Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-01-12

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All times shown according to UTC.

Time Nick Message
08:14 Gpox joined #bioclipse
08:28 jonalv joined #bioclipse
08:28 jonalv hi
08:29 zarah hi jonalv
08:29 jonalv zarah: seen olass
08:29 zarah olass was last seen 2 d 16 h 22 m 25 s ago in #farmbio saying 'bye'
08:29 jonalv zarah: seen olas
08:29 zarah I have not seen olas
08:31 jonalv zarah: seen masak
08:31 zarah masak was last seen 1 d 21 h 30 m 26 s ago in #november-wiki saying 'OH HAI'
08:31 jonalv zarah: senn egonw
08:31 zarah jonalv: are you making fun of me?
08:31 jonalv zarah: senn egonw
08:31 zarah jonalv: you've just exceeded my capabilities :/
08:31 jonalv zarah: seen egonw
08:31 zarah egonw was last seen 2 d 21 h 51 m 53 s ago in #bioclipse saying 'bye'
08:32 jonalv where is everyone?
08:35 Gpox i dont know
08:52 CIA-54 bioclipse: jonalv * r8183 /bioclipse2/trunk/plugins/net.biocl​ipse.structuredb/src/net/bioclipse/​structuredb/domain/BaseObject.java: implemented setResource as throwing UnsupportedException since structuredb domain objects does not currently use Resources
08:52 CIA-54 bioclipse: jonalv * r8184 /bioclipse2/trunk/plugins/net.biocl​ipse.structuredb/src/net/bioclipse/​structuredb/domain/BaseObject.java: removed method duplication unknowingly caused by me (it seems)
08:53 jonalv aha I must have forgotten to do git svn dcommit!
08:53 jonalv that explains it
09:09 shk3 joined #bioclipse
09:09 jonalv shk3: hi
09:22 masak joined #bioclipse
09:30 edrin joined #bioclipse
09:30 jonalv zarah: tell edrin We will not be able to use your scripting solution in Bioclipse core because it is GNU GPL which is not compatible with Eclipse Public License
09:30 zarah Consider it noted.
09:30 jonalv lol hi edrin!
09:30 shk3 hi jonalv
09:30 edrin hi
09:31 zarah hi edrin
09:31 zarah edrin: You have new messages. Write '/msg zarah @messages' to read them.
09:31 edrin @msg
09:31 masak edrin: well, we'll be able to _use_ it, but not to distribute it with Bioclipse
09:31 zarah edrin: 2 d 21 h 10 m 44 s ago, olass said xmpp.isAvailable(IFunction f) is requested
09:31 zarah edrin: 2 d 19 h 57 m 5 s ago, olass said I have emailed you my error
09:31 zarah edrin: 2 d 17 h 45 m 27 s ago, olass said is the xws4j.jar up to date in plugin net.bioclipse.xws4j?
09:31 zarah edrin: 2 d 17 h 25 m 26 s ago, olass said http://wiki.bioclipse.net/index​.php?title=HIVpred_XMPP_service
09:31 zarah edrin: 27 s ago, jonalv said We will not be able to use your scripting solution in Bioclipse core because it is GNU GPL which is not compatible with Eclipse Public License
09:31 shk3 I have some maintainence stuff to do
09:31 shk3 and will then catch up with bioclipse
09:32 jonalv masak: hence "Bioclipse core" but okey that wasn't very clear I realize...
09:32 masak jonalv: well, _we_ are perfectly allowed to use a GPL plugin. there is a difference.
09:33 masak just not to ship it w/ Bioclipse.
09:33 jonalv masak: we are not allowed to use one in core
09:33 jonalv since core is what it shipped with Bioclipse
09:33 masak right.
09:33 jonalv masak: right?
09:33 masak right.
09:33 jonalv good
09:34 jonalv edrin I can not recreate your problem
09:34 jonalv edrin: I get another one...
09:35 jonalv edrin: http://pastebin.com/f7122607c
09:36 edrin jonalv: why is it gpl?
