Camelia, the Perl 6 bug

IRC log for #cdk, 2007-08-13

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All times shown according to UTC.

Time Nick Message
05:56 CIA-1 jmol: nicove * r8066 /trunk/Jmol-FAH/projects/p3680.xyz.gz: Folding@Home
06:21 CIA-1 jmol: nicove * r8067 /trunk/Jmol-FAH/ (2 files in 2 dirs): Folding@Home
06:45 egonw joined #cdk
07:11 mashuuk joined #cdk
07:11 egonw hi mashuuk
07:12 mashuuk Hi
07:14 egonw mashuuk: just looking around (which is just fine :), or is there anything I can help you with?
07:15 mashuuk neksa helped me yesterday.. I just got hibernated laptop and didnt quit irc client
07:16 mashuuk but thx:)
07:17 egonw ack
07:54 neksa joined #cdk
08:20 carsten_ joined #cdk
08:21 jpansanel hi
08:21 carsten_ changed the nick to carsten
08:23 egonw hi carsten, jpansanel
08:23 carsten Guten morgen
08:23 mashuuk hi
08:45 * carsten is loved by dleidert :)
08:45 egonw :)
08:46 * carsten replied to him in private
08:46 carsten and sticked to the technical parts of the mail
08:46 carsten (on public)
09:01 egonw well, your advertisement was bound to give that kind of reply :)
09:01 egonw it's a natural law...
09:17 jbrefort joined #cdk
09:18 CIA-1 bioclipse: biocoder * r3694 /trunk/plugins/net.bioclip​se.statistics/plugin.xml: Fixed file so that bioclipse can use the new grid editor widget
09:19 steinbeck joined #cdk
09:32 egonw hi steinbeck
09:32 egonw let me know when you want to talk about a CDK 1.0.2 release...
09:32 steinbeck sure :-)
09:32 steinbeck thanks
09:33 steinbeck I guess it will need some backports and I need to get an overview regarding the current status of tests in 1.0.2
09:33 egonw about the backports...
09:33 egonw there is a file in the SVN branch listing the possible patches...
09:34 egonw they have to be analyzed one by one for suitability...
09:34 egonw and is not up to date... but can you easily check what the last revision taken into account is from that list...
09:35 egonw for the test status, check the CDK Nightly reports for the 1.0.x branch
09:37 egonw http://cheminfo.informatics.indiana.​edu/~rguha/code/java/nightly-1.0.x/
09:37 lambdabot2 Title: CDK Nightly Build - 2007-08-13 (01:28) [SVN Revision 8677], http://tinyurl.com/2ycobk
09:38 egonw and just ignore the smarts package
09:39 egonw btw, adding Andreas Schuller as developer... so that he can commit his two bug fixes...
09:40 egonw steinbeck: they both involve the SDG
09:41 steinbeck sure - please add him.
09:41 steinbeck I'm currently testing if he is right
09:41 steinbeck I would be surprised.
09:41 egonw ack, great
09:41 steinbeck We have been displaying bridges ring systems all the time
09:41 egonw oh, this might be interesting too: http://wiki.cubic.uni-koeln.d​e/cdkwiki/doku.php?id=cdk1.0
09:42 lambdabot2 Title: The Chemistry Development Kit: cdk1.0
09:42 steinbeck I'm in the situation again that I cannot access CUBIC servers.
09:42 egonw :(
10:32 neksa joined #cdk
10:56 CIA-1 cdk: steinbeck * r8678 /trunk/cdk/src/data/mdl/bug1772609.mol: Test file for bug #1772609 "NPE with bridged rings in SDG/RingPlacer"
10:56 neksa joined #cdk
11:01 neksa joined #cdk
11:01 neksa joined #cdk
11:02 egonw steinbeck: andreas will commit his code and tests himself...
11:03 steinbeck egonw: but I'm currently testing the stuff and need to get things going :-)
11:04 egonw please add a comment in the bug track system that you already uploaded the file... so that he doesn't duplicate what you already did...
