Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-05-19

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All times shown according to UTC.

Time Nick Message
05:06 egonw joined #bioclipse
05:15 egonw moin
05:15 zarah hi egonw
06:14 masak joined #bioclipse
06:29 Gpox joined #bioclipse
06:30 Gpoks joined #bioclipse
06:40 edrin joined #bioclipse
06:40 edrin hi
06:41 zarah saluton edrin
06:41 masak hi
06:41 zarah saluton masak
06:41 zarah masak: You have new messages. Write '/msg zarah @messages' to read them.
06:41 masak @messages
06:41 zarah masak: 13 h 50 m 24 s ago, shk3 said ctrl+c does not work sorry
06:41 masak :/
06:41 rojasm joined #bioclipse
06:48 edrin masak: do you have access to pele?
06:48 edrin masak: like access to upload files with ftp
06:48 masak edrin: yes, I guess I do. zarah is on pele.
06:54 edrin masak: can you access the following dir
06:55 edrin http://pele.farmbio.uu.se/xmpp-services/dl/
06:55 zarah edrin's link is also http://tinyurl.com/p7os7d
06:55 edrin and upload/delete stuff...
06:56 * masak tries
06:57 edrin hm
06:57 edrin well, i need to upload 250 MB...
06:57 masak edrin: yes, seems I can.
06:57 edrin maybe it's not a good idea anyway to do this from home...
06:57 masak maybe not.
06:58 edrin so I will try this from institute...
06:58 edrin masak: do you know when ola will be here?
06:58 masak edrin: it shouldn't be long now. he usually turns up around this time.
06:59 edrin ok
07:16 olass joined #bioclipse
07:17 olass hi
07:17 zarah oh hai olass
07:18 masak olass: you just missed edrin. :/
07:33 edrin joined #bioclipse
07:34 edrin hi
07:34 zarah oh hai edrin
07:34 edrin hi olass
07:34 edrin around?
07:37 olass yes
07:37 olass edrin: did you manage to build?
07:37 edrin yes
07:37 olass saw your email
07:37 olass you need ftp access to pele
07:38 olass I'll set that up
07:38 olass now
07:38 edrin ok, cool :)
07:38 olass done
07:38 olass chmod to 777 (for now)
07:38 olass can you try?
07:39 edrin ok
07:39 olass it looked like you already uploaded linux 64 bits
07:39 edrin no
07:39 edrin i did not
07:39 olass ok
07:40 edrin ehm... olass can you mail me an account!?
07:40 olass you already have one
07:40 edrin ah, the wiki account
07:40 edrin ?
07:40 olass no not wiki
07:40 edrin the pelezilla?
07:56 egonw joined #bioclipse
07:57 egonw moin
07:57 zarah hello egonw, you fantastic person you
07:57 edrin egonw: i need help
07:58 egonw how so?
07:59 edrin egonw: see private message
08:04 edrin egonw: still there?
08:10 edrin egonw: ?
08:11 shk3 joined #bioclipse
08:11 masak edrin: people are in a meeting, discussing the ongoing problems with exporting.
08:11 edrin ok
08:12 edrin masak: can you tell me why my account on pelezilla to use sftp/SCP does not work?
08:12 masak edrin: I'm afraid I can't.
08:12 edrin ok
08:12 masak edrin: but mostly because your question is a bit ill-posed.
08:12 masak edrin: in what way doesn't it work? what is it you're doing.
08:13 masak s/\./?/
08:13 edrin access denied
08:13 edrin egon takes care now
08:13 masak ok.
08:20 rojasm in the net.bioclilpse.ui.business manifest the org.eclipse.ui.navigator has added a bundle-version which produce a error! should it not be removed?
08:22 masak @tell olass rojasm asked 'in the net.bioclilpse.ui.business manifest the org.eclipse.ui.navigator has added a bundle-version which produce a error! should it not be removed?'
08:22 zarah Consider it noted.
08:29 CIA-40 bioclipse: shk3 * r10538 /bioclipse2/trunk/_playgroun​d_/net.bioclipse.medea.case/ (2 files in 2 dirs): using the wcc calculation from spectrum manager
08:30 CIA-40 bioclipse: ospjuth * r10539 /bioclipse2/trunk/features/ne​t.bioclipse.product_feature/: Initial import.
08:32 egonw all: IMPORTANT NOTICE
08:33 egonw we are setting up a product feature
08:34 egonw which will contain the bioclipse.product
08:34 CIA-40 bioclipse: egonw * r10540 /bioclipse2/trunk/features/ne​t.bioclipse.product_feature/: Wrong name
08:34 egonw which will be removed from net.bioclipse.ui
08:34 egonw to solve a circular dependency when usign Buckminster
08:34 CIA-40 bioclipse: ospjuth * r10541 /bioclipse2/trunk/features/net​.bioclipse.platform_feature/: Initial import.
08:35 edrin k
08:35 edrin :)
08:35 egonw shk3: can you relay the message at the EBI, to Chris and Gilleain
08:35 egonw please?
08:35 CIA-40 bioclipse: shk3 * r10542 /bioclipse2/trunk/_playground_/net.bio​clipse.medea.case/src/net/bioclipse/pl​ugins/extensions/WCCMedeaJudge.java: using the wcc calculation from spectrum manager
08:35 shk3 both not here
08:36 shk3 sorry
08:36 CIA-40 bioclipse: ospjuth * r10543 /bioclipse2/trunk/features/ne​t.bioclipse.platform_feature/ (5 files): Committed product feature that factors out products to a separate platform feature. This means we can have multiple products for different purposes.
08:40 CIA-40 bioclipse: ospjuth * r10544 /bioclipse2/trunk/plugins/net.b​ioclipse.ui/bioclipse.product: Removed the product from ui plugin since moved to net.bioclipse.platform_feature.
08:46 olass joined #bioclipse
08:46 olass zarah: wb
08:46 zarah olass: that was not so easy for a little bot to understand
08:46 zarah olass: You have new messages. Write '/msg zarah @messages' to read them.
08:46 olass zarah: just tell me..
08:46 zarah olass: 24 m 25 s ago, masak said rojasm asked 'in the net.bioclilpse.ui.business manifest the org.eclipse.ui.navigator has added a bundle-version which produce a error! should it not be removed?'
08:47 jonalv joined #bioclipse
08:47 olass rojasm: you are absolutely correct
08:48 olass I'll do it now
08:49 CIA-40 bioclipse: ospjuth * r10545 /bioclipse2/trunk/plugins/net.bioclip​se.ui.business/META-INF/MANIFEST.MF: Removed bundle versions since pointing to a too specific eclipse version.
08:49 CIA-40 bioclipse: egonw * r10546 /bioclipse2/trunk/features/net.bioclip​se.platform_feature/bioclipse.product: Fixed .product file for feature rename from product to platform
09:02 egonw_ joined #bioclipse
09:15 egonw shk3: can you please stick to 80 characters max?
