Camelia, the Perl 6 bug

IRC log for #cdk, 2008-06-18

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All times shown according to UTC.

Time Nick Message
02:41 CIA-23 jmol: hansonr * r9501 /branches/v11_4/Jmol/src/org/jmol/viewer/ (Jmol.properties Viewer.java): 11.5.4_dev # bug fix: spin thread not stopped for applet destroy()
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04:24 CIA-23 jmol: hansonr * r9502 /trunk/Jmol/src/org/jmol/ (9 files in 5 dirs):
04:24 CIA-23 jmol: version=11.5.42_dev obscure data/quaternion state bug; axes dotted; spin memory leak
04:24 CIA-23 jmol: # bug fix: state script fails to save data for atoms created using the quaternion command
04:24 CIA-23 jmol: # bug fix: axes/boundbox/unitcell dotted not working since 11.5.6
04:24 CIA-23 jmol: # bug fix: spin thread not stopped for applet destroy()
05:52 CIA-23 cdk: egonw * r11391 /cdk/trunk/src/ (2 files in 2 dirs): Added comparing of IBonds
05:52 CIA-23 cdk: egonw * r11392 /cdk/trunk/src/main/org/opensci​ence/cdk/io/cml/CMLStack.java: Added missing unit test annotation
05:52 CIA-23 cdk: egonw * r11393 /cdk/trunk/src/test/org/op​enscience/cdk/io/formats/ (. ChemFormatTest.java ResourceFormatTest.java): Start with adding unit tests for the IChemFormats
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08:28 thomas_ku moin
08:29 egonw hi thomas_ku
08:29 shk3 moin
08:29 shk3 egonw: I have a debian question
08:30 shk3 how do I switch off startup of apache on startup of machine?
08:31 egonw while it is not the proper way, I normally delete the entry from
08:31 egonw /etc/rc2.d/SXXapache
08:31 egonw entry == synbolic link
08:32 egonw http://wiki.debianhelp.org/pmwiki.ph​p/DebianHelpPages/DebianInitScripts
08:32 egonw the proper way is to use the config script for it...
08:32 egonw but not sure what the name is
08:36 shk3 I found there is update-rc.d, but I didn't understand it...
08:36 shk3 so I will go your way
08:51 azeem egonw: hi
08:51 azeem shk3: there's also the update-rc.d tool, though it's not very human friendly
08:54 azeem ok, I'm wondering about which SDK's can be used to build/run cdk and jmol, anybody konw?  Has it been tested with anything else than Sun java?
09:08 egonw azeem: yes, I used classpath in the past
09:08 egonw azeem: openjdk or icedtea are good candidates
09:09 azeem egonw: yeah, but they're both not in Debian yet, due to licensing issues
09:09 egonw azeem: then try classpath
09:09 egonw Jmol compiles but was slow
09:09 egonw CDK should be no problem, I think
09:09 azeem lenny freeze is approaching, so I wondered whether there's a chance to have cdk/jmol in
09:10 azeem ok
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09:10 egonw azeem: CDK is already in main
09:10 azeem ah, d'oh
09:10 azeem sorry for the noise then
09:11 jpansanel moin
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09:13 egonw azeem: jmol is a different thing
09:13 egonw that's not pacakged yet...
09:14 egonw when is the lenny freeze?
09:14 azeem library freeze is end of the month I think
09:14 azeem package freeze in 1,5 months or so, maybe, not sure
09:17 egonw ok, let's take this to debian-java or debian-science...
09:17 egonw will try to brush up the debian/ stuff on alioth
09:17 egonw or at least be around for support
09:38 CIA-23 cdk: egonw * r11394 /cdk/trunk/src/test/org/op​enscience/cdk/io/formats/ (3 files): Tuned: helper methods to set the tested format; null MIME is valid; some textual explanation for some tests
09:39 CIA-23 cdk: egonw * r11395 /cdk/trunk/src/test/org/openscience/cdk/ (10 files in 2 dirs): More missing unit tests
09:59 egonw lunch
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10:31 shk3 I am trying to figure out what's wrong with the applet build.
10:31 shk3 Still getting "Problem creating jar: Negative seek offset"
10:31 shk3 it seems to be related to the indexing. If I remove index="true" from the jar command,
10:31 shk3 it works.
10:31 shk3 Anybody an idea?
10:42 egonw shk3: did you recreate the index?
10:42 egonw how is the index created anyway?
10:51 shk3 that's part of jar creation
10:51 shk3 at least in ant
10:51 shk3 I am trying to do it separatly via jar right now
10:53 egonw this is cdk 1.0.x based, correct?
10:53 egonw shk3: are you subscribed to cdk-jchempaint@ ?
10:54 shk3 yes
10:54 shk3 got your email
10:54 egonw ok, perfect
10:55 shk3 yes, still trying cdk 1.0.x
10:55 egonw ok, good
10:55 shk3 I think the problem needs to be solved anyway
10:55 * egonw did not get the applet compile for the cdk 1.0.3 release
10:55 egonw yes, likely
10:55 egonw anyway, we're still months away from a new applet, depending on man power
11:21 shk3 managed to create the index, but the applet still is not runnig :-(
11:21 shk3 crashes my firefox
11:22 egonw :(
11:23 shk3 do you want to try?
11:24 shk3 run ant -f build-applet.xml dist-applet and then jar i dist/jar/jchempaint-applet-core.jar
11:25 egonw which folder?
11:25 egonw cdk/tags/<what>?
11:25 shk3 in cdk-1.0.x checkout
11:26 shk3 oh sorry,
