Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-12-01

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All times shown according to UTC.

Time Nick Message
06:31 masak joined #bioclipse
08:13 egonw joined #bioclipse
08:19 Gpox joined #bioclipse
08:57 edrin joined #bioclipse
09:08 gilleain joined #bioclipse
09:16 jonalv joined #bioclipse
09:16 jonalv hi
09:16 zarah hi jonalv
09:56 thomasku joined #bioclipse
10:03 CIA-32 bioclipse: jonalv * r7909 /bioclipse2/trunk/plugins/net.bioclipse.s​tructuredb/src/net/bioclipse/structuredb/ (14 files in 3 dirs):
10:03 CIA-32 bioclipse: [structuredb] Made all tables into "cached tables" meaning that they are not 100% in memory. (Now also bigger amounts of data can be fitted in one structuredb instance...)
10:03 CIA-32 bioclipse: Also tried to fix a NPE realted to failing to calculate fingerprint. This needs further testing...
10:07 edrin hi
10:07 zarah hi edrin
10:08 edrin egonw: it's now online
10:08 edrin http://xws4j.sourceforge.net/
10:10 shk3 joined #bioclipse
10:12 shk3 I am getting a Java bug when trying to run Bioclipse.
10:12 shk3 Anybody ever had that?
10:15 egonw edrin: cheers!
10:15 egonw shk3: yes, now and then
10:19 edrin masak: i tried the js console at weekend - and it did not work (windows)
10:20 masak edrin: ok. do you recognize the symptoms among any of the reported bugs?
10:20 masak @pz console
10:20 zarah [Bug 76] Bioclipse crashes when text ... http://tinyurl.com/5bad2u
10:20 zarah [Bug 78] CR/LF problems on windows       http://tinyurl.com/5zcr45
10:20 zarah [Bug 113] The js console says "unexpe... http://tinyurl.com/55zoc7
10:20 zarah [Bug 123] scripting hangs the UI         http://tinyurl.com/6m2nku
10:20 zarah [Bug 139] Exception upon added a firs... http://tinyurl.com/6zzx3q
10:20 zarah Entire list at http://tinyurl.com/6pke5y
10:22 masak edrin: I plan to replace the js console with something else this week, and in the meantime I will probably only patch things that are (a) critical and (b) trivial. I've tried fixing things on Windows before, but so far that has only made it worse.
10:23 shk3 egonw: I have it all the time since friday, can't start bioclipse any longer
10:23 egonw try rerunning target platform
10:23 egonw and, 2. removing all features from the bioclipse.product
10:23 egonw then save (important!)
10:23 egonw and add them again, and save again
10:23 egonw then start
10:24 edrin masak: there urls were not found
10:24 egonw http://pele.farmbio.uu.se/show_bug.cgi?id=123
10:24 zarah egonw's link is also http://tinyurl.com/6m2nku
10:24 egonw masak: there bugzilla/ missing in that
10:24 masak egonw: you're right. I'll fix that.
10:25 egonw wait
10:25 egonw might be a problem of bugzilla
10:25 egonw I see log in on front page is broken again too...
10:26 masak yes, it is actually a problem of bugzilla's
10:27 masak I can work around it, though, but now right now.
10:27 egonw one sec
10:27 masak must be the Atom feed that contains faulty links
10:28 egonw @pz console
10:28 zarah [Bug 76] Bioclipse crashes when text ... http://tinyurl.com/5eaofv
10:28 zarah [Bug 78] CR/LF problems on windows       http://tinyurl.com/6eznsa
10:28 zarah [Bug 113] The js console says "unexpe... http://tinyurl.com/5hey86
10:28 zarah [Bug 123] scripting hangs the UI         http://tinyurl.com/67c3my
10:28 zarah [Bug 139] Exception upon added a firs... http://tinyurl.com/54rkap
10:28 zarah Entire list at http://tinyurl.com/6pke5y
10:28 egonw ok, fixed
10:28 egonw edrin: thanx for noting
10:28 masak egonw++
11:41 charlgren joined #bioclipse
11:46 CIA-32 bioclipse: egonw * r7910 /bioclipse2/trunk/cdk-externals/trunk/o​rg.openscience.cdk.core/src/org/opensci​ence/cdk/dict/data/cdk-atom-types.owl: Updated version to CDK r13232, which includes newer atom types, such as S.trioxide
12:43 sneumann joined #bioclipse
12:59 jonalv egonw: is voting deactivated in 'pelezilla'?
13:03 edrin joined #bioclipse
13:07 egonw jonalv: I have neither activated not deactivated it...
13:10 gilleain joined #bioclipse
13:20 jonalv egonw: so it is off then_
13:21 jonalv ?
13:50 egonw if it is not working... then I guess it is turned off
13:51 jonalv perhaps we should turn it on_
13:52 egonw yeah, if I only knew how
14:00 egonw ok, found something
14:02 egonw jonalv: ok, turned on
14:02 jonalv egonw: cool
14:16 jonalv stupid nacintish swallowed my cd
14:17 jonalv It refuses to admit that there is a cd in the cd player
14:21 gilleain the nacintosh is an inferior machine. get a mac. :)
14:22 jonalv gilleain: that ws not helpful
14:22 gilleain (sorry)
14:22 gilleain are cd's mounted?
14:22 gilleain In /Volumes ?
14:23 jonalv not this one anyway
14:24 gilleain oh.
14:52 masak joined #bioclipse
15:18 jonalv 35% of the time it takes to import molecules into structuredb is spent on calculating figerprints...
15:19 jonalv 33% is java.io.RandomAccessFile.readFully
15:19 jonalv 14% is java.util.ArrayList.contains
15:19 jonalv that last on could perhaps be optimzed a bit_
