Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-05-17

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All times shown according to UTC.

Time Nick Message
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07:48 olass moin moin
07:48 olass hola
07:48 zarah privet olass
07:48 olass salut zarah
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08:25 CIA-61 bioclipse.core: Arvid Berg 2.4.x * r823a01b / (2 files):
08:25 CIA-61 bioclipse.core: Removed tests/ form src classpath
08:25 CIA-61 bioclipse.core: Directory tests does not exist in net.bc.scripting.ui.tests - http://bit.ly/dcD5ui
08:31 jonalv oh hai
08:31 zarah hello jonalv, you fantastic person you
08:35 egonw_ joined #bioclipse
08:40 egonw_ annzi: yeah, feel free to make an extra repository for the ChEMBL functionality
08:41 annzi egonw: ok grat!
08:41 annzi great
08:47 egonw_ annzi: so, what repositories are involved now? can you add them to the bioclipse wiki please?
08:47 egonw_ also, would be nice if we can ensure they all push there commits to this channel via the CIA
08:56 annzi egonw_: I made some test against the SPARQL endpoint…It seems like there is a cut-off  at 10000 as we expected. Could you look into it?
08:59 egonw_ yes, I should
09:51 olass jonalv: ping
09:52 olass jonalv: could it be so that the Java 1.6 port of scripting in JS has afected the exception handling outputting exceptions to the console?
09:53 olass I see some discrepancies but I guess it could be my fault
10:26 annzi joined #bioclipse
10:36 olass @pz propertysource
10:36 zarah [1968] ArrayOutOfBoundsEsxception in ... http://tinyurl.com/35wo7yx
10:36 zarah [1969] CDKMoleculePropertySource thro... http://tinyurl.com/36sxu5w
10:36 zarah [1647] Properties view is buggy for M... http://tinyurl.com/yabxuzc
10:36 zarah [874] Jmol should show static propert... http://tinyurl.com/klzbsr
10:36 zarah [893] Jmol should show properties in ... http://tinyurl.com/mq9k88
10:36 zarah Entire list (7) at http://tinyurl.com/34pv6el
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11:23 olass egonw: about 1969... did you have tiem to look at it?
11:23 olass can be no RC without that annoyance (which I think might be InChI spooking)
11:24 * olass wonders if 1968 and 1929 are duplicates
11:24 egonw oh, crap
11:24 egonw I never get to finish that CDK patch this way ...
11:24 egonw I'll check
11:25 olass egonw: another sad thing; com.hp.hpl.hena and jena.arq do not compile for me either :(
11:26 olass some damn xerces.impl problem
11:26 egonw do you have patch 6aa1fc4d?
11:26 egonw oh, that xerces problem again?
11:27 egonw the one that is happening randomly...
11:27 egonw and I have no clue how to get that right
11:27 egonw you had it before
11:27 egonw as did I
11:27 olass yes
11:27 olass any idea what the reason is?
11:27 egonw nope
11:27 olass wrong xerces picked up?
11:28 egonw possibly
11:28 egonw I'm thinking of trying the same trick Arvid has done
11:28 egonw remove a hardcoded dependency
11:28 egonw and use an Import-Package: instead...
11:29 egonw let me try that
11:30 olass thanks
11:58 olass egonw: any luck?
11:59 egonw yeah, some progress...
11:59 * olass is trying hard to get RDF to compile
12:00 CIA-61 bioclipse.rdf: Egon Willighagen 2.4.x * rf006850 / externals/com.hp.hpl.jena/META-INF/MANIFEST.MF : Replaced the dependency into an Import-Package - http://bit.ly/bJsoEP
12:00 egonw ok, now we wait for Gpox' comments ...
