Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-10-02

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All times shown according to UTC.

Time Nick Message
03:13 mgerlich joined #bioclipse
05:45 egonw joined #bioclipse
06:57 olass joined #bioclipse
06:57 olass moin
06:57 zarah hi olass
06:58 olass egonw: did everything go well with updating to new cdk?
06:58 egonw sort of...
06:58 egonw there are the few compile errors that need resolving
07:02 Gpox joined #bioclipse
07:10 egonw Gpox: I have updated the CDK export
07:10 egonw did not encounter problems with cdk-eclipse
07:10 egonw Gpox: but there are some code updates needed
07:10 egonw can you have a look at those?
07:14 olass Gpox: would be nice if you could resolve them asap, I want to try to build
07:14 olass egonw: we need to update id's for devel build, and also to branch
07:14 olass egonw: how about calling the branch 2.2.x?
07:15 olass let's do the branch after the build is successful, shall we?
07:15 egonw yes, sounds good
07:15 egonw both
07:17 olass we should set the ID for all plugins and features in master to 2.1.1.v20091002
07:18 olass egonw: sounds ok?
07:18 CIA-51 bioclipse.cheminformatics: Egon Willighagen master * rc527094 / plugins/net.bioclipse.jmol/jars/Jmol.jar : Updated to the bug fix release 11.8.7 - http://bit.ly/1747qm
07:18 egonw yes, sounds OK
07:19 Gpox egonw: there is no problem just running the ant export on cdk-eclipse, no compilation takes place it is all source
07:19 egonw I know that, I wrote that code :)
07:19 Gpox is is when building it stand alone there is problems
07:19 egonw ok
07:20 egonw the compile issues I am talking about are updates needed in the bioclipse wrapping code
07:20 egonw for JCP
07:20 Gpox but it doesn't matter I font out why jchempaint-primary did not compile
07:20 egonw I tried it again, and it compiled fine for me
07:22 Gpox well when doing dist-all on jchempaint-primary i got error related to missing cdk-annotations.jarr in *.cdkdepends for the new control and render modules
07:22 egonw oh...
07:22 egonw that should have showed up for me too...
07:25 Gpox it was an exception in javac for the annotation stuff, maybe it is different in the compiler for linux and mac
07:25 egonw possibly
07:26 egonw please do file such things as bug reports
07:42 Gpox egonw: i am missing bundle org.openscience.cdk.annotation
07:42 egonw that's in bioclipse.core
07:44 Gpox of course...
07:53 egonw but it is missing there then?
07:53 Gpox no, I found it
08:09 egonw ok, good
08:10 samuell joined #bioclipse
08:23 olass Gpox: if you had time to look at bug 1648 before release that'd be very much appreciated
08:25 Gpox @pz 1648
08:25 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1648
08:32 egonw olass: I noted that for the ChEMBL SD file too
08:43 * egonw will have to upgrade the firmware of his internet router
08:43 egonw I hope to be back in some 15 minutes
08:52 egonw joined #bioclipse
08:52 egonw and I'm back
08:52 egonw hoping that my internet connection is more stable now
09:00 Gpox it seams cdk don't read in the properties for the SDfiles
09:01 egonw ok, reassign the bug to me
09:01 egonw or even file on sf.net/projects/cdk
09:01 Gpox and i get exceptions when trying to load the molopt-9634.sdf file from the js-console
09:02 egonw ok, cc me on that too
09:04 Gpox it is all in bug #1648
09:04 egonw ack
09:38 * samuell needs to reboot
09:39 egonw argh...
09:39 egonw typical friday...
09:39 egonw can't focus at all
09:40 olass egonw: you looking at 1648? or is Gpox?
09:40 olass does BC cheminfo compile?
09:40 egonw I am trying to confirm the bug in the CDK
09:41 olass ah
09:41 egonw cheminfo is not for me yet
09:41 olass ack
09:42 samuell joined #bioclipse
09:44 * samuell solved the printer problem (It was due to an embarrasing error by me)
09:45 egonw samuell++ (for being honoust)
09:45 samuell :)
09:56 egonw olass: can I share that 20mols.sdf in the CDK as LGPL for unit tests?
09:57 olass mom, need to check
09:57 olass 99% sure it's ok
09:57 egonw please check and give me that last 1%
09:58 olass hmm, will try..