09:36 jonalv edrin: because your file headers say it is
09:36 edrin jonalv: ah
09:36 edrin ic
09:37 edrin yes, not compatible then
09:37 edrin but i can change it
09:37 masak !?
09:37 edrin to lgpl
09:37 masak edrin: is it your product?
09:37 edrin sure
09:37 masak oh, good.
09:37 jonalv that would work
09:37 masak edrin: I thought you had used someone else's editor.
09:38 edrin no, it's mine
09:38 masak excelllent.
09:38 masak edrin++
09:38 edrin great :) do you like it?
09:38 masak edrin: it looks very nice so far.
09:38 edrin thanks
09:38 edrin jonalv: said there is a problem
09:39 jonalv perhaps masak wants to tweak some color choices?
09:39 masak perhaps.
09:39 jonalv edrin: did you see my stack trace?
09:39 * masak doesn't fully like pink
09:39 edrin jonalv: yes, when does it occur ?
09:40 jonalv after I added the manager stuff
09:40 jonalv after I removed the commetns that is
09:40 edrin jonalv: this only happens if you activate the outcommented code as i rworte in the email?
09:40 edrin yes
09:41 jonalv edrin: yea but it's not the same error as you got is it?
09:41 edrin ok, so probably it's the same problem on another platform with different symptoms
09:41 edrin no
09:41 edrin but as i said, i get a similar error with the New scripting console...
09:41 jonalv but strange it happens before itäs run the manager code...
09:42 edrin jonalv: yes, i think it is OSGI related
09:42 edrin but so far only a guess
09:42 jonalv yea well most things are...
09:42 edrin maybe i have to change something in the settings to make it OSGI compatible
09:43 edrin but no clue yet
09:44 edrin jonalv, masak: I will now have to return to work...
09:44 edrin have to do a stuff that needs some hours...
09:44 jonalv edrin: oki, have fun! :)
09:44 edrin but i will be here all few hours
09:44 edrin so i'll be here
09:45 jonalv I get the same error with that outcommented now...
09:47 edrin so maybe it is another error...
09:48 edrin maybe both scipting engines are using the same rhino instance (there is a putative global instance with in rhino, maybe i should use a newly created one)
09:48 edrin maybe the error only occurs if you use the scripting console before... ?
09:49 edrin (and when stuff is activated there already ?=)
09:49 edrin me gone
09:51 edrin jonalv: currently the plugin does an import* in manifest i think... you can comment this out for debugging...
09:51 egonw joined #bioclipse
09:52 edrin i will remove it later
09:52 edrin anyway
09:52 jonalv hi egonw
09:52 jonalv edrin: I can't get your editor to work and you can't get ours to work...
09:52 edrin hi egonw
09:53 edrin jonalv: the editor has a problem?
09:53 egonw moin
09:53 zarah hi egonw
09:53 edrin i thought the scripts in general where running?
09:53 jonalv edrin: yes, or rather the running of the script has a problem. It's not working...
09:53 jonalv edrin: no I am yet to succed in ruynning a script from your editor
09:54 jonalv I get the same NoSuchMethodException...
09:55 edrin even if you comment out the code again?
09:55 jonalv masak: could you try as well?
09:55 jonalv edrin: yuyp
09:55 edrin jonalv: try this:
09:55 jonalv +it dies before it even reaches that code
09:55 masak jonalv: aye.
09:56 edrin rhino.showMessage("hi");
09:57 jonalv edrin: that does not work
09:57 edrin ok
09:57 edrin what js.jar version are you using?
09:58 jonalv I don't know. I haven't changed anything
09:58 jonalv I just checked out all of it...
09:58 edrin jonalv: can you remove the js.jar from the plugin's classpath and depend for now on the version in bilcipse.scripting ?
09:58 edrin maybe these two .jar versions are conflicting?
09:59 edrin i guess the bioclipse.javascript plugin should export/offer this .jar to other plugins? or at least for now to find the error
10:00 * jonalv is testing this idea
10:01 jonalv edrin: this might be what is going on
10:01 jonalv I now have an error on row 52 in ScriptExecution
10:01 jonalv there is no method enterContext...
