Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-03-07

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All times shown according to UTC.

Time Nick Message
07:29 rojasm joined #bioclipse
07:56 viklund joined #bioclipse
07:56 viklund l
08:11 egonw joined #bioclipse
08:14 EskilA joined #bioclipse
08:30 masak joined #bioclipse
08:37 olas joined #bioclipse
08:42 egonw olas: can't commit to SF
08:42 egonw see email to -devel
08:42 egonw bloody annoying...
08:42 egonw already changed my pwd... but does not seem to help :(
08:43 olas strange
08:43 olas is it only ou or something global?
08:44 olas ok
08:44 olas read your email
08:44 olas SG tend to mess up things
08:44 olas SF that is
08:51 egonw dunno about global or not
08:51 egonw please try
08:57 jonalv joined #bioclipse
08:58 olas will do
08:59 olas nope
08:59 olas error for me too
09:03 olas changed my pwd
09:03 olas can't commit anyway
09:03 olas maybe it takes time to propagate to SVN credentials?
09:05 CIA-22 bioclipse: ospjuth * r5029 /bioclipse2/trunk/plugins/net.bioclip​se.services/src/net/bioclipse/service​s/business/ServiceManagerHelper.java: Added helper class for service manager
09:05 olas ah, now it works
09:05 olas new password = works
09:05 olas to all: you need to update your SF password
09:06 Annzi joined #bioclipse
09:08 egonw olas: well, there was more than an our inbetween for me...
09:10 CIA-22 bioclipse: egonw * r5030 / (trunk/xws-backuped/ xsw/trunk/xws-backuped/): Moved into new hierarchy.
09:11 egonw ok, works for me too now
09:11 egonw seems that between you pwd update and commit, they unbroke things
09:13 olas right :-)
09:23 thomas_ku joined #bioclipse
09:29 steinbeck joined #bioclipse
09:30 CIA-22 bioclipse: egonw * r5031 / (trunk/xws-client/ xsw/trunk/xws-client/): Moved into new hierarchy.
09:31 CIA-22 bioclipse: egonw * r5032 / (trunk/xws-component/ xsw/trunk/xws-component/): Moved into new hierarchy.
09:32 CIA-22 bioclipse: egonw * r5033 / (2 files in 2 dirs): Moved into new hierarchy.
10:02 rojasm joined #bioclipse
10:04 CIA-22 bioclipse: carl_masak * r5034 /bioclipse2/trunk/plugins/net.bioclip​se.core/src/net/bioclipse/recording/ (JsScriptGenerator.java MethodRecord.java):
10:04 CIA-22 bioclipse: [MethodRecord.java]
10:04 CIA-22 bioclipse: * fixed comment
10:04 CIA-22 bioclipse: [JsScriptGenerator.java]
10:04 CIA-22 bioclipse: * boxed types are no longer stored, because they have no unique IDs
10:41 * olas @ lunch
11:10 CIA-22 bioclipse: carl_masak * r5035 /bioclipse2/trunk/plugins/net.bioclipse.co​re.tests/net.bioclipse.recording/net/biocl​ipse/recording/ScriptGenerationTests.java:
11:10 CIA-22 bioclipse: [ScriptGenerationTests.java]
11:10 CIA-22 bioclipse: * now the expected results are traversed instead of the actual
11:10 CIA-22 bioclipse: * corrected some tests
11:11 CIA-22 bioclipse: carl_masak * r5036 /bioclipse2/trunk/plugins/net.bioclip​se.core/src/net/bioclipse/recording/ (4 files):
11:11 CIA-22 bioclipse: [JsScriptGenerator.java]
11:11 CIA-22 bioclipse: * implemented tests
11:11 CIA-22 bioclipse: * all tests now pass
11:11 CIA-22 bioclipse: [other files]
11:11 CIA-22 bioclipse: * renamed Paramater -> Parameter
11:15 CIA-22 bioclipse: jonalv * r5037 /bioclipse2/trunk/plugins/​net.bioclipse.usermanager/ (16 files in 5 dirs): Made all rows shorter than 80 columns to follow the Bioclipse 2 coding convention
11:49 CIA-22 bioclipse: jonalv * r5038 /bioclipse2/trunk/plugins/net.bioclip​se.usermanager.tests/tests/net/biocli​pse/usermanager/UserManagerTest.java: forgot to commit the tests project in last commit..
