do for the CDK..
08:32 stain if we really wanted to.. but we don't have time to learn how to do that! ;)
08:32 egonw though people can now pull from a pure git mirror too
08:33 egonw stain: read my blog:
08:33 egonw ...
08:33 stain do you use this early git-plugin for eclipse, or just the command line?
08:33 egonw http://chem-bla-ics.blogspot.com/2008/09/cd​k-development-with-branches-using-git.html
08:33 egonw command line
08:33 egonw git plugin for eclipse does not seem mature enough yet
08:34 egonw stain: but the merging with git is brilliant
08:34 stain is it because you can do partial merges?
08:34 egonw really allows me to merge much more in the same time
08:34 egonw yeah, that too...
08:34 egonw but I can branch and merge whenever I like...
08:35 stain what happens when some silly developer (me) does Source->Reformat and Source->Sort  in Eclipse?
08:35 egonw that was really getting a limiting factor for the CDK
08:35 egonw stain: good point... have not tried that one yet :)
08:35 egonw mom, will try
08:36 stain maybe we can get Tom to try out your approach.. he'll be working on something that is quite "branchy" for the next months
08:36 stain oh no
08:36 stain Git doesn't work properly on Windows
08:36 stain crappers
08:36 egonw in that case I'd recommend to keep one git-svn tree, to allow pushing things to SVN, but do all the branching in a pure Git set up
08:37 egonw moving patching from one to another is easy enough
08:37 egonw stain: via cygwin
08:37 egonw but there is a native compile too
08:37 stain he likes to ahve a minimal system, he doesn't even have Solitaire on his machine
08:37 egonw hahaha :)
08:37 egonw but he *is* using windows?
08:37 egonw mmm...
08:37 egonw so much for 'minimal' :)
08:37 stain he's the only one :(
08:38 stain we should also do it
08:38 egonw http://code.google.com/p/msysgit/ <- native git on win32
08:38 stain as most of our users are on Windows
08:38 egonw yeah, testing on win32 is important
08:38 stain they said in the 90s that Java was cross platform, but really it's not that easy
08:38 egonw but development in Linux is so much faster (to me)
08:38 stain yeah, and we're all mac-fanboys here now :)
08:39 egonw most biolcipse people are :)
08:39 olas the smart ones
08:39 stain oh, the myExperiment guys are on Windows.. which is funny as Ruby on Rails don't work properly on Windows
08:39 egonw hehehehe
08:47 edrin joined #bioclipse
08:48 edrin hi
08:48 zarah hi edrin
08:48 edrin hi olas
08:48 edrin did the thing work for you?
08:49 olas hi edrin
08:49 olas is your server online?
08:49 olas got nothing to test with...
08:50 olas working home and all info about ws1 is in Uppsala
08:50 olas :-)
08:50 olas but wrote a client in java
08:50 edrin ah
08:50 edrin no, i am not at home
08:50 olas one thing I must say should be improved is error messages
08:50 edrin but you can run the testserver yourself, too
08:50 edrin that's quite simple
08:51 olas how?
08:51 olas can't run ejabberd on my computer
08:51 egonw_ joined #bioclipse
08:51 olas not until after I upgrade to leopard
08:51 olas which will be late next week earliest
08:51 edrin no
08:51 egonw_ oops
08:51 edrin you can use the ayena.de test component account
08:52 edrin hi egonw
08:52 olas ok?
08:52 olas what is the account info?
08:52 edrin olas: i think i mailed this to you once in an email
08:52 olas ok
08:52 olas will look at that
08:52 olas thx
08:53 olas found it
08:53 edrin 14.8.08
08:53 edrin yes
08:53 edrin and then just make the component connect to it
08:54 edrin and another thing: can you describe the JUnit problem in an email to me? I am not sure if i understood the problem
08:54 olas ok
08:54 olas will do so
08:54 olas oh, a question
09:02 gilleain joined #bioclipse
09:13 edrin what question?
09:21 egonw gilleain, Gpox: meeting at #jchempaint?
09:21 egonw gilleain: is stefan around too?
09:21 gilleain there's a #jchempaint?
09:21 gilleain :)
09:21 gilleain , and no.
09:22 gilleain At least, he's not in yet.
09:22 egonw ack
09:22 jonalv umbrello won't run on Mac OS X :(
09:22 * jonalv neeeds linux
09:22 gilleain not much will in my recent experience
09:25 shk3 joined #bioclipse
09:26 gilleain but what about this :
09:26 gilleain http://uml.sourceforge.net/s​creenshots/umbrello2-mac.png
09:28 jonalv yea...
