Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-12-10

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

All times shown according to UTC.

Time Nick Message
08:15 egonw joined #bioclipse
08:16 egonw moin
08:16 zarah hi egonw
08:28 olass joined #bioclipse
08:28 olass hi
08:28 zarah hi olass
08:28 olass karma
08:28 zarah olass has a karma of 2
08:28 egonw yeah, my title sheet is finished...
08:28 olass karma olas
08:28 zarah olas has a karma of 45
08:29 egonw only 25 sheets to go :)
08:29 olass egonw: did you remove depictSybylAtomType from cdkmanager?
08:29 olass if not, where did it go?
08:29 egonw cdkdebug
08:29 olass ?
08:29 olass why?
08:29 egonw because it is CDK internals?
08:29 olass that broke a lot of tests
08:30 olass is it?
08:30 egonw ummm... I though I had moved all tests too ... :(
08:30 olass hmm
08:30 olass maybe I haven't updated the tests...
08:30 olass anyways
08:30 olass what if I want to depict sybyl atom types from console?
08:30 egonw and in the console?
08:30 olass cdk.depictSybyl(mol)
08:31 egonw or jcp.depictAtomTypes() ?
08:31 olass ??
08:31 olass please explain how the latter gives me sybyl atom types
08:31 olass and why this is a jcp call
08:31 olass and not cdk
08:31 egonw ah, you mean perceiveSybylAtomTypes() ?
08:32 olass yes
08:32 olass how?
08:32 egonw that should be in cdk. ...
08:32 egonw but that should not output...
08:32 egonw IMHO
08:32 olass it is not in cdkmanager
08:32 olass anymore
08:33 olass please get it back
08:33 egonw please file a bug report
08:33 olass I need it
08:33 olass ok, but need it now
08:33 egonw need to finish my presentation for the afternoon first
08:33 olass hmmm
08:33 egonw then just use the cdkdebug plugin?
08:33 olass ok
08:34 olass donät like the name
08:34 egonw manager: cdkdebug.depictBla
08:34 egonw OK
08:34 olass I don't want to debug, I want to percieve sybyl data types
08:34 egonw agreed
08:34 egonw but could not think of a better one so far
08:34 egonw open to suggestions
08:34 egonw cdkdebug := power tools for the cdk
08:34 olass what is the aim of cdkdebug?
08:34 egonw but that's so long...
08:34 olass ok
08:35 egonw but you actaully are a cdk power user
08:35 olass cdkx
08:35 olass cdk eXtended
08:35 olass (just brainstorming)
08:35 egonw yes...
08:35 egonw actually in the end I hope different script managers can contribute to the same namespace
08:36 olass yes, that would be nice
08:36 egonw so that the power method are simply available as cdk.
08:36 olass file a bug report to jonalv
08:36 egonw talked about this with him already...
08:36 olass a bug report is always a good thing
08:36 egonw but we did not give it high priority so far
08:36 egonw true
08:36 egonw ok, back to slide 2
08:58 Gpox joined #bioclipse
08:59 Gpox left #bioclipse
08:59 Gpox joined #bioclipse
08:59 olass hi Gpox
09:01 Gpox hi
09:01 zarah hi Gpox
09:06 CIA-32 bioclipse: ospjuth * r8014 /bioclipse2/trunk/plugins/net.biocli​pse.cdk.debug/META-INF/MANIFEST.MF: Made Activator package visible for access to debug manager via OSGI from another plugin.
09:07 * olass committed for the first time in 5 weeks
09:07 olass :-)
09:13 CIA-32 bioclipse: ospjuth * r8015 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.debug/src/net/bioclipse/cdkdebug/business/ (CDKDebugManager.java ICDKDebugManager.java): Renamed depict_xx_AtomTypes() to perceive..().
09:20 gilleain joined #bioclipse
09:22 edrin joined #bioclipse
09:22 jonalv joined #bioclipse
09:22 jonalv oh hai
09:22 edrin hi
09:22 zarah hi jonalv
09:22 zarah hi edrin
09:24 gilleain ohai
09:26 Gpox left #bioclipse
09:32 Gpox joined #bioclipse
09:57 edrin egonw: , olass http://www.slideshare.net/mattjive/​open-source-xmpp-for-cloud-services
09:57 zarah edrin's link is also http://tinyurl.com/62c2y7
09:58 edrin but it's not as good as our /IO Data
09:59 olass is that another XEP?
10:00 olass what number is our XEP?
10:00 edrin s44
10:00 edrin 244
10:01 gilleain heh. I love diagrams like the one in slide 7; An arrow connecting : [computer, brick wall, cloud labelled 'Internet', computer].
10:01 olass yes
10:01 olass sooooo not needed
10:01 edrin it's ->not an xep
10:01 olass no?
