Camelia, the Perl 6 bug

IRC log for #bioclipse, 2007-10-03

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All times shown according to UTC.

Time Nick Message
07:25 masak joined #bioclipse
07:50 olas joined #bioclipse
08:05 jonalv joined #bioclipse
08:20 CIA-31 bioclipse: jonalv * r3888 /trunk/playground/plugins/ne​t.bioclipse.structuredb/src/ (4 files in 2 dirs): Now all dao tests for structure except update works. But the hasValuesEquals to method does not check the AtomContainer molecule. Not sure of how bad this is, it might give false positives and how bad would that be?
08:27 CIA-31 bioclipse: ospjuth * r3889 /trunk/plugins/net.bioclipse.cdk.jchemp​aint/src/net/bioclipse/plugins/bc_jchem​paint/editors/JCPMultiPageEditor.java: Uncommitted fixes to some selection and save problems.
08:28 CIA-31 bioclipse: ospjuth * r3890 /trunk/plugins/net.bioclip​se.jmol/logger.properties: Correction to an outcommented string, but still... who knows...
08:41 CIA-31 bioclipse: jonalv * r3891 /trunk/playground/plugins/ne​t.bioclipse.structuredb/src/ (2 files in 2 dirs): All dao tests passes. The bar is green! Party! ehm I mean time to write more tests...
08:41 CIA-31 bioclipse: jonalv * r3892 /trunk/playground/plugins/net.bioclipse.str​ucturedb.tests/tests/net/bioclipse/structur​edb/persistency/dao/StructureDaoTest.java: All dao tests passes. The bar is green! Party! ehm I mean time to write more tests...
09:23 CIA-31 bioclipse: ospjuth * r3893 /trunk/ (2 files in 2 dirs): Moved to include in release 1.1.5
09:25 CIA-31 bioclipse: ospjuth * r3894 /trunk/features/net.bioclipse.s​tatistics-feature/feature.xml: Added net.bioclipse.chart to statistics feature
09:32 CIA-31 bioclipse: ospjuth * r3895 /trunk/plugins/net.bioclipse.chart/ (META-INF/MANIFEST.MF build.properties jars/pcmcopy1.1.jar): Fixed build path, removed unused dependencies and exported JfreeChart.jar
09:33 CIA-31 bioclipse: ospjuth * r3896 /trunk/plugins/net.bioclips​e.chart/src/net/bioclipse/ (chart/ChartUtils.java model/PcmXYDataset.java): Removed unused classes.
09:34 CIA-31 bioclipse: jonalv * r3897 /trunk/plugins/ (4 files in 4 dirs): Moved net.bioclipse.database to net.bioclipse.hibernate and net.bioclipse.database.hsqldb to net.bioclipse.hibernate.hsqldb
09:34 olas joined #bioclipse
09:34 CIA-31 bioclipse: ospjuth * r3898 /trunk/plugins/ (2 files in 2 dirs): Updated CP
09:35 jonalv olas, database is moved into hibernate now
09:35 olas good
09:35 jonalv So I will begin work on a new net.bioclipse.database
09:35 olas Please write about this on the ML as well so everyone can update their workspaces
09:36 olas also please describe what you will achieve with the new plugins in a wiki page
09:37 jonalv yes will do
09:40 * jonalv lunch
09:56 CIA-31 bioclipse: ospjuth * r3899 /trunk/features/net.bioclipse-feature/feature.xml: Updated plugins and features for release with Eclipse 3.3
09:57 CIA-31 bioclipse: ospjuth * r3900 /trunk/plugins/net.bioclipse/ (META-INF/MANIFEST.MF bioclipse.product): Updated for release 1.1.5 with Eclipse 3.3
11:35 CIA-31 bioclipse: ospjuth * r3901 /trunk/features/net.bioclipse.chem​oinformatics-feature/feature.xml: Updated versioning and deps for release 1.1.5 with Eclipse 3.3
11:35 CIA-31 bioclipse: ospjuth * r3902 /trunk/plugins/net.bioclipse.bi​ojava.ui/META-INF/MANIFEST.MF: Updated versioning and deps for release 1.1.5 with Eclipse 3.3
11:36 CIA-31 bioclipse: ospjuth * r3903 /trunk/features/net.bioclipse.bio​informatics-feature/feature.xml: Updated versioning and deps for release 1.1.5 with Eclipse 3.3
11:38 CIA-31 bioclipse: ospjuth * r3904 /trunk/features/net.bioclipse.s​tatistics-feature/feature.xml: Updated versioning and deps for release 1.1.5 with Eclipse 3.3
11:38 CIA-31 bioclipse: ospjuth * r3905 /trunk/features/net.bioclips​e.qsar-feature/feature.xml: Updated versioning and deps for release 1.1.5 with Eclipse 3.3
11:42 EskilA joined #bioclipse
11:45 CIA-31 bioclipse: ospjuth * r3906 /trunk/features/net.bioclips​e.data-feature/feature.xml: Updated versioning and deps for release 1.1.5 with Eclipse 3.3
11:46 viklund joined #bioclipse
11:46 viklund hello...
