Camelia, the Perl 6 bug

IRC log for #bioclipse, 2012-11-06

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
01:17 ilogger2 joined #bioclipse
06:22 olass joined #bioclipse
06:28 sneumann joined #bioclipse
06:37 samuell1 joined #bioclipse
06:50 egonw__ joined #bioclipse
07:02 olass joined #bioclipse
07:10 olass joined #bioclipse
07:17 samuell1 joined #bioclipse
07:31 konditorn joined #bioclipse
07:50 zaetnick joined #bioclipse
07:55 olass joined #bioclipse
08:08 samuell1 joined #bioclipse
08:13 Gpox joined #bioclipse
08:33 olass joined #bioclipse
08:57 jonalv joined #bioclipse
09:03 egonw__ joined #bioclipse
09:07 olass joined #bioclipse
09:09 samuell1 joined #bioclipse
10:14 egonw jonalv, Gpox: can you assist with getting BC2.6 to boot?
10:14 egonw which features do I need in the bioclipse.product?
10:14 egonw it cannot find the CDK plugins...
10:15 jonalv aren't they in the target.platform now?
10:15 jonalv Gpox?
10:15 egonw they are...
10:15 egonw and it finds them...
10:16 egonw that does not seem to be the problem
10:16 jonalv okay, I must admit that I don't start Bioclipse from within Eclispe much lately.
10:17 Gpox run with features add bioclipse.core_feature and click 'select required' should work
10:17 Gpox and add the main features you want
10:18 Gpox or are you trying to export?
10:18 egonw Gpox++ (it indeed tried to launch with plugins...
10:18 egonw no clues given about bioclipse.product about that...
10:19 egonw it's been months since I last reinstalled Eclipse and had forgotten about that
10:19 egonw a shame bioclipse.product cannot be configured to default to 'launch with features'... :(
10:38 egonw can file dialogs only show directories?
10:39 olass joined #bioclipse
10:39 jonalv egonw: I would think os, what do you want to show?
10:40 egonw at least with a filter, right?
10:40 jonalv honestly I have no idea :)
10:40 jonalv maybe Gpox or olass knows something?
10:40 egonw R prefs setting for R_HOME, Browse... -> that should file dialog should only show folders, not files...
10:42 egonw ah, there is a DirectoryDialog for that...
10:45 egonw already used :(
10:50 commitbot joined #bioclipse
10:50 commitbot [bioclipse.core] goglepox pushed 1 new commit to 2.5.x: http://git.io/aoJ-Fw
10:50 commitbot bioclipse.core/2.5.x 9264836 Arvid Berg: Schedule the job so it actually runs....
10:50 commitbot left #bioclipse
10:51 egonw zaetnick: when you have a sec...
10:52 zaetnick egonw: I'm here, but have to leave for sushi in ~ 5 min
10:54 egonw de.walware.rj.RjInitFailedException: The version of the loaded RJ server 1.0.0 is not compatible to RJ version 1.1.0. Make sure that the correct R package 'rj' is installed and in the R library path.
10:54 egonw at de.walware.rj.server.jri.loader.JRIServerL​oader.loadServer(JRIServerLoader.java:106)
10:54 egonw at de.walware.rj.server.srvImpl.AbstractServerCont​rol.initREngine(AbstractServerControl.java:180)
10:54 egonw at de.walware.rj.servi.internal.NodeCont​roller.start(NodeController.java:60)
10:54 egonw at de.walware.rj.servi.internal.NodeCon​troller.main(NodeController.java:48)
10:54 egonw </LOG>
10:54 egonw --------
10:54 egonw at de.walware.rj.servi.internal.LocalNodeFact​ory.createNode(LocalNodeFactory.java:478)
10:54 egonw at de.walware.rj.servi.internal.EmbeddedM​anager.start(EmbeddedManager.java:83)
10:54 egonw at net.bioclipse.r.RServiManager.star​tEmbedded(RServiManager.java:178)
10:54 egonw this info should propagate to the GUI...
10:54 egonw I got that when running r.ls()
10:54 egonw also, setting R_HOME in the prefs page should reinitiate the R manager...
10:54 egonw jonalv: is that even possible?
10:55 zaetnick egonw: after restart
10:55 egonw then the prefs page should open a dialog saying that :)
10:55 jonalv egonw: I am not sure what you mean with reinitiate the R manager
10:55 egonw reload the manager?
10:55 jonalv egonw: it's probably something inside the R-manager that needs reinitiation
10:56 jonalv egonw: and that should be totally possible
10:56 egonw zaetnick: shall I file tracker reports?
10:56 zaetnick egonw: about the RJ error: didn't you get any error message in the R console when you opened it
10:56 egonw no
10:57 egonw ... ummm... not in the JS console...
10:57 egonw R console... mmm... checking
10:57 zaetnick egonw: I haven't done anything regarding the JS console so far
10:57 jonalv it's close to such time here
10:57 egonw zaetnick: it only says: Embedded R instance could not created.
10:57 jonalv *sushi time
10:58 jonalv :)
10:58 egonw I had that too after r.ls()
10:58 egonw but it should give clues how to fix it, or at least say *what* goes wrong
