Camelia, the Perl 6 bug

IRC log for #bioclipse, 2007-10-04

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All times shown according to UTC.

Time Nick Message
06:46 thomas_ku joined #bioclipse
07:14 viklund morning
08:04 jonalv joined #bioclipse
08:22 masak joined #bioclipse
08:46 EskilA joined #bioclipse
09:27 masak this is deeply weird
09:28 * masak wishes egonw were here
09:49 masak anyone else running Eclipse 3.2.2 having trouble with the HEAD revision of Bioclipse?
09:50 masak specifically, the imported IApplication in BioclipseApplication
09:50 * jonalv has the problem in 3.2.2 will check 3.3 now
09:53 masak seems like a 3.3 addition
09:53 jonalv It works in 3.3
09:53 masak time to upgrade! :)
09:53 jonalv yes ... :(
10:02 masak lunch &
11:43 CIA-31 bioclipse: carl_masak * r3924 /trunk/plugins/net.bioclipse.cdk.ui/src/net/b​ioclipse/plugins/views/Structure2DView.java:
11:43 CIA-31 bioclipse: [Structure2DView.java]
11:44 CIA-31 bioclipse: * fixed inexplicable bug in which all molecules always showed
11:44 CIA-31 bioclipse:  up in backwards order
11:56 CIA-31 bioclipse: carl_masak * r3925 /trunk/plugins/net.bioclipse.cdk.ui/src/net/b​ioclipse/plugins/views/Structure2DView.java:
11:56 CIA-31 bioclipse: [Structure2DView]
11:56 CIA-31 bioclipse: * Slight improvement to readability
12:07 masak I'm going to write aloud here for a while
12:07 masak I'd really like to talk to shk3 about this
12:08 masak but he doesn't seem to be here too often
12:08 masak so I'll just talk to myself and anyone willing to listen
12:08 masak as of now, the Structure2DView contains two columns, created statically as the table is created
12:09 masak one "Structure" and one "Properties"
12:09 masak if I understand shk3 correctly, the "Properties" column should really be several dynamically allocated columns, one for each kind of property encountered in all the molecule files
12:10 * masak is not sure he likes that
12:11 masak OTOH, not sure how I want it to look
12:14 masak the problem is further complicated by the fact that there seem to be no real good uses of the properties fields
12:15 masak mostly, people just put random garbage there, or the molecular formula
12:15 masak well, I'm done talking now
12:15 * masak feels a little better
12:30 viklund joined #bioclipse
12:32 viklund hello guys
12:33 viklund just reinstalled my system so that I can get eclipse 3.3 and apache-axis...
12:33 * masak should do that too
12:33 viklund I tried starting eclipse now, but it said "A JRE or JDK must be available in order to run Eclipse."
12:34 viklund I kind of thought that apt-get would take care of deps...
12:34 viklund so which version should I use? 5? 6?
12:34 masak either
12:36 viklund the eclipse version from gutsy was 3.2...
12:37 viklund do you think that works?
12:37 masak as of today, no...
12:37 viklund hmm, need to get an updated eclipse for gutsy then...
12:38 masak we just discovered a 3.3 dep that olas introduced before he went to a conference abroad
12:38 viklund :(
12:38 masak that's why I, too, need 3.3
12:38 viklund I was looking around a bit yesterday
12:38 masak but I solved it by "updating" to an earlier version of a file
12:39 masak and then things worked
12:39 viklund and saw that you specify deps in the plugins
12:39 masak yes
12:39 masak apparently, this dep wasn't specified
12:39 viklund those deps, are they only deps on other plugins in the package
12:39 masak because 3.3 includes it automagically
12:39 viklund not deps on general java libraries?
12:40 masak viklund: dunno
12:40 jonalv you specifiy plugin deps for each plugin
12:40 viklund ok...
12:40 jonalv did I missunderstand the question?
12:41 viklund dont think so
12:41 viklund the ....align plugin for example is dependent on apache-axis, but since thats not a _plugin_ it's not a dependency
12:41 viklund right?
