Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-02-12

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All times shown according to UTC.

Time Nick Message
06:12 sneumann joined #bioclipse
06:17 egonw joined #bioclipse
06:27 egonw joined #bioclipse
07:18 olass joined #bioclipse
07:20 olass moin
07:21 olass hi egonw
07:21 egonw oh hai
07:21 olass where are the CIA bots and zarah?
07:21 egonw CIA-71: ping
07:21 egonw zarah I do not know
07:21 egonw will reboot it
07:21 olass k
07:22 egonw question
07:22 egonw I was looking at the EP stuff...
07:22 egonw long time since I done that
07:22 olass sure
07:22 egonw how does a factory work?
07:22 olass perspectivefactory you mean?
07:22 egonw are you using factories to reduce automatic loading of the full classpath deps?
07:22 olass or generally?
07:22 egonw ummm...
07:23 egonw eclipse commer qual book
07:23 egonw page
07:23 olass please explain more..
07:23 olass don't have the book here..
07:23 egonw 635
07:23 egonw ok, no worries
07:23 egonw it writes:
07:24 egonw where is it...
07:24 egonw ah
07:24 egonw "if you EP is intended for general consumption... then lazy initialization
07:25 egonw for example, in our case the targetClass is used to determin which Favorites item should be used
07:25 egonw *before* the plug-in that defines it is actually loaded
07:25 egonw "
07:25 egonw I don't get that...
07:25 egonw if the factory is part of the plugin..
07:25 egonw the plugin must be loaded for using the factory too, I'd say...
07:26 egonw meaning it would have to load up the plug-ins deps too...
07:26 egonw have you been using this approach in EPs?
07:26 egonw of implementations and factories to implement this lazy loading?
07:28 zarah joined #bioclipse
07:30 olass egonw: I don't think I have been
07:30 olass but then again
07:31 olass if it means that the targetClass is not loaded until needed
07:31 olass that is a factory approach
07:31 olass anyway, you should ask jonalv, masak, or Gpox
07:31 * olass just realized that egonw is holding that book :)
07:32 egonw no, don't think so... I bought my own copy
07:32 olass @karma olas
07:32 zarah olas has a karma of 50
07:32 olass @karma ola
07:32 zarah ola has a karma of 1
07:32 olass @karma jonalv
07:32 zarah jonalv has a karma of 200
07:32 olass hmm
07:32 egonw do you want me to secretly raise your karma?
07:32 olass something is strange here..
07:32 egonw oh damn... the logger
07:32 egonw hahahah :)
07:33 egonw @karma egonw
07:33 zarah egonw has a karma of 150
07:33 egonw mmm...
07:33 jonalv olas++
07:33 olas thanks jonalv
07:34 olas egonw: I created the mailing list bioclipse-bugs
07:34 egonw ack, sounds good
07:39 sneumann joined #bioclipse
07:58 annzi joined #bioclipse
08:01 sneumann morning
08:04 Gpox joined #bioclipse
08:27 egonw Gpox: I am setting up a repository for the CDK plugins
08:27 egonw http://github.com/egonw/org.openscience.cdk
08:27 zarah egonw's link is also http://tinyurl.com/yffqt2y
08:27 egonw empty yet, though
08:33 egonw_ joined #bioclipse
08:35 egonw joined #bioclipse
08:49 egonw @jonalv can you please close this BOx question: http://blueobelisk.stackexchange.com/quest​ions/20/why-do-i-get-a-nullpointerexceptio​n-while-trying-to-generate-inchi-with-cdk
08:49 zarah egonw's link is also http://tinyurl.com/yc4x4u6
10:07 masak joined #bioclipse
10:09 egonw masak: took another liberty of rebooting zarah... but it seems I messed up! karma's have been moded 50
10:09 egonw it was missing from this channel
10:09 masak zarah: karma egonw
10:09 zarah egonw has a karma of 150
10:09 egonw @karma masak
10:09 zarah masak has a karma of 142
10:09 egonw @karma jonalv
10:09 zarah jonalv has a karma of 200
10:09 masak seems to work.
10:09 egonw @karma olas
10:09 zarah olas has a karma of 51
10:10 egonw @karma ola
10:10 zarah ola has a karma of 1
10:10 egonw well, we tried is ++ was stilll working, so 51
10:10 egonw @karma Gpox
10:10 zarah Gpox has a karma of 138
10:10 egonw mmm...
10:10 olas what has ahppened to all my karma?
10:10 egonw was that just co-incidence then??
10:10 * olas had 178 a few days ago
10:11 egonw masak: oh, and don't read the logs
10:11 egonw @karma annzi
10:11 zarah annzi has a karma of 0
10:11 * masak reads the logs
10:11 egonw annzi++ (for starting a blog)
10:11 egonw annzi++ (for picking me as supervisor)
10:11 egonw annzi++ (for going to meet Mark in Canada)
10:11 egonw annzi++ (for the ChEMBL SPARQL examples)
10:12 egonw annzi-- (for not having commited the MoSS manager methods yet :)
10:12 egonw annzi: had to do that, otherwise masak would have been forced to reset your karma for alledgedly illegally boosting your karma ;)
10:12 egonw ask olas about that
10:13 olas annzi: beware of masak
10:13 masak I see olas is still confused about his karma levels.