10:01 edrin ok
10:01 edrin this means
10:02 edrin really
10:02 edrin it's the js.jar
10:02 edrin there is a new version at mozilla
10:02 edrin it's quite new
10:02 edrin and they depracted some code
10:02 edrin i was using the new api therefore...
10:03 edrin maybe you could update js.jar in bioclipse.javascript to the newest js.jar from mozilla?
10:03 jonalv aha
10:03 jonalv masak: could we upgrade?
10:03 masak jonalv: I don't remember the details of this.
10:03 edrin i am pretty sure it will work with the new js.jar, too
10:04 masak especially, I don't remember a js.jar
10:04 masak just a rhino.jar
10:04 masak will look.
10:04 edrin i expect it to be 100% upwards compatible
10:04 edrin masak: it is js.jar in the bioclipse , too
10:04 edrin i have seen it somewhere..
10:05 masak edrin: ok.
10:05 edrin http://www.mozilla.org/rhino/download.html
10:05 zarah edrin's link is also http://tinyurl.com/a7dnjx
10:07 masak found it :) now checking which version we have.
10:12 masak looks like we're currently running Rhino 1.6R4
10:15 jonalv &me has checked out all stuff in Windows now and si gonna test a little in Windows after lunch
10:25 gilleain joined #bioclipse
10:26 gilleain morning all
10:32 olass joined #bioclipse
10:32 olass moin
10:32 zarah hi olass
10:32 zarah olass: You have new messages. Write '/msg zarah @messages' to read them.
10:32 olass @msg
10:32 zarah olass: 2 d 18 h 1 m ago, edrin said xws4j.jar in plugin net.bioclipse.xws4j should be up-to-date
10:32 olass edrin: danke
10:32 olass sry, had forgotten to log into irc today
10:59 egonw hi olass
11:17 olass joined #bioclipse
11:17 * olass is back from lunch
11:18 egonw I have no clue what provisioning is, or p2... but: http://henrik-eclipse.blogspot.com/2009/01​/presentation-in-stockholm-jan-27-p2.html
11:18 zarah egonw's link is also http://tinyurl.com/8q8pbq
11:19 olass egonw: I will go on that
11:19 olass p2 is eclipse new provisioning system
11:19 CIA-54 bioclipse: shk3 * r8185 /bioclipse2/trunk/externals/org.xmlcml.cmlxom/ (html/maintopic.html toc.xml): changed the help, which was still of the old cml plugin
11:20 gilleain provisioning == service discovery?
11:20 olass not really
11:20 olass it's a replacement for online updates
11:20 olass if you see in Eclipse 3.4, the online update is new
11:20 gilleain oh
11:21 egonw oh, right
11:21 olass it's completely rewriten
11:21 egonw that's where I've seen the term before...
11:21 olass and much better management of dependencies
11:21 olass however
11:21 olass I think it has become more complex
11:21 olass and harder to use for novice users
11:21 olass hence p2 will have to wait a while for Bioclipse IMO
11:21 gilleain well more features => more complex...
11:22 olass hmm, yes
11:22 olass really not that much more features though
11:25 jonalv joined #bioclipse
11:25 gilleain well, two new features are the "drop-in directory" and "bundle pooling", it appears :)
11:25 jonalv edrin, olass: Must net.bioclipse.xws4j depend on Eclipse 3.4.1?
11:26 olass mom, tel
11:34 CIA-54 bioclipse: shk3 * r8186 /bioclipse2/trunk/externals/org.xmlcml.cmlxom/ (html/maintopic.html toc.xml): changed the help, which was still of the old cml plugin
11:34 edrin jonalv: no
11:34 edrin why?
11:34 CIA-54 bioclipse: shk3 * r8187 /bioclipse2/trunk/plugins/net.bioclipse.xom/ (html/artistic.html html/maintopic.html toc.xml):
11:34 jonalv I wil change it then
11:34 edrin why?
