Camelia, the Perl 6 bug

IRC log for #bioclipse, 2007-12-14

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All times shown according to UTC.

Time Nick Message
07:09 jonalv joined #bioclipse
07:55 steinbeck joined #bioclipse
08:00 egonw moin
08:00 steinbeck moin Egon
08:03 egonw steinbeck: do you have the latest C&EN?
08:03 steinbeck on the phone
08:03 egonw ack... will ask later
08:21 steinbeck back
08:21 steinbeck depends on what the latest is.
08:21 steinbeck I get the print issue with a small delay
08:21 steinbeck of course
08:24 egonw the latest apparently has a nice piece on metabolomics...
08:24 steinbeck ack
09:38 olas joined #bioclipse
09:38 olas egonw: got my mail?
09:38 olas regarding stefans bug 1850268
09:38 olas I can't run JCP on mac :-(
09:38 olas so I can't fix
09:39 olas but as he says, it's a real showstopper
09:39 olas so I will hold release 1.2.0 until we sort it out
09:39 olas jonalv: around?
09:40 olas jonalv: could you (as you are on linux) reproduce bug 1850268 in 1.2.0 binary? if so, could you reproduce it when run from eclipse?
09:45 egonw olas: working on the makeHTML tool...
09:45 egonw got visotors now...
09:45 egonw will chat later...
09:46 olas ok
09:52 jonalv olas: I am trying to see if I can find the bug in 1.2rc2
09:59 jonalv hm I can't install stuff from the update site at: http://update.bioclipse.net/dev into 1.2rc2
10:00 jonalv What could I do wrong?
10:00 jonalv I get the text:  ----- Current configuration problems -----
10:00 jonalv in the dialog when I check something for instatllaion..
10:03 olas damn
10:03 olas seems Rc2 is not working
10:03 olas I will not have time to fix it today
10:03 olas Martin Nervall is defending his thesis
10:03 jonalv oh
10:05 jonalv in rc1 I  can draw a mdl molecule but when I try to open it I get an empty texteditor
10:05 jonalv Not sure what's supposed to happen since I haven't tried this before...
10:09 olas right-click and select open with JCP?
10:09 olas seems not to work then :-(
10:09 olas I can't fix JCP issues as I'm on mac
10:09 jonalv when I just doubleclicked it I got a nullpointerexception
10:10 olas what is the stack trace?
10:10 olas could you paste the first ones?
10:10 jonalv Oh I can try to reget it
10:10 jonalv Should I run it from Eclipse?
10:10 olas please try that as well
10:10 olas should be the same
10:10 jonalv need to check out alot then...
10:11 jonalv but this was rc1 you know...
10:12 olas nothing has changed regarding this to rc2
10:12 olas rc2 just contained chart and matrix updates
10:12 olas WAAAAAAH
10:12 olas :-(
10:12 * olas hates that we donät have junit tests
10:13 olas This will most likely be the last release I will make for 1.x
10:13 olas I have spent a week on it now
10:13 jonalv hm now things are working better... :(
10:13 jonalv strange
10:13 olas and I can't even reproduce errors as I'm on mac
10:13 olas better inside of eclipse?
10:14 jonalv no I am still running the rc1
10:14 jonalv the problem occurs when I draw two separate molecules in the same file
10:15 jonalv that is non connected
10:16 jonalv as for stack trace I dont get one
10:16 jonalv Eclipse is catching the exception and throwing up a dialog but the details button give no more details
10:17 jonalv In bioclipse2 we should log all exceptions to prompt so that it at least is possible to see what's going wrong
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10:22 jonalv here are strange things happening with the submolecules with those mdl files
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10:39 egonw jonalv: describe in detail what you did... like click menu this, open wizards that... then do such and so...
10:39 egonw and file a bug report...
10:39 egonw I will try to reproduce it next week then...
10:39 egonw seems 1.2 will not be out today...