12:42 jonalv what's apache-axis?
12:43 viklund ;)
12:43 viklund it's a framework for working with webservices, SOAP and such
12:43 jonalv oh but isn't that .jar file included in the plugin+
12:43 viklund I could have written biojava instead of axis...
12:44 viklund huh?
12:45 viklund which eclipse should I download?
12:45 jonalv I think I have come into this discussion from the wrong end. What was the problem from the beginning?
12:45 jonalv 3.3
12:46 viklund for "Java developers", for "java ee developers" or "classic"?
12:46 viklund maybe for "plug-in developer"?
12:46 viklund http://www.eclipse.org/downloads/
12:46 jonalv the one for plugin developers is probably the best
12:47 jonalv but it's just which plugins are included from the start that differs and you will probably install plugns afterwards anyway
12:47 viklund oh, the ...align plugin depend on biojava and apache-axis, but they are not part of bioclipse, so I wondered if you only specify plugin dependencies in plugins...
12:48 jonalv yes that's right. But my guess is that either the align plugin or some other plugin which the align plugin needs contains the biojava jar file
12:48 EskilA_ joined #bioclipse
12:49 viklund but not axis?
12:50 jonalv probably axis aswell
12:51 viklund ok, I'll check that once I get the latest eclipse dowload (their server was overloaded, but luckily there was a bittorrent file)
12:51 jonalv goo
12:52 jonalv d
13:41 edrin joined #bioclipse
13:41 edrin hi
13:41 edrin anyone here?
13:42 edrin jonalv ?
13:42 jonalv hi
13:42 edrin hi there
13:42 jonalv what's up doc? :)
13:42 edrin jonalv: did you get my private message?
13:43 * jonalv is fighting with Hibernate. Things are going badly for me...
13:46 masak edrin: short question. do you know anything about Eclipse interactive shells?
13:47 edrin masak: no, i am sorry, i am currently not thinking in this direction
13:47 masak oki, no worries
13:47 masak just checking
13:52 viklund Mmm, cinamon buns...
13:52 masak viklund: is that your commit candy of choice?
13:52 masak I'm using toffiffees
13:53 masak and don't come back!
13:53 masak :)
13:53 viklund joined #bioclipse
13:54 masak welcome back :)
13:54 jonalv <masak> I'm using toffiffees
13:54 jonalv * viklund has quit (Read error: 104 (Connection reset by peer))
13:54 jonalv <masak> and don't come back!
13:54 jonalv <masak> :)
13:54 jonalv * viklund (n=johan@molev195.ebc.uu.se) has joined #bioclipse
13:54 jonalv <masak> welcome back :)
13:54 jonalv LOL
13:54 masak ha ha :)
13:54 masak jonalv: you keep quiet next time, you hear?
13:55 * masak grumbles
13:55 viklund joined #bioclipse
13:55 masak can't even talk behind people's backs anymore
13:55 masak viklund: oh, hi
13:55 viklund help, my irc-client is crashing
13:55 jonalv switch irc client
13:55 viklund mm
13:55 viklund maybe
13:56 masak ERC is nice
13:56 viklund started from terminal to see what happens...
13:56 viklund it's not really crashing, more like quitting.
13:56 jonalv which are you using+
13:56 viklund xchat-gnome
13:56 jonalv xchat is beter
13:56 viklund why?
13:57 jonalv oh I justthink so
13:57 jonalv :)
13:57 masak doesn't have a spell checker, though :P
13:58 jonalv I donät ned one anyvay ;)
13:58 masak of course you don't
13:58 * masak was talking about someone else
13:59 * viklund scratches his head
13:59 masak viklund: no, not you either
13:59 masak ha ha :)
13:59 jonalv stable..
13:59 masak extremely
14:00 CIA-31 bioclipse: carl_masak * r3926 /trunk/plugins/net.bioclipse.statistics/sr​c/net/bioclipse/model/MatrixResource.java:
14:00 CIA-31 bioclipse: [MatrixResource.java]
14:00 CIA-31 bioclipse: * different regular expression to recognize several whitespace characters in a row
14:06 viklund joined #bioclipse
14:06 viklund phew...