11:35 CIA-54 bioclipse: shk3 * r8188 /bioclipse2/trunk/plugins/net.bioclipse.cml/ (html/artistic.html html/maintopic.html toc.xml): changed the help, which was still of the old cml plugin
11:35 olass jonalv: please explain
11:35 olass what and why
11:35 edrin jonalv: did it help? did the new js.jar now make things running?
11:35 jonalv edrin: wow did you swap_
11:35 jonalv masak: I think edrin already has swapped
11:35 edrin ?
11:36 edrin wow?
11:36 jonalv yea World of Warcraft
11:36 jonalv I didn't know you had swapped...
11:36 olass swapped bioclipse devel in favor of WoW?
11:36 olass :)
11:36 edrin what are you talking about?
11:36 jonalv lol
11:36 * olass doesnät understand either
11:37 edrin ok, me must continue experiment
11:37 gilleain A WoW plugin for bioclipse, you say?
11:37 olass sounds logical
11:37 jonalv edrin: have you swapped in the new js.jar for the old one in Bioclipse_
11:47 masak I think you guys are misunderstanding each other.
11:47 jonalv yea you are probably right...
11:48 masak installing the new js.jar as we speak.
11:52 CIA-54 bioclipse: jonalv * r8189 /bioclipse2/trunk/plugins/net.bioclips​e.spectrum.test/META-INF/MANIFEST.MF: only require Eclipse 3.4 not 3.4.1
11:53 CIA-54 bioclipse: jonalv * r8190 /bioclipse2/trunk/plugins/net.bioc​lipse.xws4j/META-INF/MANIFEST.MF: only require Eclipse 3.4 not 3.4.1
11:59 olass jonalv++ (3.4 is enough)
11:59 CIA-54 bioclipse: carl_masak * r8191 /bioclipse2/trunk/plugins/net.bioclipse.scripting/ (.classpath META-INF/MANIFEST.MF build.properties libs/js.jar): [net.bioclipse.scripting] replaced old js.jar (probably Rhino 1.6R4) with new one (1.7R1)
12:01 edrin now in course
12:01 edrin :(
12:02 jonalv edrin: I can at least confirm that the javascript console is broken in wondows
12:02 jonalv *window
12:02 jonalv *windos
12:02 masak jonalv: give up.
12:02 jonalv you know...
12:02 edrin almost
12:02 gilleain wandows?
12:03 masak wundows.
12:03 gilleain oh, and it so is.
12:03 jonalv gilleain+1
12:04 olass jonalv, masak: console broken on windows is not super...
12:04 masak olass: we were just talking about that here. :/
12:04 jonalv that is what I am trying t osay...
12:04 masak olass: I'm even contemplating installing Parallels...
12:05 olass please do
12:05 masak hokay
12:05 masak zarah: hokay
12:05 zarah masak: so, basically.
12:05 jonalv I think I will send masak to Magnus to get parallells
12:05 olass sounds good
12:05 olass we seem to need it
12:05 jonalv yup
12:23 masak olass: I CAN HAZ NEW COMPUTER
12:23 masak on Friday.
12:23 olass masak: nice
12:23 masak no Parallels until then, it seems.
12:24 masak (*phew*)
12:24 masak in the meantime, please concentrate on testing and QA-ing the new console.
12:24 masak please.
12:25 masak edrin: jonalv gets the new js console to work under Windows. what about you.
12:25 masak s/.$/?/
12:29 jonalv edrin: it works fine for me. I don't know what you are doing wrong...
12:41 jonalv zarah: tell edrin I have tried to run your editor with the new js.jar and I get another sort of strange error: http://pastebin.com/f62479ad4
12:41 zarah Consider it noted.
12:57 jonalv zarah: tell edrin It works in Windows though... strange...
12:57 zarah Consider it noted.
12:58 CIA-54 bioclipse: jonalv * r8192 /xws/trunk/net.bioclipse.r​hino/META-INF/MANIFEST.MF: only require Eclipse 3.4 not 3.4.1
13:05 jonalv zarah: tell edrin I don't get any error messages at all when I am writing non copiling code and runnign it wiht your editor. Is there something that is not working for me?
13:05 zarah Consider it noted.
