Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-06-30

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All times shown according to UTC.

Time Nick Message
07:00 Gpox joined #bioclipse
07:05 olas joined #bioclipse
07:27 olas morning
07:51 edrin joined #bioclipse
07:51 edrin hi
07:56 olas h iedrin
07:57 olas saw your commits
07:57 olas just a quick question:
07:57 edrin yes?
07:57 olas why GPL and not LGPL?
07:57 olas or EPL?
07:57 olas We try to build trust so that even companies want to use Bioclipse
07:58 olas and people are generally scared of GPL
07:58 olas and besides,
07:58 olas that means we cannot have WS based on your code in our standard features, they must be distributed in a separate features
07:58 olas in most cases
07:59 olas I mean, the decision is yours
07:59 olas I have no objection to GPL
07:59 olas just wanted to ask if you've considered it
08:02 olas edrin?
08:05 shk3 joined #bioclipse
08:15 edrin left #bioclipse
08:17 edrin joined #bioclipse
08:17 edrin sorry connection was broken...
08:18 edrin olas: did not think too much about it yet
08:18 edrin but i will think about it
08:19 edrin and read up about these licenses again
08:19 olas great
08:19 olas I think it would be wise to at least consider LGPL
08:20 edrin i know
08:20 olas I think that would give your code much better spread
08:20 olas spreading?
08:20 olas :-)
08:20 olas you know what I mean
08:20 edrin i think you are right.
08:20 edrin yes, sure
08:20 jonalv joined #bioclipse
08:20 olas hi jonalv
08:21 olas jonalv: I think the cdk10 and cdk externals in the SVN are broken
08:21 olas I guess I could be the reason
08:21 jonalv okey?
08:21 * edrin is currently optimizing the spreading-function. it will probably use mail, instant messages and probably executables...
08:21 olas could you please verify them?
08:22 olas edrin: let me know if I can help
08:22 jonalv right
08:22 jonalv in what way are they broken
08:22 jonalv =
08:22 olas working on a nasty bug in Bioclipse-jmol
08:22 edrin that was a joke
08:22 olas jonalv: they donät show up in my SVN
08:23 olas edrin: oh
08:23 olas :-)
08:23 olas how's progress btw?
08:23 jonalv brb
08:24 edrin the mail, instant messages and executables are spreading trojan horses and virii ;)
08:24 edrin olas:will test the service side this week
08:25 edrin client will be started next week
08:27 olas edrin: will you also build a client for Bioclipse?
08:27 olas script-based?
08:27 edrin yes
08:27 edrin well, the client is a .jar
08:28 edrin that will be used as a lib from extern
08:28 edrin meaning Bioclipse can do a plugin with it
08:28 jonalv olas: Where are you expecting them to show up? Are you using subclipse? Are they complete plugins or just jar-files?
08:29 olas jonalv: I'm using subclipse
08:29 olas didn't you add them as svn:Externals?
08:29 olas so that I can chekc them out from biocliopse2/trunk/plugins?
08:29 edrin olas: i have certain ideas . lets see if it works like i expect it
08:29 jonalv cdk10? nope not me :)
08:29 edrin or hope it
08:30 olas jonalv: and cdk?
08:30 olas did you add that?
08:30 jonalv olas: cdk egonw fixed
08:30 egonw joined #bioclipse
08:31 jonalv brb
08:33 olas hi egonw
08:33 olas we need you
08:33 olas egonw: I could be that I have messed up, but svn:externals to CDK and CDK10 in bc2/trunk/plugins is broken
08:34 olas if you could fix that I'd be greatful
08:34 egonw moin
08:34 * olas played with subversive
08:34 olas and subversive is nothing I recommend
08:34 egonw olas: org.openscience.cdk is not using svn:externals anymore
08:35 egonw subversive seems stable on my machine
08:35 olas maybe I just didnät use it correctly
08:35 olas egonw: could we not have a link to it in bc SVN?
08:35 egonw huh?
08:35 olas so that users don't need to set check out from 2 different repos?
08:36 olas hmm, developers that is
08:36 olas and -set
08:36 egonw does that matter?