09:28 jonalv I just tried building the neeeded stuff with maport but it failed... :(
09:30 * jonalv at lunch
10:13 egonw edrin: http://pipl.com/directory/people/Johannes/Wagener
10:13 egonw quote:
10:13 egonw A quick fact about Johannes Wagener:
10:13 egonw Johannes Wagener was born on 13 Sep 1758 in Schieren, Luxembourg...
10:13 egonw hahahaha
10:20 gilleain hello, egon? are we done? :)
10:21 egonw for now, yes
10:21 gilleain okey-dok.
10:29 CIA-30 bioclipse: ospjuth * r7137 /xws/trunk/xws4j-coffee-machine-sample/src/net/b​ioclipse/xws/component/functions/Functions.java: Corrected size of funtions array.
10:30 olas @task jonalv what is the status of the usermanager plugin?
10:30 olas @ask jonalv what is the status of the usermanager plugin?
10:31 thomasku joined #bioclipse
10:31 olas @tell jonalv what is the status of the usermanager plugin?
10:31 olas zarah?
10:31 olas hi zarah
10:31 olas zarah: hi
10:31 zarah hello olas :)
10:31 olas zarah: tell jonalv what is the status of the usermanager plugin?
10:31 zarah Consider it noted.
10:32 olas zarah: ping
10:32 zarah olas: are you making fun of me?
10:32 olas zarah: no, wanted a pong back
10:32 zarah olas: I see.
10:32 olas zarah: please do that next time
10:32 zarah olas: are you making fun of me?
10:32 olas zarah: no
10:32 zarah olas: I see.
10:33 olas zarah: you are the REALLY  STUPID one
10:33 zarah olas: no, YOU are the REALLY  STUPID one!
10:33 olas zarah: boo
10:33 edrin egonw: uh, I am really old.
10:34 edrin now they know my secret ...
10:45 olas @tell jonalv: is the http://wiki.bioclipse.net/index.p​hp?title=Checking_out_Bioclipse_2 updated?
10:45 zarah Consider it noted.
10:52 jonalv joined #bioclipse
10:53 jonalv hi
10:53 zarah hi jonalv
10:53 zarah jonalv: You have new messages. Write '@messages' to read them.
10:53 jonalv zarah: tell me
10:53 zarah jonalv: olas said what is the status of the usermanager plugin?
10:53 zarah jonalv: olas said is the http://wiki.bioclipse.net/index.p​hp?title=Checking_out_Bioclipse_2 updated?
10:53 jonalv -names
10:53 jonalv olas: ping
10:54 olas pong
10:54 olas jonalv: pong
10:54 jonalv status of usermanager is that it is working for Brunns needs
10:55 jonalv status of that install page is that as far as I know it's updated
10:55 olas ok
10:55 olas could the usermanager be used to store other accounts than for brunn?
10:55 jonalv you need the usermanager for something?
10:55 jonalv olas: yes
10:55 olas well, it would be nice if it could store my jabber ID and passwd
10:56 olas so we get a singlöe signon into Bioclipse
10:56 jonalv that should work
10:56 olas edrin will work tomorrow on getting XWS into bioclipse2
10:56 olas would be great if you could assist him with the usermanager
10:56 jonalv it should work out of the box I think
10:56 olas he might need help to get started
10:56 jonalv There is a license issue with it though.So it might be needed to ship it in a separate feature...
10:56 olas or is there a wiki page describing this?
10:57 olas jonalv: can we ship usermanager with core?
10:57 olas I think it is a core plugin...
10:57 olas so be in bioclipse-feature
10:57 olas what you say?
10:57 jonalv olas: I think the license needs to be seperate
10:57 olas what is the license?
10:57 jonalv so I think it needs a seperate plugin
10:58 olas yes, but plugin in bioclipse-feature
10:58 olas it already is a separate plugin
10:58 jonalv http://www.jasypt.org/license.html
10:59 jonalv Mustn\t the entire feature have the same license since licenses are accepted for features not plugins?
10:59 olas yes
10:59 olas but I think apache license is compatible with EPL
10:59 jonalv I think not
11:02 olas ok
11:02 jonalv the apache is GPL compatible the EPL is not
11:02 jonalv http://www.fsf.org/licensing/licenses/
11:02 egonw apache is GPL3 compatible, not GPL2
11:02 edrin is lgpl compatible with epl ?
11:02 egonw yes
11:02 edrin ok
11:02 egonw lgpl basically allows embedding in anything...
11:03 edrin good
11:03 egonw bc2 plugins using GPL software should be GPL too
11:03 olas yes
11:03 olas MUST be
11:03 jonalv the usermanager should probably be apache licensed for simplicity...
11:04 jonalv and just make a feature for it...
11:04 olas this is tricky
11:04 olas can we depend on a GPL plugin in an EPL plugin if they are in different features?