13:27 gilleain joined #bioclipse
13:51 jonalv zarah: tell edrin I can't help you. When I try running a JavaScript script calling the cdk manager in your editor I get no error at all. Nothing happens. In fact that happends as soon as I write anything that isn't legal JavaScript as well. Until I get some error messages I can not try to work out what is going on...
13:51 zarah Consider it noted.
13:58 CIA-54 bioclipse: carl_masak * r8193 /bioclipse2/branches/masak-new-console/: [masak-new-console] new branch
14:10 egonw joined #bioclipse
15:03 masak @plan bc2
15:03 zarah masak: bc2/console-test-jcterm: 1 h planned
15:03 zarah masak: bc2/managerdocs-improvements: 45 m planned
15:04 masak @plan bc2 old
15:04 zarah masak: bc2/console-egonw-single-line-refactor: 2 h planned, 1 h 49 m elapsed
15:04 zarah masak: bc2/managerdocs-finder: 1 h 30 m planned, 1 h 37 m elapsed
15:04 zarah masak: bc2/managerdocs-finder-html-skin: 1 h 15 m planned, 1 h 10 m elapsed
15:04 zarah masak: bc2/scriptconsole-backspace-bug: 30 m planned, 2 m elapsed
15:04 zarah masak: bc2/scriptconsole-literal-tab-bug: 30 m planned, 15 m elapsed
15:05 masak @start console-egonw-single-line..
15:05 zarah masak: Starting task 'bc2/console-egonw-single-line-refactor'.
15:05 masak zarah: the clock is ticking!
15:05 zarah masak: I did not understand that
15:35 CIA-54 bioclipse: jonalv * r8194 /bioclipse2/branches/jonalv-​RunJSCommandsAsJobs/plugins/ (4 files in 3 dirs): made graphical progressmonitor for addStructuresFromSDF when running it from js console
15:36 CIA-54 bioclipse: jonalv * r8195 /bioclipse2/branches/jonalv-RunJSComma​ndsAsJobs/plugins/net.bioclipse.struct​uredb/src/net/bioclipse/structuredb/ (2 files in 2 dirs): made graphical progressmonitor for deleteWithMolecules when running it from js console (couldn't test it though):
15:47 CIA-54 bioclipse: carl_masak * r8196 /bioclipse2/branches/masak-new-cons​ole/plugins/net.bioclipse.scripting​.ui/src/net/bioclipse/scripting/ui/ (2 files in 2 dirs): [net.bioclipse.scripting.ui] made the JsConsoleManager print its output to the NewScriptingConsoleView
15:48 CIA-54 bioclipse: carl_masak * r8197 /bioclipse2/branches/masak-new-console/ (4 files in 3 dirs):
15:48 CIA-54 bioclipse: removed all traces of ConsoleEchoer
15:48 CIA-54 bioclipse: this is one more step towards making the R mode unusable. will fix when the
15:48 CIA-54 bioclipse: need arises -- the plan is to have a dedicated scripting console for R
15:49 CIA-54 bioclipse: carl_masak * r8198 /bioclipse2/branches/masak-new-console/plugins/​net.bioclipse.scripting.ui/src/net/bioclipse/sc​ripting/ui/views/NewScriptingConsoleView.java: [net.bioclipse.scripting.ui] set the background color of the output field to white
15:58 CIA-54 bioclipse: goglepox * r8199 /bioclipse2/branches/gpox-newMoleculeTable/plugins​/net.bioclipse.cdk.ui.sdfeditor/src/net/bioclipse/​cdk/ui/sdfeditor/editor/MoleculeTableViewer.java: Viewer for viewing lists of molecules
15:59 CIA-54 bioclipse: goglepox * r8200 /bioclipse2/branches/gpox-newMoleculeTab​le/plugins/net.bioclipse.cdk.ui.sdfedito​r/src/net/bioclipse/cdk/ui/sdfeditor/edi​tor/MoleculeTableContentProvider.java:
15:59 CIA-54 bioclipse: Content provider for MoleculeTableViewer.