11:47 CIA-31 bioclipse: ospjuth * r3907 /trunk/features/net.bioclipse.data​.blueobelisk-feature/feature.xml: Updated versioning and deps for release 1.1.5 with Eclipse 3.3
11:47 olas hi wiklund
11:47 olas hi viklund
11:47 olas wiki account coming up
11:48 viklund I'm syncing the repository currently, it takes quite a while for some reason... (I started with revision 3905)
11:48 viklund great
11:49 olas sent
11:52 olas take latest from head
11:53 viklund I'm trying to, but it's a moving target, your committing faster than svk is syncing ;) (I'm just putting a copy of it in svk, so that I can work against it in a sane way)
11:56 CIA-31 bioclipse: ospjuth * r3908 /trunk/features/net.bioclips​e.qsar-feature/feature.xml: Updated versioning and deps for release 1.1.5 with Eclipse 3.3
11:56 CIA-31 bioclipse: ospjuth * r3909 /trunk/features/net.bioclipse.data​.blueobelisk-feature/feature.xml: Updated versioning and deps for release 1.1.5 with Eclipse 3.3
11:57 viklund oops, what happened here
11:57 viklund must have middleclicked on the irc-window..
11:58 masak viklund: hola!
11:58 viklund masak: aloha!
11:58 masak I've been thinking more about those pointer thingies into genetic fragments
11:59 viklund ahh
11:59 masak it's an interesting topic
11:59 masak complicated
11:59 viklund and usefull
11:59 masak yes
12:00 masak and obviously meant for a computer to do
12:00 viklund I thought getting a bit acquainted with the codebase
12:01 masak good idea
12:01 viklund svk dosn't give any status output when syncing though...
12:01 masak heh
12:01 viklund but my networktraffic is peaking!
12:02 jonalv hi viklund
12:03 viklund hej
12:03 jonalv checking out bioclipse?
12:03 viklund yep
12:03 jonalv w00t
12:03 jonalv have you seen wiki.bioclipse.net?
12:04 viklund I just got an account from Ola!
12:04 jonalv nice
12:04 masak viklund: welcome abord
12:05 masak do we have an AUTHORS file? :)
12:05 viklund I need to commit something first though
12:05 masak not according to the pugs development model
12:05 jonalv masak, I haven't seen one...
12:05 viklund I'm mostly just getting a feel for it...
12:05 viklund ahh
12:06 masak besides, adding yourself to AUTHORS is a commit :)
12:06 viklund I have made a small change to the wiki though!
12:06 masak perfect
12:06 viklund I could allways add the AUTHORS file... ;)
12:06 masak please do
12:06 masak I don't know where it goes, though
12:06 masak probably somewhere near the top
12:07 viklund oh well, I haven't managed to mirror the thing yet so Im currently in the dark as to what the codestructure is...
12:07 jonalv masak, ask olas
12:07 * masak narrowly avoids word play on 'being in the darcs'
12:07 viklund lol
12:08 masak jonalv: good idea
12:11 CIA-31 bioclipse: ospjuth * r3910 /trunk/bioclipsUpdateSite/site.xml: Finally got all dependencies right to build update site
12:11 viklund is anyone not using eclipse to work on bioclipse??
12:11 masak olas: if Bioclipse had an AUTHORS file, where would it go?