09:15 shk3 i try to
09:16 egonw there is an editor option to help you
09:16 egonw it puts a grey line in your editor
09:16 egonw at 80 character position
09:21 masak shk3: instructions here: http://wiki.bioclipse.net/i​ndex.php?title=Style_guide
09:21 zarah masak's link is also http://tinyurl.com/5wlqjo
09:33 egonw edrin++
09:33 egonw for fixing the last few blockers for the Bioclipse-XMPP bundle
09:36 * edrin is currently concentrating on a clinical issue
09:38 jonalv olass: I get the same error in Windows as well
09:38 olass jonalv: damn
09:39 olass this makes me wonder if edrin has the latest things checked out
09:39 olass since all of us here, on alla platforms, get this error
09:39 olass alla->all
09:46 masak olass++ # not using the equals sign any more
09:46 olass :)
09:50 * olass = learning
09:51 olass masak-- //for not reacting on this
09:51 jonalv well I am trying to olass this stupid things
09:52 masak olass: :) you're such a tease.
09:52 olass hehe
09:52 CIA-40 bioclipse: ospjuth * r10547 /bioclipse2/trunk/ (54 files in 53 dirs): Set version to 2.0.0.B20090519 for the first NWO export.
09:52 masak well, live and olass, I guess.
09:52 olass has anyone ever told you how slow subclipse is?
09:52 olass is there no alternative to this shiit?
09:52 masak olass: well, you should olass to use something else, then.
09:52 masak olass: yes.
09:52 olass ah, yes
09:52 olass subversive!
09:53 jonalv olass: you can do the update from the commandline. and then refresh your workspace. That's much faster
09:53 masak :/
09:53 masak olass: yes, at least do that. that's what jonalv and I did before git-svn.
09:53 olass jonalv: but I am committing, so update would really not resolve my problem
09:53 CIA-40 bioclipse: ospjuth * r10548 /bioclipse2/trunk/features/ (14 files in 13 dirs): Set feature versions to 2.0.0.B20090519 for the first NWO export.
09:54 jonalv olass: ah no, it doesn't really speed up commit's unless you wanna do them from commandline as well...
09:54 CIA-40 bioclipse: ospjuth * r10549 /bioclipse2/trunk/plugins/ (7 files in 7 dirs): Set version to 2.0.0.B20090519 for the first NWO export.
09:56 CIA-40 bioclipse: ospjuth * r10550 /bioclipse2/trunk/plugins/ (10 files in 10 dirs): Set version to 2.0.0.B20090519 for the first NWO export.
09:56 egonw jonalv: http://chemicalrcp.blogspot.com/2009/05/​eclipse-spring-export-problem-uses.html
09:56 zarah egonw's link is also http://tinyurl.com/p2xppr
09:56 egonw will hit Planet Eclipse
09:56 egonw so far, most of my posts gave some feedback
09:56 egonw sometimes useful, sometimes not
09:57 masak olass: I now have git on Windows.
09:57 egonw ha, you think it can fix windows?
09:57 egonw by merging some Linux?
09:57 masak egonw: slowly corrupting it from within...
09:58 jonalv egonw: yes let's hope we can get some help from somewhere...
10:10 egonw Gpox: ping
10:10 egonw Gpox: can you come over?
10:10 egonw I have a BM fail
10:11 egonw about org.rosuda.jri
10:11 egonw never mind
10:11 egonw SVN time out :(
10:11 egonw svn--
10:12 jonalv egonw: what's a "BM-fail"? Do I even want to know? :)
10:12 egonw and now the Resolve to Wizard has to start again... :(
10:12 egonw BuckMinster
10:15 egonw OK, we need to go for lunch now
10:15 egonw bbl
10:17 olass @lynch
10:17 masak lunch &
11:19 maclean joined #bioclipse
11:38 egonw another bundle not found
11:38 egonw :(
11:39 * egonw hopes Gpox will bring the local sources online soon
11:44 egonw all: IMPORTANT
11:45 egonw gonna rename the net.bioclipse.inchi.business/ folder name
11:45 egonw you may want to update your workspace afterwards
11:52 masak *lol* http://xkcd.com/585/
11:56 jonalv masak: oh keep up ;)
11:56 masak :)
11:57 CIA-40 bioclipse: egonw * r10551 /bioclipse2/trunk/plugins/ (37 files in 15 dirs): Renamed folder name to match the plugin name, to make BuckMinster happy
11:57 * masak is going through BioJava tutorials, thinking about what to wrap in the BioJava manager
11:59 egonw blast (and friends)
11:59 egonw DNA 2 RNA 2 protein
12:01 egonw well, all of: http://biojava.org/wiki/BioJava:CookBook
12:01 zarah egonw's link is also http://tinyurl.com/oxtxpq
12:03 masak egonw: that's one of the resources I'm looking at.
12:03 masak egonw: I already have a long list of manager methods to expose.
12:03 egonw good :)
12:03 masak however...
12:03 egonw for PCM... protein 2 numerical representation
12:03 masak I don't see how we'll be able to pull off something like IMolecule this time.
12:03 egonw not sure if BioJava does that, or if CDK comes in...
12:03 masak so I think I'll just not do that.
12:04 egonw wondering if the CDK does numerical representation for protein
12:04 egonw why not?
12:04 egonw there is IDNASequence
12:04 egonw there is IRNASequence
12:04 masak egonw: oh, good.
12:04 masak egonw: in that case, I'll simply standardize on those.
12:04 egonw (well... not pratically... yet)
12:04 egonw protein sequences are more difficult
12:05 egonw PDB files can go in as IMolecule
12:05 egonw (so does mmCIF)
12:05 masak egonw: what do you mean by 'there is' and then 'not yet'?
12:05 egonw these are concepts, not actual interfaces yet
12:05 masak egonw: I don't understand.
12:06 masak I you mean what I think you mean, I don't see how we could do that.
12:06 egonw huh?
12:06 masak and that's the problem right now.
12:06 egonw now you lost me
12:06 masak egonw: no, you're not entitled to say "huh?"
12:06 masak you were the confusing one first.
12:07 egonw your confusing me with which bits you understood (if any) and which not
12:07 egonw or
12:07 egonw your confusing me with which bits I was unclear or not (if any)
12:07 maclean joined #bioclipse
12:07 masak well, if I understood you correctly, you propose that I introduce a couple of interfaces IDNASequence etc.
12:07 maclean what is this chat I see about biomolecules in cdk?!
12:07 jonalv egonw: masak why don't you guys talk face2face instead?
12:07 masak jonalv: that's cheating. :)
12:07 maclean jonalv : how antiquated! :)
12:08 masak no, let's not. I have work to do. :)
12:09 egonw masak: yes, I propose to introduce new domain objects...
12:09 egonw masak: how would you otherwise want to design a biojava manager?
12:09 masak egonw: well, thing is, you might be right.
12:09 masak it might be the right way to do it.
12:10 masak I just think we should ask ourselves if and why we need to, before we start wrapping everything up in our own domain objects.
12:10 * maclean agrees
12:10 masak I'm sure jonalv doesn't.
