Camelia, the Perl 6 bug

IRC log for #bioclipse, 2011-07-21

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All times shown according to UTC.

Time Nick Message
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07:24 CIA-120 bioclipse.statistics: Egon Willighagen master * r782d1f4 / plugins/net.bioclipse.r.business/src/net/b​ioclipse/r/business/RBusinessManager.java : Fixed installing of rj on Linux - https://github.com/bioclipse/bioclipse.statistics​/commit/782d1f4065fee11540e55ba7428be2ed869e530a
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09:09 CIA-120 bioclipse.statistics: Egon Willighagen master * rd4b9e8a / (2 files in 2 dirs): Add the user.home-located lib path where the rj package gets installed by default - https://github.com/bioclipse/bioclipse.statistics​/commit/d4b9e8a79af4aaad0a77c526d5de2a16132b7438
09:09 egonw > r.eval("1+1")
09:09 egonw [1] 2
09:10 egonw > r.eval("library(pls)")
09:10 egonw [1] "pls"       "rj"        "stats"     "graphics"  "grDevices" "utils"    [7] "datasets"  "methods"   "base"
09:10 egonw mmm.... that's a line break missing :)
09:10 egonw ok, got visitors now
09:10 egonw bbl
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12:27 egonw @help
12:27 zarah egonw: avaliable commands are ask bcwiki botsnack clear-messages gist google help hi hug karma messages pelezilla ping plan planet pong ps replan restart seen slap start stop tell thank thanks tutorial unplan welcome
12:27 egonw @seen cande
12:27 zarah cande was last seen 23 h 5 m 17 s ago in #bioclipse saying 'egonw: mac is stable, win will be next week'
12:28 jonalv @botsnack
12:28 zarah ;)
12:47 egonw ok, full speed ahead...
12:47 egonw let's try to move a StringMatrix from Bioclipse to R
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14:20 CIA-120 bioclipse.core: Arvid Berg 2.5.x * ra43688b / net.bioclipse.target.platf​orm/target-platform.target : Readded zest to target platform - https://github.com/bioclipse/bioclipse.core/co​mmit/a43688bc909273d945b5181351119c4a3a167ea5
14:20 CIA-120 bioclipse.core: Arvid Berg 2.5.x * r3eba4c0 / net.bioclipse.target.platf​orm/target-platform.target :
14:20 CIA-120 bioclipse.core: Changed walware site
14:20 CIA-120 bioclipse.core: now using statistics p2 site - https://github.com/bioclipse/bioclipse.core/co​mmit/3eba4c0924a6bf90172df3a60446c5e20361b098
14:21 egonw Gpox: will you issue a rebuild of the target platform?
14:22 Gpox is that needed? need to point the builds to the right branch
14:24 egonw I guess so...
14:24 egonw we want to build against an up to date target platform on jenkins too, not?
14:25 egonw oh...
14:25 egonw sorry... these are the same patches as yesterday!
14:25 Gpox well the changes are cherrypicked from master so the target platform should be the same, I wont trigger it untill the rest of the builds are set to 2.5 branch
14:25 egonw yeah, makes sense!
14:27 CIA-120 bioclipse.qsar: Arvid Berg 2.5.x * r7568cc1 / plugins/net.bioclipse.cdk.qs​ar.xmpp/META-INF/MANIFEST.MF :
14:27 CIA-120 bioclipse.qsar: Added net.sf.xws4j
14:27 CIA-120 bioclipse.qsar: Needed for net.bioclipse.xws imports - https://github.com/bioclipse/bioclipse.qsar/co​mmit/7568cc1232ef6930ad6f14c671cb373836cd040c
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14:28 Gpox hm maybe I should copy the build jobs so that we have one set of jobs for release and one for master, I have to go into every repo and change the branch anyways
14:29 egonw sounds like a true freeze
14:29 egonw if it's not too much work...
14:29 egonw btw, are you not going on holiday
14:29 Gpox got any ideas for naming of the release jobs?
14:30 Gpox no not yet :)
14:30 egonw ummm... good one...
14:31 egonw just "foo 2.5" ? or "foo 2.6"?
14:31 Gpox Bioclipse.release.core or maybe Bioclipse.stable.hivdrc, Bioclipse.integration.ons
14:32 Gpox would be nice to not have the version nummerb htere so that they can be reused for 2.6, 2.7
14:32 egonw good point
14:32 egonw .stable. might be misleading...