10:02 edrin no
10:02 olass just plain xmpp?
10:02 edrin yes
10:02 edrin seems so at least
10:02 olass it mentions XEP-114
10:03 edrin this is nothing interesting
10:03 edrin xws component is using xep114, too
10:03 olass ok
10:03 edrin Xep 114 This specification documents the existing protocol used for communication between servers and "external" components over the Jabber network.
10:04 edrin xws4j is using the same technique to run the component
10:04 olass egonw: Why a JCP feature? Is the Chemoinformatics feature not sufficient?
10:11 jonalv I think I am suffering froim the same problems that shk3 had... :(
10:16 gilleain A horrible cold?
10:16 gilleain :)
10:17 gilleain Seriously : jonalv, is it rendering troubles?
10:17 jonalv no a Bioclipse that refuses to start
10:17 gilleain oh noes.
10:17 gilleain that really is bad.
10:18 gilleain stefan did everything to get it working again.
10:18 gilleain I think that it was egonw++ 's advice in the end that fixed it, I think.
10:18 jonalv it is only the workspace containing my branch that refueses to start
10:18 jonalv my trunk workspace runs fine...
10:19 jonalv it seems at least
10:19 gilleain huh. are they quite different?
10:20 jonalv I have no diea
10:20 jonalv they shouldn't be...
10:33 jonalv but it doesn't work
10:39 jonalv gilleain. egonw, shk3: So what was the trick? I am sort of stuck here...
10:48 gilleain sorry, I went for coffee
10:48 gilleain and shk3 is at home, ill.
10:48 gilleain I was backlogging to monday, mom
10:49 jonalv gilleain: mhm
10:50 gilleain 13:59shk3it looks like I need to choose plugins manually in the run configuration
10:50 gilleain hmm. that copy/paste didn't work very well...
10:52 gilleain but it might be features that are the problem?
10:52 gilleain could you try without using a feature?
10:52 jonalv gilleain: I have tried that..
10:52 gilleain oh.
10:53 jonalv actually it might  be another problem...
10:53 jonalv It's not necessarily the same...
10:53 gilleain true
10:53 gilleain what are the symptoms?
10:54 jonalv I don't get any good errormessage but the managers just don't get published to the OSGI container
10:54 jonalv http://pastebin.com/f6649d548
10:55 jonalv that is from only the core feature
10:55 jonalv but I basically get the same no matter what I do...
10:55 gilleain hmmm. and it happens for all managers?
10:56 jonalv yea I think so
10:56 jonalv it seems to be some osgi related thing...
10:56 gilleain osgi magic, yes
10:56 jonalv I am a bit afraid it might be some race going on...
10:57 jonalv with the wrong winner...
10:57 gilleain that sounds possible.
10:58 jonalv yea but I was so sure we had gotten rid of that
10:58 jonalv anyway I am gonna break for lunch
10:58 gilleain what was the cause before?
10:58 gilleain oh, right 'k. later.
10:58 jonalv before what?
10:59 * jonalv afk
11:12 shk3 joined #bioclipse
11:48 CIA-32 bioclipse: shk3 * r8016 /bioclipse2/trunk/plugins/net.bioclip​se.specmol/src/net/bioclipse/specmol/​editor/SpecMolDrawingComposite.java: no context menu needed
12:51 jonalv uhm help. "The Eclipse executable launcher was unable to locate its companion
12:51 jonalv shared library"
12:52 jonalv all I did was remove the git-feature...
13:18 gilleain joined #bioclipse
13:19 gilleain jonalv : sounds bad. did you do all the usual, such as restarting eclipse, cleaning code (not sure how that would help in this case), uhmm.. and..
13:24 gilleain you're not on windows, are you?
13:29 gilleain http://snipurl.com/7qhcl
13:29 gilleain (possible fix for mac eclipse, to do with .ini files)
14:37 egonw joined #bioclipse
14:38 gilleain hey egonw, did you make your presentation yet?
14:38 egonw yes, just got back
14:38 gilleain howditgo?
14:38 egonw ok, I think
14:39 gilleain link?
14:39 gilleain :)
14:40 egonw yes, will follow
14:40 egonw first some coffee
14:40 egonw olass, jonalv: with some german cake?
14:41 jonalv cake?
14:48 olass /me doesn't like german cake
14:49 * olass
14:49 olass /me
14:49 olass oh, a space in the beginning
14:49 olass :-)
15:52 masak joined #bioclipse
16:21 CIA-32 bioclipse: carl_masak * r8017 /bot/trunk/zarah.pl: [zarah] add reply "zarro boogs" to null pelezilla search
16:21 zarah joined #bioclipse
16:22 gilleain @pele unobtanium
16:22 zarah gilleain: Zarro boogs found.