11:04 jonalv I don't see why not
11:04 olas having a core plugin, such as usermanager, as non-EPL seems like a bad idea
11:05 jonalv good point
11:05 olas we should consider using eclipse password management as we talked about
11:05 olas it really resembles usermanager
11:05 olas could we not find encryption jar in EPL?
11:05 jonalv or we could rewrite the encryption code in the Usermanager...
11:06 jonalv there is some ecryption code in java but it's a bit messier to use...
11:07 olas might be worth it
11:07 jonalv yea
11:09 jonalv although when we talked to the people behind jasypt they seemed very intrested in getting their program into Bioclipse
11:09 jonalv perhaps they have just picked a license without thinking about the effects...
11:09 olas not likely
11:10 olas but you could ask them
11:10 olas anyway, it is my belief that usermanager plugin should be in bioclipse-feature
11:10 olas it should be central to bioclipse
11:10 olas and hence we need to resolve the license issue
11:11 olas will file a bug for this and assign to jonalv
11:21 olas egonw: around?
11:21 olas rguha made a patch for the CMLReader
11:21 olas did you merge it with cdk trunk and 1.2?
11:22 olas if not, please do
11:22 olas and let me know
11:23 egonw where did he send the patch?
11:23 olas no idea
11:23 olas BTWm I just uploaded a patch to the bug report I just filed. So if you need it in a hurry, you can apply the patch to your local CDK copy
11:23 olas that was guhas mail to me
11:24 olas so maybe in cdk/bugs?
11:24 egonw when did he send that?
11:24 olas Well, the bug is in CMLCoreModule and is related to wrong setting for unspecified implicit H count.  Unfortunately, I don't know enough of the CML code to give a quick fix - I've filed a bug report and will have to wait for Egons view on this
11:24 olas sept 17
11:24 egonw ah, ok, that one
11:24 egonw no, not applied
11:24 olas could you please?
11:24 egonw mom, let me check
11:24 olas or schedule for soon :-)
11:25 olas CMLReading is broken in many bc2 places because of this
11:25 olas I'm happy if you just put it on your tot list
11:25 olas todo
11:25 olas haha
11:25 olas tot != todo
11:28 egonw the patch might actually be applied...
11:28 egonw seen the test file...
11:28 egonw will check now
11:50 olas let me know
11:54 egonw yeah... really tired today...
11:55 egonw things are not going so fast
11:57 egonw olas: btw, when do you plan to make a new BC2 releaes?
11:58 jonalv things are not going too fast either. I miss Ubuntu...
12:02 egonw I miss the coffee
12:02 egonw so, I bought a capucchino Ritter sport :)
12:02 jonalv okey
12:02 olas new bc2 release when we have something new
12:02 egonw good
12:02 olas currenlty no real improvements
12:03 * egonw is manually applying Rajarshi's patch
12:03 jonalv egonw: Are you gonan get a Mac too?
12:03 egonw nope
12:03 olas he is trying to resist it
12:03 egonw had to fight for it
12:03 egonw if it only had ubuntu preinstalled on it...
12:03 olas egonw REALLY wanted to run windows
12:04 olas and Jarl said OK
12:04 jonalv I like my mac but it's totally not compatible with the work I ahve done with Brunn
12:04 olas good with multiple platforms in developer group IMO
12:04 jonalv I am severly crippled when it comes to develop Brunn now...
12:04 * olas must run of and get vaccinated for his trip
12:05 olas be back in 30 mins
12:05 jonalv olas: good point. You wanna head up the Windows developer group?
12:05 * olas away
12:05 jonalv :)
12:13 egonw Gpox: please please int the copyright header found in other CDK files
12:13 egonw as in:
12:13 egonw http://cdk.svn.sourceforge.net/viewvc/cdk​/cdk/branches/cdk-1.2.x/src/main/org/open​science/cdk/modeling/builder3d/AtomPlacer​3D.java?revision=12161&amp;view=markup
12:13 egonw lines 1-20
12:14 egonw where you update line 3
12:14 egonw [14:13] <egonw> Gpox: please please int the copyright header found in other CDK files
12:14 egonw ???
12:14 egonw make that:
12:14 egonw [Gpox: please add the copyright header as found in other CDK files
12:15 gilleain I am also guilty of missing off copyright files. I will set my eclipse to do it..
12:15 Gpox will do
12:16 gilleain joined #bioclipse
12:32 egonw olas: the patch was in functionality already applied to the cdk1.2.x branch
12:32 egonw not in the way Rajarshi did it, but with the same effect
12:57 * olas away
12:57 * olas is back
13:01 edrin this fast
13:01 egonw but fixing a related bug too now
13:01 egonw which has been present since eternity
13:13 CIA-30 bioclipse: carl_masak * r7138 /xws/trunk/xws4j-coffee-machine-sample/src/net/b​ioclipse/xws/component/functions/Functions.java:
13:13 CIA-30 bioclipse: [Functions.java]
13:13 CIA-30 bioclipse: * replaced repetitive assignment to array elements with array assignment
13:44 jonalv KTable--
13:45 gilleain what is a "KTable"?