15:59 CIA-54 bioclipse: If input is not a IMoleculesEditorModel it tries
15:59 CIA-54 bioclipse: to adapt to file and starts indexing the file.
15:59 CIA-54 bioclipse: goglepox * r8201 /bioclipse2/branches/gpox-newMoleculeTable​/plugins/net.bioclipse.cdk.ui.sdfeditor/sr​c/net/bioclipse/cdk/ui/sdfeditor/editor/ (MoleculeTableContentProvider.java MoleculeTableViewer.java): Gave adapting to IFile priority over MoleculesEditorModel
16:00 CIA-54 bioclipse: goglepox * r8202 /bioclipse2/branches/gpox-newMoleculeTable/plugin​s/net.bioclipse.cdk.ui.sdfeditor/src/net/bioclips​e/cdk/ui/sdfeditor/editor/MoleculesEditor.java: Changed to use MoleculeTableViewer and removed references to CompositeTable
16:16 CIA-54 bioclipse: carl_masak * r8203 /bioclipse2/branches/masak-new-console/plugins/​net.bioclipse.scripting.ui/src/net/bioclipse/sc​ripting/ui/views/NewScriptingConsoleView.java: [NewScriptingConsoleView] copied history from old console
16:20 edrin joined #bioclipse
16:20 edrin hi
16:20 zarah hi edrin
16:20 zarah edrin: You have new messages. Write '/msg zarah @messages' to read them.
16:21 edrin @message
16:21 zarah edrin: 3 h 39 m 39 s ago, jonalv said I have tried to run your editor with the new js.jar and I get another sort of strange error: http://pastebin.com/f62479ad4
16:21 zarah edrin: 3 h 23 m 50 s ago, jonalv said It works in Windows though... strange...
16:21 zarah edrin: 3 h 15 m 6 s ago, jonalv said I don't get any error messages at all when I am writing non copiling code and runnign it wiht your editor. Is there something that is not working for me?
16:21 zarah edrin: 2 h 29 m 7 s ago, jonalv said I can't help you. When I try running a JavaScript script calling the cdk manager in your editor I get no error at all. Nothing happens. In fact that happends as soon as I write anything that isn't legal JavaScript as well. Until I get some error messages I can not try to work out what is going on...
16:21 edrin @msg
16:21 zarah edrin: You have no new messages.
16:23 edrin jonalv: can you give me a summary about what is working for you now and what is not?
16:23 jonalv edrin: The new jsconsole works
16:23 jonalv edrin: the old does not
16:24 jonalv edrin: your editor works for the showmessage example
16:24 edrin jonalv: ok
16:24 edrin and when does it not work?
16:24 jonalv edrin: but I don't get any error messages from it
16:24 edrin ah
16:24 edrin yes you do
16:24 edrin please open the eclipse console
16:25 edrin i forgot to add "show eclipse console" code
16:25 jonalv edrin: so I don't know what I am doing wrong when I am trying with the managers
16:25 jonalv aha
16:25 edrin jonalv: in your views, add the Eclipse dafault console
16:25 edrin do you see it?
16:26 jonalv edrin: that was not so eady fro a little bot to understand... :)
16:26 jonalv edrin: I am gonna try it
16:27 edrin jonalv: yes, sorry, my mistake
16:27 jonalv np
16:27 edrin i will add a show console code...
16:27 edrin xws' using it, too
16:27 jonalv aha
16:29 edrin back going to students... cu later
16:29 jonalv masak, edrin: You two _really_ should talk to eachother....
16:29 edrin back in 1h
16:29 masak jonalv: I don't doubt that.
16:29 masak edrin: unfortunately, I'll be gone in 1h.
16:30 masak edrin: will be here later this week.
16:30 edrin cu later
16:30 masak edrin: yes, cu.
16:30 masak try the new console.
16:35 grandm44 joined #bioclipse
16:35 egonw grandm44??
16:36 grandm44 hello
16:36 zarah hi grandm44
16:36 egonw hi
16:36 zarah hi egonw
16:36 egonw zarah: shut up
16:36 zarah egonw: no, YOU shut up!