08:36 egonw rather not, as svn:externals does not work nicely with git-svn
08:36 egonw but not impossible...
08:36 olas ok
08:36 CIA-34 bioclipse: ospjuth * r6011 /bioclipse2/trunk/plugins/net.bioclipse.jmol​/src/net/bioclipse/jmol/views/JmolView.java: Cleaned up JmolView reactOnSelection() a lot.
08:36 egonw we could just have both
08:37 egonw an svn:externals in bioclipse2/plugins
08:37 egonw an svn:externals in bioclipse2/trunk/plugins
08:37 olas how about cdk10?
08:37 olas that was with externals
08:37 egonw AFAIK, that's still using externals
08:37 olas it's broken :-(
08:37 olas Think I might have caused that
08:38 olas on checkout, I get no CDK classes
08:38 olas only the activator
08:38 olas ok, then I check out cdk from cdk SVN
08:38 olas I'm OK with that
08:38 olas but we have a big problem
08:38 olas when it comes to exporting
08:38 olas due to an eclipse bug, we can't filter out classes from package/export
08:39 olas it's a known eclispe bug
08:39 olas but will not be fixed within reasonable time
08:39 olas it was reported in 2005 I think...
08:39 egonw :(
08:39 egonw ok, please write it up...
08:39 olas I did write about it on the cdk bug
08:39 egonw and email
08:40 olas but have no solution
08:40 olas the only thing I can think of
08:40 olas if to have a net.bioclipse.cdk.runtime
08:40 olas with the jars
08:40 olas for releases
08:40 egonw that's a rather pain to keep up to date
08:40 olas I know
08:40 egonw but for releases that should work
08:40 egonw which are less frequent
08:41 olas that's my proposal
08:41 egonw ok, sounds reasonable
08:41 olas egon: you are an ant master, right?
08:42 olas could you not add an ant target cdk-bioclipse
08:42 olas that builds and adds the jars for Bioclipse
08:42 olas to a dist folder
08:42 olas that could be copied to the net.bc.cdk.runtie plugin
08:42 olas hmm
08:42 egonw ant dist-large
08:43 olas hmm
08:43 olas that includes some other jars we already have, like log4j?
08:43 egonw ant dist-pure
08:43 egonw that one does not
08:43 olas would that be ok?
08:43 olas I could try that
08:44 egonw yes, tonite
08:45 olas will work after tonight?
08:45 egonw i hope
08:45 olas ok
08:45 olas will you set up the net.bc.cdk.runtime or shall I do it?
08:45 egonw please do
08:45 olas ok
08:45 egonw then maybe it can be finished before tonite
08:46 olas great
08:46 egonw have not been able to do much work last week, so behind schedule at PRI...
08:46 egonw so, don't have much CDK/Bioclipse time
08:46 olas no worries
08:46 olas your help is appreciated
08:47 olas but cdk10 seems broken in svn:externals
08:47 olas if you have 2 mins to look at that I'd be very greatful
08:47 olas hmm
08:47 olas I guess I could get it from cdk svn...
08:47 * egonw is checking (running svn update now)
08:51 egonw olas: mmm... svn:externals for cdk10 seems to work for me
08:51 egonw Fetching external item into 'plugins/net.bioclipse.cdk10/src/org'
08:51 egonw A    plugins/net.bioclipse.cdk10/src/org/openscience/​cdk/applications/undoredo/ConvertToAtomEdit.java
08:51 egonw ....
08:51 egonw U    plugins/net.bioclipse.cdk10/src/org/​openscience/cdk/io/MDLRXNWriter.java
08:51 egonw Updated external to revision 11462.
08:54 olas I get no org
08:54 olas at all
08:55 egonw please do:
08:55 olas I see no org.x in subclipse either
08:55 egonw (command line)
08:55 egonw cd net.bioclipse.cdk10/src/
08:55 egonw svn proplist
08:55 egonw Properties on '.':
08:55 egonw svn:externals
08:55 olas svn does not work from command line for me :-(
08:55 egonw the latter two should be given
08:55 egonw oh....