12:11 egonw masak: because we need something beyond a particular implementation
12:11 jonalv masak: if you choose to not implement IBioObject then you are on your own
12:11 masak egonw: that, too.
12:11 egonw otherwise, you cannot exchange data between e.g. biojava, jmol and cdk maangers
12:11 masak jonalv: well, exactly.
12:11 masak jonalv: it kinda goes outside of the design.
12:12 masak egonw: good point.
12:12 egonw masak: the sole raison-d'existance of Bioclipse is integrating tools
12:12 masak aye.
12:13 masak well, if we managed to wrap everything into managers and domain objects, then it would be really, really cool.
12:13 masak but it'll take a lot of work to do so, and quite a few things can be mis-designed along the way.
12:13 masak in fact, I'm pretty sure quite a few things will be the first few times around.
12:14 masak so perhaps it's best to keep the BioJava wrapper APIs liquid for a while.
12:15 jonalv okey egonw, olass  I have merged net.bioclipse.managers and net.bioclipse.recording into net.bioclipse.core. I can not get any NWO managers to be initialised but I can export now. Not exactly super...
12:15 maclean mis-design of bio-interfaces is highly likely if they are made by chemists :p
12:15 egonw maclean: plugging yourself?
12:15 egonw :)
12:15 maclean anyway. I'm off for coffee (and incidentally, lunch)
12:15 maclean :)
12:15 olass jonalv: ok...
12:16 * olass is coming over
12:16 masak maclean: I'd very much like to discuss ideas.
12:16 maclean No, I'm too busy pretending to be a mathematician today (automorphism orbits of partitions on graph groups.... etc)
12:16 maclean masak : well, I would be happy to - when?
12:17 maclean (I know those sentences contradict each other; so what? :)
12:18 maclean masak : briefly, the problem of making good interfaces seems like the problem of language design. viz : hard.
12:18 masak maclean: sometime after-hours, perhaps. and maybe not this week.
12:18 maclean ok, cool.
12:18 masak I prefer IRC, but Skype works too.
12:19 * maclean much prefers irc...
12:20 masak splendid.
12:23 CIA-40 bioclipse: carl_masak * r10552 /bioclipse2/trunk/plugins/net.bioclipse​.scripting.ui/src/net/bioclipse/scripti​ng/ui/views/ScriptingConsoleView.java:
12:23 CIA-40 bioclipse: [ScriptingConsoleView] removed premature keypress forwarding
12:23 CIA-40 bioclipse: Turns out the "Paste" forwarding done on Windows was more of a "Ctrl"
12:23 CIA-40 bioclipse: forwarding. (r9903 which introduced this forwarding doesn't seem to
12:24 CIA-40 bioclipse: be aware of this.) This doesn't cut it, because we still want to be able to
12:24 CIA-40 bioclipse: Copy from the output part of the console.
12:24 jonalv svn--
12:25 masak SVN--
12:28 egonw svn--
12:29 egonw ok, reboot buckminster once more :(
12:34 * jonalv is trying to commit...
12:34 jonalv SVN--
12:34 * egonw votes for an earlier move to git
12:34 egonw svn@sf is holding us back
12:35 egonw I'm now just waiting for jonathan's fixes, so that he can help debug the manager initialization :(
12:37 CIA-40 bioclipse: shk3 * r10553 /bioclipse2/trunk/plugins/net.bioclips​e.spectrum/src/net/bioclipse/spectrum/ (3 files in 2 dirs): added method for file type detection
12:37 CIA-40 bioclipse: shk3 * r10554 /bioclipse2/trunk/plugins/net.bioclipse.​spectrum.test/src/net/bioclipse/spectrum​/business/test/SpectrumManagerTest.java: test for file type detection
12:38 CIA-40 bioclipse: jonalv * r10555 /bioclipse2/trunk/ (113 files in 84 dirs): merged net.bioclipse.managers into net.bioclipse.core
12:39 egonw rojasm, shk3, edrin: don't upgrade to 10555
12:39 masak :)
12:39 egonw it fixes export, but still breaks running the managers...
12:39 egonw jonalv: there is a second patch coming, right?
12:39 jonalv egonw: I got conflict here during commit
12:39 jonalv egonw: no idea what that means...
12:40 egonw that SVN was so slow, your commiting was not finished while stefans commits arrived
12:40 * egonw thinks...
12:41 masak SVN--
12:41 jonalv olass: could we please move to git? I get conflcits mid commit here...
12:42 masak olass: move to git? please?
12:42 olass left #bioclipse
12:42 CIA-40 bioclipse: jonalv * r10556 /bioclipse2/trunk/ (41 files in 7 dirs): merged net.bioclipse.recording into net.bioclipse.core
12:43 egonw all: which Java class should I use for first in, first out?
12:43 CIA-40 bioclipse: jonalv * r10557 /bioclipse2/trunk/plugins/ (10 files in 6 dirs): removed remains of net.bioclipse.managers and net.bioclipse.recording plugins.
12:43 jonalv egonw: linkedlist?
12:44 egonw '?' as in: 1. but I am not sure, or 2. didn't you know that ?!?!
12:44 masak egonw: there's also a Queue in later versions of Java.
12:44 jonalv as in but there might be even beter options
12:45 masak http://java.sun.com/j2se/1.5.0​/docs/api/java/util/Queue.html
12:45 zarah masak's link is also http://tinyurl.com/d4pn8
12:45 egonw "Queues typically, but do not necessarily, order elements in a FIFO"
12:45 egonw emph one 'do not necessarily"
12:45 masak hm, and LinkedList implements that. :)
12:45 egonw on, not one
12:46 egonw ok
12:46 egonw addFirst, getLast
12:46 egonw that seems to do it
12:47 * egonw is booting a third Eclipse instance
12:56 egonw and another missed fika :(
12:56 jonalv egonw: we have more important things to do
12:58 * masak boycotts fika
12:58 * egonw is exiting his buckminster workspace
12:58 egonw SVN it too slow
12:58 egonw svn keeps changing
12:58 masak and olass went away, so we cannot nag him any more. :/
12:59 egonw so inthe middle of a run, net.bioclipse.managers dissappaers
12:59 jonalv he is still in #farmbio ;)
12:59 masak jonalv: I noticed. :)
12:59 masak jonalv: on 3? 1..2..
13:01 egonw jonalv: did you also update [managers|recording].tests ?
13:01 masak "The programmers are at the gate! They demand git!"
13:01 jonalv egonw: nope
13:01 jonalv egonw: sry..
13:01 CIA-40 bioclipse: jonalv * r10558 /bioclipse2/trunk/plugins/net.biocl​ipse.cdk.jchempaint/src/net/bioclip​se/cdk/jchempaint/Activator.java: corrected error message. The jchempaint manager is hardly an "example manager"
13:01 jonalv egonw: I am trying to get things to work first and cleaning up later...