11:04 steinbeck already done
11:04 egonw OK :)
11:04 steinbeck I took up the bug and set it to pending
11:04 steinbeck and will continue to comment
11:07 jonalv joined #cdk
11:19 egonw do you want to hear something impressive?
11:19 carsten I do
11:19 egonw CDK ranks somewhere between 100 and 1000 on SF, right?
11:19 carsten no clue :)
11:19 egonw depending on the time of year...
11:19 egonw SF has a new page...
11:19 egonw which gives the Rank History...
11:19 egonw turns out that CDK does around 2000 in terms of Logo and Site Hits...
11:20 egonw sorry... make that rank 1200 or so...
11:20 egonw downloads: around rank 1500
11:21 egonw however, were we do best is the rank for SVN:
11:21 egonw on good days, that around <50 !
11:21 egonw today, it's now 626
11:21 egonw but end of July it was place 45
11:22 egonw see http://sourceforge.net/project/stats/ran​k_history.php?group_id=20024&amp;ugn=cdk
11:22 lambdabot2 Title: SourceForge.net: Rank History For The Chemistry Development Kit, http://tinyurl.com/yutvpz
11:22 egonw oh, and here's the formula:
11:22 egonw http://sourceforge.net/project/stats/rank_calc.​php?group_id=20024&amp;ugn=cdk&amp;day=20070813
11:22 lambdabot2 Title: SourceForge.net: Rank History For The Chemistry Development Kit, http://tinyurl.com/237yyo
11:23 egonw that last page is great :)
11:24 egonw we do worst in terms of communication...
11:24 egonw no forum posts... few tracker entries...
11:25 egonw too bad the don't count IRC lines...
11:32 * carsten ordered a MS natural keyboard 4000. RSI starts in my right hand (mouse hand)
11:32 egonw :(
11:33 carsten yes. I hope it has an equally good "Anschlag"
11:33 carsten I am currently using a Genius keyboard I got for something like 5€ :)
11:33 carsten and that is the best possible Anschlag
11:36 jbrefort joined #cdk
11:39 dleidert joined #cdk
11:42 Nielsout egonw, we could just post irc logs in the forum :P
11:42 egonw hehehe
11:57 CIA-1 cdk: fichte01 * r476 /trunk/protonprediction/Data/output2/Models/ (14 files in 3 dirs):
12:02 CIA-1 bioclipse: biocoder * r3695 /trunk/plugins/net.bioclipse.statistics/sr​c/net/bioclipse/model/MatrixResource.java: Fixed parser bug, added methods hasColHeader and hasRowHeader
12:04 dleidert egonw: ping
12:04 egonw pong
12:04 dleidert xmllint --noout --schema schemas/cml23.xsd dicts/blueobelisk-dictionary.xml
12:04 dleidert schemas/cml23.xsd:5136: element complexType: Schemas parser error : local complex type: The content model is not determinist.
12:04 dleidert WXS schema schemas/cml23.xsd failed to compile
12:04 dleidert Any idea?
12:04 egonw URL?
12:04 dleidert local system
12:05 dleidert I'm currently checking bodr
12:05 egonw ack, mom
12:05 egonw local changes? or SVN version?
12:05 dleidert SVN version
12:06 egonw dicts/blueobelisk-dictionary.xml validates
12:06 egonw just did a fresh checkout...
12:06 egonw what xmllint version?
12:07 egonw xmllint: using libxml version 20627
12:07 egonw   compiled with: Threads Tree Output Push Reader Patterns Writer SAXv1 FTP HTTP DTDValid HTML Legacy C14N Catalog XPath XPointer XInclude Iconv ISO8859X Unicode Regexps Automata Expr Schemas Schematron Modules Debug Zlib
12:08 dleidert newer: 2.6.29.dfsg-1
12:08 egonw interesting...