12:12 masak viklund: unlikely
12:12 jonalv viklund, why would someone want to do that? :)
12:12 viklund ok, is it possible to use vim in eclipse?
12:12 masak viklund: unlikely
12:13 masak it's a tough call, both programs (eclipse/vim) have features that the other lacks
12:13 olas masak: what is an AUTHIORS file?
12:13 viklund have you looked for a vimplugin
12:13 masak olas: a list of committer, basically
12:14 masak viklund: no
12:14 jonalv You wont't need vim and if you need a to do fancy refactoring using vim you can always fire it up and edit just the one file...
12:14 viklund Yay! http://satokar.com/viplugin/
12:14 masak I've added a few essential Emacs key bindings to eclipse, and now it's quite a nice experience
12:14 masak I always did C-xC-s, so I added that, for example
12:14 olas dunno where AUTHORS should go
12:14 olas any suggestions?
12:14 viklund olas: to the pub?
12:15 masak olas: is there a "root" folder?
12:15 jonalv olas, no as to where it should go but I think it's a great idea to have one
12:15 masak would it feel dirty to add it there?
12:16 olas in trunk I suppose...
12:16 * masak doesn't have the whole of trunk checked out
12:16 olas thats similar to CVSROOT
12:16 masak sounds good
12:17 masak pugs, the most successful open source project in the history of mankind, has an AUTHORS file
12:18 masak I'm not saying it's a good idea to have one, I'm just... you know... hinting that it might be :)
12:22 jonalv shouldn't it be in the root of the repo?
12:22 jonalv not in trunk but in the real root?
12:22 viklund I'd say trunk
12:22 jonalv what about the branches then?
12:23 viklund No-one should checkout the root. So it should be in the trunk, it's like CHANGELOG, INSTALL or COMPILE...
12:24 masak viklund: ah, true
12:24 viklund oh well. It will be copied to the branch when branching, that the old branches dosn't have it is not that big problem
12:24 viklund you could of course copy it over to the branches if you want to...
12:24 jonalv alright
12:24 jonalv whatever
12:24 masak olas: installing StatET now
12:27 olas ok
12:28 olas it's not great
12:28 olas and sort of buggy
12:28 olas but has potential
12:28 olas We should use it or something similar in BC2
12:28 masak yes.
12:29 jonalv for running matlab in bioclipse?
12:29 masak ok, so it installed properly, but where do I find it now?
12:29 masak is there a perspective or a menu alternative somewhere?
12:34 masak olas?
12:34 olas window -> show view
12:34 olas other
12:34 masak mm
12:35 olas or window -> open perspective
12:35 olas don't really remember
12:35 olas you have to set preferences too
12:35 olas that is important
12:35 masak ah! found it
12:35 CIA-31 bioclipse: jonalv * r3911 /trunk/playground/plugins/net.bioclipse.database/: Created database plugin
12:35 masak under perspective
12:42 masak olas: why are the preferences important? I find nothing there
12:42 masak seems I'm missing something, I get two errors when I try to Run the R console
12:43 masak or should I say, I find nothing there that pertains to getting the console to run...
12:43 olas soory, cannot help from memory
12:43 CIA-31 bioclipse: jonalv * r3912 /trunk/playground/plugins/ (net.bioclipse.database.demo/ net.bioclipse.hibernate.demo/): moved net.bioclipse.database.demo in playground to net.bioclipse.hibernate.demo
12:43 masak olas: ok
12:44 olas do you get a StatET preference section?
12:44 olas with 5 sub-topics?
12:44 masak in Preferences? yes
12:44 masak but only 4 sub-topics
12:44 olas What have you selected in R interaction?
12:45 masak the default: a console in Eclipse
12:45 olas ok
12:45 masak should work
12:45 olas Have you installed R?
12:45 masak yes
12:45 olas create a new R project then
12:45 masak hm, ok
12:46 olas and under menu Run -> External tools...
12:46 olas configure the path to R that you have installed
12:46 masak yes, I did that
12:46 olas hmm
12:46 olas maybe there is no R console after all...
12:47 olas I might have been mistaken
12:47 masak a bit unsure what to write as executable, since Mac OS does trickery with .app folders
12:47 olas :-(
12:47 olas yes, true
12:47 masak olas: that just means we're pioneers :)
12:47 olas you are looking for an R console, right?
