Camelia, the Perl 6 bug

IRC log for #cdk, 2008-01-04

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All times shown according to UTC.

Time Nick Message
06:15 jbrefort joined #cdk
07:58 _thomas_k joined #cdk
08:20 _thomas_k moin
08:45 steinbeck joined #cdk
09:08 jonalv joined #cdk
09:23 carsten joined #cdk
09:32 masak joined #cdk
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12:18 CIA-17 cdk: egonw * r9821 /trunk/cdk/src/org/openscience/cdk/ (3 files in 3 dirs): Added perception of As+R4 and SnR4
12:18 egonw moin
12:20 CIA-17 cdk: egonw * r9822 /trunk/cdk/src/org/openscience/cdk/qsar/descri​ptors/atomic/AtomHybridizationDescriptor.java: Use the CDKAtomTypeMatcher and no need to configure the atom
12:21 CIA-17 cdk: egonw * r9823 /trunk/cdk/src/org/openscience/cdk​/test/qsar/descriptors/atomic/Atom​HybridizationDescriptorTest.java: Better testing; use the super.descriptor
12:55 dleidert joined #cdk
13:18 masak joined #cdk
13:23 jpansanel moin
13:56 jpansanel egonw : Web Site for http://sourceforge.net/projects/cdk has the same issue as for bodr
14:01 egonw jpansanel: ack, thanx for letting me know
14:19 CIA-17 bioclipse: carl_masak * r4619 /branches/bioclipse2/core/plugins/net.b​ioclipse.ui/src/net/bioclipse/ui/views/ (JsConsoleView.java ScriptingConsoleView.java): (log message trimmed)
14:19 CIA-17 bioclipse: [ScriptingConsoleView.java]
14:19 CIA-17 bioclipse: * moved actionTable from constructor into anonymous initialization block
14:19 CIA-17 bioclipse: * created the following methods:
14:19 CIA-17 bioclipse: ** startOfCommandLine
14:19 CIA-17 bioclipse: ** positionOnCommandLine
14:19 CIA-17 bioclipse: ** scriptSpecificKeyBindings
14:20 egonw jpansanel: what's the 2.1 webpage again?
14:21 jbrefort joined #cdk
14:22 egonw jpansanel: never mind... found it
14:26 jpansanel http://www.alchem.org/breve.php3?id_breve=40
14:28 jpansanel egonw : could alchem.org news collected  on chemical blog space ?
14:28 egonw jpansanel: no, Cb does not collect news feeds
14:28 egonw only personal blogs
14:29 egonw so, make sure to blog about it too :)
14:29 egonw and add some personal touch to it
14:31 jpansanel ok
14:31 jpansanel egonw : do you know if my blog (pansanel.blogspot.com) is collected on Cb ?
14:33 egonw AFAIK it is
14:34 jpansanel thk
14:38 egonw http://wiki.bioclipse.net/ind​ex.php?title=Dataset_plugins
14:48 jpansanel egonw : http://depth-first.com/articles/2007/09/06/from-​inchi-to-image-with-ruby-open-babel-and-ruby-cdk is really interesting
14:48 egonw yes, it is... Rich has indeed been doing really interesting thing...
14:49 egonw btw, did I tell you that Bioclipse2 has Ruby support?
14:49 egonw masak, jonalv: did Uppsala contact Rich on DextroKit... or what was that name again? :)
14:50 egonw Deuterium?
14:50 * jonalv has no idea
14:50 egonw rubidium
14:51 jonalv masak?
14:51 egonw that's it
14:51 egonw http://depth-first.com/articles/2007/​11/21/simple-installation-of-rubidium
14:51 masak egonw: yes, I did
14:51 masak and he replied
14:51 egonw oh, goodies...
14:51 egonw what did he reply?
14:51 egonw sod off?
14:51 egonw :)
14:51 jonalv so what did he say?
14:52 jpansanel egonw : Yes, I think you told me that
14:52 jonalv do bioclipse 2 has ruby support yet btw?
14:52 masak seems like a nice fellow
14:53 masak jonalv: yes
14:53 masak I haven't really had time to announce it, that' all
14:53 jonalv oh show me
14:53 masak it happened just before cristmas
14:54 egonw but, but... what did he answer?
14:55 masak egonw: I was about to tell you
14:55 masak jonalv sidetracked me by asking for a demo :)
14:55 jonalv and I gor one :) thanx :)
14:55 jonalv and sorry...
14:56 masak np
14:56 masak he replied "Once you have a working JRuby interpreter embedded, which it sounds like you do, adding jar should be as simple as dropping them (or their aliases) into the JRuby 'lib' directory."
14:56 masak which sounds like good news
14:56 egonw ah, really cool
14:56 masak :)
14:56 egonw anyway to get JRuby aware about the plugin's classpath?
14:57 masak "any way". I don't know
