Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-11-04

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All times shown according to UTC.

Time Nick Message
05:44 CIA-63 joined #bioclipse
06:31 egonw_ joined #bioclipse
06:32 Gpox joined #bioclipse
06:53 sneumann__ joined #bioclipse
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08:28 edrin joined #bioclipse
08:29 egonw_ joined #bioclipse
08:31 CIA-63 bioclipse.cheminformatics: Egon Willighagen 2.2.x * r6765739 / (2 files in 2 dirs): Added GUI action for calculating the RMSD distance matrix which opens in a separate editor (fixes #1664) - http://bit.ly/z0zKV
08:31 zarah bug #1664 | http://tinyurl.com/yzc98r9
08:34 olass joined #bioclipse
08:34 olass moi
08:34 olass moin
08:34 zarah saluton olass
08:34 olass moi moi
08:52 egonw_ hi olass
08:53 olass hi egonw_
08:54 egonw_ hej
08:54 egonw_ not in meeting yet?
08:54 olass yup
08:54 olass so only here briefly
08:54 egonw_ ack
08:55 olass thx for the pointers in gdoc
08:55 egonw_ yeah, finally...
08:55 olass let's write it up together after lunch
08:55 egonw_ sorry... I have been tired, and finishing too many papers :(
08:55 olass you had good points
08:55 egonw_ indeed
08:55 egonw_ I am actually working on 4+ papers right now...
08:56 egonw_ 3 of which need hard work today...
08:56 olass egonw_: please, first the blog posts..?
08:56 egonw_ yes....
08:56 egonw_ bc2 paper is highest on list right now...
08:56 egonw_ I'll try to get that third pop up working
08:57 egonw_ tricky
08:57 * olass is afk
08:57 egonw_ ack
08:57 egonw_ cu later
09:15 samuell joined #bioclipse
09:24 edrin hi
09:24 zarah oh hai edrin
10:31 olass hi edrin
10:32 edrin left #bioclipse
10:32 edrin joined #bioclipse
10:32 edrin hi
10:32 zarah privet edrin
10:32 edrin olass: did you reset the server?
10:32 olass yes, unfortunately had to
10:32 edrin what happened?
10:33 olass edrin: do you know if you can reload the config file without restarting ejabberd?
10:33 * olass will go for lunch now
10:33 edrin i dont think this is possible :/
10:33 edrin but you would have to read the ejabberd docu to be sure
10:55 egonw_ Gpox: ping
10:55 egonw_ can you help me with a generics problem?
10:55 Gpox pong
10:55 Gpox sure
11:18 masak joined #bioclipse
11:26 jonalv joined #bioclipse
11:26 jonalv oh hai
11:26 zarah saluton jonalv
11:26 * jonalv @ lunch
11:35 samuell Anybody knows where to find uu-style latex templates for stuff like degree project reports?
11:38 egonw_ I don't
11:44 egonw_ masak: did you also bump the feature versions ?
11:45 CIA-63 bioclipse.cheminformatics: Egon Willighagen 2.2.x * rb532bf3 / (2 files in 2 dirs):
11:45 CIA-63 bioclipse.cheminformatics: Added GUI action for doing an Kabsch alignment (fixes #1665).
11:45 CIA-63 bioclipse.cheminformatics: The results are saved as SD file and opened the prefered editor for
11:45 CIA-63 bioclipse.cheminformatics: 3D SD files (Jmol by default). - http://bit.ly/11EWkY
11:45 zarah bug #1665 | http://tinyurl.com/yjhpozs
11:47 egonw_ masak: I use:
11:47 egonw_ grep -r 2.1.1.v20091002 * | cut -d':' -f 1 | xargs replace 2.1.1.v20091002 2.2.0.RC1 --
11:48 CIA-63 bioclipse.cheminformatics: Egon Willighagen 2.2.x * rf81ce34 / (16 files in 16 dirs): Bumped version to 2.2.0.RC1 for the upcoming release candidate - http://bit.ly/N2HLc
11:49 CIA-63 bioclipse.social: Egon Willighagen 2.2.x * r5831960 / plugins/net.bioclipse.myexperiment/src/net/bioclip​se/myexperiment/business/MyExperimentManager.java : Fixed URL: the SPARQL results now contains the data type - http://bit.ly/19e8tF
11:49 CIA-63 bioclipse.social: Egon Willighagen 2.2.x * r219f97d / (2 files): Bumped version to 2.2.0.RC1 for the upcoming release candidate - http://bit.ly/16HxCL
11:50 CIA-63 bioclipse.rdf: Egon Willighagen 2.2.x * rc9b8443 / (11 files in 9 dirs): Bumped version to 2.2.0.RC1 for the upcoming release candidate - http://bit.ly/2hx2hi
11:51 CIA-63 bioclipse.joelib: Egon Willighagen 2.2.x * r519f288 / (5 files in 4 dirs): Bumped version to 2.2.0.RC1 for the upcoming release candidate - http://bit.ly/1nIq6M
13:10 egonw_ samuell: http://www.semanticoverflow.com/ques​tions/129/how-do-i-build-a-reasoner
13:10 zarah egonw_'s link is also http://tinyurl.com/ylhvahj
13:26 samuell Hmm... getting a StackOverflowError as soon as I load more than 1000 triples. Anybody knows of some typical jvm param that can be set=
13:26 samuell ?
13:27 samuell Some stack parameter seems to be restricted to 1000. :(
13:33 edrin samuell: when running in an eclipse environment ?
13:33 samuell edrin: yes
13:35 edrin samuell: in the run parameters are an option to increase mem
13:36 samuell edrin:Yes... I've increased Bioclipse's standard memory usage to the double
13:36 samuell I have quite a special environment though, since I'm talking to prolog via the Prolog / Java api, so it might be something specific to that.
13:36 edrin ok, then I cannot help
13:37 samuell Thanks anyway
13:37 samuell I was thinking that there might be some very typical thing that use to happen when loading more than 1000 items, since the limit was really exactly at 1000.
13:41 stain something recursing when it should not?
13:43 stain -Xss<size>        set java thread stack size
13:43 stain samuell: perhaps that would work
13:43 samuell stain: Will try...
13:43 stain for most java programmers a stack of 1000 means you've forgotten the final clause in your recursion
13:44 stain or that you have made a lovely listener that listens to itself or something
13:50 samuell stain:Yeah, true. Trying out different stack sizes now...
13:52 samuell stain: Changing the stack size indeed helped! Thanks a lot!
15:09 CIA-63 bioclipse.cheminformatics: Arvid Berg 2.2.x * r2a0bb7c / plugins/net.bioclipse.cdk.jchempain​t/src/net/bioclipse/cdk/jchempaint/​handlers/ChangeModuleHandler.java :
15:09 CIA-63 bioclipse.cheminformatics: Changed to IBond.Stereo in toolbar handler
15:09 CIA-63 bioclipse.cheminformatics: Fixes bug #1598 - http://bit.ly/30tQJr
15:09 egonw_ Gpox: I applied three patches
15:09 CIA-63 bioclipse.cheminformatics: Arvid Berg 2.2.x * r862f81c / plugins/net.bioclipse.cdk.jchempain​t/src/net/bioclipse/cdk/jchempaint/​widgets/JChemPaintEditorWidget.java : Might solve bug #1699 the bug is still not reproducible - http://bit.ly/3sFN32
15:09 zarah bug #1598 | http://tinyurl.com/yg4mb4q
15:09 zarah bug #1699 | http://tinyurl.com/ykak4ch
15:09 CIA-63 bioclipse.cheminformatics: Arvid Berg 2.2.x * r50f51b6 / (2 files in 2 dirs):
15:09 CIA-63 bioclipse.cheminformatics: Add drawNumbers to jcp-popup
15:09 CIA-63 bioclipse.cheminformatics: Solves bug #1176 - http://bit.ly/2q5ChV
15:09 zarah bug #1176 | http://tinyurl.com/yf36crk
15:13 jonalv java.lang.UnsatisfiedLinkError: Cannot load 32-bit SWT libraries on 64-bit JVM :(
15:15 CIA-63 bioclipse.core: Ola Spjuth 2.2.x * r700f244 / plugins/net.bioclipse.webse​rvices/META-INF/MANIFEST.MF : Removed spring.aop dep that made eclipse complain. - http://bit.ly/1BDmz2
15:15 olass joined #bioclipse
15:21 CIA-63 bioclipse.core: Carl Masak 2.2.x * r3e16eb6 / plugins/net.bioclipse.scripting.ui/src/net/bi​oclipse/scripting/ui/views/JsConsoleView.java :
15:21 CIA-63 bioclipse.core: [JsConsoleView] only says 'not found' if not found
15:21 CIA-63 bioclipse.core: Fixes #1704. - http://bit.ly/1W9C57
15:21 zarah bug #1704 | http://tinyurl.com/yf9qvs6
15:21 egonw_ masak: ping
15:21 egonw_ masak: regarding that...
