Camelia, the Perl 6 bug

IRC log for #cdk, 2009-05-15

| Channels | #cdk index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
05:01 bag joined #cdk
05:59 jbrefort joined #cdk
06:47 edrin joined #cdk
06:59 egonw joined #cdk
07:12 Gpox joined #cdk
07:24 rojasm joined #cdk
07:25 rojasm moin
07:25 zarah oh hai rojasm
07:33 sneumann joined #cdk
08:22 jonalv joined #cdk
08:25 steinbeck joined #cdk
08:27 dleidert joined #cdk
08:27 dleidert egonw: Around?
08:29 dleidert left #cdk
08:29 dleidert joined #cdk
08:33 mgerlich joined #cdk
08:33 mgerlich_ joined #cdk
08:47 egonw_ joined #cdk
08:57 CIA-42 cdk: dleidert * r35 /trunk/bodr/TODO:
08:57 CIA-42 cdk: TODO for bodr 9: Write test-scripts.
08:57 CIA-42 cdk: - compare our database with the IUPAC Atomic Weight table.
08:57 CIA-42 cdk: - spell-check our database
08:58 egonw_ moin
08:58 zarah privet egonw_
08:58 egonw_ dleidert: I am now
09:01 dleidert egonw_: Just wanted tio let you know, that I was already working on the reported issues.
09:04 egonw_ ack
09:04 egonw_ dleidert++
09:13 steinbeck_ joined #cdk
09:13 CIA-42 cdk: dleidert * r36 /trunk/bodr/TODO: Error values of atomic weights can be compared too.
09:30 mgerlich joined #cdk
09:41 Gpox joined #cdk
09:45 steinbeck joined #cdk
09:49 rojasm joined #cdk
09:58 rojasm joined #cdk
10:20 Gpox joined #cdk
10:50 Mike_v_V joined #cdk
12:06 jonalv joined #cdk
12:38 shk3 joined #cdk
12:47 jpansane1 joined #cdk
13:18 CIA-42 cdk: dleidert * r37 /trunk/bodr/ (ChangeLog elements/elements.xml):
13:18 CIA-42 cdk: * elements/elements.xml (Cm): Fixed electronic configuration (KDE #192616).
13:18 CIA-42 cdk:  (Bh,Db,Hs,Mt,Rf,Rg,Sg,UUh): Fix atom weights accordingly to the 2005 Atomic
13:18 CIA-42 cdk:  Masses table by the IUPAC (KDE #192551).
13:18 CIA-42 cdk:  (Lu,Mo,Yb,Zn): Fix atomic masses accordingly to the 2007 Atomic Masses
13:18 CIA-42 cdk:  table by the IUPAC (KDE #192551).
13:21 CIA-42 cdk: dleidert * r38 /trunk/bodr/ (6 files in 2 dirs):
13:21 CIA-42 cdk: * tests/AtWt.xsl, tests/Makefile.am: Added a stylesheet to check the
13:21 CIA-42 cdk:  atomic weights in our database against the IUPAC table. The check
13:21 CIA-42 cdk:  target will do the test.
13:21 CIA-42 cdk: * configure.ac (AC_CONFIG_FILES), Makefile.am (SUBDIRS): Added tests.
13:58 CIA-42 cdk: dleidert * r40 /trunk/bodr/tests/AtWt.xsl:
13:58 CIA-42 cdk: * tests/AtWt.xsl: Some fixes and improvements. Fix error value test to not
13:58 CIA-42 cdk:  return false positive. Normalize the space to not fail on leading or trailing
13:58 CIA-42 cdk:  whitespace. Fix xsl:param declarations. Improve output in case symbols are
13:58 CIA-42 cdk:  different.
13:59 dleidert left #cdk
14:10 CIA-42 cdk: dleidert * r41 /trunk/bodr/ (ChangeLog elements/elements.xml):
14:10 CIA-42 cdk: * elements/elements.xml (Bh,Db,Hs,Lu,Mo,Mt,Ni,Rf,Rg,Sg,UUh,Yb,Zn): Fix
14:10 CIA-42 cdk:  atom weights accordingly to the 2007 Atomic Masses table by the IUPAC
14:10 CIA-42 cdk:  (KDE #192551).
14:17 CIA-42 cdk: dleidert * r42 /trunk/bodr/NEWS: * NEWS: Added notes about recent fixes/changes.
14:39 CIA-42 cdk: dleidert * r43 /trunk/bodr/TODO: * TODO: NIST Atomic Weights and Isotopic Compositions for All Elements
15:29 jerome__ joined #cdk
15:33 jpansanel moin
15:33 zarah oh hai jpansanel