10:58 egonw otherwise, you'll get an awfull amount of cryptic bug reports
10:59 zaetnick egonw: sure
11:09 egonw installing rj 1.1
11:09 egonw zaetnick: I guess it is only checking if rj is installed, but not the right version?
11:15 samuell1 joined #bioclipse
12:31 zaetnick egonw: it should install the right rj version, which version of BC do you run
12:31 egonw 2.5.x
12:32 egonw I had rj installed, but did not install rj 1.1
12:32 egonw I had to do that manually...
12:34 zaetnick what message did the R console print when you started
12:35 egonw I no longer have that :(
12:35 egonw I'll try to reproduce
12:37 zaetnick you can manually go back to rj 1.0  and reproduce
12:38 zaetnick my point is that the R console should print proper error message and a link to help a troubleshooting page in help
12:38 egonw right
12:38 egonw the "R console" only wrote: "Embedded R instance could not created."
12:38 zaetnick where the rj installation issues in linux are addressed
12:38 egonw that I can reproduce :)
12:39 zaetnick only this? is there no link
12:39 egonw no
12:40 konditorn joined #bioclipse
12:41 egonw zaetnick: confirmed now...
12:41 egonw reinstall rj 1.0
12:41 egonw reinstall*ed* rj 1.0
12:41 egonw only "Embedded R instance could not created."
12:42 egonw shall I gist the full eclipse console log output?
12:42 zaetnick egonw: yes, please, even better if you file a bug
12:48 egonw http://pele.farmbio.uu.se/bug​zilla36/show_bug.cgi?id=3423
12:49 zaetnick tack egonw :)
13:03 jonalv egonw: would you mind verifying and closing or reopening your five bugs for 2.6.0?
13:05 jonalv egonw: oh, we have done it
13:05 egonw jonalv: got a link to those five?
13:05 jonalv bug: 3042
13:05 egonw I replied to the pings you gave this morning already
13:05 zarah bug #3042 | http://pele.farmbio.uu.se/bug​zilla36/show_bug.cgi?id=3042
13:05 jonalv bug: 3074
13:05 zarah bug #3074 | http://pele.farmbio.uu.se/bug​zilla36/show_bug.cgi?id=3074
13:05 jonalv three closed
13:06 egonw 3042 -> see comment
13:06 jonalv karma
13:06 zarah jonalv has a karma of 360
13:06 egonw jonalv: cannot close things without verifying...
13:06 egonw 3074 will take time...
13:07 egonw btw, developers feel encouraged to leave a note when a bug got fixed...
13:07 jonalv @tell olass would you mind verifying and closing or reopening your 30 or so open bugs for 2.6.0?
13:07 zarah Consider it noted.
13:13 konditorn joined #bioclipse
13:15 olass joined #bioclipse
13:15 zaetnick egonw: you did run from eclipse, didn't you
13:15 olass joined #bioclipse
13:15 zaetnick there's something wrong here
13:17 zaetnick can you download the last beta, install R and see what happens
13:19 egonw yes, running from eclipse...
13:19 egonw 2.5.x branch
13:23 zaetnick do you see s button in the R console right hand side "Open R help pages"
13:28 zaetnick same thing with bug 3053
13:28 zarah bug #3053 | http://pele.farmbio.uu.se/bug​zilla36/show_bug.cgi?id=3053
13:32 egonw one sec...
13:32 egonw reinstalling rj 1.1
13:35 zaetnick BTW, which plugin does matrix.create() come from
13:36 zaetnick it's not available in BC
13:37 egonw yeah, I need to dig up that patch...
13:37 egonw oh, but I have matrix.create...
13:39 zaetnick > matrix.create("1 2 3 4 5 6", 3);
13:39 zaetnick javax.script.ScriptException: sun.org.mozilla.javascript.internal.EcmaError: ReferenceError: "matrix" is not defined. (<Unknown source>#1) in <Unknown source> at line number 1
13:39 zaetnick I also have it when I run from eclipse
13:41 egonw part of net.bioclipse.statistics.business
13:41 zaetnick interesting
13:42 zaetnick this looks like another bug :)
13:43 zaetnick anyway, can you confirm the bugs running the BC binaries
13:43 egonw yeah, and another one...
13:43 egonw logging in with Bioclipse does not log in on OpenTox, it seems :(
13:44 egonw zaetnick: I will see... get many other things with higher priorities :/
13:48 egonw http://pele.farmbio.uu.se/bug​zilla36/show_bug.cgi?id=3425
13:51 olass_ joined #bioclipse
14:46 Gpox joined #bioclipse
15:40 konditorn joined #bioclipse
16:18 sneumann joined #bioclipse
16:52 zaetnick joined #bioclipse
17:03 commitbot joined #bioclipse
17:03 commitbot [bioclipse.statistics] valyo pushed 1 new commit to 2.5.x: http://git.io/RwNyEA
17:03 commitbot bioclipse.statistics/2.5.x 1643039 Valentin Georgiev: Change Required Features entry from ...
17:03 commitbot left #bioclipse
17:23 zaetnick joined #bioclipse
17:29 olass joined #bioclipse
18:48 sneumann joined #bioclipse
18:53 Gpox joined #bioclipse
19:20 olass joined #bioclipse
20:41 zaetnick joined #bioclipse
21:06 olass joined #bioclipse
21:25 olass joined #bioclipse

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary