Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-08-26

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All times shown according to UTC.

Time Nick Message
05:16 sneumann_ joined #bioclipse
05:18 egonw joined #bioclipse
05:19 CIA-63 bioclipse.joelib: Egon Willighagen master * ra047032 / (13 files in 11 dirs): Fixed all class and resource loading problems now - http://bit.ly/19AzzN
05:19 CIA-63 bioclipse.joelib: Egon Willighagen master * r44cd63d / plugins/net.bioclipse.joelib.qsar/src/net/bioclips​e/joelib/qsar/impl/JOELibDescriptorCalculator.java : Fixed the actual missing storage of the descriptor values - http://bit.ly/KUtxp
06:32 Gpox joined #bioclipse
06:47 olass joined #bioclipse
06:47 olass hi
06:47 zarah ni hao olass
06:56 egonw olas++ for the QSAR graphics: http://egonw.posterous.com/​qsar-in-the-bioclipse-world
06:56 zarah egonw's link is also http://tinyurl.com/lqbr9d
06:56 olass I have worked hard on this
06:58 olass what is posterous?
06:58 olass seems easy to post images
07:01 egonw yeah, I just email them there...
07:02 egonw but you can email HTML too
07:02 egonw and Gists
07:02 egonw you can email Gists too :)
07:02 egonw well, that's really just HTML, isn't it...
07:15 * olass likes teh idea of posterous and created a site
07:16 olass Many times I wish to share a screenshot or photo, this could be useful
07:16 egonw joined #bioclipse
07:44 sneumann joined #bioclipse
07:53 jonalv joined #bioclipse
08:08 shk3 joined #bioclipse
08:59 shk3 I have trouble starting Bioclipse
08:59 shk3 also from a fresh checkout
08:59 shk3 I get errors like:
08:59 shk3 org.eclipse.core.internal.dt​ree.ObjectNotFoundException: Tree element '/Virtual/.project' not found.
08:59 egonw http://egonw.posterous.com/wondering​-if-i-can-just-post-an-embedment-of
08:59 shk3 Error while booting Bioclipse: NoClassDefFoundErrororg/ecli​pse/core/resources/IProject
09:00 egonw sounds like a missing depedency somewhere...
09:00 shk3 does that ring a bell for somebody?
09:00 shk3 yes, but I checked in the run config
09:01 egonw sorry, can not help with running as list of plugins... I only work with features...
09:01 egonw if you have it listed, I am not sure why it fails...
09:01 egonw make sure the proper plugin has the dep too
09:03 shk3 looks like it's all there
09:03 shk3 hm, will do something else for now
09:04 egonw a larger stack trace could be useful too
09:07 shk3 http://pastebin.com/m10ca3323
09:10 egonw funny...
09:10 egonw when I think 'svn diff' my hands automatically types 'git diff' :)
09:12 egonw shk3: I'll look at it after a coffee
09:12 egonw bbl
09:42 egonw ok, that was a long fika
09:44 jonalv joined #bioclipse
09:44 masak joined #bioclipse
09:44 jonalv and we are back
09:45 egonw from what?
09:45 masak power outage.
09:45 egonw fika too?
09:45 egonw ah, again ??
09:45 jonalv egonw: power outage again... :(
09:45 masak fike? no, of course not.
09:45 egonw masak: :)
09:45 masak again.
09:46 egonw vattenfall--
09:46 jonalv masak and me had a ncie game of Bucky after we realised that we couldn't do anything without internet
09:46 masak vattenFAIL
09:46 masak I got outclassed by jonalv who claimed he "didn't remember the game at all". :/
09:47 egonw shk3: that classnotfound seems to be in the net.bioclipse.ui plugins
09:47 egonw and I'm sure it is set as dep properly there...
09:47 egonw seems to be related to your local set up...
09:47 egonw I know Eclipse can be a pain in that respect
09:47 egonw I hope you get it working again...
09:47 egonw shk3: happes to us all now and then...
