Camelia, the Perl 6 bug

IRC log for #cdk, 2010-07-18

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All times shown according to UTC.

Time Nick Message
02:24 CIA-47 cdk: Egon Willighagen cdk-1.2.x * r483c856 / (2 files):
02:24 CIA-47 cdk: Replace special chars where spaces are supposed to occur, fixing the fail of the unit tests every now and then
02:24 CIA-47 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/aG1hx4
02:28 CIA-47 cdk: Egon Willighagen cdk-1.2.x * rcd83236 / src/test/org/openscience/cdk/aromaticity​/CDKHueckelAromaticityDetectorTest.java :
02:28 CIA-47 cdk: Unit test fix: the molecules *is* aromatic, as we should assume it is. Fixes a big goof up
02:28 CIA-47 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/cf0dSO
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11:28 azeem egonw: thanks for the quick reply, FWIW JMol builds fine if I check those two out of subversion
11:29 egonw ack
11:29 egonw signing is not stricktly needed...
11:29 egonw it allows a Jmol applet to read/write on the clients desktop...
11:29 egonw and only applies for Jmol as applet...
11:30 egonw if the deb is only going to provide the application, I guess signing is not needed at all
11:31 azeem there's an libjmol-applet-java .deb in Steffen's original packaging and it still contains jars with 11.8.25
11:31 azeem but I haven't tested it yet
11:35 egonw oh, that's cool
11:35 egonw I had not noted that
11:35 egonw but even the applet works unsigned...
11:37 azeem the certificate is binary, so it's a bit of a PITA to integrate it via the Debian patch
11:37 azeem I could try to patch it out of build.xml
11:38 egonw btw, what about packaging 12 instead?
11:38 egonw Bob's RCs are pretty much stable
11:49 azeem the applet load, but seems crashy (with non-sun jdk)
11:49 azeem loads*
11:51 egonw with openjdk?
11:51 azeem yeah, I think
11:52 azeem well, at least I only see a black background for the examples from http://www.uwosh.edu/faculty_staff/gutow/Jmol​_Web_Page_Maker/Export_to_web_tutorial.shtml
11:52 zarah azeem's link is also http://tinyurl.com/39krtll
11:52 egonw and the Jmol logo?
11:53 azeem that appears
11:53 egonw right click on background?
11:53 egonw do you get the popup menu?
11:53 azeem nope
11:53 egonw if you do, it seems a problem with finding the file...
11:53 egonw ah, ok...
11:54 azeem maybe some adblock stuff
11:54 egonw mom... will try 11.8.25 here with OpenJDK
11:55 azeem (Jmol stand-alone works fine)
12:00 egonw perhaps the browser applet plugin code?
12:00 azeem I'm using icedtea6-plugin
12:04 egonw does that work for online applets?
12:05 azeem apparently not, because I now tried with sun-java, and that works fine
12:06 egonw that is, icedtea6-plugin does not run any Jmol applet?
12:07 azeem well, the jmol applet "loads" (you get the logo, and something like "loading 2,1 seconds"), but then I get a black screen with "jmol" in the lower-right corner
12:07 azeem "Jmol" thatis
12:09 egonw ok, so this is not so much a jmol bug
12:09 egonw but a iceadtea bug
12:09 azeem yeah, I guess
12:09 egonw and neither the Jmol app nor the applet depend on this
12:09 egonw because the applet is aimed at consumption by others
12:10 egonw so, I'd say, this issue does not introduce a dependency on non-main stuff, correct?
12:10 azeem it should probably Recommend: icedtea6-plugin | sun-java6-plugin
12:11 egonw why?
12:11 egonw the applet on the server does not
12:11 azeem oh, hrm
12:11 egonw I would not expect a lot of people using Jmol locally via the applet
12:11 egonw that would be a bit silly
12:12 egonw or does mediawiki also Recommend: firefox | reasonable-browser ?
12:12 egonw not read the DSFG recently :)
12:12 azeem no, no
12:13 azeem I was just confused about java
12:13 azeem my bad
12:13 azeem Package: libjmol-applet-java
12:13 azeem Description: Extra libraries for Jmol I am not fully confident that the dependency on libjmol-java exists.
12:13 azeem that could be improved upon :)
12:14 egonw :)
12:14 egonw the applet jars normally do not depend on (via classpath) to the application jar
12:15 azeem ok
12:15 egonw so, in the current set up, there would be some binary code duplication
12:15 egonw I am not aware that the current build.xml allows building of applet jars that do, however...