08:55 olas will get leopard soon
08:55 olas then it will be fixed (I hope)
08:56 olas hmm
08:56 egonw WTF???
08:56 egonw I type "subversive svn:externals" in GG
08:56 egonw and he autotranslates that to "subversion svn:externals" ??
08:57 olas egonw: my SVn installation is broken
08:57 olas I will redo it when I install leopard
08:57 olas then it will work
08:57 olas that's what I meant
08:58 olas properties seems to be correct...
08:58 olas I can see the svn:externals
08:59 olas it's just not updated
08:59 olas grr
08:59 egonw :(
08:59 egonw no idea how to solve that
08:59 olas will start over again
08:59 egonw seems to be a problem with your subversive version
08:59 olas subclipse
09:00 olas maybe
09:00 olas seems like it
09:00 olas still no löuck
09:00 olas ok
09:00 olas thx
09:00 olas for the help
09:00 olas will solve this another way
09:02 olas egonw: a quick question
09:03 olas in cdk, all tests are in src/tests?
09:03 egonw yes
09:03 olas and all code in cdk/main?
09:03 egonw yes
09:03 olas is the info in META-INF required at runtime?
09:03 egonw no
09:03 olas and the cdk-apps.manifest and jmol.javafiles?
09:03 egonw no, don't think so
09:03 olas ok, good
09:04 olas egonw: about the src/data
09:04 olas what is reuired at runtime and what at test time?
09:04 olas could we not have that as a hierarchy?
09:04 olas data/tests/ and data/runtime
09:05 olas that would mean less sampledata in a dist
09:06 egonw yes, good idea
09:07 egonw please file a feature request, so I don't forget about it...
09:08 olas another thing
09:08 olas cdk does not compile for me
09:08 olas import com.sun.tools.doclets.Taglet;
09:08 olas need to add a jar?
09:08 olas in package net.sf.cdk.tools.doclets
09:09 egonw yes
09:09 olas which one?
09:09 olas and is this a new bug?
09:09 olas new addition?
09:09 egonw see develjar
09:10 egonw you do not need to compile this taglet
09:10 olas it's in src/main, hence I need to build it
09:10 olas for my export
09:10 olas all in src/main must be compiled
09:10 olas for eclipse
09:10 egonw develjar/com-sun-javadoc.jar
09:10 egonw develjar/com-sun-tools-doclets-Taglet.jar
09:10 olas seems included...
09:11 olas updated CP did the trick
09:11 egonw mmm
09:12 olas strange that survided a clean()
09:12 olas ok, works now
09:13 egonw good
09:13 * egonw will try to write a 12 page paper today
09:14 olas egonw: which of the devel-jars are required to compile src/main?
09:14 olas obviously the com_sun_doclets is required
09:15 egonw it seems only junit-4.3.1
09:15 olas ?
09:15 olas for src/main?
09:16 olas you said there are no tests in src/main!
09:16 egonw yeah, seems so...
09:16 egonw true :)
09:16 olas and?
09:16 egonw so skip that one
09:16 olas *puh*
09:16 egonw cat src/META-INF/*.devellibdepends | sort | uniq
09:16 egonw but command does not seem to work...
09:17 egonw actually, except for those two taglet related thing, it should be none
09:17 egonw brb
09:53 masak joined #bioclipse
10:05 egonw lunch
10:06 thomas_ku joined #bioclipse
10:36 * olas is enjoying a thunderstorm in Stockholm
10:58 * EskilA as well :)
11:01 egonw NL is sunny and preparing for 30+ starting tomorrow
11:04 EskilA oh well, better weather tomorrow hopefully
11:05 olas who cares, I'm working
11:05 * olas likes rain when working
11:05 masak EskilA: better? it hardly gets better than this
11:06 EskilA My windows are leaking :(
11:06 masak :)
11:06 * EskilA needs silikon
11:06 * masak struggles to find a joke about the OS
11:06 masak dang
11:06 EskilA at least you tried :)
12:11 jonalv joined #bioclipse
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12:59 edrin egonw: what 12 page paper will u write up?
