Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-03-02

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All times shown according to UTC.

Time Nick Message
07:50 masak joined #bioclipse
08:01 Gpox joined #bioclipse
08:08 * masak . o O ( maybe rename the biojava manager 'bio' instead? )
08:11 olass joined #bioclipse
08:11 olass moin
08:11 zarah hi olass
08:11 masak hi olass
08:11 olass privet masak
08:12 Gpox hi olass
08:12 olass hi Gpox
08:12 masak :)
08:12 masak hi zarah
08:12 olass great work all of you last week
08:12 Gpox hi masak
08:12 masak hi Gpox
08:12 olass glad we could get beta3 out
08:12 olass let's just hope it works :-)
08:13 masak 哈哈
08:13 olass hah
08:13 olass 29 downloads so far
08:13 olass even one for SPARC
08:13 * masak has 14 bugs to fix before 2.0
08:14 olass :-)
08:14 olass something like this with me too...
08:14 * masak can't haz a lunch box today
08:15 olass Gpox: I realy like the new moltable! Great job
08:15 olass Gpox++
08:15 olass masak: did you find inspiration for icons last friday?
08:15 masak olass: unfortunately not. I spent the bus journey in some zombie-like half-sleep.
08:16 masak but I'll get right on the icons now.
08:16 olass zombies are scary
08:16 masak braaaaains.
08:16 masak er. I mean... yes.
08:44 sneumann joined #bioclipse
08:45 masak @pz 45
08:45 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=45
08:45 masak olass: so the above bug ticket concerns the icon representing the Bioclipse app?
08:46 olass yes
08:46 olass on all platforms
08:46 olass it requires some icon program of some sort
08:46 masak O RLY?
08:46 * olass is not good at this at all
08:46 olass O RLY?
08:47 masak NO WAI!
08:47 olass ???
08:47 masak !!!
08:47 masak ¿¿¿
08:48 olass masak gone mad
08:48 masak :)
08:48 masak olass: http://en.wikipedia.org/wiki/O_RLY%3F
08:48 olass zarah: reboot masak
08:48 zarah masak's link is also http://tinyurl.com/8k74w
08:51 * olass need to switch to eclipse 3.4.2 now
08:54 egonw joined #bioclipse
08:54 egonw moin
08:54 zarah saluton egonw
08:55 sneumann bongiorno
08:55 masak dobre rano
08:55 sneumann zarah: this means "moin" ;-)
08:55 zarah sneumann: I did not understand that
08:56 masak sneumann: hold on.
08:56 egonw goedemorgen
08:56 egonw morguh
08:56 sneumann Guten Morgen
08:56 CIA-55 bioclipse: carl_masak * r9193 /bot/trunk/zarah.pl: [zarah] now understands 'bongiorno'
08:57 masak zarah: reboot, plz
08:57 zarah joined #bioclipse
08:57 rojasm joined #bioclipse
08:57 sneumann bongiorno
08:57 zarah ni hao sneumann
08:57 masak :)
08:57 sneumann thx.
08:57 masak np.
08:57 egonw hi rojasm
09:00 jonalv joined #bioclipse
09:01 jonalv y0
09:01 zarah ni hao jonalv
09:05 rojasm hi egonw, hi all
09:06 masak hi rojasm
09:54 olass there will be a status meeting tomorrow for the Uppsala group
09:54 olass is that OK with all UA developers?
09:54 olass to sum up things to do for RC1
09:54 olass and see current status with bugs
09:54 jonalv yes
09:54 olass gut
09:55 masak \o/
09:55 jonalv at last!
09:55 masak finally!
09:56 olass we're getting there :-)
09:56 * masak has missed those progress meetings
09:57 masak olass: this will sound a bit strange, but...
09:57 masak ...I'm putting in a lot of work time at the beginning of this week...
09:57 masak ...on the rare possibility that I might have to leave the country on Thursday.
09:57 masak :)
09:58 olass lol
09:58 olass yes, sounds strange
09:58 olass but legal
09:58 masak more explanations on a need-to-know basis. :P
09:58 olass you will come back, right?
09:58 masak aye.
09:58 jonalv so masak: you might have to leave the country for Korea?
09:59 masak jonalv: incidentally, yes.
09:59 masak but nothing certain yet.
09:59 olass masak: no worries
10:00 masak I'll see how I arrange that with vacation days. I'll be incommunicado at least during the flights.
10:02 olass masak: let's talk more tomorrow
10:02 masak olass: yes.
10:02 masak nothing certain yet. I might just as well stay put. we'll see.
10:07 thomasku joined #bioclipse
10:07 olass hi thomasku
10:07 thomasku hi olass
10:07 thomasku moin
10:07 zarah privet thomasku
10:08 masak ni hao thomasku
10:12 olass masak: I would like to vote for bug #35 for 2.0 if possible (and not too much work)
10:12 olass it cannot interfere with bug fixing
10:12 masak @pz 35
10:12 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=35
10:13 olass it's definitely more important to get proper error messaging in console
10:13 olass but I have a feeling that sorting out how different consoles should work is an important design issue
10:13 masak olass: well, since I'm stuck on the error messaging issue...
10:13 olass maybe we can at least talk about it briefly tomorrow?
10:13 masak absolutely.
10:13 olass gut
10:16 masak olass: between icons and #35, which one would you prioritize the highest?
10:17 olass icons
10:17 * masak thought so
10:17 olass looks is everything!
10:17 olass (almost)
10:17 olass :-)
10:17 masak indeed.
10:18 egonw can I vote for being able to 'cancel' a running script?
10:18 masak egonw: sure you can, but that's non-trivial.
10:18 masak as in Rhino internals.