16:36 egonw grandm44: how can we be of assistence? that is, what brings you here? btw, welcome!
16:37 grandm44 what a warm welcome !
16:37 grandm44 well, i'm trying to get stated with bioclipse
16:37 egonw happy to hear that
16:37 egonw which version?
16:38 grandm44 I downloaded the last svn snapshot with subclipse
16:38 CIA-54 bioclipse: jonalv * r8204 /bioclipse2/branches/jonalv-​RunJSCommandsAsJobs/plugins/ (6 files in 3 dirs): Changed cdk business plugin to support new progressmonitors during javascript console running
16:38 egonw OK, impressed :)
16:39 egonw getting it running from there is rather tricky...
16:39 egonw which probably brings you here?
16:39 grandm44 the base works, but...
16:39 grandm44 I can't get the chemoinformatics plugins to work :(
16:40 egonw have you tried running it via features?
16:40 egonw or by selecting a list of plugins?
16:41 egonw both should work, though
16:42 grandm44 I selected the plugins in the trunk, got cdk from cdk.svn.sourceforge.net/svnroot/cdk/cdk/trunk
16:43 egonw one sec...
16:45 grandm44 org.openscience.cdk and net.bioclipse.chemoinformatics are ok, but there is errors with org.bioclipse.cml, cdk.ui, cdk.ui.sdfeditor, cdk.business, cml and cdk.jchempaint
16:46 egonw yeah...
16:46 egonw you need a different version of the CDK...
16:47 egonw the org.openscience.cdk.* plugins in Bioclipse SVN
16:47 grandm44 which on should I use and where to get it ?
16:47 masak you're a smart girl, zarah.
16:47 zarah masak: So they keep telling me.
16:47 egonw grandm44: in bioclipse/bioclipse2/cdk-externals/trunk
16:48 grandm44 thank you very much, i'm trying this now
16:51 egonw you'll also need the plugins from cdk-externals/ itself...
16:52 egonw like javax.vecmath
16:53 * jonalv usually just imports all plugins. If you have a decent computer that is faster I think...
16:56 CIA-54 bioclipse: carl_masak * r8205 /bioclipse2/branches/masak-new-console/plugins/​net.bioclipse.scripting.ui/src/net/bioclipse/sc​ripting/ui/views/NewScriptingConsoleView.java: [NewScriptingConsoleView] added class JavaDoc
16:57 CIA-54 bioclipse: carl_masak * r8206 /bioclipse2/branches/masak-new-console/plugins/​net.bioclipse.scripting.ui/src/net/bioclipse/sc​ripting/ui/views/NewScriptingConsoleView.java:
16:57 CIA-54 bioclipse: [NewScriptingConsoleView] implemented general tab completion
16:57 CIA-54 bioclipse: still needs to be hooked up in NewJsConsoleView to work for js
16:58 * grandm44 downloading all plugins in cdk-externals...
17:09 grandm44 I still have errors, I'm going to chek out all plugins in bioclipse/bioclipse2/plugins
17:10 egonw yes, advisable
17:10 egonw it's a rather large project...
17:10 egonw and not so easy to start with...
17:10 egonw I hope we can soon offer a tar.gz for download...
17:11 jonalv sadly yea it seems to be complicated to get started. I hope you will help us make it easier
17:12 egonw grandm44: by expressing where you find it difficult :)
17:12 egonw we'll solve the problems
17:12 grandm44 Yes, it's a bit tricky to start with it... and I'm not used to java and eclipse. But anyway thank you for your help !
17:13 jonalv just ask away! :)
17:16 * jonalv just broke a lot of cdk methods and is very glad he is working in a branch :)
17:16 egonw hahaha :)
17:16 jonalv branches++
17:17 * egonw mubles 'oh, let's just drop svn and move git all the way'
17:17 * jonalv didnt quite hear something
17:18 masak @plan stop
17:18 zarah masak: Syntax: @plan <task name> <number>h
17:18 masak zarah: don't ypu tell me what the syntax is!