12:09 dleidert unfortunately I'm not an expert for schemas, so I don't know, if the validation result is right or if xmllint makes an error here
12:09 egonw I'm downloading the gutsy tribe 4 CD... should be able to give some feedback later this week
12:10 dleidert BTW: bod.sf.net rewrites to the old cubic address, maybe you could fix that
12:10 egonw oh, crap...
12:10 egonw thanx for reporting
12:12 egonw fixed
12:28 thomas_ku joined #cdk
12:29 thomas_ku moin
12:31 egonw hi thomas_ku
13:05 CIA-1 cdk: dleidert * r4 /trunk/bodr/ (9 files in 6 dirs): (log message trimmed)
13:05 CIA-1 cdk: 2007-08-13 Daniel Leidert <daniel.leidert@wgdd.de>
13:05 CIA-1 cdk:  * bodr.pc.in: Removed unnecessary paths (closes #1713504 sf.net).
13:05 CIA-1 cdk:  * configure.ac: Added backwards-compatible snippet to determine the
13:05 CIA-1 cdk:  docdir variable/option value, that is available in newer autoconf
13:05 CIA-1 cdk:  versions, to ste the installation path of biblio HTML output.
13:05 CIA-1 cdk:  * bibtexml-xslt/html-harvard.xsl: Output PUBLIC and SYSTEM IDs for
13:48 shk3 joined #cdk
14:27 CIA-1 cdk: steinbeck * r8679 /trunk/cdk/src/org/openscience/cdk/gra​ph/invariant/MorganNumbersTools.java:
14:27 CIA-1 cdk: getMorganNumbes may fail due to an overflow of an int.
14:27 CIA-1 cdk: Deprecated old method and added a new one returning a long[] array
14:35 shk3 left #cdk
14:38 CIA-1 cdk: steinbeck * r8680 /trunk/cdk/src/org/openscienc​e/cdk/layout/AtomPlacer.java:
14:38 CIA-1 cdk: Fixed bug #1773119 "SDG wrongly folds short chains connecting two rings". We now calculate the degreeSum of atoms in chains and thereby find the one
14:38 CIA-1 cdk: without terminal atoms. This one is then layed out first.
14:41 CIA-1 cdk: steinbeck * r8681 /trunk/cdk/src/org/openscienc​e/cdk/layout/RingPlacer.java: Applied pathes by Andreas Schueller. Fixes bug #1772609 "NPE with bridged rings in SDG/RingPlacer"
14:41 egonw steinbeck: is happily hacking on the 'crown jewel' of the CDK :)
14:42 * steinbeck was very proud when reading Rich's comment :-)
14:42 egonw :)
14:43 steinbeck I've written a test which read the NCI file and does layout for many, many structures. It looks very good now.
14:44 * egonw looking forward to the blog with the screenshot :)
14:46 steinbeck I have to move my blog to some other place and still do not know where. Or if I should host my own wordpress version.
14:47 egonw blogger.com worked well for me...
14:47 egonw but you got a server anyway... and that allows you to tweaks things a bit more...
14:47 egonw but also requires you to do so...
15:06 egonw bbl
16:10 CIA-1 cdk: archvile18 * r8682 /trunk/cdk/src/org/openscience/cdk/ (RingSet.java test/RingSetTest.java):
16:10 CIA-1 cdk: Applied patch for bug #1772613 (RingSet.getConnectedRings() returns duplicate rings) and added a test case.
16:10 CIA-1 cdk: Also had to correct test case testGetConnectedRings_IRing() in RingSetTest.java.
16:16 dleidert joined #cdk
18:04 carsten joined #cdk
18:09 CIA-1 cdk: mario_baseda * r8683 /trunk/cdk-taverna/src/main/ (4 files in 3 dirs): Classes modified/added
18:33 steinbeck joined #cdk
19:10 mashuuk joined #cdk
19:10 mashuuk Hi
19:11 mashuuk where I can find online k-mer or k-tuple implementation in order to check if mine works fine ?
19:36 shk3 joined #cdk
20:26 steinbeck left #cdk

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