Camelia, the Perl 6 bug

IRC log for #bioclipse, 2012-03-02

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All times shown according to UTC.

Time Nick Message
00:08 CIA-137 bioclipse.speclipse: Egon Willighagen master * r6cad6ce / features/net.bioclipse.spe​clipse_feature/feature.xml : Removed versioning of dependencies in the feature - http://git.io/0IFnzA
00:14 CIA-137 bioclipse.speclipse: Egon Willighagen master * ra1c1a38 / features/net.bioclipse.spe​clipse_feature/feature.xml : A possible provider for log4j? - http://git.io/bCt47Q
06:34 egonw joined #bioclipse
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09:25 CIA-137 bioclipse.cheminformatics: Ola Spjuth 2.5.x * rfc01345 / plugins/net.bioclipse.chemoinformatics/plugin.xml : Added missing dataset menu. Fixes #3149. - http://git.io/SO6D6A
09:25 zarah bug #3149 | http://tinyurl.com/7psqxgs
09:27 CIA-137 bioclipse.ds: Ola Spjuth 2.5.x * rcfe1663 / plugins/net.bioclipse.ds.signatures/plugin.xml : Renamed UI commands for clarity - http://git.io/HLJ7SQ
09:27 * olass likes to close bugs
11:44 egonw i fixed a number of cosmetic bugs
11:44 egonw last night
11:44 egonw and added compiling of bioclipse.latex
11:45 egonw olass: oh, btw, can you update the redirects of jenkins.bioclipse.net and hudson.bioclipse.net
11:45 egonw the first crashes, the second does a double redirect right now
11:48 egonw olass: btw, the update site was updated, but plugin/feature descrptions were not
11:48 olass ok, is it fixed now?
11:48 egonw no idea what goes wrong...
11:49 egonw only see that some things are updated, like new features showing up, but feature descriptions not getting updated...
11:49 egonw but if I'm the only one observing it, it may just be something local
11:49 egonw zaetnick: ping
11:49 egonw zaetnick: I got R bug reports
11:50 egonw the installing went fine, btw!
12:00 zaetnick egonw: pong
12:13 olass egonw: what is a feature description?
12:13 olass don't understand what you mean...
12:13 egonw sorry, skype call in a moment, so please forgive me delays :)
12:13 egonw feature.xml <description>
12:13 olass what about it?
12:13 egonw and that shows up for the user prominently on the first 'install extra's' page
12:13 egonw had a number or problems...
12:14 olass what shows up?
12:14 egonw typo's, missing, uninformative
12:14 egonw those descriptions
12:14 egonw zaetnick: try ls()
12:14 olass and you edited them but not picked up on update?
12:14 egonw zaetnick: it seems to not remember variables here
12:14 egonw yes, so I fixed those issues indeed, but did not show up last night
12:15 olass but commits to plugins did?
12:15 olass maybe just commits to features don't get updated?
12:15 egonw yeah, and hudson recompiled stuff too
12:15 olass Gpox: can you comment on this?
12:15 zaetnick egonw: which variables
12:15 egonw yeah, it seems to be a cache or so...
12:15 olass egonw: what repo was that?
12:15 egonw zaetnick: try this:
12:15 olass egonw: even after restarting bioclipse?
12:15 egonw r.eval("foo = c(1,2)")
12:15 egonw r.eval("ls()")
12:16 egonw the latter shows up nothing
12:16 egonw not in the R console itself either
12:16 zaetnick foo = c(1,2)
12:16 olass egonw: please file a bug about changes in feature.xml not picked up by jenkins on rebuild
12:16 olass that needs to work
12:17 egonw zaetnick++ (for installing the R stuff in zarah :)
12:18 zaetnick egonw: r.eval("foo <- c(1,2)")
12:18 zaetnick :)
12:18 egonw yes, followed by a  r.eval("ls()")
12:18 egonw then foo should show up, but doesn't here
12:19 zaetnick egonw: the "=" operator doesn't seem to work in JSconsole or R console
12:19 egonw ah!
12:19 zaetnick egonw: and never did
12:20 egonw ok, good to know!
12:20 egonw will test later with <- instead!
12:20 zaetnick it works in a normal terminal R session, so maybe it's good if we implement it
12:21 egonw feature request level, sounds good
12:21 egonw in my opinion more important to get data exchange fully working... not sure what the state is of that...
12:21 egonw not played with that yet
