Camelia, the Perl 6 bug

IRC log for #bioclipse, 2011-02-01

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All times shown according to UTC.

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05:29 CIA-91 bioclipse.statistics: Egon Willighagen master * r09ea9ce / README : Details about setting R_HOME - http://bit.ly/hcanVA
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08:15 CIA-91 bioclipse.rdf: Arvid Berg master * rca26a1a / (24 files in 8 dirs): Moved test projects to corresponding plugin and feature folders. - http://bit.ly/fjmBoS
08:26 egonw__ Gpox++
08:26 egonw__ is now known as egonw
08:29 egonw Gpox: do you know how I can recover my hudson password?
08:32 Gpox I can do it manualy
08:32 zarah Gpox: You have new messages. Write '/msg zarah @messages' to read them.
08:32 egonw Gpox: ok, please reset, tack!
08:33 Gpox egonw: you are away cant msg you the password
08:34 egonw try now
08:35 egonw ok, autobuild after scm polled kicked in :)
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09:14 CIA-91 bioclipse.rdf: Arvid Berg master * ra4a5a45 / sites/net.bioclipse.rdf_site/feature.xml : Added pellet feature to rdf site - http://bit.ly/hRYDzh
09:25 CIA-91 bioclipse.statistics: Egon Willighagen master * r3134831 / plugins/net.bioclipse.r/src/net/bio​clipse/r/ui/views/RConsoleView.java : Output commands and results to the console - http://bit.ly/f0P38B
10:21 CIA-91 bioclipse.rdf: Arvid Berg master * r9df4749 / features/net.bioclipse.pellet_feature/feature.xml : Changed version of dependency on net.bioclipse.rdf_feature - http://bit.ly/ggGevz
10:29 CIA-91 bioclipse.statistics: Egon Willighagen master * rd93aa30 / (3 files): Added a R feature - http://bit.ly/feAzDH
10:29 CIA-91 bioclipse.statistics: Egon Willighagen master * r6f870c7 / features/net.bioclipse.statistics_site/feature.xml : Added the R feature to the update site - http://bit.ly/hNvRjY
10:34 egonw Gpox: I'm debugging the .statistics fail...
10:35 Gpox egonw: it is a buckminster problem
10:35 egonw is it?
10:35 egonw how so?
10:35 * egonw assumed he just messed up
10:36 Gpox it is trying to find net.bioclipse.r_feature but does not know where to look
10:36 egonw should be in features/
10:36 egonw so, I did mess up then? :)
10:37 egonw [2011-02-01 11:30] <CIA-91> bioclipse.statistics: Egon Willighagen master * rd93aa30 / (3 files): Added a R feature - http://bit.ly/feAzDH
10:39 egonw https://github.com/bioclipse/biocli​pse.statistics/tree/master/features
10:40 Gpox no it is blue again
10:40 egonw cool :)
10:40 egonw so, where can the update site be found?
10:40 egonw that is, what URL do I need to pass to Bioclipse 2.5?
10:41 Gpox http://pele.farmbio.uu.se/hudson/view/Release​/job/Bioclipse.statistics/lastSuccessfulBuild​/artifact/buckminster.output/net.bioclipse.st​atistics_site_1.0.0-eclipse.feature/site.p2/
10:41 zarah Gpox's link is also http://tinyurl.com/6ktmddy
10:41 egonw heheheh...
10:41 egonw maybe we should define some apache rewrites :)
10:41 Gpox it is under Last Successful Artifacts
10:42 Gpox I will be working on an aggregator site
10:42 egonw OK
10:42 egonw sounds promosing :)
10:42 * egonw wishes Gpox blogged :)
10:43 egonw Gpox++
10:43 egonw (for good work on Hudson!)
10:52 Gpox egonw: maybe you can help me. If you search for Error in the latest console log for Bioclipse.rdf it is trying to get version 2.4.0.RC1 of both net.bioclipse.core_feature and net.bioclipse.rdf_feature and I can't figure out why
10:52 egonw Gpox: so, if I bump the version number, e.g. the date part at the end, of a feature... the update site will not change, and the update thus be picked up by a 2.5.0 installation?
10:53 egonw Gpox: can you point me to the full stack trace, debug messages?
10:53 Gpox http://pele.farmbio.uu.se/hudson/vie​w/Main/job/Bioclipse.rdf/35/console
10:53 zarah Gpox's link is also http://tinyurl.com/4orl34l
10:53 Gpox search for net.bioclipse.rdf_feature
10:54 Gpox it is a buckminster error
10:54 egonw what makes it a BM error?