15:46 gilleain joined #bioclipse
16:17 jonalv egonw: is bioclipse running a copy of the cdk repo these days?
16:18 egonw jonalv: yes
16:18 egonw sort of that is
16:18 egonw an export of the source code really
16:18 egonw bioclipse2/trunk/cdk-external​s/trunk/org.openscience.cdk.*
16:18 jonalv so should I make changes in cdk or in Bioclipse?
16:18 jonalv ...or borth?
16:19 egonw make that bioclipse
16:19 egonw commit that, and file a patch report over at sf.net/projects/cdk
16:19 egonw pointing to that commit
16:19 egonw I will get it reviewed for inclusion upstream (==cdk)
16:20 jonalv okey I will look into this now that I think I have gotten the brunn repo back again... :/
16:20 egonw yeah, thank god for revision control :)
16:23 jonalv commiting complete src folder takes a while though...
16:23 jonalv 27%
16:29 jonalv 58%
16:29 jonalv slow... :(
16:30 egonw if only it was git
16:30 jonalv is that faster?
16:30 jonalv I would probably not have gotten into this trouble with git...
16:31 masak jonalv: git is pretty fast
16:32 masak because most common operations are local
16:32 jonalv masak: ah
16:32 jonalv 70% now :)
16:39 jonalv 98%
16:42 masak exciting!
16:43 jonalv done
17:03 CIA-32 bioclipse: jonalv * r7911 /bioclipse2/trunk/cdk-externals/trunk/org​.openscience.cdk.standard/src/org/opensci​ence/cdk/fingerprint/Fingerprinter.java: change from list to map. Reduced import time for structuedb aprox 2/3.
17:09 jonalv egonw: I don't know how to create a patch... :(
17:10 egonw you just did
17:10 jonalv egonw: uhm won't that cdk page want a patch file?
17:11 egonw go to sf.net/projects/cdk -> patches
17:11 egonw submit a new report there...
17:11 egonw pointing to bioclipse commit 7911
17:12 egonw e.g. copy/paste the commit email content
17:12 egonw bbl
17:12 egonw dinner
17:12 jonalv ah commit email. Good plan! :)
17:25 jonalv egonw: found another bottleneck that probably could be removed with a hash...
17:25 jonalv egonw: hope to see you tomorrow if you feel better!
17:25 * jonalv is out of here!
18:42 edrin left #bioclipse
19:32 edrin joined #bioclipse
19:32 edrin hi again
19:32 edrin egonw
19:44 egonw hi edrin
20:31 CIA-32 bioclipse: edrin_t * r7912 /xws/trunk/xws4j/src/net/bioclipse/xws/client/ (4 files in 4 dirs): replaced remaining collections with concurrent class stuff
21:14 edrin egonw: i did some modification to the xws component :)
21:14 edrin (and to client)
21:14 CIA-32 bioclipse: edrin_t * r7913 /xws/trunk/xws4j/src/net/bioclipse/xws/ (5 files in 5 dirs): blah blah
21:15 edrin egonw: there is now an admin function ...
21:15 egonw yeah, saw something about that...
21:15 egonw each service now has an admin function?
21:15 edrin this function shows info about the component
21:15 egonw ok, nice
21:15 edrin what is your JID?
21:15 egonw egonw@jabber.org
21:17 edrin ok, when you browse to xws.ayena.de, can you see the admin function with psi?
21:17 edrin "ComponentStatus"
21:18 egonw how do I browse to xws.ayena.de?
21:18 edrin egonw: you can execute the function in PSI... a window will pop up and show info about the component
21:18 edrin egonw:with PSI Service Discovery
21:19 egonw but I need to get an account on xws.ayena.de first then?
21:19 edrin no
21:19 edrin just use your egonw@jabber.org account
21:19 edrin i set your JID in the component cfg
21:20 edrin to be admin
21:20 egonw huh?
21:20 edrin you should be able to see the function
21:20 egonw sorry...
21:20 edrin you are a "component admin" ;)
21:21 edrin yes
21:21 egonw ok, forgot that in 'Service Discovery' I could set the server
21:22 egonw but it's via ws1.bmc
21:22 edrin ag
21:22 edrin ah
21:22 edrin ok, moment, will add this JID, too
21:22 edrin ok
21:22 edrin try again
21:23 egonw now there via jabber.org
21:23 egonw but that one you already had, right?
21:23 edrin yes
21:23 egonw ok, I see the XEP-0050 stuff
21:23 edrin well, i added both your JIDs
21:23 edrin ok
21:23 egonw "Get status info about the component"?
21:23 edrin egonw: 2click this :)
21:24 edrin yes
21:24 edrin ok...
21:24 edrin i will now run a stress test against the component...
21:24 edrin you should be able to see how the jobs or tasks are done
21:26 edrin the sample client is now executing the delayedTestFunction 200 times...
21:26 egonw yes
21:26 edrin with the getComponentStatus you should be able to see the functions to pass by :)
21:26 edrin Number of active processes in memory: 165
21:26 edrin Number of terminated/deleted processes: 4
21:26 edrin Number of active processes in memory: 191
21:26 edrin Number of terminated/deleted processes: 13
21:26 egonw right
21:26 edrin Number of active processes in memory: 162
21:26 edrin Number of terminated/deleted processes: 42
21:27 egonw ok, going offline now...
21:27 egonw will be back tomorrow
21:27 edrin ok :)
21:27 egonw need sleep
21:27 edrin cu tomorrow
21:27 edrin sleep well
21:27 egonw bye

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