10:00 egonw ummm...
10:00 egonw olass: did you check that file?
10:00 egonw I'm pretty sure no fixing will ever give props in the moltable
10:01 egonw the files does not have any!
10:01 egonw olass--
10:02 egonw Gpox:
10:02 egonw did you look at bug 1632?
10:03 egonw olass requests there to have the molecule title in the mol table too, via the prop CDKConstants.TITLE
10:03 egonw and that is actually read properly
10:07 egonw olass: what about molopt-9634.sdf ?
10:07 egonw is that LGPL sharable?
10:12 egonw olass: either way...
10:12 egonw I can confirm the NPE for that file
10:12 egonw olass: I'd very much appreciate being able to share that file...
10:12 egonw as LGPL, please let me know with 100% certainty
10:22 olass egonw: how can I be sure?
10:22 egonw did you make the file yourself?
10:22 egonw do you have copyright?
10:22 olass no
10:22 egonw then ask the source you got it from
10:22 olass will try
10:23 egonw yes, that's fine
10:43 masak joined #bioclipse
11:04 egonw Gpox: are you still working on the compile fixes?
11:04 Gpox for what?
11:04 egonw in bioclipse.cheminformatics
11:04 egonw due to the CDK/JCP-Prim update
11:10 egonw olass: which repositories do I need to version for?
11:10 egonw bioclipse.cheminformatics, sure
11:10 egonw which others?
11:10 egonw .rdf
11:10 olass well, all that you are head of...
11:10 olass joelib for example
11:10 egonw right
11:11 olass any news on the props bug?
11:11 olass a tough bastard?
11:11 egonw grep -r 2.*.v200 * | grep Bundle-Version | cut -d':' -f1 | xargs replace 2.1.0.v20090807 2.1.1.v20091002 --
11:12 egonw yes, difficult to trace down
11:12 egonw it's not in the CDK
11:12 egonw can that test file be part of cdk.business.test ?
11:13 CIA-51 bioclipse.cheminformatics: Egon Willighagen master * r1c84be4 / (17 files in 17 dirs): Dumped version number to 2.1.1.v20091002 for imminent release - http://bit.ly/3WRW1J
11:17 CIA-51 bioclipse.joelib: Egon Willighagen master * rdbb14c3 / (4 files in 3 dirs): Dumped version number to 2.1.1.v20091002 for imminent release - http://bit.ly/tPpG6
11:18 egonw oh, please also add bioclipse.social
11:20 CIA-51 bioclipse.rdf: Egon Willighagen master * rbdf99fd / (8 files in 6 dirs): Dumped version number to 2.1.1.v20091002 for imminent release - http://bit.ly/3lbRGJ
11:22 CIA-51 bioclipse.social: Egon Willighagen master * r115ef7a / (2 files): Dumped version number to 2.1.1.v20091002 for imminent release - http://bit.ly/rQbm7
11:24 olass egonw: yes it can //about the test file
11:24 egonw tack
11:24 olass sry but cannot determine origine to 100%
11:26 olass I got it from Lars at AZ
11:26 olass so will ask him
11:36 egonw Gpox: tack!
11:37 CIA-51 bioclipse.cheminformatics: jonalv master * r7d41951 / plugins/net.bioclipse.cdk.business/src/ne​t/bioclipse/cdk/domain/ICDKMolecule.java : can return null - http://bit.ly/BxPZ3
11:37 CIA-51 bioclipse.cheminformatics: Arvid Berg master * r8458bd6 / (9 files in 4 dirs): Added getAvaiableProperties() to IMoleculesEdiotrModel - http://bit.ly/X4Awy
11:37 CIA-51 bioclipse.cheminformatics: Arvid Berg master * r5fbcffe / (8 files in 5 dirs):
11:37 CIA-51 bioclipse.cheminformatics: Added setProperty to IMoleculesEditorModel to enable calculation of property
11:37 CIA-51 bioclipse.cheminformatics: Changed property calculation to take a IMoleculesEditorModel - http://bit.ly/1UG3Ew
11:37 CIA-51 bioclipse.cheminformatics: Arvid Berg master * rc275271 / (2 files in 2 dirs):
11:37 CIA-51 bioclipse.cheminformatics: Added sorting of sorting enabled IMoelcuesEditorModels
11:37 CIA-51 bioclipse.cheminformatics: Added new interface to indicate sort-ability of model - http://bit.ly/xe3hm
11:37 CIA-51 bioclipse.cheminformatics: Arvid Berg master * r80c0f41 / (2 files):
11:37 CIA-51 bioclipse.cheminformatics: Created IMoleculesEditorModel for lists, this model is sortable
11:37 CIA-51 bioclipse.cheminformatics: Also replaced two inner classes with this new model - http://bit.ly/7yWdj
11:39 CIA-51 bioclipse.cheminformatics: Ola Spjuth 2.0.x * r64d4fc0 / plugins/net.bioclipse.webservi​ces.tests/META-INF/MANIFEST.MF : Added core.resources as dep since CDK.business requires it. - http://bit.ly/3gTUE8
11:43 olass egonw: ok, so what is status after this update?