12:24 egonw joined #bioclipse
12:50 CIA-22 bioclipse: carl_masak * r5039 /bioclipse2/trunk/plugins/net.bioclipse.scripting​/src/net/bioclipse/scripting/JsEnvironment.java:
12:50 CIA-22 bioclipse: [JsEnvironment.java]
12:50 CIA-22 bioclipse: * environment now keeps track of which managers are imported
12:50 CIA-22 bioclipse: * this is to be able to tab complete better
12:53 CIA-22 bioclipse: jonalv * r5040 /bioclipse2/trunk/plugins/net.bioclipse.core/​src/net/bioclipse/core/domain/BioObject.java: BioObject.getId is no longer final. It doesn't need to be and it breaks the AOP if it is...
13:05 CIA-22 bioclipse: jonalv * r5041 /bioclipse2/trunk/plugins/net.bioclipse.co​re.tests/net.bioclipse.recording/net/biocl​ipse/recording/ScriptGenerationTests.java: Fixed broken test. It now fails. As it should...
13:52 egonw masak: I'll do the releng and updatesite now
13:52 egonw I think the updatesite should indeed go into bioclipse/trunk
13:53 CIA-22 bioclipse: egonw * r5042 / (bioclipse/trunk/updateSite/ trunk/bioclipsUpdateSite/): Moved into new hierarchy.
13:54 masak egonw: sounds good
13:54 CIA-22 bioclipse: egonw * r5043 /releng/ (. branches/ tags/ trunk/): Set up a releng project
13:56 CIA-22 bioclipse: egonw * r5044 / (2 files in 2 dirs): Moved into new hierarchy.
13:57 CIA-22 bioclipse: egonw * r5045 /trunk/: Removed obsolete dir
13:59 CIA-22 bioclipse: egonw * r5046 / (bioclipse/tags/N20060212/ tags/N20060212/): Moved into new hierarchy.
14:00 CIA-22 bioclipse: egonw * r5047 / (bioclipse/tags/R0_2_0/ tags/R0_2_0/): Moved into new hierarchy.
14:01 CIA-22 bioclipse: egonw * r5048 / (2 files in 2 dirs): Moved into new hierarchy.
14:02 CIA-22 bioclipse: egonw * r5049 / (bioclipse/tags/release-1.0.0/ tags/release-1.0.0/): Moved into new hierarchy.
14:02 CIA-22 bioclipse: egonw * r5050 / (bioclipse/tags/release-1.0.1/ tags/release-1.0.1/): Moved into new hierarchy.
14:03 CIA-22 bioclipse: egonw * r5051 / (bioclipse/tags/release-1.1.3/ tags/release-1.1.3/): Moved into new hierarchy.
14:04 CIA-22 bioclipse: egonw * r5052 / (bioclipse/tags/start/ tags/start/): Moved into new hierarchy.
14:04 CIA-22 bioclipse: egonw * r5053 /tags/: Removed obsolete dir
14:05 CIA-22 bioclipse: egonw * r5054 / (bioclipse/branches/b1/ branches/b1/): Moved into new hierarchy.
14:06 CIA-22 bioclipse: egonw * r5055 / (2 files in 2 dirs): Moved into new hierarchy.
