Camelia, the Perl 6 bug

IRC log for #bioclipse, 2011-09-13

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All times shown according to UTC.

Time Nick Message
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07:53 jonalv egonw++ //for instructive mail to Bioclipse list
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09:20 egonw hi de_maas
09:20 egonw hi Kr8bit
09:20 egonw Kr8bit: not seen you here before
09:22 egonw de_maas: got your mail... will reply later
09:22 egonw blogs you actually via the website...
09:22 egonw but I guess that just adds the entry to that table, but not entirely sure
09:23 egonw Gpox: ping
09:23 Gpox egonw: pong
09:23 egonw what's your Jenkins schedule looking like?
09:24 de_maas egonw: ok
09:24 egonw when you have time, I could use some help, and was hoping to soon see the aggregated update site working... this is purely informational... any answer is fine, just curious about your plans :)
09:25 egonw Gpox: I haven putting more stuff on jenkins of the past week or two
09:25 egonw and will likely add more later, e.g. more test suites
09:26 egonw regarding that, I do have a question... I could not get the test.qsar working, because of XMPP stuff
09:26 egonw the other thing I like to ask, is if you could (at some point) have a look at Bioclipse.rdf...
09:26 egonw that stopped compiling...
09:27 egonw I don't know the cause, but it has to do with net.bioclipse.chemoinformatics.rdf not being found...
09:27 egonw I'm still exploring that one, but with the XMPP/QSAR one I am left clueless
09:31 Gpox egonw: qsar uses 2.5.x branch while the test uses master
09:33 egonw ah, good catch
09:33 egonw set test.qsar to use 2.5.x too now
09:33 egonw and rebuilding
09:36 CIA-96 bioclipse.qsar: Egon Willighagen master * ra9eae47 / features/net.bioclipse.qsa​r.xmpp_feature/feature.xml : Capitalized XMPP - http://git.io/S-1PDA
09:36 CIA-96 bioclipse.qsar: Egon Willighagen master * r603a3cc / features/net.bioclipse.qsar_site/feature.xml : Human readable feature name + 2.5.0 version number - http://git.io/Wk9CrA
09:37 CIA-96 bioclipse.qsar: Egon Willighagen 2.5.x * r0564437 / (12 files in 3 dirs): Added test suite stuff for the QSAR feature - http://git.io/rbZ9uA
09:37 CIA-96 bioclipse.qsar: Egon Willighagen 2.5.x * rd0fd97b / features/net.bioclipse.qsa​r.test_feature/feature.xml : Updated the list of plugins: the test plugins, not the QSAR feature ones - http://git.io/ih6BHQ
09:37 CIA-96 bioclipse.qsar: Egon Willighagen 2.5.x * r194feab / features/net.bioclipse.qsa​r.xmpp_feature/feature.xml : Capitalized XMPP - http://git.io/eXJ62w
09:37 CIA-96 bioclipse.qsar: Egon Willighagen 2.5.x * r24373c2 / features/net.bioclipse.qsar_site/feature.xml : Human readable feature name + 2.5.0 version number - http://git.io/P5P3Mg
09:44 Gpox egonw: chemoinformatics or cheminformatics?
09:44 egonw no o
09:44 egonw is the error about chemO ?
09:45 Gpox egonw: in the cheminformatics.rdf_feature it points to net.bioclipse.cheminformatics.rdf plugin in the branding field there in only a net.bioclipse.chemoinformatics.rdf plugin
09:45 egonw ah :/
09:45 egonw fixing
09:46 egonw btw, the QSAR/XMPP problem persists:
09:46 egonw Error: file /home/hudson/jobs/Bioclipse.test.qsar/work​space/plugins/net.bioclipse.cdk.qsar.xmpp: The project was not built since its build path is incomplete. Cannot find the class file for net.bioclipse.xws.exceptions.XmppException. Fix the build path then try building this project
09:48 CIA-96 bioclipse.rdf: Egon Willighagen 2.5.x * rd9fa423 / features/net.bioclipse.cheminfo​rmatics.rdf_feature/feature.xml : Fixed branding plugin name - http://git.io/B2oK8w
09:52 egonw ok, bioclipse.rdf is blue again
09:52 egonw Gpox++ (for observent eyes)
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10:45 Gpox egonw: qsar tests is up and running
10:45 egonw cool
10:46 egonw what was the problem?
10:46 egonw something in the jenkins config?
10:47 egonw don't see commits to the hudson repos, nor the bioclipse.qsar one
10:48 Gpox removed the import of qsar.cquery and fixed the location of the test launch file it was pointing to an opentox feature
10:51 egonw ah...
10:51 egonw makes sense... did not spot the opentox thing
10:51 egonw Gpox++
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11:09 egonw hi olass
11:09 olass hi egonw
11:09 olass egonw: sent you an email 1 min ago
11:09 olass about export BC-OT
11:10 egonw ok
11:10 egonw need to make a call first now
11:10 olass I had the same problem as you, I added stuff to TP and then the "export for multiple platforms" appeared in the wizard
11:10 olass as far as I remember...
11:10 egonw sounds good
11:10 egonw your email explains how to add it to the TP?
11:12 egonw ah, it does not...
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11:15 olass egonw: no, I don't remember that.... :(
11:26 egonw Gpox: do you know that?
11:31 egonw jonalv: CIA update time... can you please add bioclipse.seneca ?
11:33 jonalv egonw: done
11:33 egonw tack!
11:35 Gpox egonw: download the deltapack and unpack it, add that directory to the target platform
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11:38 egonw steinbeck: have you seen this yet: http://pele.farmbio.uu.se/jen​kins/job/Bioclipse.speclipse/ ?
11:39 egonw mmm... not interested, I guess :)
11:44 egonw Gpox, olass: that did not help so far...
11:46 egonw jonalv: http://pubs.acs.org/doi/abs/10.1021/ci200235e
11:46 jonalv egonw: hm is that worth reading you think? I have discarded it as too technical once but maybe I actually should look at it?
11:48 olass egonw++ //for answering mail on ML
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12:01 egonw jonalv: dunno... but it's at least relevant :)
12:01 jonalv egonw: I will look into it some day :)
12:01 egonw yeah, depends on where your research goes...
12:02 egonw Gpox: are you aware of an OSGi bundle for JFreeChart? is stuff other than Seneca using that in Bioclipse?
12:03 Gpox egonw: no I am not. Don't know
12:03 egonw Gpox: ok, thanx
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12:07 egonw ok, delta pack / target platform thingy working
12:08 egonw making an export now
12:11 egonw Gpox, olass: thanx for the explanation on the delta pack stuff
12:12 egonw it's still running, which is prob a positive thing :)
12:14 olass it takes a while...
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12:23 egonw CPDB regression tells me aspartic acid is mutagenetic :)
12:23 egonw but, up the upside... the export worked :)
12:33 egonw loving pigz for parallel proc support for gzip
12:37 egonw uploading files to pele:/var/www/dl at 10MB/s
13:18 olass egonw: CPDB regression will probably be deprecated...
13:18 egonw OK :)
13:22 egonw no worries... there always false positives
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23:25 CIA-96 bioclipse.ds: Ola Spjuth modeling * r2ae3c1b / (33 files in 20 dirs): Implemented DS modeling. - http://git.io/s5PyRw
23:58 CIA-96 bioclipse.ds: Ola Spjuth modeling * r0101781 / plugins/net.bioclipse.ds.modeling/src/net/bio​clipse/ds/modeling/handlers/ModelFromSDF.java : Fixed bug max height - http://git.io/CjdWTw

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