Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-01-04

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All times shown according to UTC.

Time Nick Message
07:58 _thomas_k joined #bioclipse
08:45 steinbeck joined #bioclipse
09:08 jonalv joined #bioclipse
09:31 masak joined #bioclipse
09:37 thomas_ku joined #bioclipse
13:04 rprins joined #bioclipse
13:18 masak joined #bioclipse
13:56 kaskelot herro
13:57 kaskelot can anyone tell me how one can find the path of a file in the bioclipse distribution inside bioclipse
13:57 kaskelot I need to exec a binary which is in the bioclipse directory...
13:58 kaskelot so I need to find out where bioclipse is in the filesystem, basically
14:00 masak kaskelot: sounds like that isn't what you want to do, frankly
14:01 masak sounds very brittle
14:01 kaskelot ?
14:01 jonalv ?
14:01 masak best would be if   bc somehow knew where it was already
14:01 kaskelot so should I install the binary into PATH or what
14:01 masak no
14:01 jonalv masak, what do you mean?
14:01 kaskelot either I put it into path or I know where it is...
14:01 masak jonalv: I'm coming to that
14:02 masak my point is that there more or less has to be a variable somewhere that already keeps track of where the bc executable is
14:02 kaskelot yes, which is what I want to read
14:02 masak no need to reinvent the wheel
14:02 masak kaskelot: yes
14:02 kaskelot I'm not trying to reinvent it, I'm asking where it is!
14:02 masak I know
14:02 masak I don't know
14:03 jonalv the class loader know
14:03 jonalv which is why suggested using it
14:03 kaskelot the class loader was funny like
14:03 jonalv but that didn't work for some strange reasnom
14:12 egonw http://wiki.bioclipse.net/ind​ex.php?title=PubChem_plugins
14:14 jonalv egonw, looks nice. Will in be bc2 soon? :)
14:14 egonw not sure...
14:14 egonw agenda is pretty full...
14:15 egonw working on grant proposals right now
14:15 jonalv mhm
14:19 CIA-20 bioclipse: carl_masak * r4619 /branches/bioclipse2/core/plugins/net.b​ioclipse.ui/src/net/bioclipse/ui/views/ (JsConsoleView.java ScriptingConsoleView.java): (log message trimmed)
14:19 CIA-20 bioclipse: [ScriptingConsoleView.java]
14:19 CIA-20 bioclipse: * moved actionTable from constructor into anonymous initialization block
14:19 CIA-20 bioclipse: * created the following methods:
14:19 CIA-20 bioclipse: ** startOfCommandLine
14:19 CIA-20 bioclipse: ** positionOnCommandLine
14:19 CIA-20 bioclipse: ** scriptSpecificKeyBindings
14:21 masak CIA-20: is there any particular reason you feel like trimming my log message?
14:27 * masak counts the maximal number of lines 'allowed' so he knows until next time
14:27 masak six
14:27 masak egonw: is it your bot?
14:28 egonw masak: yeah, CIA is eager to teach you too commit often :)
14:28 egonw no, CIA
14:28 egonw they are checking for terrorism here...
14:28 egonw don't say he B-word :)
14:32 masak :)
14:32 jonalv Bioclipse?
14:32 masak I do commit often
14:32 masak but some commits are large, and need large comments
14:33 masak anyway, the good news that got clipped away is that the js console now has tab completion
14:33 masak do try it out
14:33 egonw ah, cool
14:33 egonw played with R script yesterday
14:33 masak nice
14:33 egonw after trying the problem jonalv was having with biojava
14:34 masak ah
14:34 jonalv <http://wiki.bioclipse.net/index.php?title=Instruc​tion_for_how_to_check_out_and_compile_Bioclipse_2>
14:36 jonalv Am I the only one getting: "java.lang.NoClassDefFoundError: org/eclipse/core/internal/runt​ime/auth/AuthorizationHandler" in bioclipse 2?
14:38 egonw http://wiki.bioclipse.net/ind​ex.php?title=Dataset_plugins
14:38 egonw jonalv: no, I had that too
14:39 jonalv Hm it dissapeared when I clicked in the clear the configuration are before launching
14:40 jonalv but I got other errors instead
14:41 jonalv anyone seen thses erros: <http://pastebin.com/m25ac4a01>?
14:48 shk3 joined #bioclipse
14:59 masak hi shk3
15:02 egonw hi shk3
15:02 egonw nice to see you online
15:15 shk3 hi
15:15 shk3 can't be online during the day too much
15:15 shk3 hi thomas_ku
15:15 thomas_ku hi shk3
15:15 shk3 how are things going?
15:16 shk3 finished?
15:16 thomas_ku so far so good, no will need one more year!
15:16 shk3 is the betreuung clear now?