15:51 edrin joined #cdk
17:00 egonw_ shk3: ping
17:00 shk3 pong
17:00 egonw_ replied to your question about loadReactions()
17:01 egonw_ I think the ICDKManager.loadReactions() should no longer have the IProgressMonitor params
17:01 egonw_ that will fix it, I think
17:01 shk3 ok
17:01 shk3 I will try
17:01 shk3 did we get any comments on the one-or-many-containers-in-jcp problem?
17:02 egonw_ no, forgot to discuss that with Gpox
17:02 egonw_ the NWO merge took most of my time yesterday...
17:04 shk3 hm
17:05 shk3 changed the load reactions in cdkmanager
17:05 shk3 now getting errors in other places
17:05 shk3 public ICDKMolecule fromCml(String molstring)
17:05 shk3 does
17:05 shk3 return loadMolecule( (InputStream)bais,
17:05 shk3 (IChemFormat)CMLFormat.getInstance(),
17:05 shk3 new NullProgressMonitor() );
17:05 egonw_ good
17:05 shk3 but eclipse complains
17:05 egonw_ remove the last argument
17:05 egonw_ yes, it should
17:05 shk3 ah
17:06 shk3 but why didn't eclipse complain before?
17:06 shk3 anyway
17:06 egonw_ because the proxy will figure out when to use a progress monitor
17:06 egonw_ shk3: not sure about that...
17:06 egonw_ umm... called away for doing the dishes
17:06 egonw_ bbl
17:07 shk3 mom
17:07 shk3 the cdk test has many errors at places like
17:07 shk3 cdk.loadMolecule( mf, new NullProgressMonitor());
17:07 shk3 no monitor needed?
17:07 shk3 well, I will do an update
17:07 shk3 perhaps there were recent changes
17:09 shk3 still problems in TestCDKMolecule
17:09 shk3 will mail the mailing list
17:11 egonw_ right
17:11 egonw_ remove the new NullPM()
17:12 egonw_ yes, please do updates
17:12 egonw_ don't worry about CDKManagerTest
17:12 egonw_ that will be removed shortly
17:12 egonw_ better: already removed that one from svn
17:13 egonw_ shk3: please update to rev 10465
17:15 shk3 ok
17:15 shk3 looks like problems with monitors are done
17:15 shk3 now I get ERROR - org.springframework.aop.fra​mework.AopConfigException: Could not generate CGLIB subclass of class [class net.bioclipse.cdk.domain.CDKReaction]: Common causes of this problem include using a final class or a non-visible class; nested exception is java.lang.IllegalArgumentException: Superclass has no null constructors but no arguments were given
17:15 shk3 does that tell you anything?
17:16 egonw_ nope, that one is new to me...
17:16 egonw_ if you file me a bug report, I will look at it
17:17 shk3 I try to figure out what's going on
17:17 shk3 and file bug report if I can't
17:17 shk3 injoy the dishes
17:17 egonw_ shk3: I think I see the problem
17:17 egonw_ note line 61-69 in CDKMOlecule
17:17 egonw_ and the note in the JavaDoc
17:18 egonw_ just add this code to CDKReaction
17:18 egonw_ at line 32
17:18 egonw_ public CDKReaction() {
17:18 shk3 just came across that
17:18 egonw_ }
17:18 egonw_ and copy the JavaDoc from CDKMolecule
17:19 shk3 looks good
17:24 shk3 will commit reaction changes
17:24 egonw_ ok
17:24 egonw_ will check them
17:26 shk3 great
17:26 shk3 can commit reaction plugin now
19:18 edrin joined #cdk
19:58 CIA-42 cdk: aherraez * r14592 /jchempaint/trunk/po/es.po: Spanish
21:13 bag joined #cdk
21:54 edrin joined #cdk

| Channels | #cdk index | Today | | Search | Google Search | Plain-Text | summary