10:21 jonalv egonw: I sort of have solution for that. If you are okey with canceling on manager method calls that is...
10:21 jonalv egonw: for the general solution I donät have an idea...
10:21 masak that's the one that's non-trivial.
10:22 masak (and it might slow down js execution, if it's at all possible)
10:22 egonw so, the system sort of works, but is just not practical :(
10:22 egonw at least we should disable the cancel functionality then
10:22 masak aye.
10:22 egonw if it's too hard
10:22 jonalv masak: slow down the execution?
10:23 jonalv if the script uses manager methods we already have a solution in place that does the trick
10:23 masak jonalv: because of possibly time-consuming checks at regular intervals instead of running the js commands.
10:24 jonalv masak: they are not very time consuming and it is the way the rest of Bioclipse already works so the checks will still be there no matter what...
10:24 masak jonalv: ok, point taken. still non-trivial, though.
10:25 masak Rhino compiles source code down to byte code, and runs that, IIRC.
10:25 jonalv We might be able to just klill the thread. But I am not sure about how good an idea that actually is...
10:25 masak with the present setup, it'd also kill the js env.
10:26 jonalv masak: yes but aren\t we creating a new one for each script?
10:26 masak I think we are nowadays, yes.
10:26 masak so that might not actually be a problem.
11:08 egonw olass: ping
11:08 olass pong
11:08 egonw can you send me a copy of the NT proposal of last year...
11:08 egonw I have it in print
11:08 egonw but
11:09 olass if I have...
11:09 egonw cannot find the PDF in my email archive
11:09 olass you should ask jarl
11:11 egonw ack
11:58 egonw joined #bioclipse
12:01 olass egonw: seen this? http://www.biomedcentral.com/1471-2105/10/S2/S4
12:01 zarah olass's link is also http://tinyurl.com/bw4foc
12:03 olass could be interesting reading for us as well
12:03 olass I know soo little of caBIG
12:04 olass but they seem to do cool stuff
12:04 charlgren joined #bioclipse
12:06 jonalv charlgren: hi
12:15 charlgren jonalv hi
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12:24 thomasku joined #bioclipse
13:19 shk3 did we come to a decision if new wizard should have filenames preset?
13:20 masak not that I know.
14:16 egonw joined #bioclipse
14:19 * masak might have found the part of the js env that stringifies exceptions
14:20 egonw sounds promosing
14:21 masak there was a method explanationAboutParameters which got all the EvaluatorExceptions and returned a String.
14:22 masak problem was, if it turned out that it shouldn't be the one to diagnose the error, it returned the message of the exception,
14:22 masak when it really should have re-thrown it.
14:22 shk3 should we have a poll on that naming stuff?
14:22 masak shk3: no, we should do it in the way that best benefits the user.
14:22 masak that is non-negotiable.
14:23 egonw what naming stuff?
14:23 masak egonw: there's a bug ticket that overheated somewhere.
14:23 masak I can dig it out for you.
14:23 egonw @pz overheated
14:23 zarah egonw: Zarro boogs found.
14:23 shk3 so should we have a poll on what's best for the user ;-)
14:23 shk3 I am really not sure about it
14:23 egonw masak: please let me know
14:24 masak egonw: hang on.
14:24 egonw I can put some oil on the fire then :)
14:24 masak @pz 189
14:24 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=189
14:24 masak egonw: go right ahead. :)
14:37 jonalv who is in the Molecular Informatics group at cologne University |Bioinformatcs Center?
14:38 masak zarah: ping me
14:38 zarah masak: ping
14:39 masak zarah: pong
14:39 olass jonalv: why do you ask?
14:39 olass several are there
14:39 jonalv do we have Bioclipse developers there?
14:39 olass [15:42] < olass> jonalv: why do you ask?
14:39 jonalv I didn't know this so now I got curious about who they might be...
14:40 jonalv and if we don't then I think some Bioclipse wiki page needs updating...
14:40 olass wiki page needs updating
14:40 olass 100% sure of that
14:40 jonalv I am reading chalgrens repport and he says that Bioclipse is actively developed by people there. I was a bit suprised becasuue I was not aware of this...
14:41 olass actively, no
14:41 olass but in a sense, yes
14:41 jonalv olass: now it's my turn to have my qwuestion answedred. Who is there? :)
14:41 olass we rely heavily on CML, which is actively developed there, and we have a collaboration with them
14:41 olass PMR
14:41 jonalv aha
14:41 olass Robert Glen
14:41 olass Sam Adams
14:41 olass and many others
14:42 jonalv okey
14:42 jonalv so I will not correct him then. it's somewhat true I guess...
14:46 jonalv olass: I thought PMR was in Cambridge...
14:46 olass jonalv: yes
14:46 olass oh
14:46 olass I see
14:46 olass mol informatics at cologne was Christophs old group
14:46 olass I read Cambridge before
14:46 olass ok
14:47 olass COlogne is out
14:47 olass should be replaced with EBI
14:47 jonalv olass: so it's old and should be removed?
14:47 olass Christoph is there now
14:47 jonalv oki thankyou
14:47 olass sry
14:47 olass read to fast :-)
14:47 olass to=too
14:48 masak no, it isn't :)
14:48 jonalv then bioclipse.net needs updatting...
14:48 shk3 yes
14:48 shk3 and wiki as well
14:48 shk3 as soon as bc2 is out
14:49 shk3 both need major updating
14:49 shk3 cubic should be updated to ebi right now, though
15:34 jonalv shk3: "cubic"?
15:35 masak shk3: "cubic"?
15:35 shk3 cologne University |Bioinformatcs Center?
15:35 shk3 =cubic
16:14 jonalv shk3: aha :)
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