12:47 masak yes
12:47 * olas is thinking
12:48 olas Don't know if there exists an interactive console
12:48 olas but there must
12:48 olas hmm
12:48 olas maybe ask in %eclipse?
12:48 masak will do
12:48 olas or create a new yourself :-)
12:48 * olas is struggling with packaging bioclipse in 3.3
12:48 masak olas: good luck
12:50 olas it's tricky to get dependencies for multiple platforms and OS in place
12:50 viklund why is software updates under help in eclipse??
12:50 olas that is Eclipse standard
12:50 olas But I agree it's not ideal
12:50 jonalv viklund, good question where would you want it?
12:51 viklund I know, it's eclipse i'm talking about
12:51 olas YES! Finally got Eclipse building for multiple platforms
12:51 masak viklund: because plugins are a good help? :)
12:51 jonalv w00t
12:51 olas * PUH *
12:51 olas or intl: * PHEW * I suppose
12:52 viklund shuldn't it be "* Phu *" in swedish... hmm, maybe not.
12:54 jonalv in the "empty plugin" why is the view in net.bioclipse.plugins.views wouldn't net.bioclipse.views be enough?
12:55 olas yes
12:55 olas an error in empty
12:55 olas please correct and commit
12:55 jonalv oki
12:56 masak hm, the #eclipse ppl didn't really know either
12:56 masak they liked the Bioclipse screenshots, though
12:56 jonalv who?
12:57 jonalv you pointed people to bioclipse screenshots?
12:57 masak jonalv: no, I wrote "Bioclipse"
12:57 masak and they kinda found them themselves
12:57 masak spooky
12:57 jonalv google did the rest... :)
12:57 masak guess so
12:59 CIA-31 bioclipse: jonalv * r3913 /trunk/playground/plugins/net.bioclipse.empty/ (4 files in 3 dirs): moved views out of the plugins package
13:01 CIA-31 bioclipse: ospjuth * r3914 /trunk/features/net.bioclipse-feature/feature.xml: Updated even more deps for release 1.1.5 with Eclipse 3.3 to get export for multiple platforms working
13:01 jonalv what's in all jar files that comes with the "empty plugin"?
13:02 masak olas: it turns out that the R colsole "works" already
13:03 * jonalv thinks the empty plugin is quite big...
13:03 masak it's just that id doesn't respond
13:03 masak the real session is in a proper R window elsewhere
13:03 masak I noticed when I was switching apps and found 7 R applications running
13:05 masak so maybe there isn't an R console...
13:05 olas I guess you are right
13:05 olas it would be EXTREMELY good if we could hook in R to your console
13:06 masak :)
13:06 olas that is a feature people have asked for for a long time...
13:06 masak yes
13:06 jonalv sounds VERY fancy
13:06 masak I was looking for a way to run R directly from terminal
13:06 masak but didn't really find anything
13:08 viklund masak: R
13:08 CIA-31 bioclipse: jonalv * r3915 /trunk/playground/plugins/net.bioclipse.database/ (META-INF/MANIFEST.MF src/net/bioclipse/model/): Removed model stuff left from the empty plugin
13:08 masak viklund: R
13:08 viklund to run R from terminal that is, but maybe you ment something else??
13:09 masak no, I meant that
13:09 masak but just `R` don't cut it
13:09 viklund it works for me;)
13:09 masak it fires up some useless frigging graphical environment for me
13:09 masak that I can't get rid of
13:10 masak it doesn't respond to comman line argument flags
13:10 viklund man R?
13:10 masak no such beast
13:10 viklund man --vanilla might work,,,
13:10 masak hunh?
13:10 viklund I have it, do you want it??
13:10 viklund sry: "R --vanilla"
13:10 * masak 'll try
13:11 masak nope, and not --chocolate either
13:11 jonalv what about --strawberry?
13:11 masak jonalv: trying
13:12 viklund hmm, maybe you should come over from the dark side and install ubuntu on that thing?
13:12 masak it worked!
13:12 masak kidding...
13:12 jonalv taste it!
13:12 masak viklund: what? no...
13:12 masak jonalv: what? no...
13:12 jonalv moving right along...