10:13 annzi first of all what is karma levels?
10:13 masak olas: if you add up the karma for your different accounts on IRC, you have about the same as the rest of us.
10:13 olas masak: it seems you have now set me to 50. thanks
10:13 masak annzi: it's just a number.
10:13 masak @karma annzi
10:13 zarah annzi has a karma of 3
10:14 masak olas: I haven't changed anything.
10:14 olas right
10:14 olas maybe zarah did it herself?
10:14 annzi and second I didn't commit yesterday since I feel that the current code will change a lot
10:14 olas zarah: you are the evil one
10:14 zarah olas: no, YOU'RE the evil one!
10:14 annzi egonw: want me to commit anyway?
10:15 masak zarah: don't listen to olas. you're the cute one!
10:15 zarah masak: no, YOU are the cute one!
10:16 olas *grmf*
10:21 egonw annzi: no, it's fine... you have to establish your own commit habits...
10:21 egonw annzi: I will only complain about incomplete, unusable, bad commit *messages*
10:22 egonw http://www.phdcomics.com/comics.php?f=1279
10:22 zarah egonw's link is also http://tinyurl.com/ybqy2c4
10:22 annzi I have a problem with commits, I always intend to write to much ;)
10:22 egonw ah, well, then:
10:23 egonw commit not with: git commit -m ""
10:23 egonw but
10:23 egonw use an editor, and then have the first line be brief, and then skip one line and give the long version after that...
10:24 annzi ok
10:24 egonw like: http://github.com/egonw/chembl.rdf/commit​/e4ebb93979a7e2f3ac95a92cf4b527d1f1b224d7
10:24 zarah egonw's link is also http://tinyurl.com/yg4kqyl
10:25 egonw so, first line a summary, then followed by the fine details
10:25 egonw annzi++ (for caring about commit messages)
10:26 egonw masak: btw, with your reluctance expressed yesterday, I have added those wiki pages I requested for Sequence
10:26 masak oh, ok.
10:27 masak predictably, my afternoon was filled with a lot of other things, so I never got around to editing wikis... :/
10:27 egonw no worries...
10:28 egonw as said, from my perspective, the wiki is like a social contract, explaining me what to expect from something
10:28 egonw unlike the actual implementation
10:28 egonw I see them as complementary
10:28 egonw I also see the wiki as drafting place for the Bioclipse Book content
10:35 egonw http://wiki.bioclipse.net/index.php​?title=Bioclipse2_core_object_model
10:35 zarah egonw's link is also http://tinyurl.com/ykf9ykn
10:35 egonw done. One less broken link on the front page
10:59 egonw annzi: the thing with commits is...
11:00 egonw the more often you commit, the earlier you can expect comments
11:00 egonw which could improve your programming habits
11:00 egonw (depending on the number and level of people taking the time to actually comment)
11:20 CIA-71 org.openscience.cdk: Egon Willighagen master * r9a34f86 / (5 files in 3 dirs): Added first draft of CDK150 - http://bit.ly/aIJlEg
11:20 CIA-71 org.openscience.cdk: egonw master * rfcb1465 / cdk-externals/net.sf.jniinchi/META-INF/MANIFEST.MF :
11:20 CIA-71 org.openscience.cdk: Fixed Bundle-ClassPath
11:20 CIA-71 org.openscience.cdk: git-svn-id: https://bioclipse.svn.sourceforge.net/s​vnroot/bioclipse/bioclipse2/trunk@7407 fcb5ba71-d80d-0410-8237-ba3920747fcc - http://bit.ly/aGpuSP
11:20 CIA-71 org.openscience.cdk: egonw master * r1b7e77e / (5 files in 3 dirs):
11:20 CIA-71 org.openscience.cdk: Upgraded JNI-InChI to 0.5
11:20 CIA-71 org.openscience.cdk: git-svn-id: https://bioclipse.svn.sourceforge.net/s​vnroot/bioclipse/bioclipse2/trunk@7992 fcb5ba71-d80d-0410-8237-ba3920747fcc - http://bit.ly/bib74k
11:20 CIA-71 org.openscience.cdk: egonw master * r9fe69cc / cdk-externals/net.sf.jniinchi/META-INF/MANIFEST.MF :
11:20 CIA-71 org.openscience.cdk: Fixed version number for current jar
11:20 CIA-71 org.openscience.cdk: git-svn-id: https://bioclipse.svn.sourceforge.net/s​vnroot/bioclipse/bioclipse2/trunk@7995 fcb5ba71-d80d-0410-8237-ba3920747fcc - http://bit.ly/bm83jt
11:20 CIA-71 org.openscience.cdk: Egon Willighagen master * refeab1d / (10 files in 6 dirs): Moved net.sf.jniinchi from cdk-externals to externals - http://bit.ly/cKWUJ8
11:34 egonw masak: ping
11:34 masak egonw: pong
11:34 egonw masak: regarding JRI etc...
11:34 masak yes?