16:22 gilleain heh.
16:22 olass pz?
16:23 masak @pz works too
16:23 zarah [109] missing manager unit test for r... http://tinyurl.com/6crhlx
16:23 zarah Entire list at http://tinyurl.com/6m8xcv
16:23 olass meaning?
16:23 masak olass: pelezilla.
16:23 olass ah
16:23 olass @pz ospjuth
16:23 zarah [86] missing unit tests for has2d and... http://tinyurl.com/62zqah
16:23 zarah [87] missing unit test for getInfo(St... http://tinyurl.com/5ldv8y
16:23 zarah [88] missing unit test for getNoMolec... http://tinyurl.com/6rapvc
16:23 zarah Entire list at http://tinyurl.com/6jc6y3
16:23 masak @pelezilla masak
16:23 zarah [76] Bioclipse crashes when text is d... http://tinyurl.com/5eaofv
16:23 zarah [77] paths in windows slash problems     http://tinyurl.com/578aen
16:23 zarah [78] CR/LF problems on windows           http://tinyurl.com/6eznsa
16:23 zarah [79] Properties menu item does not sh... http://tinyurl.com/5zc2jj
16:23 zarah [97] missing unit test for fromCml( S... http://tinyurl.com/5lxvyh
16:23 zarah Entire list at http://tinyurl.com/6rqkry
16:24 olass @pz ola.spjuth
16:24 zarah olass: Zarro boogs found.
16:24 olass @pz ola.spjuth@farmbio.uu.se
16:24 zarah olass: Zarro boogs found.
16:24 masak olass: not sure that search works that way.
16:24 olass what does it do?
16:24 masak it's a kind of 'quick search', whatever that means.
16:24 masak olass: I'm not really sure. I should find out.
16:24 olass @pz jcp
16:24 zarah [165] Color atoms and bonds in JCP fr... http://tinyurl.com/5q4sks
16:24 zarah [150] Mark isDragging in JCP editor a... http://tinyurl.com/63px67
16:24 zarah [158] ChangeModule Action should only... http://tinyurl.com/6ow99v
16:24 zarah [162] SDFeditor has same toolbar as JCP  http://tinyurl.com/5krqbm
16:24 zarah [160] Unable to open new JCP in Biocl... http://tinyurl.com/5ru7cu
16:25 zarah Entire list at http://tinyurl.com/65hbv9
16:25 masak at least it scans the titles.
16:25 masak but probably more.
16:25 olass ok
16:25 olass @pz missing
16:25 zarah [79] Properties menu item does not sh... http://tinyurl.com/5zc2jj
16:25 zarah [65] CDKManager should be completely ... http://tinyurl.com/68rpol
16:25 zarah [94] missing unit test for createConf... http://tinyurl.com/674rgn
16:25 zarah [106] missing manager unit test for m... http://tinyurl.com/5s4wyd
16:25 zarah [107] missing manager unit test for s... http://tinyurl.com/65p3jp
16:25 zarah Entire list at http://tinyurl.com/6l7922
16:26 masak zarah: you should write how many bugs the full list contains.
16:26 zarah masak: Hokay. You provide the commits, I provide the "should"-ing
16:26 masak zarah: hokay
16:26 zarah masak: so, basically.
16:34 CIA-32 bioclipse: carl_masak * r8018 /bot/trunk/zarah.pl: [zarah] now reports how many hits there were in a @pelezilla search
16:34 zarah joined #bioclipse
16:34 gilleain @pz jcp
16:34 zarah [165] Color atoms and bonds in JCP fr... http://tinyurl.com/5q4sks
16:34 zarah [150] Mark isDragging in JCP editor a... http://tinyurl.com/63px67
16:34 zarah [158] ChangeModule Action should only... http://tinyurl.com/6ow99v
16:34 zarah [162] SDFeditor has same toolbar as JCP  http://tinyurl.com/5krqbm
16:34 zarah [160] Unable to open new JCP in Biocl... http://tinyurl.com/5ru7cu
16:34 zarah Entire list (10) at http://tinyurl.com/65hbv9
16:34 masak zarah++
16:34 gilleain ho-hoh.
16:34 gilleain zarah++
16:35 masak zarah: you are a smart girl.
16:35 zarah masak: Not so loud, dear. I don't want my boyfriend to hear.
16:35 olass zarah: YOU ARE A SMART GIRL
16:35 zarah olass: eh... wha'?
16:36 olass zarah: you are the stupid one
16:36 zarah olass: no, YOU'RE the stupid one!
16:36 masak :P
16:36 olass zarah: you are stupid
16:36 zarah olass: I did not understand that
16:36 masak haha
16:36 masak she's funny.
16:36 olass zarah: do you like me?
16:36 zarah olass: are you talking to *me*?