13:01 egonw no worries... just wondering :)
13:02 jonalv although my last commit might have been a cleanup... :)
13:03 egonw oh no
13:06 egonw (git-svn)-- for not removing empty folders
13:06 CIA-40 bioclipse: egonw * r10559 /bioclipse2/trunk/plugins/ne​t.bioclipse.inchi.business/: Removed empty folders
13:08 * masak is checking out Bioclipse using git-svn on Windows
13:08 masak @ask olass git?
13:08 zarah Consider it noted.
13:12 egonw who made balloon part of the bioclipse product?
13:13 jonalv egonw: it should be I think...
13:13 egonw really?
13:13 egonw ok
13:13 jonalv I am not sure but it ws there in the latest release...
13:14 jonalv you will have to ask olass about it...
13:14 masak I was surprised too.
13:14 masak when he has finished installing git...
13:14 edrin egonw: so i better do not chekout?
13:14 edrin what is the current status?
13:15 edrin i am very occupied today, can work a little bit on bc tonight only
13:15 egonw no, just upgrade to the commit with the version changes
13:15 edrin egonw: so i just update "all" my plugins later?
13:16 edrin egonw: build is working for you now again?
13:16 egonw exporting is
13:17 edrin yes
13:17 edrin ok, so everything is good now!?
13:17 egonw initialization of NWO managers not
13:17 egonw no, not yet
13:17 edrin so i better do not update?
13:17 egonw [15:15:13] <egonw> no, just upgrade to the commit with the version changes
13:18 edrin can you mail me how to do this in eclipse?
13:18 egonw jonalv:
13:18 egonw INFO - Bioclipse manager: js added to Javascript environment.
13:18 egonw INFO - Bioclipse manager: ui added to Javascript environment.
13:18 edrin i must go to student course now
13:18 egonw jonalv: that seems to work
13:18 egonw edrin: ok
13:18 egonw talk to you later
13:18 jonalv egonw: yes...
13:18 edrin ok
13:20 jonalv egonw: The instance data location has not been specified yet., can you help?
13:20 egonw yes
13:20 CIA-40 bioclipse: egonw * r10560 /bioclipse2/trunk/plugins/net.biocl​ipse.cdk.jchempaint/src/net/bioclip​se/cdk/jchempaint/Activator.java: Removed unused imports
13:21 olass joined #bioclipse
13:21 olass hi
13:21 zarah ni hao olass
13:21 zarah olass: You have new messages. Write '/msg zarah @messages' to read them.
13:21 olass oh no
13:22 * olass has a feeling what awaits him
13:22 olass zarah: clear all messages from jonalv
13:22 zarah olass: Messages cleared.
13:22 olass hah
13:22 olass jonalv: got you
13:23 masak :)
13:24 maclean joined #bioclipse
14:16 rojasm is the plugin net.bioclipse.managers eleminated?
14:16 rojasm it is empty
14:18 rojasm and there are still a lot of classes which depends of him. I guess
14:22 rojasm ooh
14:22 rojasm I see now
14:22 rojasm marged to core
14:23 rojasm but there are a lot plugins looking for the managers plugin
14:23 jonalv rojasm: update
14:24 jonalv yes, it was removed
14:24 rojasm jonalv: but I found a lot of plugins still depending of him
14:24 rojasm and they are not updated
14:25 masak rojasm: jonalv asks 'which one?'
14:26 rojasm I think more of 20. I tried to copy the list
14:27 rojasm but I think there was a similar problem with cdk. Before submiting something test if there are some errors for other plugins!
14:27 rojasm I know it can be hard
14:28 rojasm And I don't know who has the responsibility of that
14:29 jonalv me is egon
14:29 jonalv have you run set target platform again
14:29 jonalv did you also note the folder name change of the inchi plugin
14:29 jonalv which was incorrect_
14:29 jonalv you may have the inchi plugin closed in your workspace now
14:29 jonalv can you check
14:31 rojasm It is not close. Looks fine. The problems is with the MANIFEST.MF it contains the net.bioclipse.managers bundle
14:31 rojasm is = are
14:33 * rojasm trying to clean and refresh all again
14:33 jonalv http://bioclipse.svn.sourceforge.net/viewvc/biocli​pse/bioclipse2/trunk/plugins/net.bioclipse.inchi/M​ETA-INF/MANIFEST.MF?revision=10555&amp;view=markup
14:33 zarah jonalv's link is also http://tinyurl.com/ozdtmu
14:34 jonalv rojasm
14:34 jonalv that URL indicates the manifest does not refer to managers anymore
14:36 rojasm Plugins which I see it still contains the dependences. cdk,
14:36 rojasm cml
14:36 rojasm gist
14:37 rojasm jmol
14:37 rojasm qsar
14:37 rojasm but maybe it is failing my updating process
14:38 rojasm I try again
14:41 rojasm sorry. I see that in my laptop is all correct!
14:41 rojasm I don't know what is happening with the Desktop machine
14:53 rojasm sorry jonalv. I was my mistake. Still I have the problem that my desktop computer doesn't recognize the svn is different
14:56 CIA-40 bioclipse: jonalv * r10561 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.jchempaint/src/net/bioclipse/cdk/jchempain​t/business/JChemPaintManagerFactory.java: use JavaScript flavor instead of Java flavored manager
14:57 CIA-40 bioclipse: jonalv * r10562 /bioclipse2/trunk/externals/org.xmlcml.cmlxom/ (7 files in 6 dirs): gave unique name to Activator in org.xmlcml.cmlxom to not give classpath conflicts in net.bioclipse.cml
14:58 CIA-40 bioclipse: jonalv * r10563 /bioclipse2/trunk/plugins/ (8 files in 4 dirs):
14:58 CIA-40 bioclipse: moved pick workspacedialog to ui plugin because that's where it's needed for setting up the workspace before depending code is run.
14:58 CIA-40 bioclipse: Also moved Spring extender starting code from ui to core to no success... :(
15:00 masak rojasm: if you update with an SVN tool external to Eclipse, you need to refresh the workspace with F5 before continuing work in Eclipse.
15:09 rojasm I was using full eclipse. But I realize that I need to go the svn perspective and make a refresh directly svn repository. With F5 was not working.
15:09 rojasm I can remember that before it was enough with F5
15:09 rojasm mmm
15:10 masak it's been a while since I used SVN from within Eclipse.
15:30 edrin what is the status? everything working again?
15:47 edrin egonw: what is the current strategy to get stuff working again?