11:34 egonw please have a look at the bioclipse.cheminformatics/cdk-externals folder
11:34 egonw perhaps too outdated...
11:34 * masak looks
11:34 egonw but there is JRI bundles there
11:35 egonw bundleD
11:37 masak I see them.
11:37 masak don't know how old they are.
11:38 masak also don't know if it makes sense to create a dep to CDK in this case.
11:38 egonw ummm...
11:38 egonw there is no dep on the CDK
11:38 egonw the CDK deps on these
11:38 egonw you have the arrow in the wrong direction
11:38 masak I mean.
11:39 masak I don't know if it makes sense to depend on CDK just to get JRI.
11:39 egonw masak: but agreed... there is perhaps room for a bioclipse.orbit initiative, instead of all these externals/ folders
11:39 egonw I mean: there is no dep for JRI on the CDK
11:39 egonw where do you see that?
11:39 masak I know that :)
11:39 masak no, you misunderstood what I first said.
11:39 masak maybe I was unclear.
11:39 egonw [02/12/10 12:39] <masak> I don't know if it makes sense to depend on CDK just to get JRI.
11:39 egonw no, it does not make sense
11:40 egonw which is why there is no such dep
11:40 masak I was speaking from the perspective of the project I'm building.
11:40 egonw ?
11:40 egonw yes, indeed:
11:40 egonw [02/12/10 12:39] <egonw> masak: but agreed... there is perhaps room for a bioclipse.orbit initiative, instead of all these externals/ folders
11:40 masak egonw: IRC doesn't seem to work very well for the two of us this week.
11:40 egonw it seems, despite the communication, we are thinking in the same direction :)
11:40 egonw masak: indeed :)
11:41 egonw maybe we should try haiku-over-twitter ? ;)
11:42 egonw twaiku: haiku's with 140 chars at most
11:42 masak :-P
11:43 CIA-71 org.openscience.cdk: Egon Willighagen master * r6d4ab31 / (50 files in 30 dirs): Moved org.xmlpull.xpp3, org.rosuda.jri, org.omegahat.sjava, org.jama, org.3pq.jgrapht from cdk-externals to externals - http://bit.ly/d1a1lV
11:55 annzi joined #bioclipse
12:01 CIA-71 org.openscience.cdk: Egon Willighagen master * r7a867da / (1214 files in 289 dirs): Uploaded bundles for CDK 1.3.2 - http://bit.ly/9VxMFz
12:32 annzi joined #bioclipse
12:52 CIA-71 org.openscience.cdk: Egon Willighagen cdk-jchempaint * r85688cc / (18 files in 12 dirs): Removed bundles which are not supposed to be used - http://bit.ly/dgZzkn
12:52 CIA-71 org.openscience.cdk: Egon Willighagen cdk-jchempaint * r1f87257 / .gitignore : Ignore autogenerated bin/ folders - http://bit.ly/dpQsBT
12:54 CIA-71 org.openscience.cdk: Egon Willighagen master * r8678639 / .gitignore : Ignore autogenerated bin/ folders - http://bit.ly/9g6E55
12:54 CIA-71 org.openscience.cdk: Egon Willighagen master * r316eb01 / (18 files in 12 dirs): Removed bundles which are not supposed to be used - http://bit.ly/9Vk6Wr
12:54 egonw mmm... need to figure out how to filter these commits for only the cdk-jchempaint branch... because only that one matter for bioclipse
13:40 egonw masak: yes, incompatible...
13:40 egonw in the sense, that a relicensing is required, which is allowed, but needed nevertheless
13:40 masak ok.
14:07 jonalv joined #bioclipse
14:11 CIA-71 org.openscience.cdk: Egon Willighagen master * re4dd573 / (120 files in 64 dirs): Added missing data files - http://bit.ly/9cvhrG
14:17 CIA-71 org.openscience.cdk: Egon Willighagen cdk-jchempaint * rfc2ccae / (128 files in 72 dirs): Added missing data files - http://bit.ly/anNdxT
18:55 sneumann joined #bioclipse
20:17 egonw_ joined #bioclipse
20:42 sneumann joined #bioclipse
21:27 sneumann hi egonw_, just added lucid to my sources.list,
21:27 sneumann pinned lucid in preferences to -10
21:28 sneumann and apt-get install -t lucid linux-image which got me
21:28 sneumann Linux paddy 2.6.32-13-generic #18-Ubuntu
21:28 sneumann and will pull in updates from lucid whenever they come.
21:28 sneumann I love apt ;-)
21:28 egonw_ :)
21:28 * egonw_ is not moving to lucid until after the grant applications at the end of this month at least
21:28 sneumann Also you get all the ubuntu patches on top of vanilla
21:28 egonw_ reasonably happy with the backports repos
21:29 egonw_ true
21:29 * sneumann is enjoying Fritz Lang's Metropolis Directors cut
21:29 * egonw_ is not enjoying his cold
21:30 egonw_ and has a bursury to send out within 90 minutes
21:30 egonw_ been pushing it...
21:30 egonw_ but delaying it in the hope my cold would disappear
21:30 egonw_ and I could think straight...
21:31 * sneumann shuts up

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