13:18 masak still in the dark, as it were :/
13:21 viklund haha, I got java.lang.NullPointerException when starting eclipse...
13:23 masak ouch
13:23 jonalv viklund, strange... What have you done to it?
13:24 viklund ohh, just trying to get the vimplugin working, currently it crashes eclipse on startup every other time...
13:24 jonalv there is a vim plugin? :)
13:25 jonalv personally I feel a bigger need for a vim plugin for firefox than one for eclipse...
13:25 viklund there is one...
13:25 viklund of course
13:25 jonalv working good?
13:25 viklund vimperator, http://amix.dk/blog/viewEntry/19136
13:25 viklund it's cool
13:26 masak viklund: the vim plugin for firefox is insane
13:26 masak it goes at least one step too far
13:26 viklund well yes...
13:26 masak it turns _Firefox_ into vim, not its text boxes
13:26 jonalv apuch that's not what I want
13:26 viklund yep, you just have to respect those guys for doing that...
13:26 jonalv I just want tje textboxes to be vim
13:26 masak jonalv: no, it's not! trust me
13:27 jonalv why?
13:27 masak for the reason you said
13:27 viklund from one thing to another, what sdk are you guys using suns?
13:27 masak you just want the textboxes to be vim
13:27 jonalv it's the textboxes that need vim not every little thing
13:27 masak viklund: guess so
13:28 jonalv right?
13:28 masak rught
13:28 masak s/u/i/
13:28 viklund bummer, I don't think i'm going to get the vimplugin working
13:28 masak :(
13:28 viklund Cannot load AWT toolkit: gnu.java.awt.peer.gtk.GtkToolkit
13:29 jonalv why is it running awt?
13:29 jonalv sounds strange...
13:29 viklund ...
13:29 viklund i know
13:33 olas EskilA: around?
14:11 viklund Yay! I'm now checking stuff out from eclipse via subclipse from my svk mirror!!
14:12 CIA-31 bioclipse: biocoder * r3916 /trunk/plugins/net.bioclipse.statistics/src/​net/bioclipse/editors/MatrixGridEditor.java: Removed test action
14:16 CIA-31 bioclipse: biocoder * r3917 /trunk/plugins/net.bioclipse.chart/src/​net/bioclipse/dialogs/ChartDialog.java: removed debug output
14:17 CIA-31 bioclipse: biocoder * r3918 /trunk/plugins/net.bioclipse.statistics/src/​net/bioclipse/editors/MatrixGridEditor.java: Removed debug output.
14:21 olas joined #bioclipse
14:23 CIA-31 bioclipse: ospjuth * r3919 /trunk/plugins/net.bioclip​se.statistics/plugin.xml: Commented out MatrixEditor as GridEditor is the one that works
14:35 CIA-31 bioclipse: ospjuth * r3920 /trunk/plugins/net.bioclipse.statistics/ (plugin.xml src/net/bioclipse/model/MatrixResource.java): Updated resource to use GridMatrixEditor by default with new id (as class and id should always be the same in plugin.xml)
14:52 CIA-31 bioclipse: ospjuth * r3921 /trunk/plugins/net.bioclipse/ (META-INF/MANIFEST.MF bioclipse.product): Updated even more deps for release 1.1.5 with Eclipse 3.3 to get export for multiple platforms working
14:59 CIA-31 bioclipse: jonalv * r3922 /trunk/playground/plugins/ (16 files in 10 dirs): Started fooling around with databasetype extension point
15:09 masak olas: the Erlang plugin has a console
15:09 masak this looks hopeful
15:12 olas cool
15:12 olas Erlang is cool
15:12 olas as well
15:13 masak yes, even at a distance
15:13 olas ejabberd is written in Erlang
15:13 CIA-31 bioclipse: jonalv * r3923 /trunk/playground/plugins/net.bioclips​e.structuredb.tests/tests/net/bioclips​e/structuredb/DatabasesetupTest.java: removed superfluous test
15:13 * masak still hasn't succeeded writing anything in the console, though
15:13 masak but it's obviously meant for writing, and it looks nice
15:20 olas :-)
15:31 olas left #bioclipse
16:41 Nout joined #bioclipse
18:20 egonw joined #bioclipse

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