Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-07-02

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All times shown according to UTC.

Time Nick Message
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09:19 jonalv Gpox: I am trying to write an answer to Cyrus mail. But I have run into trouble. Why does the installation instructions for 2.0 talk about appache commons codecs?
09:19 jonalv Gpox: 2.4 does not seem to do that
09:19 Gpox because it is old
09:19 jonalv strange...
09:19 jonalv Gpox: are those bundles included in the new target platform?
09:20 jonalv Gpox: do you remember which bundles we are using from that?
09:20 * jonalv seems to remember using some package for converting from 64 bit encoding when doing password encryption
09:20 jonalv maybe that is all...
09:21 Gpox check it, shift-cmd-a and search for the bundle at the bottom it says from where it comes
09:21 jonalv Gpox: right, only I don't know what names they would have...
09:22 jonalv Gpox: any progress with inchi btw? :)
09:22 Gpox you can search on packages
09:22 Gpox a litle
09:22 * jonalv starts by looking at what exists in target platform
09:24 * Gpox has logback log traces from jnati
09:25 jonalv Gpox: that sounds like a good step in the right direction
09:25 Gpox [n.s.j.deploy.repository.RemoteRepository] Not found: http://jnati.sourceforge.net/jnati-repo/jni​inchi/1.03_1/jniinchi-1.03_1-MAC-X86_64.jar
09:25 zarah Gpox's link is also http://tinyurl.com/2ussmyt
09:25 jonalv Gpox: huh it tries to grab it online?
09:26 Gpox yes, that is what jnati does if it dosen't find it localy
11:32 jonalv Gpox: oh, and that doesn't work either?
11:32 jonalv soudns intresting...
11:56 Gpox java.lang.UnsatisfiedLinkError: net.sf.jniinchi.JniInchiWrapper.Lib​InchiGetVersion()Ljava/lang/String;
13:03 CIA-71 bioclipse.core: jonalv 2.4.x * rb03456e / features/net.bioclipse.platfo​rm_feature/bioclipse.product : fixed ref error in bioclipse.product - http://bit.ly/buUV3j
13:16 slyrus jonalv: thanks for the email!
13:17 jonalv slyrus: I am working on another one :)
13:17 jonalv hitting the send button any minute now :)
13:17 jonalv okey sent :)
13:17 jonalv slyrus: how are things going for you?
13:18 slyrus fine, but I just woke up :)
13:18 jonalv ah yes off course :)
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13:23 slyrus one more question (my puny brain can only handle so many layers of abstraction): am I correct in thinking that the cdk stuff is a _plugin_ (?) to bioclipse?
13:23 jonalv slyrus: the short answer: yes
13:24 slyrus so there are folks who use bioclipse but don't use cdk?
13:24 jonalv slyrus: it's actually more than just one plugin, it's quite a few
13:24 jonalv slyrus: I have no idea what people are using in Bioclipse. The version you can download from sourceforge ships with the cdk plugin though
13:24 slyrus yes, I'm beginning to think that the "plugin" name is a bit misleading :)
13:25 jonalv slyrus: well actually, everything is plugins
13:25 jonalv users normally downloads features though, which are collections of plugins
13:25 slyrus yes, so much so that the label starts to lose its meaning..
13:26 jonalv well a plugin is a seperate well defined chunk of code. Dependencies are handled on plguin level. One plugin depends on another plugin. So the label definitly has a meaning. Only maybe not the one you first would expect from the name...
13:29 * Gpox got InChI=1S/C30H48O2/c1-19(2)10-9-11-20(3)23-​18-26(32)30(8)22-12-13-24-27(4,5)25(31)15-​16-28(24,6)21(22)14-17-29(23,30)7/h10,12,1​4,20,23-26,31-32H,9,11,13,15-18H2,1-8H3
13:29 jonalv Gpox: it works?
13:29 Gpox yeah
13:30 jonalv Gpox++
13:30 Gpox now I just have to figure out what I did
13:30 jonalv \o/
13:30 jonalv *lol*
13:48 slyrus the inchi source distribution web page feels very late-90s...