15:48 egonw no fix yet
15:48 egonw :(
15:48 egonw bloody intelligent loading of things
15:50 masak software--
15:51 edrin egonw: please mail me what must be done to "update the version number"
16:00 egonw I don't know
16:00 egonw I just don't know any more
16:02 egonw edrin: one thing you could help me very much with, is zip up your workspace
16:02 egonw you use to make exports
16:02 CIA-40 bioclipse: egonw * r10564 /bioclipse2/branches/bioclipse-xmpp/: Removed old branch
16:04 egonw edrin:
16:04 egonw use the bioclipse-xmpp
16:04 CIA-40 bioclipse: egonw * r10565 /bioclipse2/branches/bioclipse-xmpp/: Branch for XMPP export
16:04 egonw branch
16:04 shk3 edrin: could not test your gist yesterday since I have no xmpp account
16:07 egonw [18:04:15] <egonw> use the bioclipse-xmpp
16:07 egonw [18:04:16] <CIA-40> bioclipse: egonw * r10565 /bioclipse2/branches/bioclipse-xmpp/: Branch for XMPP export
16:07 egonw need to go now
16:07 rojasm sorry one question more:
16:07 rojasm I get this error when I try to create a new data fro Bioclipse
16:07 rojasm ERROR - Failed to get a service: Plug-in "net.bioclipse.cdk.qsar" was unable to execute setInitializationData on an instance of "net.bioclipse.cdk.business.CDKManagerFactory".
16:07 edrin shk3: ok
16:07 edrin egonw: ?
16:07 egonw rojasm: yeah, everyone has...
16:07 rojasm ups
16:07 egonw rojasm: hang on
16:07 rojasm ok
16:08 edrin you want me to transmit my whole workspace as zip to you`?
16:09 egonw please put it on pele /tmp
16:09 egonw and send me an email when finished
16:10 egonw would be very much appreciated
16:10 edrin uh... this will be some gigabyte!?
16:10 edrin i cantry
16:10 egonw you being the only one who seem to be able to do an export
16:10 egonw rojasm: I'm reverting earlier attempts to get export working again
16:10 egonw will be 4 commits
16:11 CIA-40 bioclipse: egonw * r10566 /bioclipse2/trunk/plugins/ (8 files in 4 dirs):
16:11 CIA-40 bioclipse: Revert "moved pick workspacedialog to ui plugin because that's where it's needed for setting up the workspace before depending code is run."
16:11 CIA-40 bioclipse: This reverts commit 0506f9c13372f652d783f7d6449fcf7adafdfdd1.
16:11 edrin so export works now ?
16:11 egonw that should give you a workspace where the managers should run again
16:11 egonw but nothing else done
16:11 egonw seems to be a loose-loose situation
16:11 edrin either manager or workspace?
16:11 edrin err
16:11 CIA-40 bioclipse: egonw * r10567 /bioclipse2/trunk/plugins/ (10 files in 6 dirs):
16:11 CIA-40 bioclipse: Revert "removed remains of net.bioclipse.managers and net.bioclipse.recording plugins."
16:11 CIA-40 bioclipse: This reverts commit ff3cab1c8c3bd892d33ab07dcfe6ed81520f75b5.
16:11 edrin or export?
16:12 CIA-40 bioclipse: shk3 * r10568 /bioclipse2/trunk/plugins/net.biocli​pse.seneca/src/net/bioclipse/seneca/ (5 files in 4 dirs): input of dept info is now via the ui
16:13 CIA-40 bioclipse: shk3 * r10569 /bioclipse2/trunk/plugins/net.bio​clipse.data.seneca/data/example2/ (data.cml example.sjs): updated example to work with current seneca
16:13 CIA-40 bioclipse: egonw * r10570 /bioclipse2/trunk/ (41 files in 7 dirs):
16:13 CIA-40 bioclipse: Revert "merged net.bioclipse.recording into net.bioclipse.core"
16:13 CIA-40 bioclipse: This reverts commit b7d6efdf05ccf009df2f4ccfbc06499faede9c3e.
16:14 edrin egonw: for the build/export and version number stuff...
16:14 edrin egonw: do i have to update them?
16:17 edrin egonw: currently zipping the stuff
16:40 egonw edrin: update what?
16:40 egonw edrin: use the branch
16:41 edrin egonw: i thought i should use the current trunk
16:42 egonw that branch is the current trunk
16:42 egonw see my earlier commits
16:42 edrin !? so the nwo is removed!?
16:42 egonw [18:02:09] <CIA-40> bioclipse: egonw * r10564 /bioclipse2/branches/bioclipse-xmpp/: Removed old branch
16:42 egonw [18:04:10] <egonw> edrin:
16:42 egonw [18:04:15] <egonw> use the bioclipse-xmpp
16:42 egonw [18:04:16] <CIA-40> bioclipse: egonw * r10565 /bioclipse2/branches/bioclipse-xmpp/: Branch for XMPP export
16:42 egonw last commt message could have been clearer, indeed
16:42 egonw but maed a new brnach
16:42 edrin egonw: but my xws4j is adapted to nwo now
16:42 egonw no, the nwo is not removed
16:43 egonw where did I say that?
16:43 egonw the current r10565 is a branch from trunk just after olass submitted his version change patches
16:44 egonw http://bioclipse.svn.sourceforge.net/view​vc/bioclipse?view=rev&amp;revision=10565
16:44 zarah egonw's link is also http://tinyurl.com/p93eun
16:44 egonw it says:
16:44 egonw Directorybioclipse2/branches/bioclipse-xmpp/
16:44 egonw (Copied from bioclipse2/trunk, r10550)
16:46 edrin egonw: hm... but do i have to checkout all this again now?
16:46 edrin the whole workspace!?
16:46 egonw there are other options
16:47 egonw but nothing I can easily do
16:47 CIA-40 bioclipse: egonw * r10571 /bioclipse2/trunk/ (109 files in 84 dirs):
16:47 CIA-40 bioclipse: Revert "merged net.bioclipse.managers into net.bioclipse.core"
16:47 CIA-40 bioclipse: This reverts commit 077bd9bb8a678b9ed29a9ddfb1748625c403a12f.
16:47 egonw if you were using git, it was easy enough
16:47 egonw OK, trunk is now back to where:
16:47 egonw 1. NWO in place
16:47 egonw 2. export does not work (except for edrin)
16:48 egonw 3. managers work
16:48 egonw well, it should...
16:49 egonw if you already removed .managers and .recording from your workspace, you can savely add it again
16:49 egonw what a bumpy ride it is...
16:49 egonw spring--
16:49 egonw osgi--
16:49 egonw (spring+osgi)--
16:49 egonw (spring+osgi)--
16:49 egonw (spring+osgi)--
16:49 zarah (spring+osgi)--
16:49 egonw zarah: thank you for being so considerate
16:49 zarah egonw: you're welcome.
16:50 egonw edrin: well, you could also use current trunk
16:50 egonw which should be about the same as the current bioclipse-xmpp
16:53 edrin egonw:  ok then i will do this
17:27 edrin left #bioclipse
17:52 rojasm joined #bioclipse
17:58 egonw joined #bioclipse
18:41 edrin joined #bioclipse
18:53 edrin egonw: it says: net.bioclipse.inchi -r HEAD --force
18:53 edrin Invalid filesystem path syntax
18:53 edrin svn: Target path does not exist
18:53 edrin where is inchi now?
18:55 edrin egonw does my workspace export for you?