15:17 thomas_ku yes christoph will do it he has a position at the ebi now
15:18 shk3 that's great
15:18 shk3 so no worries
15:18 thomas_ku oh yes!! thats really cool
15:19 shk3 (i knew he had the position already, btw, but its great for you)
15:19 thomas_ku no worries any more except the typical problem ;-)
15:19 masak bioclipse wiki down -- anyone confirm?
15:19 shk3 looks like
15:19 shk3 where is this hosted now?
15:19 masak :(
15:19 shk3 sf?
15:20 masak dunno
15:20 jonalv I just reached the main page..
15:20 shk3 no, it works
15:20 shk3 slow, but works
15:20 masak yes, now it works again
15:20 masak still slow, though
15:21 shk3 thomas_ku: how is cdk-taverna going?
15:22 thomas_ku well so far. A lot of work and every now and than a new Version of Taverna.
15:22 shk3 how is feedback?
15:23 thomas_ku I do not really get much feedback on it... ;-( But for my work it was ok and stable...
15:24 shk3 that's a problem always...
15:24 shk3 I got an external tester for nmrshiftdb client in bioclipse
15:24 shk3 hopefully there will be a release soon.
15:24 thomas_ku thats good!
15:25 thomas_ku I have to go now for a while... cu later
15:25 shk3 ok, I am heading home to do some bioclipse hacking... will be in the chat later.
15:25 shk3 left #bioclipse
15:44 masak bioclipse wiki definitely has intermittent problems
15:56 egonw sorry... have been adding to much screenshots I guess :)
16:01 masak ah
16:01 masak good to know there was an external cause to it, at least :)
16:02 egonw no, was joking...
16:02 egonw I think the machine is suffering from the cold
16:03 masak how can that be? we keep it here with us in the sauna...
16:03 egonw :)
16:04 jonalv CAn someone give me an example of what we want's to do with biojava?
16:13 masak convert DNA to RNA?
16:16 shk3 joined #bioclipse
16:29 CIA-20 bioclipse: updatebjarni * r4620 /branches/bioclipse2/core/plugins/net.​bioclipse.r/src/net/bioclipse/r/pty.c: C language PTY wrapper to run R on Unix.
16:33 egonw interesting commit...
16:34 CIA-20 bioclipse: updatebjarni * r4621 /branches/bioclipse2/core/plugi​ns/net.bioclipse.r/native-bin/ (. pty-linux-i386): Directory to contain the native binaries for the PTY wrapper needed to run R on Unix.
16:35 CIA-20 bioclipse: updatebjarni * r4622 /branches/bioclipse2/core/plugins/net.​bioclipse.r/src/net/bioclipse/r/pty.c: Updated the comment box.
16:36 jonalv http://wiki.bioclipse.net/index.​php?title=Use_case_for_Recorder
16:38 kaskelot egonw: you see, the R interpreter checks to see whether its stdin is a tty, so you need to create a pseudo tty to keep it happy, which requires a native program...
16:39 kaskelot whithout this little dance, R refuses to run in "interactive mode" and dies when it normally would print an error message
16:39 CIA-20 bioclipse: updatebjarni * r4623 /branches/bioclipse2/core/plugins/net.bio​clipse.r/src/net/bioclipse/r/TextR.java: PTY wrapping for R on Unix, so I guess R doesn't work on non-Unix for now, but I'm hungry...
16:42 egonw kaskelot: interesting...
16:42 egonw also interesting to see how it works...
16:42 egonw will soon chat with a C(++) programmer, who might be interested in using Bioclipse a RCP GUI
16:42 kaskelot right now it works on linux/x86 only... :-/
16:42 kaskelot needs more cowbell
16:43 jonalv yep but it works :)
16:43 kaskelot s/cowbell/binaries/
16:43 jonalv kaskelot++
16:43 kaskelot \o/
16:43 kaskelot and now for something completely different
16:43 * kaskelot -> food
16:44 egonw should I test?
16:44 egonw got 10 minutes
16:46 jonalv kaskelot, left for food now but I guess you can test it anyway
16:46 jonalv stupid tab I didn't mean that ','
16:46 egonw yeah, but then not now
16:48 jonalv It worked without any problem for me so if you are curious just update r and try...
16:54 egonw OK, going home now
16:54 jonalv bye
16:54 egonw will try to give it a go this weekend
16:54 egonw cu next week!
16:55 linus_ joined #bioclipse
17:55 edrin joined #bioclipse
17:55 edrin hi
17:56 edrin alle ausgeflogen?
18:31 edrin http://xkcd.com/322/
19:29 DrGTO joined #bioclipse
19:37 DrGTO good evening
19:37 DrGTO has Stefan been here already?
19:38 edrin i did not notice him the last 1.5 h
19:38 edrin gtg
19:38 edrin cu
19:38 edrin left #bioclipse
20:34 edrin joined #bioclipse

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