09:48 egonw shk3: randomly trying things is the only working solution pattern
09:48 egonw "The bundle's start level is not met" sounds like your run configuration is messed up
09:48 egonw consider deleting it, and create a new one from scratch
09:49 jonalv "The bundle's start level is not met" usually is fixed by resteting target platform
09:49 jonalv but yea remove the run config to
09:49 jonalv o
09:54 shk3 I did a completely new chechout, but I will try again later
12:05 jonalv http://jonalv.blogspot.com/2009/08/i-ju​st-realized-databases-arent-always.html
12:05 jonalv :)
12:08 masak jonalv++ # nice post!
12:17 jonalv @pz 1658
12:18 zarah joined #bioclipse
12:18 jonalv @pz 1658
12:18 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1658
12:19 jonalv @pz 1569
12:19 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1569
12:26 CIA-63 bioclipse.cheminformatics: Stefan Kuhn master * re0dbe40 / plugins/net.bioclipse.chemoinformati​cs/src/net/bioclipse/chemoinformatic​s/wizards/AddMoleculeWizardPage.java :
12:26 CIA-63 bioclipse.cheminformatics: made the AddMoleculeWizardPage more flexible
12:26 CIA-63 bioclipse.cheminformatics: Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> - http://bit.ly/qNmgL
12:26 CIA-63 bioclipse.cheminformatics: Stefan Kuhn master * r586f623 / (2 files):
12:26 CIA-63 bioclipse.cheminformatics: new sdf wizard uses AddMoleculeWizardPage
12:26 CIA-63 bioclipse.cheminformatics: Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> - http://bit.ly/kBolD
12:29 egonw I second masak:
12:29 egonw jonalv++ (for the blog item)
12:31 edrin joined #bioclipse
12:31 edrin hi
12:31 zarah ni hao edrin
12:34 egonw hi edrin
12:34 sneumann Hi,
12:34 sneumann is there an official license behind http://wiki.bioclipse.net/ ?
12:35 jonalv not that I know...
12:35 jonalv hm...
12:35 jonalv egonw?
12:35 sneumann I just asked shk3 if I could use a picture, (and I still would tell him even if there is a CC something)
12:35 sneumann but others might not know to ask on +bioclipse
12:35 egonw ah, for the wiki content...
12:36 egonw mmm...
12:36 egonw olass?
12:36 olass yes?
12:36 sneumann Card game "schwarzer Peter"
12:36 egonw :)
12:36 olass egonw: you called?
12:36 egonw olass: what's the license of the wiki content?
12:36 olass good question
12:37 olass we are fairly open with anything I'd say
12:37 olass at least I don't mind
12:37 egonw yeah, so we should make it CC-BY
12:37 egonw let's add that to the footer
12:37 olass sounds reasonable
12:37 olass file me a bug
12:37 egonw sneumann: that works for you?
12:38 sneumann I'm already happy because shk3 answered positive.
12:38 egonw ack
12:38 sneumann I just thought about your blogs on licensing.
12:38 sneumann Would that need approval of all authors ? Theoretically ?
12:40 egonw yes, theoretically...
12:40 egonw just sent an email to bioclipse-devel
12:40 egonw "Object now and/or remove your wiki contributions..."
12:41 egonw any objects from the people now here online?
12:43 egonw @pz 1573
12:43 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1573
12:43 egonw @pz wiki.bioclipse.net
12:43 zarah [1573] Please formalize Open aspect o... http://tinyurl.com/lhnsf3
12:43 zarah [743] Main page could use a bit of co... http://tinyurl.com/mr5dmz
12:43 zarah [801] Refactor JsConsoleManager into ... http://tinyurl.com/mk2wla
12:43 zarah [65] CDKManager should be completely ... http://tinyurl.com/68rpol
12:43 zarah [66] JmolManager should be fully cove... http://tinyurl.com/bnta2p
12:43 zarah Entire list (13) at http://tinyurl.com/m9fs2v
12:45 masak bugzilla--
12:45 egonw huh?
12:45 masak egonw: I wrote a comment to a ticket, posted it, and it disappeared.
12:46 egonw oh, wow
12:46 egonw our pelezilla?
12:47 masak yes.
12:48 egonw "dat doet ie anders nooit"
12:48 egonw famous Dutch ad where a dog ate someone elses dog
12:48 egonw "he otherwise never does that"
12:48 egonw don't remember what the ad was about...