18:58 egonw in plugins/net.bioclipse.inchi
18:58 egonw previously, the folder was named net.bioclipse.inchi.business
18:58 egonw while the plugin was already named .inchi
18:59 egonw bbl
19:01 edrin @pz 1070
19:01 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1070
19:04 edrin egonw: i now updated my workspace but in bioclipse.product it is still 2.0.0.B20090515
19:04 edrin ah, in the others it is not
19:04 edrin will just adapt
19:05 jonalv joined #bioclipse
19:07 edrin well, my export now created a strange very small biclipse... when i run it a small window pops up and shows me diverese parameters...
19:07 edrin what is this now!?
19:08 edrin and i cannot start stuff anymore...
19:08 edrin jonalv what was now done to the trunk?
19:09 jonalv edrin: what wasn't? :/
19:10 edrin jonalv: what do you mean?
19:10 edrin jonalv how to start bc in eclipse now?
19:11 jonalv edrin: there is a mail about htat on the lsit
19:11 jonalv edrin: read that and give me 5 min
19:12 jonalv egonw: have you been doing stuff lately?
19:14 jonalv egonw: ping
19:16 edrin jonalv: what will you do in these 5 minutes?
19:17 edrin jonalv: the manifest of net.bioclipse.core gives me an error: Manifest has no main section
19:18 jonalv edrin: egonw has reverted my patches
19:18 jonalv edrin: I had everythig working here but I can not commit because my patches are reverted
19:18 jonalv egonw: ping
19:18 jonalv where is he?
19:21 edrin jonalv: he said:
19:21 edrin [20:59] <egonw> bbl
19:21 jonalv okey I don't know how to fix this with git-svn
19:21 jonalv I don't know enogh
19:21 jonalv i ahven't eaten since lunch... :(
19:21 jonalv I am leaving now
19:22 jonalv Ican not help you
19:22 jonalv I can't even get things to run myself for the moment
19:22 edrin jonalv: oh?
19:22 edrin jonalv didnt you say: [21:18] <jonalv> edrin: I had everythig working here but I can not commit because my patches are reverted
19:23 jonalv zarah: tell egonw In order to get things to work here is what you do: Recommit my pathces that you reverted. Move net.bioclipse.core/META-INF​/spring/spring/context.xml into ../managers.xml. Done. cya tomorrow
19:23 zarah Consider it noted.
19:24 jonalv edrin: yes I said. But I don't know how to revert two reverted patches using git-svn and I am not planning to learn right now since clearly egonw knows...
19:24 jonalv cya
19:25 edrin egonw!
19:25 edrin I want to build
19:27 edrin ok, it's time to play some quake
19:33 olass joined #bioclipse
19:33 edrin olass:
19:33 olass hi
19:33 zarah ni hao olass
19:33 edrin hi
19:33 edrin [21:17] <jonalv> edrin: egonw has reverted my patches
19:33 edrin [21:18] <jonalv> edrin: I had everythig working here but I can not commit because my patches are reverted
19:33 zarah privet edrin
19:33 edrin [21:23] <jonalv> zarah: tell egonw In order to get things to work here is what you do: Recommit my pathces that you reverted. Move net.bioclipse.core/META-INF​/spring/spring/context.xml into ../managers.xml. Done. cya tomorrow
19:34 edrin olass: currently i cant build since the current svn seams to be broken...
19:34 edrin i can neither run bc
19:34 olass @tell jonalv jonalv++ //for solving the exporting
19:34 zarah Consider it noted.
19:34 olass egonw: around?
19:34 edrin nor does the export create a bc but only a tiny strange msg box program
19:35 * edrin plays quake till egon returns
19:35 olass edrin: you have to wait until egonw fixes things
19:35 olass lol
19:40 olass joined #bioclipse
19:56 * egonw is briefly back
19:57 edrin egonw: long enough to do the things jonalv suggested?
19:57 olass egonw: please...
19:57 egonw perhaps
19:57 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
19:57 egonw trying
19:57 egonw so if you would not disturb me :)
19:57 * olass will not disturb egonw
19:58 edrin me also
20:00 egonw setting target platform
20:01 egonw ...
20:03 egonw confirmed, export working, running working...
20:03 egonw cdk.fromSMILES("CCC") *not* working
20:04 egonw NullPointerException
20:04 egonw need advice...
20:04 egonw commit or not?
20:05 edrin commit
20:05 edrin since nothing does start up here at all
20:05 egonw are you sure?
20:06 egonw it will not lead to a working bioclipse...
20:06 edrin testing
20:06 egonw there is one more thing to fix
20:06 egonw olass: ping
20:06 edrin let me test
20:08 egonw OK, will be back in 10 minutes
20:08 edrin egonw
20:08 edrin if i try to start now i get
20:09 edrin http://de.pastebin.ca/1427793
20:10 edrin ah
20:10 edrin there is a new prodcut
20:10 edrin testing this
20:10 edrin seems to start
20:12 edrin now testing with xws4j features
20:12 edrin seems to work
20:12 edrin now trying export
20:13 edrin Problem during export: cycle... will clean manifest now...
20:14 egonw back
20:14 egonw olass: ping
20:17 edrin egonw: what is a net.bioclipse.baloon_feature? why do i need this?
20:18 egonw edrin: best to make a xmpp feature...
20:18 egonw net.bioclipse.xmpp.platform_feature
20:18 egonw to be precise
20:18 edrin egonw: ehm, i did not add this feature...
20:19 egonw edrin: balloon is part of the BC2 release
20:19 egonw been for a while
20:19 edrin but
20:19 edrin it is not in my workspace
20:19 edrin nor can i find a file in the workspace that links to it
20:19 edrin but when i try to export it asks for it
20:20 egonw it's listed in the net.bioclipse.platform_feature
20:20 edrin can i remove it?
20:20 egonw [22:18:25] <egonw> edrin: best to make a xmpp feature...
20:20 egonw [22:18:39] <egonw> net.bioclipse.xmpp.platform_feature
20:20 edrin egonw: does this already exist?
20:21 egonw no, but I can do that in minutes...
20:21 edrin egonw: i dont understand
20:21 edrin ok, then do this :)
20:21 egonw did you read Ola's email of this afternoon on -devel ?
20:21 edrin yes, sort of
20:21 egonw well, that explains things
20:21 edrin maybe not carefully enough?
20:22 edrin i downlaoded this thing
20:22 edrin and run from it and not from ui product (since uiproduct does not run)
20:22 edrin egonw: ok what should i do now?
20:22 edrin can you create this feature?
20:22 egonw what did you download?
20:22 egonw yes, will do...
20:23 edrin i downloaded platform_feature
20:23 egonw you can locally remove the balloon from the feature.xml in the folder
20:23 egonw so that you can proceed
20:24 edrin ok, so i do not need the xmpp platform feature ?
20:25 edrin ok, done, added chemoinformatics, xmpp and hivpred
20:25 egonw good
20:25 edrin and core
20:25 egonw the xmpp feature will formalize the bundle
20:26 edrin trying to build
20:26 edrin it now says 26%
20:26 edrin is this good?
20:26 edrin how far did you get?