14:06 CIA-22 bioclipse: egonw * r5056 /branches/: Removed obsolete dir
14:06 egonw OK, clean up finished
14:07 CIA-22 bioclipse: egonw * r5057 /playground/: Removed unused dir
14:29 CIA-22 bioclipse: Annzi * r5058 /bioclipse2/trunk/plugins/net.bioclipse.moss/ (4 files in 3 dirs): still developing errors
14:56 Annzi left #bioclipse
15:28 CIA-22 bioclipse: jonalv * r5059 /bioclipse2/trunk/plugins/ (7 files in 5 dirs): The scripting use case now works. I also took the opportunity to rename BioObjectList into BioList which is much shorter and better :)
15:44 CIA-22 bioclipse: jonalv * r5060 /bioclipse2/trunk/plugins/net.bioclipse.core​/src/net/bioclipse/core/domain/BioList.java: removed @Recorded from iterator method
16:34 olas left #bioclipse
17:17 rklancer joined #bioclipse
18:11 rojasm left #bioclipse
18:16 egonw joined #bioclipse
18:16 EskilA left #bioclipse
18:17 rklancer hi egonw
18:17 egonw hi rklancer
18:18 rklancer you work on cdk principally?
18:19 egonw yes
18:19 egonw interested in the CDK? or already using it?
18:20 egonw you're the one who wrote about logging in Bioclipse, not?
18:20 rklancer yeah
18:20 rklancer actually i don't know much about cdk
18:20 rklancer but I guess it's a pretty mature library? I noticed in CIA.vc that bioclipse is a child project of cdk
18:21 egonw bioclipse uses the cdk
18:21 egonw would not call it a child project
18:21 egonw bioclipse uses more libraries
18:21 egonw but it uses CDK for much of the chemoinformatics
18:23 rklancer I figured ... just noticing that the bioclipse page at cia.vc is http://cia.vc/stats/project/cdk/bioclipse
18:23 egonw yeah, that's from before #bioclipse was really crowded...
18:23 egonw at that time the bioclipse guys from uppsala hang out on #cdk
18:24 rklancer one of the strengths of the bioclipse idea seems to be that there are a lot of useful opensource libraries like CDK, BIojava, Jmol, Jalview...
18:24 rklancer and these can be exposed to scripters and users via bioclipse
18:24 rklancer ah, now that makes sense
18:24 egonw yeah, and what these libs lack is integration
18:28 rklancer hmm..
18:28 rklancer java.lang.NoClassDefFoundError: net/bioclipse/scripting/OutputProvider
18:28 egonw BC2, I guess?
18:28 rklancer yeah
18:28 rklancer won't open a javascript console
18:29 egonw too bad the Uppsala guys are not here...
18:29 egonw can't be of much help with BC2...
18:29 egonw haven't had much time for BC much lately
18:29 rklancer natch
18:29 rklancer are you working on a dissertation?
18:30 egonw no, post-doc who just finished his PhD thesis, and having my defense in 4 weeks
18:30 rklancer good luck :)
18:30 egonw and this post-doc does not primarily involve Bioclipse (yet)
18:33 egonw rklancer: http://chem-bla-ics.blogspot.com/2008/03​/todo-april-2nd-defend-my-phd-work.html
18:33 rklancer oh, cool
18:34 rklancer can't come watch though (I'm in Boston()
18:34 egonw :)
18:34 egonw what's your background?
18:34 egonw never been in Bosten, but there is an interesting metabolomics conference in September there...
18:37 rklancer My background is: worked in C. elegans genetics for 2 years, joined Boston Uni's biomed engineering Ph.D. program, decided I liked software more, switched to Masters program,  recruited to bioclipse project by Deanne Taylor @ Harvard School of Public Health, now she wants to collaborate with a  biostatistics/epidemiology group at Harvard School of Public Health and ultimately adapt bioclipse to help them with some o
18:37 rklancer computer science undergrad degree though
18:38 egonw ah, ok
18:38 rklancer that's like a paragraph, sorry
18:38 egonw :)
18:40 rklancer well if you can get to the metabolomic conf it's an interesting city ... nice and crawling with scientists
18:53 rklancer ah nice ... I have full debug logging in BC2 showing up in my console
19:02 egonw good

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