12:48 egonw but the line sticked
12:53 olass egonw: den enes bröd, den andres död
12:54 olass a good swedish line to remember
12:54 egonw huh?
12:54 egonw oh, that was not German
12:54 egonw ?
12:54 egonw with a typo here and there...
12:54 olass swe
12:56 egonw olass: ping
12:56 olass pong
12:56 egonw BaseEPObject
12:56 olass yes?
12:56 egonw is that supposed to be edited?
12:56 egonw or autogenerated?
12:56 olass edited how?
12:56 egonw manually
12:56 olass yes
12:57 egonw BaseEPObject.setNamesapce() <- please fix
12:57 egonw it hurts my eyes
12:57 olass ok
12:59 egonw btw, is there a way to test the dcat.setDate() and descriptor.setDate() ?
13:02 CIA-63 bioclipse.qsar: Ola Spjuth master * rbf684d1 / plugins/net.bioclipse.qsar/src/net/bio​clipse/qsar/business/QsarManager.java : Added check for Salt when reading mols. - http://bit.ly/899Kc
13:02 CIA-63 bioclipse.qsar: Ola Spjuth master * r5b36bcf / (3 files in 2 dirs): Added icons to MoleculesPage. - http://bit.ly/jgW0X
13:02 CIA-63 bioclipse.qsar: Ola Spjuth master * rf104ef3 / (8 files in 5 dirs): Corrected type in BaseEPObject: NameSpace - http://bit.ly/HDJJK
13:03 olass egonw: there is a failing pluginJunitTest in net.bc.qsar.test
13:03 egonw ack
13:05 egonw olass: you have not update the QSAR manager tests to the NWO ?
13:06 olass no
13:06 egonw oh, and OntologyHelper does not have a copyright notice
13:06 olass will fix that
13:06 olass but no NWO, no time for that
13:06 egonw and the BO namespace in OntologyHelper and TestQsarManager is wrong
13:06 egonw lacks the hash at the end
13:06 egonw is -> are
13:06 olass please file a bug
13:08 olass egonw++ //for the deep checks
13:09 egonw ok, three bugs filed
13:10 olass thx
13:10 CIA-63 bioclipse.qsar: Ola Spjuth master * rf6b1865 / (7 files in 5 dirs): Added missing copyright header. - http://bit.ly/34pazl
13:56 masak CIA-63: you don't report on my commits. why?
13:57 egonw bioclipse.biojava ?
13:57 masak aye.
13:57 egonw werid
13:57 egonw it is listed
13:57 egonw for the bot
13:57 masak it used to report them.
13:58 egonw maybe it is just slow...
14:01 olass masak: did it contain more than 5 commits? For me it does not relay them in that case..
14:02 masak it contained exactly 1 commit.
14:09 egonw ah, that's the problem... too few commits
14:09 egonw with only one commit you are not important enough
14:10 egonw btw: http://baoilleach.blogspot.com/2009​/08/using-openbabel-from-java.html
14:10 zarah egonw's link is also http://tinyurl.com/nth5lc
14:14 egonw olass: no way I can get your tests to run...
14:14 olass sad
14:15 egonw it's a plugin test, right?
14:15 olass I only create plugin-junit-tests
14:15 egonw it complains about a missing classloader for qsar.test
14:15 egonw when I try to run it...
14:15 egonw never seen that one before
14:15 olass ok
14:17 egonw can you check your Runtime tab?
14:17 egonw the list of exported pkgs was empty here
14:18 egonw but that does not make any difference... :(
14:19 egonw and no '.' in the classpath in the same tab
14:19 CIA-63 bioclipse.qsar: Egon Willighagen master * r6a20d90 / plugins/net.bioclipse.qsar.ui/src/net/bi​oclipse/qsar/ui/builder/QSARBuilder.java : Escape commas to not break the CSV format - http://bit.ly/1fROW1
14:22 olass egonw: is the namespace really ending with /# ?
14:22 egonw yes
14:22 olass ok
14:22 egonw check line 7 of descriptor-algorithm.owl
14:24 egonw olass: OK, no time to bugfix that local fail for running the unit tests...
14:24 olass ack
14:37 CIA-63 bioclipse.qsar: Ola Spjuth master * rac19552 / (5 files in 3 dirs):
14:37 CIA-63 bioclipse.qsar: Factrored out BO_NAMESPACE to QSARConstants class.