16:36 olass zarah: no
16:36 zarah olass: I see.
16:36 olass zarah: your MAMA
16:36 zarah olass: that was not so easy for a little bot to understand
16:37 olass zarah: boo
16:37 zarah olass: are you making fun of me?
16:37 olass @pz olas++
16:37 zarah [76] Bioclipse crashes when text is d... http://tinyurl.com/5eaofv
16:37 zarah [97] missing unit test for fromCml( S... http://tinyurl.com/5lxvyh
16:37 zarah [101] missing unit test for loadMolec... http://tinyurl.com/5s3c2p
16:37 zarah [108] missing manager unit test for l... http://tinyurl.com/5ok8h9
16:37 zarah [109] missing manager unit test for r... http://tinyurl.com/6crhlx
16:37 zarah Entire list at http://tinyurl.com/6rbdly
16:37 olass karma
16:37 zarah olass has a karma of 2
16:37 olass olas++
16:38 olass aaah!!!
16:38 masak hey!
16:38 masak olas--
16:38 olass :-)
16:38 olass NOOOOO
16:38 olass karma olas
16:38 zarah olas has a karma of 46
16:38 olass :-(
16:38 olass I remember a time... not so distant...
16:38 masak olas--
16:38 olass then masak came along
16:38 olass olas++
16:38 jonalv olas--
16:38 masak olas--
16:38 olass cleared olas karma
16:38 olass olas++
16:38 olass olas++
16:38 olass olas++
16:38 zarah olas++
16:38 jonalv karma olass
16:39 zarah olass has a karma of 2
16:39 olass zarah: thanks
16:39 zarah you're welcome, olass :)
16:39 masak olass: that's it. I'm resetting your olas karma on the server.
16:39 olass NOOOOO!!!
16:39 masak (to 46, to be fair.)
16:39 olass can you do that!?
16:39 masak sure.
16:39 masak me++
16:39 olass NOT AGAIN!
16:39 olass this is the second time
16:40 gilleain And so, the karma wars began...
16:40 masak olass: second time you misbehaved, yes.
16:40 olass jonalv-- //for not stopping masak
16:40 masak jonalv++
16:40 jonalv olass: I am working...
16:40 jonalv olass: not playing..
16:40 olass right
16:40 olass jonalv++
16:40 masak olass: furthermore, I think I will block karma requests from all users named 'olas*'
16:41 olass :-(
16:41 masak olass: ...until you rehabilitate.
16:41 masak haha
16:41 masak olaz: you're beyond help.
16:41 olass I know
16:42 * masak considers giving the 46 karma points to that olaz guy.
16:42 olass he's a nice guy
16:42 olass met him once
16:42 olass friendly
16:42 olass polite
16:42 olass generous
16:42 olass but most of all, very modest
16:42 masak extremely.
16:43 masak olass: so you don't mind my delegating the karma points to olaz?
16:44 olass copying that is, right?
16:44 olass karma olas
16:44 zarah olas has a karma of 47
16:44 olass 47 it is
16:44 olass not 46
16:44 masak olass: I haven't changed anything yet. requires a zarah reboot.
16:45 masak olass: that last point was from you.
16:45 olass let's not do it then
16:45 olass olas++ //for being so honest
16:45 masak @restart
16:45 olass olas-- //for being away
16:45 zarah joined #bioclipse
16:46 olass karma olas
16:46 zarah olas has a karma of 46
16:46 olass :-(
16:46 masak olass: resistence is futile.
16:46 olass zarah: masak is mean. Do you agree?
16:46 zarah olass: I'm just a bot, you expect me to understand that?
16:46 masak zarah: if olass misbehaves I will reset his score again, this time to a random number between 0 and 46.
16:46 zarah masak: you've just exceeded my capabilities :/
16:47 olass zarah: mine too
16:47 zarah olass: excuse me?
16:47 masak olass: I have very sensitive monitor equipment to detect if you have been cheating. so don't.
16:47 olass :-S
16:48 olass I wouldn't dream of it
16:48 masak 'course not.
16:50 masak zarah: you are excused.
16:50 zarah masak: you want me to leave?
16:50 masak zarah: yes.
16:50 zarah masak: I see.
18:34 egonw joined #bioclipse
18:48 egonw @tell masak http://scienceblogs.com/twominds/2008​/12/check_your_chinese_characters.php
18:48 zarah egonw's link is also http://tinyurl.com/5esb7e
18:48 zarah Consider it noted.
18:50 edrin egonw: btw. masak, did he set a new console now?
19:08 egonw he's working on it
19:08 egonw but remember he is only working 25%
19:31 edrin ok what kind of job is he doing?
20:14 edrin ok, me goes home
20:14 edrin cu later
20:14 edrin left #bioclipse

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