20:27 egonw build -> export ?
20:27 egonw it takes time
20:27 edrin yes
20:27 edrin but did it break before or after this?
20:28 egonw much before
20:28 egonw within seconds
20:28 edrin ok
20:28 edrin so looks good
20:28 egonw not while exporting
20:28 egonw but while checking things
20:28 edrin i removed this from manifest btw:
20:28 edrin org.springframework.bundle.osgi.​extender;bundle-version="1.0.2"
20:28 edrin but that's all
20:29 egonw that might not be a good idea
20:29 edrin egonw: does my workspace export for you?
20:29 egonw depending on which bundle you removed it from
20:29 egonw did not try
20:29 egonw trunk is now exporting again
20:29 egonw well...
20:29 egonw with the patches that are now being submitted
20:29 edrin i removed it from bc.ui
20:29 egonw btw, please do not commit anything right now
20:29 edrin no
20:29 edrin ok
20:30 egonw yes, it is crucial there
20:30 edrin why crucial?
20:30 edrin the build strats up very well
20:30 olass egonw: please do not call new features platform
20:31 edrin + the script runs
20:31 olass Bioclipse is the platform
20:31 egonw olass: ummm... things with .products should not be platforms?
20:31 egonw ic
20:31 egonw ok
20:31 olass definitely not
20:31 edrin egonw: do you hear me? the export starts
20:31 egonw so, something with a speclipse.product would be called, what?
20:31 egonw edrin: why?
20:31 olass speclipse feature?
20:31 egonw edrin: from master?
20:32 edrin so why is this spring crucial there?
20:32 egonw edrin: without the fixes for export, happy with your export?
20:32 edrin yes
20:32 egonw ok
20:32 olass egonw: does thinkgs work again?
20:32 egonw well, if that works for you and the builds for us, I guess it is fine
20:32 olass how much works and how much does not?
20:32 egonw olass: yes
20:32 edrin you did not commit the "fixes" for export so i cannot test
20:32 egonw not flawlessly
20:32 egonw a few issues
20:32 olass which?
20:32 egonw but managers work, and exporting works
20:32 egonw ummm...
20:32 egonw 1086
20:33 edrin no
20:33 egonw and a stacktrace about something being locked
20:33 egonw olass: btw, please don't commit anything right now
20:33 egonw or anyone for that matter
20:33 olass ok
20:33 edrin egonw: you did locally the changes jonalv suggested but you did not commit them, they killed your managers
20:33 olass can I check out trunk?
20:33 CIA-40 bioclipse: egonw * r10572 /bioclipse2/trunk/ (109 files in 84 dirs):
20:33 CIA-40 bioclipse: merged net.bioclipse.managers into net.bioclipse.core
20:33 CIA-40 bioclipse: From: jonalv <jonalv@fcb5ba71-d80d-0410-8237-ba3920747fcc>
20:33 egonw my SVN is trying to make a series of commits
20:33 egonw no, not yet
20:33 egonw hang on...
20:33 egonw it's some 5-6 commits
20:34 olass ping me when I can updates
20:34 olass ok
20:34 edrin egonw: if you say the managers do not work i better no not checout
20:34 edrin should i now export with current?
20:34 edrin i have here?
20:34 edrin or wait for egons committs?
20:34 olass wait
20:35 edrin but it's working
20:35 edrin maybe it's not afterwards
20:35 egonw edrin: then why are you using trunk, and not the branch I created?
20:35 olass edrin: you think very short now...
20:35 egonw if you wait, the export will have the minor issues
20:35 CIA-40 bioclipse: egonw * r10573 /bioclipse2/trunk/ (41 files in 7 dirs):
20:35 CIA-40 bioclipse: merged net.bioclipse.recording into net.bioclipse.core
20:35 CIA-40 bioclipse: From: jonalv <jonalv@fcb5ba71-d80d-0410-8237-ba3920747fcc>
20:35 edrin olass: egon said:
20:35 edrin [22:04] <egonw> commit or not?
20:35 edrin [22:05] <edrin> commit
20:35 edrin [22:05] <edrin> since nothing does start up here at all
20:35 edrin [22:05] <egonw> are you sure?
20:35 edrin [22:06] <egonw> it will not lead to a working bioclipse...
20:35 olass ok
20:35 olass then do not update then
20:36 edrin egonw: so why do you commit?
20:36 egonw that last is no longer true
20:36 egonw that had to do with recording
20:36 CIA-40 bioclipse: egonw * r10574 /bioclipse2/trunk/plugins/ (10 files in 6 dirs):
20:36 CIA-40 bioclipse: removed remains of net.bioclipse.managers and net.bioclipse.recording plugins.
20:36 CIA-40 bioclipse: From: jonalv <jonalv@fcb5ba71-d80d-0410-8237-ba3920747fcc>
20:36 egonw which we do not do yet...
20:36 egonw and commenting out a line fixed that NPE
20:36 egonw guys... please read what I write
20:36 edrin eh confusing ;)
20:36 CIA-40 bioclipse: egonw * r10575 /bioclipse2/trunk/plugins/ (8 files in 4 dirs):
20:36 CIA-40 bioclipse: moved pick workspacedialog to ui plugin because that's where it's needed for setting up the workspace before depending code is run.
20:36 CIA-40 bioclipse: Also moved Spring extender starting code from ui to core to no success... :(
20:36 CIA-40 bioclipse: From: jonalv <jonalv@fcb5ba71-d80d-0410-8237-ba3920747fcc>
20:37 egonw I think two more patches
20:37 CIA-40 bioclipse: egonw * r10576 /bioclipse2/trunk/plugins/net.b​ioclipse.core/META-INF/spring/ (managers.xml spring/context.xml):
20:37 CIA-40 bioclipse: Moved spring config file in the correct location (Jonathan's great idea! jonalv++)
20:37 CIA-40 bioclipse: From: Egon Willighagen <egon.willighagen@gmail.com>
20:37 egonw edrin: you can best use the bioclipse-xmpp branch I have set up
20:37 CIA-40 bioclipse: egonw * r10577 /bioclipse2/trunk/plugins/net.bioclipse.core/src​/net/bioclipse/recording/WrapInProxyAdvice.java:
20:37 CIA-40 bioclipse: Disabled recording right now, as it is giving NullPointerExceptions for me (see #1086)
20:37 CIA-40 bioclipse: From: Egon Willighagen <egon.willighagen@gmail.com>
20:37 egonw OK, that should do it
20:38 olass so I can update now?
20:38 egonw but I would not suggest this for bioclipse-xmpp
20:38 edrin better not chekout a new workspace branch
20:38 egonw olass: yes, you can
20:38 edrin why not?
20:38 egonw edrin: because it has a new set up
20:38 egonw with minor issues
20:38 olass edrin: does all gists work in your export?
20:38 edrin egonw: so i build with the thing *before* your current commits?