15:21 egonw_ masak: we should make an index that can make it report:
15:22 egonw_ Not found, but if you install Feature X...
15:27 olass egonw_: ping
15:27 egonw_ pong
15:27 olass egonw_: why is gist not in bioclipse.social?
15:27 olass and, I think we should bundle social feature in the release
15:27 jonalv there is a bioclipse.social plugin now?
15:28 egonw_ because .social did not even exist when .gist was written
15:28 olass no, but a fetaure
15:28 * jonalv must have missed that one...
15:28 masak egonw_: I'd like to see a design for such a feature before I go ahead and add it.
15:28 egonw_ masak: here's the design: List<String,String>
15:28 olass masak, jonalv http://github.com/egonw/bioclipse.social/
15:28 zarah olass's link is also http://tinyurl.com/yhmruyz
15:28 olass egonw_: ok, so we leave gist as it is for now
15:29 egonw_ List<String,String> managers and List<String,String> commands
15:29 egonw_ olass: yes, I suggest that
15:29 olass egonw_: should social go in update site or experimental?
15:29 egonw_ update site
15:29 olass I suggest update site
15:29 olass good
15:29 masak egonw_: I mean, how do we avoid having to update it all the time?
15:29 egonw_ masak: you can't, I guess...
15:29 masak then I'm disinclined to add it.
15:29 egonw_ though we can autogenerate upon building a release
15:30 masak I'm not sure the bang is worth the buck.
15:30 jonalv masak: adding what?
15:30 masak jonalv: see above.
15:30 olass egonw_: please build a system that updates the update site when the API changes
15:30 olass :)
15:30 jonalv masak: I am trying but I can't find it... Did I just arrive?
15:30 olass jonalv: no, you've been here all day
15:30 egonw_ jonalv: that you get a suggestion about what Bioclipse Feature to install
15:30 masak jonalv: let me nopaste the discussion for you.
15:31 egonw_ when a manager or manager command is 'Not Found'
15:31 egonw_ sort of, to be user friendly
15:31 jonalv egonw_: ah like in Ubunutu++
15:31 egonw_ jonalv: quite so
15:31 jonalv or even Ubuntu++
15:31 egonw_ :)
15:31 egonw_ and Kubuntu++
15:32 masak jonalv: http://gist.github.com/226131
15:32 egonw_ gist.download()
15:32 egonw_ Not Found, but you can install the Bioclipse Social feature.
15:32 egonw_ Wait, let me do that for you know... hang on...
15:33 jonalv egonw_: I like that
15:33 jonalv egonw_: How would we go about implementing it_
15:34 masak if you can make it light-weigth and easy to administer, it might work.
15:34 jonalv egonw_: a seperate plugin that can be autogenreated?
15:34 masak s/weigh/weight/
15:34 jonalv s/genre/gener
15:35 * jonalv thinks this might bequite easy to do the day we autobuild using that fancy tool Gpox++ is working on
15:36 egonw_ jonalv: indeed
15:41 olass egonw_: did you bumb version for joelib?
15:41 olass egonw_: ah, a new branch
15:41 olass nvm
15:43 jonalv egonw_: did you have problems running Bioclipse on 64 bit machine?
15:45 egonw_ there is a problem with SaveAs in the JS editor...
15:45 jonalv olass: do you have 5 sec?