11:43 * olass will now set ID for core plugins
11:43 * egonw is booting 2.1
11:43 egonw for some rough testing
11:44 CIA-51 bioclipse.cheminformatics: Arvid Berg master * ra6459fd / (3 files in 2 dirs): Implemented IGeneratorParameter getParameters() generators in bioclipse - http://bit.ly/mFI56
11:44 CIA-51 bioclipse.cheminformatics: Arvid Berg master * r690e4f5 / (4 files in 2 dirs): Fixed errors related to stereo change in cdk - http://bit.ly/2VTvc2
11:44 CIA-51 bioclipse.cheminformatics: Arvid Berg master * r777cd19 / plugins/net.bioclipse.jmol.cdk/src/net/bioc​lipse/jmol/cdk/adapter/CdkJmolAdapter.java : Added stub for required methods from super class - http://bit.ly/4aqaHE
11:44 olass a lot is happening...
11:45 egonw Gpox: compile errors gone, but no moltable or JCP editor yet
11:45 egonw not for me...
11:45 egonw Gpox: can you confirm?
11:45 egonw or does it work for you?
11:47 CIA-51 bioclipse.core: Ola Spjuth master * rcebd0d2 / (20 files in 20 dirs): Set versions to 2.1.1.v20091002 for devel release. - http://bit.ly/28gfFk
11:48 * samuell have to go back and forth to G�vle this afternoon.... (good time for reading papers :) )
11:48 olass samuell: have a nic etrip!
11:48 samuell Thx!
11:49 egonw samuell: ack
11:49 egonw samuell: next week's plan?
11:49 Gpox egonw: i can confirm it dose not work for me either.
11:49 egonw Gpox: OK
11:49 egonw I got a NPE
11:49 egonw can you have a look at it?
11:50 samuell egonw: 1 moment...
11:50 CIA-51 bioclipse: ospjuth * r11730 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/sr​c/net/bioclipse/xws4j/DefaultClientCurator.java: Better error reporting if incorrect credentials in XMPP preferences. Also disconnect if connection fails to not leave XWS in a state wher it incorrectly thinks it is connected.
11:51 samuell egonw: I plan to finish reading up on DL vs. Prolog this weekend, and write up on it on my Blog.
11:51 samuell For next week...
11:52 samuell I might need some readup on OWL (The black book), and then I'll turn into get BLIPKIT up running, and prepare for plugin development
11:53 samuell Comments?
11:53 egonw I'd tend to suggest to start working on the plugin next week, part-time
11:53 egonw half the day reading more material, half the day working on the plugin
11:53 CIA-51 bioclipse: ospjuth * r11731 /bioclipse2/trunk/ (2 files in 2 dirs): Set version to 2.1.1.v20091002 for devel release.
11:54 samuell egonw: Well, sound like a good idea
11:54 egonw reason: there is so much stuff to read... but you must deliver in the end
11:54 egonw easy to get stuck in reading
11:54 CIA-51 bioclipse.qsar: Ola Spjuth master * rbb1f8f1 / (12 files in 12 dirs): Set version for QSAR to 2.1.1.v20091002 for devel release. - http://bit.ly/IupkJ
11:54 egonw it's a not a PhD you are doing, so I don't expect you to master each and every detail
11:56 egonw samuell: oh, and take this blog with you on the train:
11:56 egonw http://www.snee.com/bobdc.blog/200​9/10/a-rules-language-for-rdf.html
11:56 zarah egonw's link is also http://tinyurl.com/ybjb6fy
11:56 samuell egonw: Yeah, IC. Well, by reading up on DL vs Prolog I think I know better now what role Prolog has really, so I think the most important pre-readup is done.