10:54 egonw that is... when is something a BM error, and when an error in some eclipse rcp file by us?
10:56 * egonw is searching his local checkout for RC1 instances...
10:56 Gpox well buckminster is trying to locate 2.4.0.RC1 but it could be that there is a reference in and rcp file that says that it needs 2.4.0.RC1
10:56 egonw right
10:57 egonw so this search should show which thing is depending on RC1
10:57 egonw I see metabolomics stuff, but that is not on hudson yet...
10:57 egonw but also rdf stuff...
10:57 egonw I'll fix that ...
10:59 Gpox Interesting I didn't find anything when I did a search
11:00 egonw it seems I was not up to date with upstream yet...
11:00 egonw but still plenty of hits...
11:00 egonw what should it read?
11:00 egonw 2.4.0.what?
11:00 egonw 2.4.0.20100709
11:00 egonw that sounds appropriate
11:00 Gpox rdf version is 2.4.1.v20100830
11:01 Gpox core is 2.4.0.20100709
11:09 CIA-91 bioclipse.rdf: Egon Willighagen master * r055e3e5 / (5 files in 5 dirs): Removed products - http://bit.ly/f3m3Ok
11:09 CIA-91 bioclipse.rdf: Egon Willighagen master * rbed3371 / (5 files in 5 dirs): Bumped version numbers to remove reference of RC1 - http://bit.ly/g437hg
11:10 egonw rebuilding
11:11 egonw yeah, blue!
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11:12 egonw ok, going for lunch now then...
11:12 egonw bbl
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11:26 CIA-91 bioclipse.rdf: Arvid Berg master * rd4c781e / features/net.bioclipse.rdf​.test_feature/feature.xml : Added n.bc.rdf.competeRepoTest to rdf test feature - http://bit.ly/egagZa
12:02 CIA-91 bioclipse.statistics: Egon Willighagen master * r662152f / plugins/net.bioclipse.r/src/net/bio​clipse/r/ui/views/RConsoleView.java : Catch Throwables - http://bit.ly/ew8KpN
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12:35 CIA-91 bioclipse.qsar: Arvid Berg master * r0da6391 / (2 files in 2 dirs):
12:35 CIA-91 bioclipse.qsar: Changed junit from Require-Bundle to Import-Package
12:35 CIA-91 bioclipse.qsar: Using Import-Package allows for more flexibility
12:35 CIA-91 bioclipse.qsar: for what bundle provide the junit classes and
12:35 CIA-91 bioclipse.qsar: simplifies dependency management. - http://bit.ly/fuoAoI
12:35 CIA-91 bioclipse.qsar: Arvid Berg master * r3ad07d0 / (3 files): Added site for qsar features - http://bit.ly/i2YZxP
12:40 egonw arvid, thanx! http://chem-bla-ics.blogspot.com/2011/02/​diy-running-r-from-within-bioclipse.html'
12:40 zarah egonw's link is also http://tinyurl.com/6f8eveg
12:40 egonw arvid, thanx! http://chem-bla-ics.blogspot.com/2011/02/​diy-running-r-from-within-bioclipse.html
12:40 zarah egonw's link is also http://tinyurl.com/5ugmdku
12:40 egonw Gpox++
12:50 sneumann_ gpox++
12:51 samuell 390 Tool config wrapper files shipped by default with Galaxy ... Guess it is better to preload the data :)
12:52 samuell (... than to read and parse these XML files on each startup)
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13:13 egonw cande: two last refactorings remaining for this week for the R integration
13:13 egonw 1. split out UI stuff
13:14 egonw 2. set up a manager
13:15 cande aha
13:26 egonw ok, big push comming...
13:29 CIA-91 bioclipse.statistics: Egon Willighagen master * r34483ed / (15 files in 11 dirs): Factored out UI stuff, to be prepared for HEADLESS - http://bit.ly/eeHrdN
13:29 egonw one down... one to go
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13:35 egonw hi jonalv
13:45 egonw ok, another big patch
13:45 egonw introducing an R manager :)
13:45 egonw > r.eval("library(\"rcdk\")")
13:46 egonw Error: null
13:46 egonw > r.eval("1+1")
13:46 egonw [REAL* (2.0)]
13:46 egonw and since you are wondering:
13:46 egonw > r.eval("data = c(1,2,3)")
13:46 egonw [REAL* (1.0, 2.0, 3.0)]
13:46 egonw > r.eval("mean(data)")
13:46 egonw [REAL* (2.0)]
13:48 egonw jonalv: ping
13:48 egonw Gpox++
13:48 egonw Gpox++
13:48 egonw Gpox++
13:48 zarah Gpox++
13:49 egonw (for beavering away with new repositories on Hudson :)
13:49 egonw jonalv: ping
13:52 CIA-91 bioclipse.statistics: Egon Willighagen master * rf35f0ba / (14 files in 6 dirs): Added a R manager for the scripting environment... just a first go - http://bit.ly/i0PNuK
13:52 egonw "Activator extends Plugin" instead of "Activator extends AbstractUIPlugin" should be enough for HEADLESS compat, correct?