12:21 jonalv Gpox: egonw is on to something. We could probably throw jasper out from the core download. Right?
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12:22 jonalv mumble
12:32 CIA-137 bioclipse.opentox: Arvid Berg master * raceff88 / features/net.bioclipse.open​tox_site/buckminster.cspex :
12:32 CIA-137 bioclipse.opentox: Removed buckminster.cspex
12:32 CIA-137 bioclipse.opentox: might interfere with qualifier replacement, and I am not sure if it is needed - http://git.io/_VT_NA
12:39 egonw Gpox: what fix type should I be thinking about, to fix something like this:
12:39 egonw Error: file /home/hudson/jobs/de.ipbhalle.msbi/wo​rkspace/plugins/de.ipbhalle.metfrag: The project was not built since its build path is incomplete. Cannot find the class file for javax.vecmath.Point3d. Fix the build path then try building this project
12:39 egonw Gpox: got a suggestion bioclipse.X repos to look at?
12:39 egonw Gpox: got a suggestion bioclipse.X repos *I can* look at?
12:44 Gpox egonw: Buckminster Installation should be Buckmisnter-auto, and setting the Target Platform shoulb solv it I think
12:50 egonw what example file in the buckminster git repos?
12:51 egonw what example file in the buckminster git repos ... should I best look at... ?
12:51 egonw sorry for being unclear
12:55 Gpox bioclipse/buckminster/cqueries/metaprint2d.cquery
13:12 egonw Gpox++ (thanx!)
13:28 CIA-137 de.ipbhalle.msbi: Egon Willighagen master * r81e30aa / features/de.ipbhalle.metfrag_feature/feature.xml : Added a missing plugin import - http://git.io/-mg25A
13:32 CIA-137 de.ipbhalle.msbi: Egon Willighagen master * r4f15e34 / features/de.ipbhalle.msbi_site/feature.xml : Require vecmatch at the site level too - http://git.io/0IASPw
15:02 egonw btw, didn't get it to find vecmath...
15:02 egonw after all those changes :/
15:06 CIA-137 bioclipse.ds: Ola Spjuth 2.5.x * r4e47d77 / (25 files in 7 dirs):
15:06 CIA-137 bioclipse.ds: Implemented regression models for NN and exact match.
15:06 CIA-137 bioclipse.ds: * Refactored all SDFmodels at the same time. - http://git.io/xEejQw
15:07 CIA-137 bioclipse.ds: Ola Spjuth 2.5.x * r73d7813 / plugins/net.bioclipse.ds.common/src/net/bio​clipse/ds/matcher/BaseSDFExactMatcher.java : handle case when stored prop in SDF is null - http://git.io/Ul5Gsw
15:07 CIA-137 bioclipse.ds: Ola Spjuth 2.5.x * rb82af28 / (3 files in 2 dirs): Cleaned up some unused imports - http://git.io/1WqyTw
15:11 Gpox egonw: I told you what was wrong before when you asked for the buckminster stuff, now it works. And there should not be a vecmath at site level
15:12 egonw Gpox: yeah, sorry... I still cannot make sense of this config stuff
15:13 egonw I guess I just did not understand what you were explaining
15:14 egonw I'll fix the _site
15:15 egonw so, just Hudson configuration stuff was wrong?
15:15 egonw I just hate it when something can be wrong at three separate places...
15:15 egonw because I just don't understand the clues the Hudson/Eclipse is telling me with those cryptic error messages
15:15 egonw (aka, I think the build system sucks)
15:16 egonw (the design, not your use :)
15:16 egonw but my apologies that I did not ask:
15:17 egonw "Arvid, you completely lost me, when you said 'Buckminster Installation should be Buckmisnter-auto'..."
15:17 egonw but, the good news...
15:17 egonw I now see this option in the Hudson config window...
15:17 egonw Gpox++ (for being patient with me)
15:33 egonw olass: yes, it's friday :)
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15:34 CIA-137 chembl.rdf: Egon Willighagen master * ra5e9130 / README.markdown : Updating for ChEMBL 13 - http://git.io/Y9W4lA
15:34 CIA-137 chembl.rdf: Egon Willighagen master * r5c31df6 / (namespaces.php targets.php): Use the PRO ontology, for protein - http://git.io/7-RFIg
15:36 CIA-137 de.ipbhalle.msbi: Egon Willighagen master * r4bcb604 / features/de.ipbhalle.msbi_site/feature.xml : Vecmath should not be imported - http://git.io/9dgHfg
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17:39 * olass will give up for the day now
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