11:56 samuell egonw: Thanks
11:56 egonw RIF was just approved as recommendation today, I think
11:57 egonw there are quite a few rule flavors, it seems :)
11:57 samuell egonw: Seems so yes :)
11:58 samuell Ok, have to disconnect now. Will read the blog.
11:58 egonw masak: that's family?
12:00 egonw samuell: have a nice weekend!
12:10 CIA-51 bioclipse.ds: Ola Spjuth master * ra08af07 / (7 files in 7 dirs): Set version to 2.1.1.v20091002 for devel release. - http://bit.ly/1KfdNw
12:11 egonw Gpox: are you looking at the run time problems iwth JCP?
12:12 CIA-51 bioclipse.balloon: Ola Spjuth master * rb78228e / (8 files in 8 dirs): Set version to 2.1.1 for devel release. - http://bit.ly/HkuJx
12:18 egonw Gpox: tack
12:19 Gpox it doesn't work for SDF, calculateBounds in Renderer can return null now and again trying to find a quick solution
12:19 egonw ok
12:19 CIA-51 bioclipse.cheminformatics: Egon Willighagen master * rcf91b9b / (2 files in 2 dirs): Added unit test confirming bug #1648 - http://bit.ly/3KMIc3
12:20 zarah bug #1648 | http://tinyurl.com/ydf4lbv
12:20 shk3 joined #bioclipse
12:25 CIA-51 bioclipse.cheminformatics: Arvid Berg master * r720afb4 / plugins/net.bioclipse.cdk.jchempain​t/src/net/bioclipse/cdk/jchempaint/​widgets/JChemPaintEditorWidget.java :
12:25 CIA-51 bioclipse.cheminformatics: Fixes NPE when opening mol files
12:25 CIA-51 bioclipse.cheminformatics: This make sure that the model is set
12:25 CIA-51 bioclipse.cheminformatics: before calculating bounds on it - http://bit.ly/4uYRzT
12:25 CIA-51 bioclipse.cheminformatics: Arvid Berg master * r50e9f65 / cdk-externals/trunk/org.openscience.​cdk.controlbasic/src/org/openscience​/cdk/controller/ControllerHub.java :
12:25 CIA-51 bioclipse.cheminformatics: Removed firing of structure changed event when changing model, pend new model changed event.
12:25 CIA-51 bioclipse.cheminformatics: Changing the model is not merely a structure change and as such should not fire a structure changed event - http://bit.ly/1lD9J
12:28 Gpox @pz 1632 egonw: cdk:Title shows up for me as a property
12:28 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1632
12:33 egonw Gpox: ack
12:40 CIA-51 bioclipse.balloon: Ola Spjuth master * r3a7ace3 / plugins/net.bioclipse.ballo​on.business/about.mappings : Updated ID in feature branding. - http://bit.ly/AfaJd
12:55 CIA-51 bioclipse.core: Ola Spjuth master * r40166ef / (3 files in 3 dirs): Set version for features to 2.1.1.v20091002. - http://bit.ly/1yl3Mq
12:58 CIA-51 bioclipse.cheminformatics: Arvid Berg master * r2e2339a / cdk-externals/trunk/org.openscience.cdk.renderext​ra/src/org/openscience/cdk/renderer/Renderer.java : Added null check to avoid NPE when no model is present - http://bit.ly/1t0r9m
12:58 egonw olass: cheminformatics is good to go
12:58 olass egonw++ Gpox++
13:02 CIA-51 bioclipse.ds: Ola Spjuth master * r652dbfb / features/net.bioclipse.ds_feature/feature.xml : Removed prel plugins not on git. - http://bit.ly/2FbhBa
13:02 olass egonw: HELP!
13:02 olass fatal: unable to create '.git/refs/remotes/origin/master.lock': File exists
13:03 olass I managed to kill git during a push..
13:03 olass how recover?
13:03 olass egonw: you know?