13:45 jonalv you don't wanna know...
13:45 gilleain Is it like a KDTree, as I am having fun with those...:)
13:46 jonalv http://sourceforge.net/projects/ktable
13:47 jonalv Brunn uses KTable
13:47 gilleain ahhh.
13:47 jonalv I used Ubuntu when I wrote most Brunn code. Now I am on a mac and things are not working... :(
13:48 jonalv Ktable works in windows and linux but not on mac...
13:48 gilleain many things don't, sadly.
13:49 gilleain as for umbrello - I use omnigraffle to draw uml diagrams.
13:49 gilleain it's not free, of course.
13:49 olas how about eUML?
13:49 olas you can get academic license for that
13:49 olas (we have)
13:50 egonw mmm... me sees a pattern
13:51 egonw ...but not on mac...
13:51 egonw well... http://landonf.bikemonkey.org/code/macosx/
13:52 gilleain I tried soylatte, but couldn't get it to work.
13:52 gilleain also, it's Xwindows only. blech.
13:53 egonw http://www.puzzlepirates.com/ :)
13:53 egonw anyway...
13:53 gilleain is http://sourceforge.net/projects/brunn/ meant to be blank? *looks innocent*
13:53 egonw why I dropped in on IRC...
13:53 egonw does UU.se not have access to JCICS/JCIM??
13:53 egonw that's a serious bug
13:54 olas JCIM yes
13:55 olas JCICS I don't know
13:55 egonw JCICS was split up into JCIM and something theory bla
14:06 jonalv gilleain: no it's not supposed to be empty...
14:06 jonalv http://www.myrtlewoodgaller​y.com/get_a_round_tuit.htm
14:20 gilleain jonalv: well, me too... http://tailor.sourceforge.net/
14:22 thomasku joined #bioclipse
14:24 jonalv okey is it just me or dourceforge suck_
14:24 jonalv ?
14:24 gilleain it has been slow lately
14:25 gilleain I'm sure it's nothing that sf has against you personally :)
14:25 egonw well, I was happy this morning about the new Remember option
14:25 egonw but all effect I see is that I now have to re-login every hour instead of every day :(
14:26 gilleain result!
14:26 gilleain (sorry)
14:26 gilleain that must be very irritating
14:26 jonalv I am actually starting to think that maybe siourceforge isn't the best solution around...
14:27 gilleain I hear all the cool kids use google code and hub gits.
14:28 jonalv yea well if it only was no good but now it's not working wtiehr...
14:28 jonalv *either
14:29 olas anyone has experience with http://semantic-mediawiki.org ?
14:31 gilleain not me.
14:31 olas egonw: you?
14:33 egonw no, only theoretical knowledge
14:34 egonw Henry Rzepa uses/d it
14:34 jonalv I am trying to write somrthign on a bug in sourceforge but it doesn't work... :(
14:34 egonw neither googlecode nor github have the full package of tools we need
14:34 egonw SF does
14:35 egonw jonalv: you should add a comment instead
14:35 jonalv launchpad?
14:35 egonw yes, that one does a reasonable job
14:35 jonalv egonw: that's what I am trying to do!!!!
14:35 egonw but only bzr :(
14:35 egonw jonalv: :)
14:35 egonw same here...
14:35 egonw but only get empty pages all the time
14:35 jonalv exactly
14:36 egonw yeah, something messed up with their system right now :*
14:36 egonw :(
14:40 edrin http://wiki.bioclipse.net/index.p​hp?title=Checking_out_Bioclipse_2 is up to date?
14:40 olas jonalv says so
14:41 edrin ok
14:41 jonalv as far as I know yea
14:41 olas ask here if you find any errors
14:41 gilleain it worked for me last month or so.
14:41 edrin ok
14:42 jonalv edrin: are you having problems?
15:00 edrin did not try yet
15:03 egonw bye all!
15:04 edrin bye
15:10 olas bye
16:08 edrin olas: mock process status created, but I can commit earliest tonight
16:09 edrin olas: the class will be called ProcessStatusMock.java
16:11 edrin and i also changed the run() methode of IFunction to public void run(IProcessStatus ps, Element input); -> IProcessStatus and not ProcessStatus. that means only the functions of ProcessStatus that are thought to be used by the users are visible...
17:14 olas edrin: sounds good
17:14 olas gotta log off now
17:14 olas bye all
17:14 olas left #bioclipse
17:40 edrin anyone still here?
17:41 edrin in bc2 how do i write stuff to the console? how do I do logging?
19:08 edrin left #bioclipse
19:24 rojasm joined #bioclipse

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