10:40 masak egonw: there's already one filed re this
10:40 masak check out https://sourceforge.net/tracker/ind​ex.php?func=detail&aid=1850268&​amp;group_id=150681&atid=778609
10:40 egonw ok
10:41 masak ...which may or may not be the same bug
10:41 masak I talked to shk3 about it yesterday
10:42 masak olas: btw, it is known that jcp does not work _at all_ on a Mac, right?
10:42 masak olas: and do you agree that that is quite bad?
10:42 masak and that somebody should fix it very soon?
10:43 * masak has a good mind to look into it
10:44 olas masak: yes, it's been known ever since we started with mac
10:44 olas if you'd like to look into it I'd be more than happy
10:44 masak it's something to do with SWT, innit?
10:45 masak I think I heard something about it this past summer
10:45 olas as it works in jmol and jfreeshart it should be possible to fix
10:45 masak yes
10:45 olas I think it's that SWT and AWT events needs some tweaking to work properly
10:45 olas but it IS a mac issue
10:45 olas which makes it harder
10:46 masak why?
10:46 olas anyway, it works in jmol
10:46 olas well, it's not a general SWT/AWT problem
10:46 olas and hence it's harder to ask people for help
10:46 masak so the way to fix it would be: (1) look in jcp how they do it, (2) look in jmol how they do it, (3) try to do the same in jcp as in jmol
10:47 olas anyway, it's the worst bug of Bioclipse currently
10:47 masak which makes it fixworthy
10:47 olas something along those lines
10:47 masak maybe something for the X-mas holidays, then :)
10:47 * masak loves a good problem
10:47 olas a box of toffiffee to the one that fixes it!
10:47 masak seriously?
10:47 olas yup
10:49 jonalv That will be needed for bc2 as well right?
10:49 olas definitely
10:50 olas I thought the new JCP would replace it
10:50 olas but it seems noone is working on that
10:50 olas AND it appears to not work on mac either...
10:50 olas due to some other issue
10:51 olas if we don't get JCP to work we will have to investigate alkternatives
10:51 egonw I heard the new JCP can't work in Mac either
10:51 egonw because the Mac JVM is broken
10:51 olas right
10:51 masak olas: anyway, have you tried the new R support?
10:51 olas no
10:51 olas how do I try it?
10:51 masak I got the async output working yesterday
10:51 olas nice
10:51 masak update all your bc2 plugins
10:51 masak and have a go
10:51 masak write "R" in the js console
10:51 olas with the syntax?
10:51 olas ah
10:51 masak and then something like 1:100
10:52 egonw that sounds cool
10:52 egonw will try that next week
10:52 olas and use java-ns in R?
10:52 masak not yet, no
10:52 masak that would be the next step
10:52 olas ack
10:52 masak I'll also make sure to flesh out one of our java ns
10:52 jonalv masak: biojava?
10:52 masak egonw: I'll blog about it for you :)
10:52 masak jonalv: sure, why not?
10:53 jonalv no reason not
10:53 masak ack
10:54 * jonalv @lunch
10:54 masak & lunch
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11:36 edrin test
11:44 edrin left #bioclipse
11:48 egonw masak: yeah, looking forward to that blog item!
12:25 masak egonw: here you go: http://bioclipse.blogspot.com/2007/12/r-matey.html
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13:37 masak our svn bot is down
13:37 jonalv :(
13:37 masak feels a bit funny to do an svn commit for bc and only the bot over at #cdk reacts
14:54 edrin http://xkcd.com/135/
14:56 masak he's right -- Miss Lenhart should have focused more on that problem
14:59 jonalv LOL
15:01 masak jonalv: you think this is funny?
15:03 jonalv yes
15:03 masak :)
15:51 masak so there _was_ a CIA bot here?
15:51 masak why then wasn't it reporting commits?
15:51 masak lazy bot...
15:51 * masak mumbles inaudibly
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