Camelia, the Perl 6 bug

IRC log for #cdk, 2008-01-01

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All times shown according to UTC.

Time Nick Message
04:17 CIA-17 jmol: hansonr * r8890 /trunk/Jmol/src/org/jmol/ (15 files in 5 dirs): (log message trimmed)
04:17 CIA-17 jmol: version=11.5.1
04:17 CIA-17 jmol: # pmesh binary "filename"
04:17 CIA-17 jmol: #
04:17 CIA-17 jmol: # * 4 bytes: P M \1 \0 (littleEndian) or
04:17 CIA-17 jmol: # * P M \0 \1 (bigEndian)
04:17 CIA-17 jmol: # *
08:15 jbrefort joined #cdk
08:27 egonw joined #cdk
10:05 CIA-17 cdk: egonw * r9770 /trunk/cdk/src/META-INF/ (forcefield.cdkdepends test-forcefield.cdkdepends): Added missing deps
10:42 CIA-17 cdk: egonw * r9771 /trunk/cdk/src/org/openscience/cdk/test/qsa​r/descriptors/bond/BondDescriptorTest.java: Setup descriptor testing for the qsarbond module
10:43 CIA-17 cdk: egonw * r9772 /trunk/cdk/src/org/openscience/cdk/ (3 files in 3 dirs): Added a missing unit test class
11:07 CIA-17 cdk: egonw * r9773 /trunk/cdk/src/ (6 files in 2 dirs): Other bond descriptors now use full descriptor testing too
12:15 CIA-17 jmol: nicove * r8891 /branches/v11_4/Jmol/src/org/​jmol/viewer/Jmol.properties: Version
12:24 CIA-17 jmol: nicove * r8892 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
12:55 CIA-17 jmol: egonw * r8893 /branches/v11_4/CVSROOT/: No need for that here, nowhere at all really.
13:07 CIA-17 jmol: egonw * r8894 /branches/v11_4/Jmol/ (7 files in 2 dirs):
13:07 CIA-17 jmol: Injected PMD analyzer. Run 'ant -f build-pmd.xml' and check build/pmd/jmol.html.
13:07 CIA-17 jmol: Currently, only unused code is being found; you can add other rule sets (see
13:07 CIA-17 jmol: pmd.sf.net, left grey menu-like list) by editing pmd.config.xml
13:45 CIA-17 cdk: egonw * r9774 /trunk/cdk/ (pmd/custom.xml pmd/migrating.xml pmd-migrating.xml): Added PMD rules to check for code cleanups for Java 1.5 (and 1.3 and 1.4 too, actually).
13:51 edrin joined #cdk
14:07 egonw edrin: please feel free to start your tutorial :)
14:57 egonw later then...
14:57 egonw bbl
16:14 CIA-17 jmol: hansonr * r8895 /trunk/Jmol/src/org/ (7 files in 4 dirs): (log message trimmed)
16:14 CIA-17 jmol: version=11.5.2 VERSION
16:14 CIA-17 jmol: # bug fix: unclosed readers in Pmesh, FileManager, Jvxl
16:14 CIA-17 jmol: # new feature: pmesh BINARY "filename"
16:14 CIA-17 jmol: # BINARY keyword is optional, but recommended for efficiency
16:14 CIA-17 jmol: #
16:14 CIA-17 jmol: # * 4 bytes: P M \1 \0
16:15 CIA-17 jmol: hansonr * r8896 /branches/v11_4/Jmol/src/org/ (5 files in 4 dirs): version=11.4.RC2_dev # bug fix: unclosed readers in Pmesh, FileManager, Jvxl
17:01 CIA-17 bioclipse: edrin_t * r4590 /trunk/xws-component/src/net/bioclipse/x​ws/component/adhoc/ProcessManager.java: now ignoring the resource in case of JID-to-process validation
17:02 CIA-17 bioclipse: edrin_t * r4591 /trunk/xws-client/src/net/bioclipse/xws/client/ (13 files in 5 dirs): added synchronous invoce functionality
18:13 CIA-17 jmol: nicove * r8897 /trunk/Jmol/build-pmd.xml: Copying PMD to the trunk
18:13 CIA-17 jmol: nicove * r8898 /trunk/Jmol/pmd.config.xml: Copying PMD to the trunk
18:14 CIA-17 jmol: nicove * r8899 /trunk/Jmol/develjars/:
19:36 CIA-17 jmol: hansonr * r8900 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: still working
20:17 CIA-17 jmol: hansonr * r8901 /trunk/Jmol/src/org/jmol/ (6 files in 3 dirs):
20:17 CIA-17 jmol: version=11.5.2
20:17 CIA-17 jmol: # new feature: "getProperty FILECONTENTS ." in the context of
20:17 CIA-17 jmol: # a zip directory defaultDirectory
20:17 CIA-17 jmol: # new feature: zip file reading extended to write FILE
20:17 CIA-17 jmol: #
20:23 CIA-17 cdk: shk3 * r9775 /branches/cdk-1.0.x/src/org/openscie​nce/cdk/smiles/SmilesGenerator.java: two minor problems in smiles generator. If a ring closure had a double bond, this was printed as = even if aromatic and chiral smiles sometimes had unnecessary []
20:25 egonw joined #cdk
20:32 CIA-17 cdk: shk3 * r9776 /trunk/cdk/src/org/openscience/c​dk/smiles/SmilesGenerator.java: two minor problems in smiles generator. If a ring closure had a double bond, this was printed as = even if aromatic and chiral smiles sometimes had unnecessary []
20:50 dleidert joined #cdk
20:59 egonw hi dleidert
21:00 dleidert egonw: hi. Happy Ney Year!
21:00 dleidert s/Ney/New
21:00 egonw yeah, same to you
21:01 dleidert thx :)
21:02 edrin joined #cdk
21:06 egonw edrin: is it difficult to set up a server?
21:18 dleidert which kind of server?
21:31 egonw xmpp
21:31 egonw for a jabber server...
21:32 egonw anything in ubuntu/debian for that?
21:32 dleidert http://www.debianhowto.de/doku.p​hp/de:howtos#jabber_xmpp-server
21:33 dleidert a german howto, but maybe you find, what you are looking for
21:45 egonw thanx