13:03 egonw no, but I can help google
13:03 egonw @google git lock clean
13:03 zarah egonw: http://lkml.indiana.edu/hypermai​l/linux/kernel/0710.1/2757.html
13:04 egonw no, bad hit
13:06 * olass is confused
13:06 olass rm .git/index.lock
13:06 olass seemed to do the trick.
13:06 olass Hopefully nothing is toasted by this...
13:06 olass read this on a page
13:06 * olass is scared to try it
13:07 olass seemd to work
13:07 olass git--
13:07 egonw olass++
13:07 olass :)
13:08 egonw well, you killed it half way
13:08 egonw git was never written to die gracefully
13:08 olass yes but git should give me better info how to resolve it
13:08 olass or offer a flag to override
13:10 olass egonw: I still get no props for the SDFile
13:10 egonw true
13:10 egonw that is not fixed yet
13:10 egonw not sure what is going on
13:11 egonw it's not a CDK bug
13:11 olass hmm
13:11 egonw and does work for some SD files...
13:11 egonw but not for yours
13:11 egonw and the unit test confirms that
13:11 olass Gpox: do you have any idea?
13:22 Gpox egonw: got it
13:23 Gpox in MDLV2000Reader you replaced "String data = line;" with "StringBuilder data = new StringBuilder();" thus losing the property that was in line at the time
13:24 egonw oh, fuck
13:24 Gpox comit http://github.com/egonw/bioclipse.cheminformatics​/commit/d075a6ee951afcd91e5356912102b7529fbdee15 line 267
13:24 zarah Gpox's link is also http://tinyurl.com/y9nnek6
13:24 egonw everywhere it was data = ""
13:24 egonw overlooked that there was an exception
13:25 egonw damn, and no unit test picked that up :(
13:30 masak time to write more tests!
13:30 egonw and start using emma
13:31 Gpox egonw: about comment on lie 276 we are no longer in the molfile block but in the data block thus this should applay
13:31 Gpox A [Data] value may extend over multiple lines containing up to 200 characters each. A blank line
13:31 Gpox terminates each data item.
13:31 egonw yes, it does
13:32 egonw this will all get cleaned up when a refactor out a SDFReader
13:32 egonw instead of having all in MDLV2000Reader...
13:37 egonw Gpox++
13:37 egonw for noting this stupid mistake
13:38 CIA-51 bioclipse.cheminformatics: Egon Willighagen master * r01186a2 / cdk-externals/trunk/org.openscience.cdk.io/sr​c/org/openscience/cdk/io/MDLV2000Reader.java : Fixed reading of properties - http://bit.ly/rrvqp
13:40 olass sweet
13:42 egonw I just keep rebooting Bioclipse to see it open 796MB of SD file in under one minute :)
13:46 olass not bad
13:46 egonw OK, will be offline for a while now...
13:47 egonw to do some work around the house
13:47 egonw bbl
13:55 CIA-51 bioclipse.core: Ola Spjuth master * r13fcdb6 / features/net.bioclipse.platfo​rm_feature/bioclipse.product : The product for 2.1.1 devel release. - http://bit.ly/3HHw1
13:56 * olass is doing an export for Mac OS X to test
14:01 olass looks good!
14:02 olass AARGH
14:02 olass error exporting for other platforms...
14:02 olass *grmf*
14:06 * olass is reinstalling the delta pack
14:07 CIA-51 bioclipse.core: Ola Spjuth master * ra5baac5 / features/net.bioclipse.platfo​rm_feature/bioclipse.product : Updated ID for product. Forgotten. - http://bit.ly/uV2dq
14:10 olass hmm, seems reinstalling the delta pack solved at least one issue...
14:21 olass egonw: ping
14:22 egonw pong
14:25 olass egonw: where do I get the org.mindswap.pellet plugin?