14:57 egonw because it would be nicest if the rubidium jar would reside in net.bioclipse.rubidium
14:57 masak hm
14:58 egonw but I'm sure you can get that done
14:58 masak I haven't really paid much attention to that kind of partition so far
14:58 masak most scripting stuff is crammed into net.bioclipse.scripting right now
14:58 egonw right, but this is where OSGi comes in...
14:59 egonw so, jonalv, you can fix it :)
14:59 jonalv sry fix what wxactly?
15:00 masak jonalv: being able to put things that need to know about each other in different packages
15:00 masak ...I think
15:00 masak it's the dreaded classpath issue
15:00 jonalv I am afraid that it all depends on what JRuby does...
15:01 masak ...which I don't know yet
15:01 masak so we'll get back to that
15:01 masak but I'm thinking we'll interface JRuby just like we interface other things, like biojava
15:02 masak maybe in that regime, the problem won't even occur
15:02 jonalv except that you want JRuby to run other stuff or what is the problem?
15:02 jonalv I am not sure I know what it is you want to be able to do?
15:02 masak me neither
15:02 jonalv what is this rubidium?
15:03 masak as I said, maybe it is a non-problem
15:03 egonw [2008-01-04 15:53:01] <egonw> http://depth-first.com/articles/2007/​11/21/simple-installation-of-rubidium
15:03 egonw jonalv: check that link
15:03 masak rubidium is a big chemistry toolkit for Ruby
15:03 jonalv which JRuby must know about
15:03 egonw (wrapping around the CDK)
15:04 jonalv oh morw CDK wrapping
15:04 jonalv =)
15:04 masak :)
15:04 jonalv Well how do you install stuff in JRuby then?
15:04 jonalv or rather what happends?
15:05 masak Bioclipse: wrapping CDK in all ways possible
15:05 masak jonalv: I don't exactly know
15:06 jonalv beacause that might not be exactly compatible with simply running an OSGI bundle...
15:06 masak I see
15:06 jonalv or rather installing a certain osgi bundle
15:09 masak I have almost no idea of what you mean
15:09 jonalv hehe
15:10 masak but if you say there'll be problems, I believe you
15:10 jonalv good but all I am saying is that there probably will be problems
15:10 jonalv I don't know how JRuby wotks
15:12 masak basically, it's a full Ruby interpreter running inside the JVM
16:16 shk3 joined #cdk
16:17 egonw shk3: you live that close to your work?
16:20 shk3 that close?
16:20 shk3 30 minutes
16:20 shk3 isn't too close
16:20 shk3 is it?
16:21 egonw no
16:21 egonw did not see that much time had passed already...
16:21 egonw I live 90mins from work :(
16:21 shk3 you live in nimwegen still?
16:22 egonw yes
16:23 egonw less easy to move a whole family
16:23 shk3 well, then it's ok
16:25 shk3 I decided to do some sport...
16:25 shk3 will hack later
16:29 CIA-17 bioclipse: updatebjarni * r4620 /branches/bioclipse2/core/plugins/net.​bioclipse.r/src/net/bioclipse/r/pty.c: C language PTY wrapper to run R on Unix.
16:34 CIA-17 bioclipse: updatebjarni * r4621 /branches/bioclipse2/core/plugi​ns/net.bioclipse.r/native-bin/ (. pty-linux-i386): Directory to contain the native binaries for the PTY wrapper needed to run R on Unix.
16:35 CIA-17 bioclipse: updatebjarni * r4622 /branches/bioclipse2/core/plugins/net.​bioclipse.r/src/net/bioclipse/r/pty.c: Updated the comment box.
16:39 CIA-17 bioclipse: updatebjarni * r4623 /branches/bioclipse2/core/plugins/net.bio​clipse.r/src/net/bioclipse/r/TextR.java: PTY wrapping for R on Unix, so I guess R doesn't work on non-Unix for now, but I'm hungry...
17:10 carsten joined #cdk
18:15 CIA-17 jmol: nicove * r8905 /trunk/Jmol-extensions/wik​i/MediaWiki/Jmol.body.php: Bug fix of the extension: missing global declaration
18:27 CIA-17 jmol: nicove * r8906 /trunk/Jmol-FAH/projects/ (p3060.xyz.gz p3061.xyz.gz p3062.xyz.gz p3906.xyz.gz): Folding@Home
20:34 edrin joined #cdk
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21:44 CIA-17 cdk: rajarshi * r9824 /trunk/cdk/src/org/openscience/cdk/qsar/result/ (DoubleArrayResult.java IntegerArrayResult.java): Removed unnessary boxing

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