15:45 olass ok
15:46 olass jonalv: shoot
15:52 CIA-63 bioclipse.core: jonalv master * r15055b2 / features/net.bioclipse.platfo​rm_feature/bioclipse.product : force 32 bit JVM on Mac - http://bit.ly/jnR10
15:56 CIA-63 bioclipse.core: jonalv 2.2.x * r135eb1d / features/net.bioclipse.platfo​rm_feature/bioclipse.product : force 32 bit JVM on Mac - http://bit.ly/1EAXXm
15:56 jonalv olass: ping
16:05 egonw_ yeah, something is not good with Eclipse running on Kubuntu Karmic...
16:05 egonw_ Import Project does not work...
16:05 egonw_ same problem I saw in Bioclipse...
16:05 egonw_ so, it's an actual Eclipse problem... :(
16:06 jonalv egonw_: okey so it's not a similar problem to ours then..
16:07 egonw_ dunno
16:08 egonw_ ah...
16:08 egonw_ it seems a egit problem
16:08 egonw_ java.io.FileNotFoundException:
16:08 egonw_ at org.eclipse.egit.core.project.GitProj​ectData.map(GitProjectData.java:455)
16:09 egonw_ well, or perhaps just correlation...
16:09 egonw_ will need to explore
16:09 egonw_ going home now
16:13 olass egonw_: how operational is the joelib feature and plugin?
16:14 egonw_ fully operational
16:14 egonw_ bye now
16:14 egonw_ let's talk later
16:14 olass egonw_: joelib does not exxport
16:14 olass will have to live without it then
16:55 CIA-63 bioclipse.core: Ola Spjuth 2.2.x * r4d7ab51 / features/net.bioclipse.platfo​rm_feature/bioclipse.product : Set product ID and included feat. to 2.2.0.RC1 - http://bit.ly/1wrxrt
17:36 CIA-63 bioclipse.core: jonalv 2.2.x * rec72925 / plugins/net.bioclipse.ui/src/net/biocli​pse/ui/prefs/UpdateSitesEditDialog.java : fixed layot - http://bit.ly/3RkKdd
17:36 CIA-63 bioclipse.core: jonalv 2.2.x * rb4cc179 / features/net.bioclipse.platfo​rm_feature/bioclipse.product : Merge branch '2.2.x' of github.com:olas/bioclipse.core into 2.2.x - http://bit.ly/1X3Usr
17:37 sneumann__ joined #bioclipse
17:46 CIA-63 bioclipse.core: Ola Spjuth 2.2.x * r597719d / plugins/net.bioclipse.ui/src/net/bioclip​se/ui/prefs/UIPreferenceInitializer.java : Set update sites for 2.2.0.RC1 - http://bit.ly/1FJYh9
17:46 CIA-63 bioclipse.core: Ola Spjuth 2.2.x * r21e39de / plugins/net.bioclipse.ui/src/net/bi​oclipse/ui/BioclipseConstants.java : Update update sites to correct URL for 2.2.0.RC1 - http://bit.ly/ev2Ch
17:46 CIA-63 bioclipse.core: Ola Spjuth 2.2.x * rf8d05bb / (2 files in 2 dirs): Remove extended data action due to P2 problems. - http://bit.ly/4ClcEg
17:48 samuell left #bioclipse
17:53 CIA-63 bioclipse.core: jonalv 2.2.x * r84818ab / plugins/net.bioclipse.ui/src/net/biocli​pse/ui/prefs/UpdateSitesEditDialog.java : new attempt at layout - http://bit.ly/1a4Lfv
17:53 CIA-63 bioclipse.core: jonalv 2.2.x * r4bd129c / (4 files in 4 dirs): Merge branch '2.2.x' of github.com:olas/bioclipse.core into 2.2.x - http://bit.ly/1qwBuS
18:01 CIA-63 bioclipse.core: Ola Spjuth 2.2.x * r90a087e / plugins/net.bioclipse.ui/src/net/biocli​pse/ui/prefs/UpdateSitesEditDialog.java : Move Textbox down in dialog. - http://bit.ly/4zBkxm
19:06 edrin left #bioclipse
19:06 egonw_ joined #bioclipse
19:33 egonw_ hi all
19:33 zarah hello egonw_, you fantastic person you
19:33 egonw_ hi jonalv!
19:33 egonw_ so many people this time of the day
19:33 egonw_ I'm not used to that :)
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