13:48 slyrus mid 90s maybe
13:52 jonalv slyrus: what does this page feel to you ? (http://bioclipse.net/)
13:52 slyrus heh
13:52 slyrus that's nice
13:52 jonalv yea they have made some new fancy stuffses there
13:55 slyrus so I should try to build bioclipse with galileo instead of helios (I didn't actually intentionally use helios, I just tried to download the RCP version and, lo and behold, it was helios)?
13:55 jonalv yes
13:55 jonalv at least I would recommend that but I have never actually tried Helios so I don't know if it works or not
13:59 slyrus ok, eclipse is downloading all sorts of stuff I hope to never have to look at
14:00 slyrus hamcrest? cheatsheets? jetty? universal? win32? osgi? what _is_ all this stuff?
14:00 * slyrus doesn't like his editor to download things of the intertubes. has to get over it i guess...
14:00 slyrus s/of/off/
14:00 jonalv slyrus: the scary things is that I know what most of them actually are. Do you want to know? :)
14:01 slyrus these java folks sure do love their jars
14:01 jonalv well, in Java there isn't very much else...
14:01 slyrus umm... there is _source code_.
14:02 slyrus the new mantra seems to be "write once, download everything!"
14:02 slyrus :)
14:03 jonalv well, yea, we like frameworks here :)
14:04 * slyrus likes the "small pieces, loosely joined" approach
14:08 jonalv slyrus: well yea, but Bioclipse is a big project so you still have many pieces
14:09 jonalv I would say that OSGI does not hinder that approach
14:09 slyrus what is OSGI?
14:09 slyrus what is spring?
14:09 jonalv oh it is the bundle (or plugin) framework which Eclipse and hence Bioclispe is built on to of
14:09 jonalv it handles dependecies
14:10 jonalv Spring is a bit more complicated to explain
14:11 jonalv it is a framework which provides us with among other stuff the power of AOP. I would say that Spring is built using your philosphy of small loosely coupled pieces if that is any comfort
14:12 slyrus ok, it built, and the bioclipse splashscreen appeared, but then it said it couldn't be run
14:12 jonalv okey did you get some error message more than it can't be run?
14:12 slyrus !MESSAGE Product net.bioclipse.ui.product could not be found.
14:13 jonalv did you update bioclipse.core after I did my fix that I explained in the mail?
14:13 jonalv slyrus: how familiar are you with git btw?
14:14 slyrus well, it's better than downloading random zip files off of ftp sites :)
14:15 slyrus I'm reasonable comfortable with git. as long as I'm not trying to rebase egonw's patch sets, I'm fine
14:15 jonalv okey
14:15 slyrus reasonably
14:15 jonalv then pull in bioclipse.core to get my fix if you haven't done that
14:15 slyrus which branch?
14:16 jonalv you ahve to refresh in Eclipse fater that by selecting all project and hitting F5
14:16 jonalv 2.4.x
14:16 jonalv slyrus: that is the one you are using right?
14:16 * slyrus checks... yes
14:17 slyrus yeah, what I just built had that "fixed ref error..." change in there already
14:18 jonalv d'oh I was hoping it would be that easy...
14:18 jonalv if you open bioclipse.product and click the Dependencies tab you do not have a red cross then I take it?
14:19 jonalv slyrus: what system are you running btw? OSX?
14:19 slyrus no, it just says "net.bioclipse.core_feature (2.4.0.RC2)
14:19 slyrus yes
14:19 slyrus is that a problem?
14:19 Gpox jonalv: why are you refering to net.bioclipse.core_feature and not net.bioclips.platform_feature in bioclipse.product
14:19 jonalv no you should be fine, most of us have Macs
14:20 jonalv Gpox: ooops ?
14:20 slyrus what's the difference between the core and the platform?
14:20 * jonalv wonders the same thing actually
14:20 jonalv Gpox: ?