21:49 dleidert egonw: BTW: I remember that you blogged or talked about some speed issues with Jmol and free JVMs
21:49 dleidert do I remember correctly?
21:49 egonw yes, I did
21:49 egonw the classpath AWT impl was rather sluggish
21:49 egonw have not tried Jmol with icedtea yet
21:49 dleidert Did you ever try this native code stuff for GIJ/GCJ?
21:50 egonw no, because I never got around getting it nicely compiled..
21:50 egonw too little .so/C++/GCC experience
21:50 dleidert There is some nice tool in the Debian toolchain called dh_nativejava
21:50 egonw sounds really interesting...
21:50 egonw that was certainly not around when I last played with it
21:51 dleidert yeah, it is some kind of new - I was experimenting a bit with speed issues building docbook-defguide using GIJ
21:51 dleidert build time decreased from 16 hours to one using native code
21:51 dleidert I would like to know, if this can also speed up Jmol
21:52 dleidert we would need -gcj packags for all depenecies of Jmol
21:52 egonw do I understand correctly that you used Java code for docbook-defguide compilation?
21:52 egonw dleidert: right...
21:52 egonw that's what I lost it...
21:52 egonw I did manage to compile some jars into a .so
21:52 egonw but did not figure out how to proceed from there
21:52 dleidert yes, I used Saxon and xml-commons
21:53 egonw *where* I lost it...
21:53 dleidert Getting and packaging the native code is easy:
21:54 dleidert http://svn.debian.org/wsvn/pkg-java/trunk/a​xis/debian/rules?op=file&rev=0&sc=1
21:55 dleidert check the stuff inside the `ifeq (..with_gcj_native..)' stuff
21:55 dleidert s/stuff/part
21:56 egonw this is that new rules stuff, right?
21:56 egonw c-something?
21:56 dleidert yes, cdbs, but here it's just an example, check the following link for a normal debian/rules file:
21:57 dleidert http://bugs.debian.org/cgi-bin/bugreport.​cgi?msg=15;filename=diff;att=1;bug=458247
21:58 edrin egonw: it's quite easy to install and run a jabber server
21:59 egonw edrin: please email me some pointers, with some details on running modules in particular
21:59 edrin in debian/ubuntu is a package with ejabberd.
21:59 egonw dleidert: I'd really hoped to have time to work on debs for Jmol and CDK these holidays...
21:59 egonw dleidert: but not so fortunate
22:00 edrin egonw: i will try to do so this week
22:01 egonw something before the end of next week would be great... I'll try to set up a server at wur.nl then...
22:01 edrin so fare there are still missing in the lib: 1. a way to parse the input/output object into the xmpp ad hoc packet.
22:02 edrin ah cool
22:02 egonw earlier than next Tuesday is not necessariy... as I'm tied up n writing grant proposals
22:02 edrin 2. missing is the service discovery stuff on the client side
22:03 edrin 3. missing is the completion and resubmission of the XMPP Extension Proposal (io-object-forms)
22:03 edrin 4. we need to discuss how to transfer big files with this stuff.
22:04 egonw ad. 4: there is no XEP for that?
22:04 edrin i think the pdb files are already quite big. a file > 50.000 byte is likely to be a problem already...
22:04 egonw really...
22:04 egonw ok...
22:04 egonw yeah, files are bound to be in the MB range...
22:05 edrin egonw: you remember, we tried to get this XEP accepted several months ago...
22:05 egonw yes, I know...
22:05 egonw with rather bad reviews
22:05 edrin yes
22:06 egonw we did not make ourselves clear enough with the goal and why other solutions are not really suitable for those goals
22:06 edrin egonw: for the big files, there is a XEP supporting direct peer2peer data transmission. i thought about using this
22:06 edrin egonw: yes
22:06 egonw yes, makes sense
22:07 edrin egonw: in any way we did not break with the ad hoc XEP. we should not worry about this XEP stuff...
22:08 egonw right...
22:08 egonw if the application is cool, then the standard will come along
22:08 edrin yes
22:08 edrin i think so, too
22:18 edrin egonw: i will leave now, i will contact you tomorrow
22:18 edrin cu
22:18 egonw bye
22:49 egonw joined #cdk
23:03 CIA-17 cdk: egonw * r9777 /trunk/cdk/src/org/openscience/cdk/test/fi​ngerprint/GraphOnlyFingerprinterTest.java: No need for this method to be static, and Nightly complaint about it
23:19 CIA-17 cdk: egonw * r9778 /trunk/cdk/src/META-INF/test-io.cdkdepends: Added missing dependency
23:20 CIA-17 cdk: egonw * r9779 /trunk/cdk/src/org/openscience​/cdk/geometry/BondTools.java: Fixed a NPE which I introduced not so long ago; overlooked the failing unit test
23:31 egonw_ joined #cdk
23:38 CIA-17 cdk: egonw * r9780 /trunk/cdk/src/org/openscience/cdk/t​est/qsar/DescriptorEngineTest.java: Proper assert calls
23:47 CIA-17 cdk: egonw * r9781 /trunk/cdk/src/org/openscience/​cdk/qsar/DescriptorEngine.java: Parameterized types

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