14:06 jonalv hi there
14:06 masak viklund: wb
14:06 viklund that's what you get for running beta software
14:07 jonalv yep
14:07 viklund btw. xchat corrects my spelling (xchat-gnome didn't)
14:07 masak beta software sucks
14:07 viklund oh, but I'm running a beta distribution
14:07 masak viklund: I wasn't talking about your spelling
14:07 viklund gutsy, beta
14:07 masak cool!
14:07 viklund I know...
14:08 viklund yep, compiz working out of the box and so forth...
14:08 jonalv Hm actually I have spell checking as well
14:14 viklund what is cdk?
14:17 masak a chemoinformatics kit
14:17 viklund ahh'
14:17 jonalv chemistry development kit: <http://en.wikipedia.org/wik​i/Chemistry_Development_Kit>
14:26 viklund I followed the exact instructions on >http://wiki.bioclipse.net/inde​x.php?title=Compile_Bioclipse>. But got 7 errors
14:27 masak which ones?
14:27 viklund net.bioclipse.descriptor seems to depend on (or want stuff from) n.b.statistics.jama
14:27 viklund and n.b.statistics
14:28 jonalv hm is descriptor part of the "at least" plugin?
14:28 jonalv intresting
14:28 viklund and 5 MatrixResource errors, also from bio.descriptor
14:28 viklund yep
14:28 jonalv this is obviuosly broken...
14:29 masak yes
14:29 jonalv too bad olas is not here....
14:29 masak I had to include n.b.statistics.jama manually, because nothing depends on it
14:29 viklund ;)
14:30 masak or rather, becuase n.b.s doesn't depend on it
14:30 viklund and if I checkout n.b.stat{,.jama}, I get 27 error (more nonincluded packages)
14:30 viklund but only from n.b.statistics
14:32 viklund so, what is n.b.descriptor?
14:32 jonalv not sure bu I think it has to do with calculating descriptors for molecules
14:33 viklund chempaint wanted it...
14:34 jonalv oh well I don't know really...
14:35 viklund oh, sorry, chempaint didn't want it
14:35 viklund when I removed descriptor I only got warnings left..
14:35 viklund s/got/had/
14:35 jonalv k
14:36 viklund 811, but that's ok, or?
14:36 jonalv what?
14:36 viklund 811 warnings...
14:37 jonalv yea that ok
14:37 masak it's just warnings :)
14:40 viklund ok, it works so far..
14:40 jonalv w00t
14:40 viklund and runs, I should add.
14:40 viklund lets see if the alignment addition works
14:41 masak viklund: alignment addition?
14:41 viklund plugin then...
14:41 * masak didn't know there was one
14:41 viklund eow, 611 errors
14:41 viklund n.b.alignment
14:41 viklund sry
14:41 masak aha
14:41 viklund n.b.align
14:42 masak oki
14:42 viklund 620 errors...
14:43 masak that's about 620 errors too many
14:43 masak good thing our customers only get the functioning binary
14:44 viklund yep
14:44 jonalv errors? not warnings?
14:44 viklund yep
14:45 jonalv but it won't work if there are errors right?
14:45 masak nope
14:45 viklund checkout only the list from the build help page + align
14:45 viklund and, tada, 620 errors
14:45 viklund and no, it dosn't work
14:45 jonalv you must be missing something
14:45 masak probably bit rot
14:45 viklund yep
14:45 viklund apache axis or smth...
14:46 viklund I don't think I'm missing bit rot.
14:46 viklund rather, I know I'm not missing bit rot
14:46 jonalv bit rot
14:46 jonalv ?
14:46 masak viklund: chat lag
14:47 masak I meant, the problem is probably due to bit rot
14:47 masak but then again, it might simply be that you're missing something
14:48 viklund I'm checking out everything from the repos now to see what happens...