13:57 CIA-91 bioclipse.statistics: Egon Willighagen master * rb753aef / (3 files in 3 dirs): Bumped version number to 2.4.1.20110201 - http://bit.ly/eVRqWr
13:59 CIA-91 bioclipse.joelib: Arvid Berg master * ra21f674 / features/net.bioclipse.joe​lib_feature/joelib.product : Bumped versions in joelib product - http://bit.ly/fr2Td3
14:05 egonw Gpox: ping
14:05 Gpox egonw: pong
14:05 egonw it seems I got something wrong with the R feature...
14:05 egonw but not sure what...
14:06 egonw can you have a look?
14:06 egonw http://pele.farmbio.uu.se/hudson/j​ob/Bioclipse.statistics/20/console
14:06 egonw it says no suitable provider at the end
14:11 egonw Gpox: r -> 2.4.1.20110201
14:11 egonw please try that version number
14:11 egonw Gpox: do I understand correctly you are hacking one of the rmap files now?
14:12 Gpox yes I did. The regex did not catch the r_ only r.
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14:17 Gpox the rmap file should probably be in the repos, but that requiers a central site for already built stuff
14:17 Gpox egonw: it works again now
14:17 egonw tack!
14:21 Gpox egonw: jolib.product is that something that is used?
14:21 Gpox *joelib
14:22 egonw nope
14:22 egonw can be removed
14:22 egonw artifact from my side
14:22 egonw did not want to change the content of bioclipse.product all the time
14:22 egonw with the risk of commiting it
14:24 CIA-91 bioclipse.joelib: Arvid Berg master * r919a640 / (2 files): Removed joelib.product - http://bit.ly/grUBv8
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14:35 egonw Gpox: any clue why it got the feature number wrong at: http://pele.farmbio.uu.se/hud​son/job/Bioclipse.statistics/
14:36 egonw where it still lists 2.4.0.something for r_feature?
14:36 egonw it does indicate to know about the commit that bumped it to 2.4.1.something
14:44 Gpox no, might need to look into it for all builds
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15:18 maclean aha! progress...of a sort. Now rconsole starts, but crashes bioclipse if used :/
15:20 maclean at : org.rosuda.JRI.Rengine.rniPa​rse(Ljava/lang/String;I)J+0
15:20 egonw :)
15:20 maclean double aha. it works!
15:20 egonw will be back in about 30min
15:21 maclean I was running the Bioclipse.app from the finder, instead of the command line
15:21 maclean ok
15:23 maclean success! the mean of (1, 2, 3) is indeed 2! :)
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16:00 maclean egonw_ : it did work in the end. It didn't like me trying to load the rCDK library, but that would be a weird thing to do anyway.
16:00 egonw_ ah,,,
16:00 egonw_ yes, that I did say in the blog :)
16:00 egonw_ weird, but the first thing I tried too :)
16:01 egonw_ loading any library fails
16:01 egonw_ dunno what that is about yet
16:01 egonw_ but cande will work with the new manager too...
16:01 egonw_ so there is critical mass in development
16:01 maclean Oh yeah. I guess I didn't really _read_ the blog post in any meaningful sense :/
16:02 maclean cool.
16:02 egonw_ thanx
16:02 egonw_ I'll take that as a compliment :)
16:02 egonw_ it means the idea is well received :)
16:02 egonw_ is now known as egonw
16:02 egonw but I need to further read up on JRI next week...
16:03 egonw and how to interact with the REngine
16:03 egonw e.g. how the threading works...
16:03 maclean It might be useful to create some use-cases for testing. I like the idea of opening plot images in bioclipse , but maybe that's not possible.
16:03 egonw and integrate that properly...
16:03 maclean ugh, threading!
16:04 maclean But I guess the main use is rounding up the data that is in the bioclipse workspace and piping it over to R for statistic analysis.
16:05 egonw right
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19:59 egonw_ moin
19:59 zarah oh hai egonw_
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20:30 egonw_ hej jonalv
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20:45 jonalv o/
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