11:26 shk3 you can't
11:26 shk3 you need a modified build-applet.xml
11:26 shk3 shall I just email you this?
11:26 shk3 would be great to see how it works for you
11:27 egonw ok
11:28 shk3 sent
11:29 shk3 the index list looks ok (never looked at it before,though)
11:33 * shk3 heads for lunch
12:22 shk3 egonw: any success?
12:23 * shk3 back fromlunch, btw
12:23 egonw no wireless at the cafeteria?
12:23 egonw no, btw
12:23 egonw have not made time to try...
12:23 egonw finishing some JSF stuff...
12:24 egonw hang on
12:25 shk3 sure
12:25 shk3 don't hurry
12:27 egonw what's 'jar i' support to return?
12:30 egonw don't get any error
12:31 CIA-23 cdk: egonw * r11396 /cdk/trunk/ (27 files in 13 dirs): Removed last bits of old renderer code
12:39 shk3 jar i seems to work
12:39 shk3 but the applet doesn't show for me
12:40 shk3 did you try a test file (e. g. viewerapplet.html) in a browser?
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12:46 egonw no
12:46 egonw shk3: will do
12:47 egonw where is that ,.html?
13:02 shk3 in the cdk-1.0.x root dir
13:03 egonw oh... thought it was there... but could not find it earlier...
13:03 egonw weird...
13:04 egonw java.lang.NoClassDefFoundError: org/openscience/cdk/smiles/SmilesParser
13:04 egonw that's what I get
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13:10 egonw so, no negative index problem
13:11 shk3 ok
13:11 shk3 let's see
13:13 shk3 ah, it should be in the editor-opts jar, but isn't
13:13 shk3 hm, try to find out why
13:16 shk3 seems there are several candidate jars, but the smiles parser seems to be nowhere
13:16 shk3 looking further - but at least something to look at...
13:32 shk3 ok, looks like I got it working with the "manual index" trick.
13:32 shk3 It seems the jar task of ant is broken.
13:49 egonw which ant version are you using?
13:49 egonw $ ant -version
13:49 egonw Apache Ant version 1.7.0 compiled on August 29 2007
13:51 shk3 same with me
13:51 shk3 it just worked, now it doesn't...
13:52 shk3 (not with ant, it worked without, but even this is no longer working)
13:52 egonw what JVM are you using?
13:54 shk3 sun 1.6
13:55 egonw ok, see no problem with that
13:55 egonw you're sure Ant is using that version too?
13:56 shk3 well, yes
13:56 egonw good
13:57 egonw then I don't see what is different with my set up
13:57 shk3 but you get the negative seek blah as well, don't you
13:57 shk3 ?
13:57 egonw no, have not seen that
13:57 shk3 really?
13:57 shk3 so ant -f build-applet dist-applet works for you?
13:58 egonw yes
13:58 shk3 (with the unmodified build-applet
13:58 shk3 )
13:58 egonw with your copy
13:58 shk3 ok, but that works for me as well
13:58 shk3 I then did the index thing with jar
13:58 egonw ok, so what's the problem then?
13:58 shk3 on command line
13:58 shk3 the applet is not working
13:58 shk3 not finding classes
13:59 shk3 like the smiles one
13:59 egonw ah, ok, now I understand the problem
13:59 shk3 which worked with a change, but now no longer does
13:59 shk3 the smilesparser class is there
14:00 shk3 when trying the editor, some other class is not found
14:00 shk3 the index list looks good
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14:03 egonw shk3: might the problem be that the classes from the cdk.smiles package are split over different jars?
14:03 shk3 but it was always like this
14:03 shk3 and the editor is missing a class from org.os.cdk.app.jcp.applet...
14:05 egonw no clue
14:09 egonw shk3: sure it worked?
14:10 egonw the specs say it uses a hash table for mapping package names to jar names
14:10 egonw http://java.sun.com/j2se/1.3​/docs/guide/jar/jar.html#JAR Index
14:10 egonw though I'm new to jar indexing...
14:11 egonw but IIRC a hash table can have only a single pacakge as key
14:11 egonw so, it would overwrite jar name upon second encounter of the same package, not?
14:11 egonw ah, no
14:12 egonw "For classes with non-null package names, mappings are recorded at the package level. Normally one package name is mapped to one jar file, but if a particular package spans more than one jar file, then the mapped value of this package will be a list of jar files."
14:27 shk3 sounds ok
14:27 shk3 well, it worked
14:27 shk3 in that sense that the applet showed up
14:27 shk3 but what is the difference - no clue
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15:24 * egonw is going home
15:32 CIA-23 cdk: egonw * r11397 /cdk/trunk/src/main/org/openscience​/cdk/renderer/Java2DRenderer.java: Fixed symbol size (mmm... not sure what will get broken now... :)
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18:12 CIA-23 jmol: aherraez * r9503 /trunk/Jmol-web/source/doc/jslibrary/ (index_en.xml index_es.xml): update for new functions in Jmol.js
18:19 CIA-23 jmol: aherraez * r9504 /trunk/Jmol-web/source/doc/jmol/ (17 files): update of applet in website (from 11.4RC4 to 11.4.4)
19:25 CIA-23 jmol: nicove * r9505 /trunk/Jmol-FAH/projects/ (p4564.xyz.gz p4566.xyz.gz): Folding@Home
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