14:48 viklund ...luckily I have it mirrored
14:50 viklund one error when checking everything out
14:51 masak as opposed to 620?
14:51 viklund "The import sun.text.CompactShortArray cannot be resolved" in net.bioclipse.chart/src/net/bio​clipse/dialogs/ChartDialog.java line 27
14:51 viklund yes
14:51 masak hm
14:52 * masak recognizes that one
14:52 masak hold on
14:52 masak just remove it
14:52 viklund what?
14:53 viklund the import statement
14:53 viklund ?
14:53 masak yes
14:53 masak take it out
14:53 masak it's marked as not used anyway
14:53 viklund gone
14:53 viklund no more errors...
14:53 masak cool!
14:53 masak I'll commit the CartDialog.java file
14:54 viklund Do you often kill your checkouts in eclipse?
14:54 viklund and if so, is there good way to do so?
14:54 masak viklund: what do you mean?
14:54 masak ah, the processes?
14:54 jonalv "kill checkout"?
14:54 masak no, that's virtually impossible
14:54 masak you have to kill eclipse
14:55 masak which sucks
14:55 viklund I delete the dirs in the left pane
14:55 viklund and check the box, remove from disk
14:55 masak yes
14:55 jonalv are we talking about the broken subclipse which is impossible to abort?
14:55 masak why do you call "delete" "kill"?
14:55 viklund more drama
14:55 masak that's two different things
14:55 masak "delete" is for files
14:55 masak "kill" is for processes
14:55 jonalv oh delete? That's something totally different...
14:55 viklund jonalv: no, it's just that I'm testing different checkouts
14:56 masak please don't use "kill" for files
14:56 masak unless you're talking about killfiles
14:56 viklund ok
14:57 viklund but I wasn't talking about a file or a bunch of files as such, I was talking about a checkout, that, I think, was the reason "kill" sprung to mind.
14:59 CIA-31 bioclipse: carl_masak * r3927 /trunk/plugins/net.bioclipse.chart/src/​net/bioclipse/dialogs/ChartDialog.java:
14:59 CIA-31 bioclipse: [ChartDialog.java]
14:59 CIA-31 bioclipse: * removed unused imports
14:59 CIA-31 bioclipse: * removed unused instance variables
14:59 CIA-31 bioclipse: * commented out dubious non-Eclipse-3.2 line
14:59 CIA-31 bioclipse: * fixed indentation
15:01 masak &
15:03 masak s/&//
15:04 viklund joined #bioclipse
15:18 masak viklund: on a scale of one to crash-prone, I'd say your client is crash-prone
15:19 viklund Oh, this last glitch wasn't a crash
15:19 masak oh, good
15:19 viklund I needed to add myself to a few groups to get full admin rights from within gnome
15:20 masak ah
15:20 viklund and to make them take affect I had to logout
15:20 masak yes
15:20 viklund I'm on xchat now actually...
15:28 viklund The sun is shining into my office!
15:43 viklund where is bc_empty?
15:43 viklund in the svn?
15:44 viklund or, where in the repository is bv_empty?
15:44 viklund s/bv/bc/
15:44 viklund I'm trying to follow the page <http://wiki.bioclipse.net/index​.php?title=Extending_Bioclipse>
15:45 jonalv there is an empty plugin in trunk/playground/pluings
15:45 viklund ahh
15:46 viklund found it, maybe I should add a pointer to the wiki?
15:46 jonalv sure
15:46 viklund yes, I'll do that.
15:52 masak viklund++
15:55 viklund has the bc_ prefix any other meaning than bioclipse?
15:56 viklund what's an activator?
15:56 masak viklund: I believe bioclipse is all that bc_ stands for
15:57 viklund ok
15:57 masak as for activator, I don't know, sry
15:59 viklund ok, whatever, I'll find out soon enough...
15:59 masak & fruit
16:04 viklund bah,
16:04 viklund time to go home
16:05 viklund c ya!
16:39 edrin me goes home
16:44 edrin left #bioclipse

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