17:18 zarah masak: that was not so easy for a little bot to understand
17:18 masak @stop
17:19 zarah masak: Stopping task 'bc2/console-egonw-single-line-refactor' after 2 h 13 m at 4 h 2 m out of 2 h (201%).
17:19 masak :/
17:19 CIA-54 bioclipse: carl_masak * r8207 /bioclipse2/branches/masak-new-consol​e/plugins/net.bioclipse.scripting.ui/​src/net/bioclipse/scripting/ui/views/ (NewJsConsoleView.java NewScriptingConsoleView.java):
17:19 CIA-54 bioclipse: [NewJsConsoleView] implemented js-style tab completion
17:19 CIA-54 bioclipse: this also required an extra method currentCommand() in NewScriptingConsoleView
17:28 grandm44 I'm going home now, see you tomorow for the result. I look forward to work with bioclipse, it looks very interesting :) Bye
17:28 CIA-54 bioclipse: jonalv * r8208 /bioclipse2/branches/jonalv-​RunJSCommandsAsJobs/plugins/ (4 files in 3 dirs): changed order of paramaters and added TODO comment for what I should pick up and work with tomorrow
17:28 egonw grandm44: ok, good luck!
17:28 egonw grandm44: just drop in here, if you need help
17:28 grandm44 I will, thx
17:40 olass edrin: around?
17:42 olass edrin: I still see xws4j-09.01.02.jar in plugin net.bioclipse.xws4j
17:42 olass did you not say you updated that?
17:42 olass @tell edrin: I still see xws4j-09.01.02.jar in plugin net.bioclipse.xws4j. Did you not update that?
17:42 zarah Consider it noted.
17:57 CIA-54 bioclipse: ospjuth * r8209 /bioclipse2/trunk/plugins/se.uu.farmbi​o.hivpred.client/src/net/bioclipse/xmp​p/hivpred/actions/HivpredAction.java: Replaced with same file uppercase. Subclipse is buggy (as we all know).
17:58 CIA-54 bioclipse: ospjuth * r8210 /bioclipse2/trunk/plugins/se.uu.farmbi​o.hivpred.client/src/net/bioclipse/xmp​p/hivpred/actions/hivpredAction.java: Replaced with same file uppercase. Subclipse is buggy (as we all know).
17:58 edrin hi olass
17:58 zarah edrin: You have new messages. Write '/msg zarah @messages' to read them.
17:59 olass hi edrin
17:59 edrin olass: i think the xws4j-09.01.02.jar is up to date, isn't it?
17:59 edrin if not i can fix it tonight
17:59 olass is it?
17:59 olass are you sure?
17:59 edrin not 100% but i thought it is...
17:59 olass it does not show teh functions for jars loaded when component starts
18:00 edrin ah
18:00 edrin then it is not
18:00 edrin :/
18:00 edrin so i will fix it tonight
18:00 olass thx
18:08 edrin olass: egonw, got my mail?
18:09 olass yes
18:09 olass replied too, did you not see?
18:10 edrin ah, it's my other emaila account
18:10 edrin checking now
18:16 edrin sound good
18:24 CIA-54 bioclipse: ospjuth * r8211 /bioclipse2/trunk/plugins/se​.uu.farmbio.hivpred.client/ (2 files in 2 dirs): Struggling with subclipse.
18:26 CIA-54 bioclipse: ospjuth * r8212 /bioclipse2/trunk/plugins/se.uu.farmbi​o.hivpred.client/src/net/bioclipse/xmp​p/hivpred/actions/HivpredAction.java: Replaced with same file uppercase. Subclipse is buggy (as we all know).
19:19 edrin going home now, will answer to your mail later ola, i think. maybe we will see here #
19:19 edrin bye
19:19 edrin ciao egonw
19:19 edrin left #bioclipse
19:52 olass joined #bioclipse
19:56 olass joined #bioclipse
21:43 edrin1 joined #bioclipse
22:00 edrin hi
22:00 zarah hi edrin
22:59 CIA-54 bioclipse: edrin_t * r8213 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/ (7 files in 3 dirs):

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