Camelia, the Perl 6 bug

IRC log for #cdk, 2007-09-11

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All times shown according to UTC.

Time Nick Message
02:50 CIA-31 jmol: hansonr * r8235 /trunk/Jmol/src/org/ (4 files in 2 dirs): 11.3.19 bug fix for PNG writing default 0 compression instead of 2, as in 11.2.0
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03:38 CIA-31 jmol: hansonr * r8236 /trunk/Jmol/src/org/jmol/ (g3d/Cylinder3D.java viewer/Jmol.properties): 11.3.19 bug fix: ragged arrow tip
03:46 CIA-31 jmol: hansonr * r8237 /branches/v11_2/Jmol/src/org/jmol/ (g3d/Cylinder3D.java viewer/Jmol.properties): 11.2.11 bug fix: ragged arrow tip
03:47 CIA-31 jmol: hansonr * r8238 /branches/v11_2/Jmol/src/org/​jmol/viewer/Jmol.properties: 11.2.11 version
04:37 CIA-31 jmol: hansonr * r8239 /trunk/Jmol/src/org/jmol/sha​pespecial/DrawRenderer.java: 11.3.19 bug fix: new arrows for 2-point arrow fail
04:39 CIA-31 jmol: hansonr * r8240 /branches/v11_2/Jmol/src/org/jmol/g3d/ (Cylinder3D.java Graphics3D.java): 11.2.11 bug fix: ragged arrow tip
04:44 CIA-31 jmol: hansonr * r8241 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: 11.3.19 version
04:52 CIA-31 jmol: hansonr * r8242 /trunk/Jmol/src/org/jmol/g3d/ (Cylinder3D.java Graphics3D.java): 11.3.19 version -- rendercone bug fix
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05:00 john_ca200 hello.  Is there anyone here to ask a simple install question to?
05:10 LaserJock john_ca200: install of what?
05:16 john_ca200 oh, great!
05:16 john_ca200 I am trying to install the cdk library.
05:18 john_ca200 I am new to java and cdk, so please pardon me.  I installed netbeans IDE on windows and downloaded the cdk library, which comes in a zip file.  The IDE works fine, but how do I actually install the cdk files so that java sees them?
05:21 LaserJock hmm
05:21 john_ca200 The cdk website says that there is a binary jar version available, but when I selected it at sourceforge I obtained the zip file and Im not sure what to do with it.
05:21 LaserJock did you unzip it?
05:22 john_ca200 yes, and there is no installation file or instructions for installation.
05:23 john_ca200 In the main folder there are some dll, javafiles, and html files, along with some subfolders
05:24 LaserJock hmm
05:24 LaserJock ok, so you went to the sourceforge site?
05:25 john_ca200 yes, and downloaded the file named cdk_1.01.jar
05:25 john_ca200 But windows saved it as a zip file.
05:25 LaserJock oh?
05:25 LaserJock hmm
05:25 LaserJock do you have Java installed?
05:25 john_ca200 yes, I can run netbeans and compile simple programs
05:26 LaserJock you should be able to just double click on the .jar file
05:26 john_ca200 maybe my zip manager wrongly changed the extension to zip instead of jar.  Hold on, I will try changing it.
05:27 john_ca200 No, that does no good.  Double clicking on it does nothing.  I think that sourceforge has zip files where there should be jar files.
05:29 john_ca200 Im trying to download the tar file to see if that contains a jar file.
05:32 LaserJock hmm, well I'm no help :/
05:33 john_ca200 the tar file just has the sourcecode in it.  I guess I will have to compile it myself with ant.  It seems that the jar file that should be on sourceforge is not there.
05:33 john_ca200 do you use cdk in your work?
05:34 LaserJock actually, I've never used cdk
05:34 LaserJock I just do some related stuff so I hang out here sometimes too
05:35 john_ca200 OK, thanks for trying to help.  Maybe tomorrow someone else will be here to help.
05:37 LaserJock well, I downloaded the .jar ,but it's not loading up
05:38 LaserJock I'm on Linux so I don't know what would be wrong
05:41 john_ca200 beats me, too.  something is wrong.
05:44 LaserJock a lot of the cdk guys are in europe
05:44 LaserJock so they should be getting up fairly soon
05:46 john_ca200 thanks again for your help
05:46 LaserJock ah, I'm getting somewhere
05:46 LaserJock cdk is a library
05:47 LaserJock so I ran java -jar cdk-1.0.1.jar
05:47 LaserJock and it told me I needed to pick a program
05:48 LaserJock so i ran java -cp cdk-1.0.1.jar org.openscience.cdk.applications.FileConvertor
05:48 LaserJock which was one of the programs they listed
05:51 john_ca200 hey, news.  For some strange reason, when I try to download from the sourceforge site I now get the jar file rather than a zip file.  So maybe it will work now.  Strange, I downloaded it twice a few minutes ago and it was a zip file each time.
05:51 egonw moin
05:51 egonw hi john_ca200
05:51 egonw still around?
05:51 john_ca200 yes
05:52 egonw good
05:52 egonw nice to meet you
05:52 LaserJock ah sweet, somebody who knows what they are talking about :-)
05:52 LaserJock hi egonw
05:52 john_ca200 nice to meet you too.  You are a cdk developer?
05:52 egonw hi LaserJock
05:52 egonw john_ca200: yes
05:52 john_ca200 very cool.  But I think my problem just fixed itself.
05:52 egonw one of the three founding farther, so to say :)
05:52 egonw Java jar files actually are plain zip files
05:53 egonw that got your archiver confused
05:53 egonw but you should not unzip it
05:53 john_ca200 oh.  So what do you do with it after unzipping?
05:53 egonw and run it from the command line as LaserJock said
05:53 egonw or use it as library...
05:53 egonw mom
05:53 egonw there should be a wiki page explaining how to set things up with netbeans...
05:53 egonw let me check
05:55 egonw http://wiki.cubic.uni-koeln.de/cdkwiki​/doku.php?id=cdkinstallation_windowsxp
05:55 egonw half way the page
05:55 egonw after the part about Eclipse
05:55 john_ca200 then I guess I have to rename it to jar rather than zip.  I did rename it and double click on it, but nothing happened.  I guess I need to run it in a command window.
05:55 egonw layout is horrible...
05:55 egonw will fix that
05:56 egonw running it as java -jar cdk-1.0.1.jar will give a few rudimentary command line utilities...
05:56 egonw more as demo than practically useful
05:57 john_ca200 ok, will download ant and give it a try.  Be back in a few.
05:59 john_ca200 egonw, is it true I should not use ant 1.7, even though apache recommends it?
05:59 egonw no, that is not true
05:59 egonw CDK from trunk/ *requires* ant 1.7
05:59 john_ca200 OK, I will use 1.7.
05:59 john_ca200 thanks
05:59 egonw but 1.0.x should be fine with ant 1.6 and upwards
06:01 CIA-31 jmol: nicove * r8243 /trunk/Jmol/src/org/jmol/viewer/Eval.java: Warning
06:02 LaserJock what is ant?
06:02 egonw Makefile for Java
06:02 LaserJock ah
06:03 egonw ummm... cmake for java
06:04 LaserJock egonw:  has there been any work on getting a python version of cdk?
06:04 egonw via jython?
06:04 egonw may Noel did bindings?
06:06 LaserJock hmm
06:06 LaserJock didn't somebody do a Ruby version?
06:06 egonw yes, Rich
06:06 LaserJock right, he seems to like Ruby ;-)
06:07 john_ca200 egonw, Im a bit confused.  The zip (jar) file I downloaded from sourceforge did not have a build.xml file in it.  It had some dll files, javafiles, and html files.  It seems that ant needs a build.xml file to work right.
06:07 egonw dll files?
06:07 egonw yes, and no...
06:07 egonw the .jar version is already compiled...
06:07 john_ca200 yes, like a few inchi dll files.
06:08 egonw ah, right indeed
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06:08 john_ca200 Oh, so then what?
06:08 egonw well, just write your CDK-based application and then compile it with:
06:08 egonw javac -classspath cdk-1.0.x.jar:. my.first.Program
06:09 egonw which you can then run with java -classspath cdk-1.0.x.jar:. my.first.Program
06:09 egonw sorry... that compile command should be:
06:09 egonw javac -classspath cdk-1.0.x.jar:. my/first/Program
06:09 john_ca200 ok, but I must need to tell java where to find cdk, no?  Also, Im not sure what classpath is.
06:09 egonw where x=1
06:10 john_ca200 Im quite new at java and cdk, sorry.
06:10 egonw that's done with the -classpath argument
06:11 john_ca200 is classpath my path to the cdk jar folder?
06:11 egonw no folder. just jar
06:11 egonw yes...
06:11 egonw the classpath is the -I/-L of C
06:11 egonw and C++
06:12 egonw john_ca200: I recommend to read up with Java programming first now...
06:12 egonw let me point you to a good (free) tutorial...
06:12 egonw hang on
06:12 egonw http://java.sun.com/docs/books/tutorial/
06:12 egonw and click the Getting Started link
06:14 john_ca200 Yes, I have a book in front of me.  I will look up classpath.  You have given me a line of code to compile my program.  Can you tell me if anything special needs to be done if I want to use netbeans?
06:14 egonw yes, I think so...
06:14 egonw not using NetBeans  myself...
06:14 egonw I use Eclipse...
06:14 egonw but
06:15 egonw you likely need to add the cdk-1.0.1.jar to your project library or something like that
06:15 egonw read that wiki page
06:15 egonw and if it does not work, please email the cdk-user mailing list
06:15 john_ca200 ok, great.  will give it a try.  I will contact the mailing list if I have troubles.  Thanks much.
06:16 egonw good luck
06:17 * egonw makes a mental note to write a good intro tutorial to get Java novice started with the CDK...
06:18 john_ca200 I look forward to it :)
06:23 CIA-31 jmol: nicove * r8244 /trunk/Jmol/src/org/jmol/translation/Jmol/ (11 files): Update of .po files
06:30 CIA-31 jmol: nicove * r8245 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
06:41 CIA-31 jmol: nicove * r8246 /branches/v11_2/Jmol/src/o​rg/jmol/translation/Jmol/ (11 files): Update of .po files
06:42 rojasm joined #cdk
06:42 rojasm moin
06:43 egonw hi rojasm
06:43 rojasm hi egonw
06:43 CIA-31 jmol: nicove * r8247 /branches/v11_2/Jmol/src/org/​jmol/viewer/Jmol.properties: Version
06:47 Nout joined #cdk
06:51 * egonw is away for meetings
06:52 * Nout is away to eat
06:55 rojasm joined #cdk
06:56 rojasm egonw: I recieved the email from Tobias Kind but
06:56 rojasm I dind't received the email that I submited to cdklist
07:14 CIA-31 jmol: nicove * r8248 /trunk/Jmol-FAH/projects/ (p2928.xyz.gz p3732.xyz.gz): Folding@Home
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07:17 thomas_ku moin
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07:32 jpansanel moin
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08:26 thomas_ku hi steinbeck: I currently evaluate if I can get funding for the Taverna meeting...
08:27 steinbeck thomas_ku: very good - the more, the better.
08:29 thomas_ku I could not reach the responsible person up to now. But we will see!
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11:25 CIA-31 bioclipse: biocoder * r3748 /trunk/playground/plugins/net.bioclipse.chart/ (8 files in 7 dirs): Added method for porting JFreeCharts to swt
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12:34 CIA-31 jmol: hansonr * r8249 /branches/v11_2/Jmol/src/org/jmol/ (shapespecial/Draw.java viewer/Jmol.properties): 11.2.12 bug fix for straight arrows not saved correctly in state
12:40 CIA-31 jmol: hansonr * r8250 /trunk/Jmol/src/org/jmol/ (3 files in 2 dirs): 11.2.20 version -- arrow rendering bug fix
14:25 Nout yo
14:26 egonw hi Nou
14:26 egonw +t
14:39 Nout egonw you said last time that I should start making some menu right?
14:39 Nout (to be able to choose the controller)
14:39 egonw yes, so that you can switch editing modes, aka controller modules...
14:39 egonw did you find the wiki page?
14:40 Nout ofc I did
14:40 Nout looks ok
14:41 Nout so shoudl this menu be like the 'icon toolbar' at the old jchempaint?
14:41 Nout or do you mean like a real dropdown menu.. or don't you care at all? :P
14:42 egonw toolbar
14:42 egonw looks nicer
14:43 Nout agree
14:43 egonw horizontal like JCP or vertical like Firefly, I do not care much about
14:43 egonw fairly easy... just copy/paste from cdk.application.jchempaint something
14:43 Nout oki i'll search for that
15:01 olas left #cdk
15:24 egonw Nout: will try to login tonight... but not sure yet
15:24 egonw bye all
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16:59 CIA-31 jmol: nicove * r8251 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
17:44 egonw joined #cdk
18:15 egonw only 2124 changes left
18:16 Nout :o
18:27 egonw will be back later..
18:27 egonw givin up on compile errors now
18:58 Nout hm egonw, that ToolBarMaker constist of only swing items
19:16 egonw yes, but don't worry about that...
19:16 egonw that has nothing to do with the renderer/controller
19:17 Nout hmkey
19:43 egonw ok, got to go
19:43 egonw email me if you need help...
19:43 egonw need to clean house tomorrow...
19:43 egonw so won't be much online I guess
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20:22 CIA-31 jmol: nicove * r8252 /branches/v11_2/Jmol/src/org/​jmol/viewer/Jmol.properties: Version
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22:07 Nout hi neksa

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