14:22 Gpox platform contains other features like ballon and chemoinformatics what we want to have in the exported product, it is kinda a bad name for it though
14:22 Gpox and core
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14:22 jonalv ah right
14:22 jonalv my misstake
14:22 * jonalv fixes
14:23 slyrus perhaps a cup of coffee will help
14:23 CIA-71 bioclipse.core: jonalv 2.4.x * raa59edc / features/net.bioclipse.platfo​rm_feature/bioclipse.product : should run platform feature not core feature - http://bit.ly/9m62FV
14:24 * jonalv needs vacation...
14:24 jonalv slyrus: okey try with that then...
14:26 slyrus works! thanks!
14:27 slyrus and the coffee is still brewing no less. amazing stuff.
14:28 slyrus now I suppose I need to figure out how to add in the cdk plugins
14:28 jonalv yea that was almost left as an exercise for the reader in the wiki
14:31 slyrus if I want 2d structure drawing, do I add jchempaint as well?
14:32 jonalv slyrus: you add the plguins from the cheminformatics repo and the cdk repo
14:32 slyrus when you say "add plugins" you mean using the "Import..." interface like I did for the bioclipse stuff, right?
14:33 jonalv I wonder if not the cheminforamtics feature is listed in the platofrm feature so you don't even have to add anything to the product
14:33 jonalv slyrus: yes
14:33 jonalv I guess I should have said imort
14:34 slyrus ok, just wanted to make sure I was doing the right thing.
14:34 slyrus that works too. I'm missing the inchi stuff, but that's my fault.
14:34 slyrus yay!
14:34 slyrus thanks jonalv!
14:34 jonalv np
14:37 jonalv Gpox: commit pending soon?
14:37 Gpox can you access Galileo - http://download.eclipse.org/releases/galileo updatesite?
14:37 zarah Gpox's link is also http://tinyurl.com/y8kqjhl
14:38 jonalv Gpox: by just clicking on that link? Yes that works...
14:39 Gpox try and resolve the target-platform
14:39 jonalv Gpox: I did that earlier today. It took quite some time but it worked at last
14:39 jonalv Gpox: do I ahve to wait for it again? :)
14:40 Gpox it didn't work for me so I changed the updatesite to http://download.eclipse.org/updates/3.5, I was wondering if I should commit that change
14:40 zarah Gpox's link is also http://tinyurl.com/38fuf6v
14:41 jonalv Gpox: it didn't work as in you got an error or as in it never finnished?
14:41 jonalv Gpox: it worked for me now
14:41 Gpox go to Install new software and selet the galileo site
14:42 jonalv apparantly it's faster when you have already done it... :)
14:42 Gpox I get a no repository found at ...
14:43 * jonalv looks at the content of the Galileo update site in his install dialog
14:43 jonalv no errors
14:45 CIA-71 bioclipse.core: Arvid Berg 2.4.x * r7bc7c75 / net.bioclipse.target.platform/l​ibs/net.bioclipse.jniinchi.jar :
14:45 CIA-71 bioclipse.core: Added jniinchi to target-platform
14:45 CIA-71 bioclipse.core: This is a OSGi bundle jar created with bnd with a Bundle-NativeCode entry - http://bit.ly/9zOXqV
14:46 jonalv Gpox++
14:46 Gpox ok update org.openscience.cdk and chemoinformatics.git form my git-hub fork and then core
14:46 jonalv so now I ahve to reset target platform anbd then it just works? :)
14:46 Gpox *from
14:47 Gpox might need to close/delete net.sf.jniinchi it is not used anymore
14:47 jonalv ah I ahve some changes to commit first
14:47 jonalv this might take a while... :(
14:47 Gpox would be nice if you could try it on different platforms
14:49 jonalv Gpox: yea I will export and try the exported versions
14:51 Gpox now lets see if I can fixe the other bugs for 2.4.0
14:53 jonalv Gpox: yea... :)
15:05 jonalv Gpox: I lost SWT again now that I rest targt platform
15:05 jonalv (gah)
15:16 jonalv okey my fix for this problem is so magical that I don't even want to talk about it
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17:07 slyrus man, when heavily-loaded java processes go down, they go down hard!
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23:29 slyrus so how do I turn on logging and where does the logging go? (for a function, say SmilesParser.parseString)?

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