12:15 egonw but the size is not horrendous
12:16 egonw actually... people should be able to install either or both jars
12:16 egonw actually... people should be able to install either or both *debs*
12:17 azeem ok
12:21 egonw mmm... i guess I need to dig up my virtualbox with lenny again then :)
12:23 azeem nah, I think I'll manage
12:24 egonw oh, but I'll want to see it in action :)
12:24 egonw and be able to provide patches anyway...
12:24 egonw at least know that I theorically could... :)
12:36 CIA-47 cdk: Egon Willighagen cdk-1.2.x * r0bd5b42 / (2 files in 2 dirs):
12:36 CIA-47 cdk: Added a test class to repeat atom type perception and test consistency
12:36 CIA-47 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/9YCHhr
13:17 CIA-47 cdk: Egon Willighagen cdk-1.2.x * r3357113 / src/main/org/openscience/cdk/aromatici​ty/CDKHueckelAromaticityDetector.java :
13:17 CIA-47 cdk: Also except N.amide as part of an aromatic ring
13:17 CIA-47 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/9WMPk8
13:21 CIA-47 cdk: Egon Willighagen cdk-1.2.x * ra454ab8 / src/test/org/openscience/cdk/aromaticity​/CDKHueckelAromaticityDetectorTest.java :
13:21 CIA-47 cdk: Added a test class to aromaticity of three compounds: the last incorrectly fails
13:21 CIA-47 cdk: Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://bit.ly/c9OrUa
13:36 egonw installed VBox 3.2, booting Lenny, and now aptitude updating ...
14:18 azeem egonw: I've got it building ignoring the shipped jars now (which I believe is required for Debian)
14:18 egonw good
14:18 azeem will try 12 next
14:18 egonw it should build fine with vecmath in Debian
14:20 azeem yes, builds and works fine apparently
14:23 egonw ok, my network is comming to a hold...
14:23 egonw seem to have be back at ISDN bandwidth today :(
14:24 egonw well, pre-ISDN really
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18:01 azeem egonw: hi, one more question: Is Jmol.jar used by anything else today?
18:01 egonw yes
18:01 egonw Bioclipse
18:01 azeem ok
18:01 egonw some more programs too
18:02 egonw but not by software in Debian at this moment, I think
18:02 azeem well, as it's not in Debian AFAIK...
18:02 egonw true, but was more thinking as optional component...
18:02 azeem according to Debian policy, library jars should be versioned, with a generic symlink
18:02 egonw what would be useful...
18:02 egonw is to make the jar OSGi compatible...
18:03 egonw not sure if that is easily done with the current Java build stuff
18:03 egonw stuff := the helpers...
18:03 azeem hrm
18:03 egonw btw, did I understand correctly that CDBS is being phased out?
18:03 azeem well, it's going to stay around
18:03 azeem for a while
18:03 azeem but dh7 seems to be preferred by lots of people
18:03 azeem not sure about java packaging though
18:04 azeem is there a reason Jmol.jar isn't versioned upstream?
18:04 egonw lack of need, I guess
18:04 azeem ok
18:05 egonw let me know if there are patches you need to make...
18:05 azeem I guess shipping a Jmol-11.8.25.jar and a Jmol.jar -> Jmol-11.8.25.jar symlink won't hurt then
18:05 egonw I'll see to it that they reach upstream, preferably get them applied there
18:05 egonw seems like a fair patch...
18:05 azeem svn://svn.debian.org/svn/pkg-escience/jmol/trunk/d​ebian/patches/jmol_search_in_usr_share_java.dpatch
18:06 azeem that's the one I kept around
18:06 azeem the other one patches build.xml, which isn't needed
18:06 egonw ah.... right...
18:07 egonw shall I write a patch for upstream to include the version number in the jar file name?
18:07 azeem well, I'm quite new to java packaging, so I'm not sure what is reasonable
18:08 azeem see http://wiki.debian.org/Java/Packaging
18:08 zarah azeem's link is also http://tinyurl.com/2v3uc3h
18:08 egonw well, I think they change it weekly...
18:08 azeem "For library packages Debian Java policy currently requires that the libraries be installed to /usr/share/java in a versioned format and with an unversioned symlink."
18:08 azeem I could easily do that in the packaging
18:09 egonw ok
18:12 azeem ah, jh_installjars automatically gets it right
18:12 egonw cool
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