14:33 egonw or confusion
14:33 egonw .beta. ?
14:33 egonw or .freeze. ?
14:45 CIA-120 bioclipse.ds: Arvid Berg 2.5.x * rec69bcb / plugins/net.bioclipse.ds.sig​natures/META-INF/MANIFEST.MF :
14:45 CIA-120 bioclipse.ds: Removed required bundle net.bioclipse.ballon.business
14:45 CIA-120 bioclipse.ds: It was not used - https://github.com/bioclipse/bioclipse.ds/com​mit/ec69bcbed76fe30f31d64c2231bf04df83dad9da
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14:54 Gpox or maybe not as the buckmisnter script isn't writen for several versions, not relaiable atleast
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15:01 egonw I'm not too strong on naming, really
15:02 egonw unless you start calling it poop or something :)
15:03 * jonalv loves naming!
15:03 jonalv Gpox: explain what you need names for again pleas?
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15:05 Gpox separate jobs on jenkins for 2.5.x branch, but I decided not to do this as I am not sure the buckminster scripts can handle it correctly
15:05 jonalv oh okey
15:08 Gpox better to do it once 2.6 is out and we want to change it back to master
15:09 jonalv okey
15:09 jonalv so any progress with hivdrc?
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15:10 Gpox it is blue, qsar it not though
15:10 jonalv Gpox: is qsar the trouble now?
15:10 jonalv always something eh?
15:10 jonalv I thought we had feature freeze...
15:13 Gpox me too
15:13 jonalv :)
15:17 CIA-120 bioclipse.statistics: Egon Willighagen master * rde36917 / plugins/net.bioclipse.r/src/net​/bioclipse/r/RServiManager.java : Added extra comment which I forgot to commit earlier today - https://github.com/bioclipse/bioclipse.statistics​/commit/de36917982e10c9ea09dacd1475d48551a3689f2
15:18 cande jonalv: vem är det som fixar commit behörighet till vaneltin på bioclipse.statistics
15:18 zarah cande: You have new messages. Write '/msg zarah @messages' to read them.
15:19 jonalv cande: antar det aer jag eller Ola
15:19 jonalv cande: har du hans anvaendare aa kan jkag goera det direkt
15:19 cande vad har du gjort med dina åäön ?
15:19 jonalv hm this is #bioclipse, we use english here cande--
15:20 jonalv shame on you for tricking me :)
15:20 cande oh, sorry :P
15:20 egonw hej cande!
15:20 jonalv egonw--
15:20 egonw what??
15:20 jonalv this is #bioclipse we use english here
15:20 egonw poop
15:20 jonalv lol
15:20 cande haha
15:21 egonw cande: the r manager is now working on linux too
15:21 cande egonw: great!!
15:21 egonw cande: I made three commits
15:21 cande egonw++
15:21 jonalv jonalv-- // this is #bioclispe we use english here..
15:21 jonalv |bioclipse
15:21 cande i just read your mesages from zarah :)
15:21 egonw bra^Wgood!
15:22 jonalv huh?
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15:22 egonw what's going on here? it's past 17 and everyone joins?!?
15:22 egonw it's not that the tour etappe has ended :)
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15:23 egonw cande: I'm implementing r.createMatrix("mVarNameInR", IStringMatrix)
15:23 zaetnick hi
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15:23 zarah hi zaetnick
15:23 jonalv hi zaetnick
15:23 zaetnick cande: I'm valyo on github
15:24 cande jonalv: valentine is valyo on github
15:24 cande :)
15:24 zaetnick cut the "e" in the end
15:24 zaetnick :)
15:25 cande ha ha sorry
15:26 jonalv zaetnick: okey try now, valyo has been added to the statistics team
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15:29 jonalv egonw: do you know what to do about all questions from ceefour on bioclipse.xws4j? Is it edrin or olass we should get to answer perhaps?
15:29 egonw edrin
15:29 egonw but I think ceefour is the same person whom edrin has been emailing with already
15:30 jonalv egonw: however I am guessing doesn't have any time over for that for the moment...
15:30 jonalv oh okey
15:30 jonalv so I shouldn't worry at all?