12:00 egonw Gpox: comments please on this commit
12:00 egonw olass: meanwhile, please give it a try
12:00 olass ok
12:02 CIA-61 bioclipse.rdf: Egon Willighagen 2.4.x * r68fd05c / externals/com.hp.hpl.jena.td​b/src/atlas/logging/Log.java : Fixed a double if statement - http://bit.ly/c88C83
12:03 Gpox I see nothing wrong with it
12:03 egonw great
12:03 egonw now, if it fixes things for Ola too...
12:19 olass no luck so far :(
12:19 olass cleaning again..
12:19 olass nope
12:20 olass well, some progress, fixed the arq plugin
12:20 olass the jena one is still red
12:20 egonw oh, interesting... that's the one I did not fix yet :)
12:20 olass sounds promising
12:20 egonw ah, no
12:20 egonw the arq I did not fix yet
12:20 olass oh no
12:20 egonw the jena one I did :)
12:21 olass teh arq turned red again :(
12:21 CIA-61 bioclipse.rdf: Egon Willighagen 2.4.x * r2e54344 / (2 files in 2 dirs): Replaced the dependency into an Import-Package - http://bit.ly/991ZSQ
12:21 olass no, nothing is fixed :(
12:21 egonw that's for the arq and tdb plugins
12:21 olass tdb compiles here
12:22 egonw Gpox: you marked 1969 as duplicate
12:22 egonw Gpox: are you fixing 1968?
12:22 Gpox I can not reproduce
12:22 olass damn
12:23 * olass hates non-reproducable problems
12:23 Gpox but I can't calculate InCHi
12:23 olass egonw: still red marks
12:24 egonw really sorry to hear that
12:24 egonw a shame this IMport-Package did not fix it...
12:24 Gpox whats the error?
12:24 egonw then I can only go back to: repeatedly, randomly reseting target platform, set classpath, and that third thingy
12:35 egonw annzi: do you have enough info to make those commits now? do you need additional help?
12:40 annzi egonw: I don't now. I think that I would have to start and then ask along the way..
12:40 egonw ok, please do
12:41 egonw try earlier than later
12:41 egonw and don't be afraid to ask practical questions
12:41 egonw git is not trivial to learn
12:41 annzi ok, thank you
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13:30 egonw olass: http://cenblog.org/newscripts/201​0/05/named-reactions-biggest-fan/
13:30 zarah egonw's link is also http://tinyurl.com/32tx9xt
13:30 egonw ok, bye all
13:30 egonw will be in Stockholm tomorrow
13:30 egonw likely no wireless
13:31 egonw cu on Wed!
13:31 olass bye egonw
13:31 egonw ah, no not Wed
13:31 egonw Thu
13:31 egonw Wed I have slip driving
13:32 egonw :)
13:32 egonw so, hopefully on Thu
13:32 CIA-61 bioclipse.moss: annzi mossUI * rc47fbf6 / plugins/net.bioclipse.moss.business/src/net​/bioclipse/moss/business/IMossManager.java : Added activity to parameters and changed method to IStringMatrix - http://bit.ly/auAvjN
13:32 egonw annzi++ (for the first commit after a very long time :)
13:32 annzi whee my first commit :)
13:32 annzi Im getting here !!
13:32 annzi :D
13:42 CIA-61 bioclipse.moss: annzi mossmanager1 * rf50acb8 / plugins/net.bioclipse.moss.business/src/ne​t/bioclipse/moss/business/MossManager.java : Improved method for protein family querying - http://bit.ly/a1nk08
13:48 CIA-61 bioclipse.moss: annzi mossmanager1 * r75def29 / plugins/net.bioclipse.moss.business/plugin.xml : xml changed for moss-chembl wizard - http://bit.ly/c7PeLs
13:48 CIA-61 bioclipse.moss: annzi mossmanager1 * r874bcf4 / plugins/net.bioclipse.moss.b​usiness/META-INF/MANIFEST.MF : Dependency changes - http://bit.ly/dvRRpI
13:49 jonalv does someone inherites or inherits?
13:50 jonalv hm or something maybe
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