14:26 olass please add that info on the site: http://wiki.bioclipse.net/index.ph​p?title=Checking_out_Bioclipse_2.2
14:26 zarah olass's link is also http://tinyurl.com/yaxkhfy
14:33 CIA-51 bioclipse.core: Ola Spjuth master * r4bd5006 / plugins/net.bioclipse.core/src/net/bioclipse/manag​ers/business/AbstractManagerMethodDispatcher.java : Fix from jonalv++ to not run methods as BioclipseJob when interface declares IProgressMonitor. - http://bit.ly/4kpftv
14:33 CIA-51 bioclipse.core: Carl Masak master * ra3b2dae / plugins/net.bioclipse.scripting.ui/src/net/biocli​pse/scripting/ui/views/ScriptingConsoleView.java :
14:33 CIA-51 bioclipse.core: [ScriptingConsoleView] added newline after tab completion
14:33 CIA-51 bioclipse.core: Fixes #1635. - http://bit.ly/3Tw4ka
14:33 zarah bug #1635 | http://tinyurl.com/ybdvlc7
14:33 masak my commits to .core show up here.
14:34 masak my commits to .bioinformatics don't.
14:34 masak they don't show up in the commits mailing list either.
14:34 olass masak: have you added the hooks on githb?
14:34 masak no, I didn't know I had to.
14:34 olass and told egonw to turn on the CIA for that repo?
14:34 olass please do
14:35 masak the latter step I'm pretty sure I've done.
14:35 masak but how do I add hooks?
14:35 olass go to github
14:35 olass hm
14:35 olass let's see if I remember..
14:35 egonw hahaha
14:35 egonw masak++
14:35 egonw for being funny
14:35 masak :)
14:36 egonw masak: btw, tony seems to be handing out google wave accounts...
14:36 masak yeah, yeah.
14:36 egonw unless his twitter account his hijacked...
14:36 olass masak: http://www.2-clicks-swords.com/images​/image/Captain-Hook-pirate-sword.jpg
14:36 zarah olass's link is also http://tinyurl.com/y8cn3rm
14:37 masak olass: ARRR! :)
14:37 masak must be dreadful to want to scratch your ear with that thing.
14:37 olass egonw: ping
14:38 olass [16:25] < olass> egonw: where do I get the org.mindswap.pellet plugin?
14:38 olass [16:25] < olass> please add that info on the site: http://wiki.bioclipse.net/index.ph​p?title=Checking_out_Bioclipse_2.2
14:38 zarah olass's link is also http://tinyurl.com/yaxkhfy
14:38 egonw pong
14:38 egonw it's in the bioclipse.rdf repos
14:38 egonw externals
14:38 olass is it?
14:38 olass hum
14:39 olass ha, yes it is
14:39 olass but you had set its Version to 2.0.0, and it was 2.0.0rc7, and hence not picked up
14:41 egonw no, the version is 2.0.0.0rc7
14:41 olass I know
14:41 egonw which, AFAIK, should match 2.0.0
14:41 egonw not?
14:41 egonw that is
14:41 olass please change the feature do require 0.0.0 of pellet plugin
14:41 olass or 2.0.0rc7
14:41 egonw is bioclipse 2.1.1 not the same as 2.1.1.v20091002 ?
14:41 olass it did not match
14:41 olass there is a dot for the qualifier
14:41 egonw ok, where's the depends?
14:42 egonw in the feature?
14:42 olass yes
14:42 olass feature.xml
14:42 egonw what dot?
14:42 egonw the third one?
14:42 egonw I got that
14:42 olass ack
14:43 olass please update build.properties of joelib
14:43 olass there is an error there
14:43 olass it should looka like: http://paste2.org/p/448163
14:43 olass with these two fixes, all features compile
14:44 olass egonw: let me know when you have pushed these 2 issues
14:44 CIA-51 bioclipse.rdf: Egon Willighagen master * r8dc8f1e / features/net.bioclipse.pellet_feature/feature.xml : Synchronized version; apparentely 2.0.0 does not match 2.0.0.0rc7 :( - http://bit.ly/2p3ypk
14:48 egonw olass: about the net.sf.joelib/build.properties
14:48 olass yes
14:48 egonw it's just the missing itext?
14:48 olass no idea how it looked before
14:48 egonw ah, it should be like the one in the pastebin?