14:37 CIA-63 bioclipse.qsar: Solves 1576. - http://bit.ly/qWu0K
14:37 CIA-63 bioclipse.qsar: Ola Spjuth master * r0d0378b / (20 files in 4 dirs):
14:37 CIA-63 bioclipse.qsar: Removed JenaReader, Jena, and all libs for this.
14:37 CIA-63 bioclipse.qsar: Now uses the RDF feature for reading OWL. - http://bit.ly/NlzQD
15:04 egonw it's can googling "bioclipse" on images.google.com
15:05 egonw can = fun
15:06 jonalv egonw: if you say so
15:06 jonalv I think it is can blogging :)
15:08 egonw i haz fun?
15:09 jonalv I haz can?
15:10 masak I can fun?
15:10 masak let's have some can together!
15:10 jonalv I like can
15:10 masak it's can to have can.
15:10 jonalv mmm can
15:10 olass no can do
15:11 jonalv olass: why you no fun do?
15:11 masak yes, why no fun do?
15:11 egonw oh, shut up...
15:11 masak I funnot understand why you're talking about.
15:11 egonw can't write grant apps with all the can here
15:11 masak fun't, you mean?
15:12 jonalv masak + 1
15:12 egonw sure can
15:12 masak oh, this is way to much can.
15:12 egonw canny actually...
15:12 egonw this typo...
15:12 masak I haven't had this much can since, um, well, I funnot remember how long.
15:13 egonw that's how my brain is working...
15:13 egonw I often make mess ups like this
15:13 masak that doesn't sounds like can at all.
15:13 * egonw funnot write proper English, or Dutch for that matter
15:13 olass egonw: how do I create a patch to send as file?
15:14 olass with git?
15:14 egonw strictly speaking, you fun use 'git send' or so
15:14 egonw google git email patch
15:14 zarah egonw: http://www.kernel.org/pub/software/​scm/git/docs/git-format-patch.html
15:14 olass egonw: just thought you knew
15:14 egonw git format-patch to create it
15:15 egonw but I haz never used git to actually send the patches too...
15:15 egonw needs some configuration I guess
15:15 olass egonw-- /haz is not a proper word
15:15 egonw I fun use whatever I think is canny
15:16 olass egonw-- /please mind your language
15:16 olass egonw++ //thx for the help wioth git
15:17 masak egonw++ # don't listen to olass: haz is a proper word, just dialectal
15:17 olass masak-- //not using Java comments
15:17 egonw just wait after I haz read Hagrid conversations :)
15:18 olass egonw: how do I choose what commits to be in the patch?
15:19 egonw dunno
15:19 masak olass: http://theurf.wordpress.com/2008/06/29/animals/
15:19 zarah masak's link is also http://tinyurl.com/3ovguk
15:19 egonw I guess line them up in a separate branch?
15:19 * egonw is away to do some cycling...
16:09 CIA-63 bioclipse.qsar: Egon Willighagen master * r31f2a9c / plugins/net.bioclipse.qsar​.test/META-INF/MANIFEST.MF : Fix for classpath - http://bit.ly/13V5kq
16:20 olass @pz 1550
16:20 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1550
16:43 edrin egonw: what means portrait page?
16:43 edrin this means it must be "normal" DIN A4 not like its now?
16:43 edrin the opposite is landscape?
16:44 edrin ah got it
17:15 egonw edrin: yeah, meant landscape, sorry
17:16 edrin egonw: the "additional files" labels were OK for you? no errors found?
17:16 egonw did not check in too much detail
17:16 egonw should I check?
17:16 edrin yes, please
17:25 sneumann joined #bioclipse
17:37 edrin egonw: pls. if it's ok write me an email
17:37 edrin have to go now
17:37 edrin cu
17:37 edrin left #bioclipse
18:18 CIA-63 bioclipse.qsar: Ola Spjuth master * rb3adc78 / (2 files in 2 dirs): Manually applied patch by egonw. Solves 1566. - http://bit.ly/2OTLy3
20:35 sneumann_ joined #bioclipse
23:36 egonw joined #bioclipse

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