15:30 egonw the idea is that ceefour gets work done
15:30 egonw no, not practically, I think
15:31 egonw perhaps give ceefour write access at some point
15:32 jonalv oki
15:32 cande zaetnick: R_console branch is merged with the master now
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15:34 zaetnick cande: should I work on master now
15:34 egonw yes
15:35 zaetnick ok, I have commits on my R_console
15:35 egonw URI?
15:35 zaetnick should I merge R_console in master before I pull or after
15:36 egonw git fetch origin master
15:37 egonw git checkout -b mergeMyRConsoleIntoMaster master
15:37 egonw oops
15:37 egonw git checkout -b mergeMyRConsoleIntoMaster R_console
15:37 egonw git rebase origin/master
15:37 egonw those three commands
15:37 egonw if that rebase works, then you can commit to master, with:
15:37 egonw git checkout master
15:38 egonw git merge mergeMyRConsoleIntoMaster
15:38 egonw git push origin master
15:40 cande egonw: there is something weird goingon with my gittish
15:40 zaetnick didn't work, there are conflicts in the rj installation part
15:41 cande the "master" branch is way old
15:41 cande it's from 2011-03-17
15:41 cande jonalvs commit
15:41 cande and your commit today, is origin/master
15:41 cande how do i fix that?
15:41 egonw cande, do this:
15:42 egonw git checkout master'
15:42 egonw git checkout master
15:42 egonw git rebase origin/master
15:42 cande ah
15:42 cande excelent! :)
15:42 cande egonw++
15:42 cande so now my local master will follow origin/master ?
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15:46 cande zaetnick: how is it going?
15:46 zaetnick messy
15:46 cande what's your git status?
15:47 zaetnick I have rw rights now
15:47 zaetnick that's ok
15:48 zaetnick but now with the branches...I have changes in the rj installation part
15:48 egonw cande: not automatically
15:49 zaetnick and they conflict with your last stuff, I wonder how to resolve these
15:49 cande zaetnick: ok, i made some changes to that aswell
15:49 egonw zaetnick: kdiff3
15:49 cande zaetnick: tell me your changes and i can add them from my puter and commit
15:49 egonw when you rebase, it will stop at a conflicting patch
15:49 egonw then run:
15:49 egonw git mergetool
15:50 egonw where you can use kdiff3
15:50 egonw zaetnick: please give cande the commit URIs on GitHub
15:50 egonw add .raw or .patch to download that commit as a single patch
15:50 cande ok
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15:54 cande egonw: nice work with the libpaths
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15:57 cande zaetnick: you have access to the wiki.bioclipse page?
15:57 zaetnick username and pass?
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16:00 zaetnick cande: should I send you my commit as a patch via email
16:01 cande yes please
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16:02 zaetnick done
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16:04 * egonw is debugging why this command does not work:
16:05 egonw r.eval("m <- textConnection(\"1 2 3 4\")")
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16:06 egonw mmm... now it works ... :/
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16:08 jonalv nah I am giving up for today
16:08 jonalv later o/
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16:17 zaetnick cande: how do I login in the wiki
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16:22 cande zaetnick: jonalv or ola can give you an account
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16:27 cande zaetnick: can you get the push URI to github bioclipse.statistics ?
16:36 zaetnick cande: what do you mean with the push URI
16:37 cande zaetnick: got it resolved :)
17:51 cande left #bioclipse
18:07 CIA-120 bioclipse.statistics: Christian Ander master * rd4b960f / plugins/net.bioclipse.r.business/src/net/b​ioclipse/r/business/RBusinessManager.java : Improved error message to R console - https://github.com/bioclipse/bioclipse.statistics​/commit/d4b960f8d54e9cf18c597f607de27790251b5927
18:19 CIA-120 bioclipse.statistics: Christian Ander master * r4c88381 / plugins/net.bioclipse.r.business/src/net/b​ioclipse/r/business/RBusinessManager.java : using logger.error() during errors - https://github.com/bioclipse/bioclipse.statistics​/commit/4c88381d9725ade84e5f86245f8ef9242bd688dd
18:19 CIA-120 bioclipse.statistics: Christian Ander master * r0261116 / plugins/net.bioclipse.r.business/src/net/b​ioclipse/r/business/RBusinessManager.java : fixed spelling errors - https://github.com/bioclipse/bioclipse.statistics​/commit/026111633a77b2f199557a7519a7e6f5590fa48a
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