14:49 olass yes
14:49 egonw ah, yes
14:49 egonw you said so
14:49 olass :)
14:50 CIA-51 bioclipse.joelib: Egon Willighagen master * r68367c4 / externals/net.sourceforge.joelib/build.properties : build.properties according to Ola: fixes exporting - http://bit.ly/14yb0m
14:50 egonw sorry, missed that line
14:50 olass thx
14:51 olass egonw: ping
14:52 olass egonw: please fix dependencies for joelib.feature to 2.1.1
14:52 olass and IDs for plugins to 2.1.1
14:52 egonw <import feature="net.bioclipse.qsar_feature" version="2.1.1.v20091002" match="greaterOrEqual"/>
14:52 egonw <import feature="net.bioclipse.platform_feature" version="2.1.1.v20091002"/>
14:52 egonw <import feature="net.bioclipse.rdf_feature" version="2.1.1.v20091002"/>
14:52 egonw ?
14:53 egonw like that?
14:53 olass ah
14:53 olass super
14:53 olass or just 2.1.1
14:53 olass if you like
14:53 egonw [10/02/09 13:17] <CIA-51> bioclipse.joelib: Egon Willighagen master * rdbb14c3 / (4 files in 3 dirs): Dumped version number to 2.1.1.v20091002 for imminent release - http://bit.ly/tPpG6
14:53 egonw no, not just 2.1.1
14:53 olass ok
14:53 egonw you just said that does not match
14:53 egonw which is why I had to fix pellet
14:54 olass there is a dot in ours
14:54 * egonw is looking for the slight difference
14:54 olass that was missing for pellet
14:54 egonw there *was* in pellet
14:54 egonw that's what I have been saying
14:54 egonw 2.0.0.0rc7
14:54 egonw three dots
14:54 olass 2.0.0rc7 != 2.0.0.rc7
14:54 egonw sure
14:55 egonw where the **** did you find either?
14:55 egonw I have/had neither of the two
14:55 egonw because I have removed neither
14:55 egonw so, the problem may still exist then
14:56 olass in manifest.mf of mindswap.pellet it says: 2.0.0.0rc7
14:57 olass in feature.xml you now require this, 2.0.0.0rc7
14:57 olass repviously it said only 2.0.0 there
14:57 olass causing a mismatch
14:57 egonw yes
14:57 egonw why?
14:57 olass don't ask me
14:57 egonw [10/02/09 16:53] <olass> or just 2.1.1
14:57 egonw I don't see the diff
14:57 egonw why can I use 2.1.1 instead of 2.1.1.foo
14:57 egonw but not 2.0.0 instead of 2.0.0.foo
14:58 olass you tried 2.0.0 instead of 2.0.0foo
14:58 olass means minor is 1foo
14:58 olass not minor is 1 and qualifier is foo
14:59 olass well, it's a guess
14:59 olass I am no master of this
14:59 egonw sorry, you lost me...
14:59 egonw you're talking gibberish
14:59 olass major.minor.revision.qualifier
14:59 olass 2.0.0rc7 has no qualifier
14:59 egonw I should have used 2.0.0rc7 because the plugin has 2.0.0.0rc7 ??
14:59 olass ?
15:00 egonw there never was a 0rc7 revision
15:00 olass no?
15:00 egonw no
15:00 olass manifest.mf in mindswap.pellet says so
15:00 olass Version=2.0.0.0rc7
15:00 egonw there has only been a 0rc7 *qualifier*
15:00 olass I am looking at it now
15:00 egonw yes, that's a qualifier, not the revision
15:01 olass ah
15:01 olass right
15:01 egonw ah, phew
15:01 olass maybe I was wrong then
15:01 olass whatever
15:01 olass there was a mismatch
15:01 olass now it works
15:01 egonw that's what matter
15:01 egonw and I am happy that I am not going crazy
15:01 * olass is building the update site for new devel
15:02 olass damn, this has taken all day
15:02 olass no thesis writing today :(
15:02 olass well, I got all weekend :)
15:13 olass ok, uploading to pele will take 45 mins
15:13 * olass will go out for a while to get some fresh air
15:14 egonw thanx
15:14 egonw will base next weeks pharmbio stuff based on the release
15:14 egonw involving SMARTS and calculation of molecular descriptors
15:32 samuell joined #bioclipse
15:37 * samuell is on a (surprisingly un-shaky, but never know how long...) 3G connection in the train
15:42 egonw :)
15:42 egonw nice
16:23 samuell joined #bioclipse
19:20 egonw joined #bioclipse
21:27 egonw joined #bioclipse
21:28 samuell joined #bioclipse

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