20:38 egonw and maybe major which we have not seen yet
20:39 egonw edrin: ummm.... one more time:
20:39 olass I say we submit the xmpp paper if we can get a release where all gists work
20:39 edrin olass: i think so, too
20:39 egonw best to use the bioclipse-xmpp branch
20:39 olass lets do it then
20:39 edrin olass: i am optimistic that the current checkout i have here works
20:39 edrin egonw: my current checkout works
20:41 * egonw needs sleep
20:41 egonw trunk seems fine
20:41 egonw but much untested
20:42 egonw r10577 that is
20:42 edrin egonw: yes
20:42 edrin hm
20:42 edrin egonw so far all cheat sheet gists work
20:43 edrin olass, egonw: you are fine with the current version number?
20:44 egonw yes, fine with me
20:44 egonw I see problems with r10577 with the navigator
20:44 * edrin still waits fo the blast gist to finish
20:44 edrin there it is
20:44 edrin navigator?
20:44 edrin r10577: is this mine!?
20:46 olass egonw: navigator? what problems?
20:46 egonw seems to need a kick in the ass
20:46 egonw /Virtual does not always show up
20:46 edrin here it showed up
20:46 edrin hivpred gist worked too
20:47 egonw seems pretty OK
20:47 * egonw is really happy NWO *and* export is now working
20:47 egonw OK, got to get sleep
20:47 edrin hivpred plugin works too
20:47 egonw nothing else I can do right now
20:47 edrin egonw: test my builds?
20:48 edrin in ~ 1 h
20:48 egonw sorry... too tired
20:48 edrin hehe
20:48 edrin ;)
20:48 egonw too little sleep last nite
20:48 egonw I'm positive it works for me if it works for you
20:48 egonw we have done enough testing in that respect
20:48 edrin good
20:48 edrin will build and upload
20:49 egonw I'll test the bundle tomorrow anyway
20:49 egonw don't expect trouble
20:49 edrin tomorrow hopfully last testing
20:49 olass egonw: one question
20:49 olass is managers and recording plugins gone now?
20:49 egonw but in case it does not work, it is not send to reviewers at that time anyway
20:49 olass can I delete them here?
20:49 egonw olass: positive on the first one
20:49 olass which?
20:49 egonw and recording is gone too I think
20:49 egonw olass: best to check on the SF SVN HTML frontend
20:49 egonw then you can make sure
20:50 egonw which first one?
20:50 egonw the first of the first first
20:50 edrin ok, i now build again
20:50 olass egonw: what about net.bioclipse.inchi?
20:50 olass what has happened?
20:50 egonw http://en.wikipedia.org/wiki/Buffalo_buffalo_B​uffalo_buffalo_buffalo_buffalo_Buffalo_buffalo
20:50 zarah egonw's link is also http://tinyurl.com/zsxl4
20:50 olass I cannot update
20:51 egonw olass: see my commit about it
20:51 olass which revision?
20:51 egonw folder name was still net.bioclipse.inchi.business
20:51 egonw giving trouble with buckminster
20:51 olass what for?
20:51 olass why add business?
20:51 olass seems very strange...
20:51 egonw check commit
20:51 egonw then you understand
20:51 olass you don't remember?
20:51 egonw (I hope)
20:51 olass ok
20:51 egonw sure I do
20:52 egonw just too lazy to read out loud what the commit says
20:52 edrin hm
20:52 egonw olass: commit 10551
20:52 edrin i like spok commits
20:53 egonw I like to be rich
20:53 olass spok?
20:53 egonw OK, really need to go now
20:53 olass ok
20:53 olass cu tomorrow
20:53 olass good job
20:53 egonw you're both all set now?
20:53 olass not yet
20:53 egonw yeah, jonalv++
20:53 olass checking out new inchi
20:53 egonw jonalv++
20:53 egonw jonalv++
20:53 edrin what is the set of meaning?
20:53 olass jonalv++
20:54 egonw (three cheers)
20:54 olass egonw: what was the error?
20:54 edrin ok
20:54 edrin jonalv++
20:54 egonw olass: about what?
20:54 egonw that inchi folder commit?
20:54 olass that jonalv++ fixed?
20:55 egonw olass: check commit r10576
20:55 egonw a spring config file in the wrong location
20:55 egonw ok, sleep well, cu tomorrow
20:55 CIA-40 bioclipse: lc69 * r10578 /bioclipse2/trunk/plugins/net.bioclip​se.ds.signsig.bursi/src/net/bioclipse​/ds/signsig/bursi/SignSIcRunner.java: Checking in a preliminary prototype. It needs restructuring and removal of a lot of print statements.
20:55 egonw @tell jonalv I applied his suggestions, and that they worked! jonalv++
20:55 zarah Consider it noted.
20:56 * egonw is happy to see that lc69 continues working as if nothing happened in the last few days :)
20:56 egonw beer in Uppsala in Thu afternoon
20:56 egonw bye!
20:59 olass egonw: will you work at bmc thursday?
20:59 olass I will
20:59 olass bye!
20:59 edrin :)
21:00 edrin me cant
21:00 olass edrin: sad to hear
21:00 * olass will grab a beer for edrin too
21:00 olass ok, need to sign off too
21:00 olass see you tomorrow
21:00 olass bye
21:01 edrin ciao
21:36 CIA-40 bioclipse: miguelrojasch * r10579 /bioclipse2/trunk/plugins/net.bioclipse.re​action/src/net/bioclipse/reaction/editor/ (ReactMolDrawingComposite.java ReactionEditor.java): Implement synchronization between boxes and JCP
21:44 olass joined #bioclipse
21:46 CIA-40 bioclipse: miguelrojasch * r10580 /bioclipse2/trunk/plugins/net.biocl​ipse.reaction/src/net/bioclipse/rea​ction/layout/HierarchicLayer.java: Difference in dimension between boxes for width and height
21:46 edrin oh, you are back
21:46 olass not really, will go to bed now
21:46 olass rally really tired
21:46 edrin ok
21:47 edrin good night
21:50 olass good night
21:58 CIA-40 bioclipse: lc69 * r10581 /bioclipse2/trunk/plugins/net.bioclip​se.ds.signsig.bursi/src/net/bioclipse​/ds/signsig/bursi/SignSIcRunner.java: Cleared a couple of lists and hashmaps that grow too much.
22:14 CIA-40 bioclipse: miguelrojasch * r10582 /bioclipse2/trunk/plugins/net.bioclips​e.reaction/src/net/bioclipse/reaction/ (2 files in 2 dirs): Removed scaled coordinates for reactions. The File should have already the corrected coordinates.
22:52 CIA-40 bioclipse: miguelrojasch * r10583 /bioclipse2/trunk/plugins/net.biocl​ipse.reaction/META-INF/MANIFEST.MF: added needed bundle
23:06 CIA-40 bioclipse: lc69 * r10584 /bioclipse2/trunk/plugins/net.bioclip​se.ds.signsig.bursi/src/net/bioclipse​/ds/signsig/bursi/SignSIcRunner.java: This is a working version except that the color is the same regardless of the prediction. The code still needs restructuring, comments etc.

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