13:01 shk3 joined #bioclipse
13:02 egonw on metware.org
13:16 jonalv joined #bioclipse
13:18 edrin egonw: nice, where do you want to submit it?
13:19 egonw not decided yet
13:19 egonw i really want to submit it to Nature...
13:19 edrin :)
13:19 egonw but don't expect that will work out the way I'd like it to be :)
13:20 edrin hehe :)
13:22 edrin egon, I am sure you know it, eigenfactor
13:23 jonalv what's latest bioclipse rev?
13:29 egonw [10:36] <CIA-34> bioclipse: ospjuth * r6011 /bioclipse2/trunk/plugins/net.bioclipse.jmol​/src/net/bioclipse/jmol/views/JmolView.java: Cleaned up JmolView reactOnSelection() a lot.
13:29 egonw I think
13:30 jonalv then I am close enough. Thabnks
13:38 EskilA Is SVN down?
13:39 EskilA nvm
13:39 egonw was just about to say that CDK's SVN works
13:40 * egonw just found out that has 0.5TB external disk does not do files >4GB :(
13:40 egonw which sucks big time
13:40 egonw now I have to buy a new one, format that one with a proper FS, then copy
13:53 egonw but the CIA is out having a lunch, it seems
14:09 stain egonw: what if you repartition it?
14:10 stain with some fancy tools that can resize it without loosing the content
14:11 egonw does that allow changing FS?
14:11 egonw the part size is no problem
14:11 egonw the max file size is
14:11 stain you can free size so that you can create a new partition of the proper file system
14:11 egonw the bloody thing uses vfat
14:11 egonw factory default
14:12 stain if you use less than 50% space you can move everything over, and then delete the FAT one
14:12 egonw ah, right
14:12 egonw well, the buy new one was more because of the idea of having 1TB of storage :)
14:13 stain they sell them with FAT so it "just works" for everyone
14:14 stain or - an alternative at least on a mac - make a disk bundle and put your big stuff inside there
14:14 stain disk bundles are made out of lots of files and are mounted as a disk image
14:14 * egonw wonders if his HD recorder will eat ext3...
14:14 egonw guess not
14:15 egonw mmm... that sounds interesting... 'disk bundle'...
14:15 egonw will check that
14:24 jonalv joined #bioclipse
14:30 shk3 olas: looks like I have trouble running bioclipse.
14:30 shk3 can we have a look at this when i am in Uppsala?
14:43 jonalv shk3: You comming to Uppsala? :)
14:44 masak ah, Uppsala
14:44 masak the Riviera of East Sweden...
14:45 thomas_ku joined #bioclipse
14:46 egonw shk3: sure
14:52 jonalv joined #bioclipse
15:55 shk3 olas:
15:55 shk3 there is the bmc hotel in Uppsala, right?
15:55 shk3 do you have a url?
15:56 egonw there is an uni hotel
15:56 shk3 I think this was called bmc hotel
15:56 shk3 but I may be wrong
15:56 egonw that I don't know
15:57 shk3 akademihotellet
15:58 jonalv shk3, when are you going to Uppsala?
15:58 shk3 next week
15:58 shk3 mo-we
15:58 jonalv cool
15:58 shk3 looking forward
15:58 shk3 we might get my bioclipse started
15:59 jonalv yea
16:00 shk3 the Akademihotellet seems to offer reasonable prices
16:01 shk3 probably this is what I remembered as bmc hotel
16:05 rojasm joined #bioclipse
17:12 edrin left #bioclipse
18:30 egonw joined #bioclipse
18:54 CIA-47 joined #bioclipse
19:09 olas egonw: working late?
19:09 olas how's the paper goin?
19:37 egonw did not make the 12 pages...
19:37 egonw but had a reasonably well start
20:00 egonw tired now
20:00 egonw won't be able to do anything tonite
20:02 rojasm joined #bioclipse
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21:32 olas left #bioclipse
23:17 edrin joined #bioclipse
23:18 CIA-48 bioclipse: edrin_t * r6018 /xws/trunk/xws-component/src/net/bioclipse/xws/ (22 files in 8 dirs):

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