Camelia, the Perl 6 bug

IRC log for #cdk, 2007-12-10

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All times shown according to UTC.

Time Nick Message
02:40 CIA-31 jmol: hansonr * r8760 /trunk/Jmol/src/ (JmolApplet.java org/jmol/viewer/Jmol.properties): version=11.3.55_dev # bug fix: applet.loadInline(String[] models) messes up
02:51 CIA-31 jmol: hansonr * r8761 /branches/v11_2/Jmol/src/ (JmolApplet.java org/jmol/viewer/Jmol.properties): version=11.2.15_dev # bug fix: applet.loadInline(String[] models) messes up
04:41 CIA-31 jmol: hansonr * r8762 /trunk/Jmol/src/ (JmolApplet.java org/jmol/viewer/Jmol.properties): (log message trimmed)
04:41 CIA-31 jmol: version=11.3.55_dev
04:41 CIA-31 jmol: # bug fix: applet.loadInline(String[] models) messes up
04:41 CIA-31 jmol: # this involves the fact that Safari will deliver null pointer when it
04:41 CIA-31 jmol: # mistakenly matches a String[] signature to a String, or vice-versa.
04:41 CIA-31 jmol: # The solution is to use
04:41 CIA-31 jmol: #
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07:17 egonw moin
07:30 carsten joined #cdk
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08:49 steinbeck joined #cdk
08:50 egonw hi steinbeck
08:50 steinbeck moin egonw
08:51 egonw one cite for CMLSpect already :)
08:51 egonw ok, it's sort of internal :)
08:51 steinbeck who cited it?
08:51 egonw robert
08:51 egonw with the specview applet paper
08:51 egonw +j
08:51 steinbeck ack
08:51 steinbeck chemistry central journal, that was, right?
08:52 egonw right
09:02 thomas_ku joined #cdk
09:02 thomas_ku moin
09:02 egonw hi thomas_ku
09:02 steinbeck moin
09:03 egonw thomas_ku: I have not been able to get the InChI code online in Taverna...
09:03 egonw the copy/paste of the jar does not seem to work out for me
09:03 egonw the unit test runs, though...
09:03 egonw so, consider it a patch for your branch
09:05 thomas_ku egonw: I have no idea why it will not work! I will have a look on it later today. To try to find the problem. If I won't find one I will copy it into the main branch
09:06 egonw OK, ping me if you do find problems
09:08 thomas_ku ok
09:59 thomas_ku egonw:
09:59 egonw yes?
10:00 thomas_ku didn't you added the inchi parser in the cdk.properties file?
10:00 thomas_ku or did you only forgot to commit?
10:00 egonw mom... will check if I forgot to commti that...
10:02 CIA-31 cdk: egonw * r9581 /branches/egonw/cdk-taverna-mb/sr​c/main/resources/cdk.properties: Added InChI to menu
10:02 CIA-31 cdk: egonw * r9582 /branches/egonw/cdk-taverna-mb/pom.xml: Attempt to create a local plugin site
10:02 egonw sorry
10:03 thomas_ku no problem
10:13 thomas_ku egonw: I can't find a problem currently... Have you looked into the faq of maven here:http://codehaus.org/~jvanzyl/maven2​/guides/getting-started/index.html  for deploying a maven jar
10:13 thomas_ku http://codehaus.org/~jvanzyl/maven2​/guides/getting-started/index.html
10:13 thomas_ku <dependency>
10:13 thomas_ku <groupId>org.apache.codehaus.plexus</groupId>
10:13 thomas_ku <artifactId>plexus-utils</artifactId>
10:13 thomas_ku <version>1.0.4</version>
10:13 thomas_ku </dependency>
10:13 egonw no, haven't had time for that
10:14 thomas_ku in the example there they have used this library for their scp command
10:14 thomas_ku perhaps you have to add this too to your pom file in order to use scp within maven
10:14 thomas_ku but i am not sure
10:15 thomas_ku also I am not sure if you have to set up the settings file for maven which contains your username and pwd
10:16 thomas_ku why the copy paste do not work I can not tell you currently! I didn't found an error up to now
10:19 egonw no worry...
10:19 egonw I will try to find time to set up a local plugin site...
10:19 egonw that's proven technology :)
10:19 thomas_ku ;-)
10:20 egonw steinbeck: I think any time is fine for me...
10:20 steinbeck ack
10:20 egonw steinbeck: as far as I can see now, at least
10:20 steinbeck please email (reply-all) :-)
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10:22 thomas_ku egonw: I just tried to compile you branch on my machine and got this error
10:22 thomas_ku JNI InChI has failed to load the native libraries required.
10:22 thomas_ku The most common problems are either the native library files being placed in
10:22 thomas_ku locations that JNI InChI does not know to search, or needing recompiling for
10:22 thomas_ku your system.
10:22 thomas_ku ERROR MESSAGE: Error loading InChI library: /home/thomas/.m2/repository/org/opens​cience/cdk/1.0.2/libinchi.so.1.01.00: Can't load IA 32-bit .so on a AMD 64-bit platform
10:22 thomas_ku JNI InChI has failed to load the native libraries required.
10:23 thomas_ku is it possible that this causes your problems within taverna?
10:25 egonw ah.... you run a 64 bit macihne...
10:25 egonw yeah... that won't work... sorry...
10:25 egonw ask Sam Adams via the mailing list for 64 bit support...
10:25 egonw or, we should consider the Rich approach with NestedVM...
10:26 thomas_ku thats not good!!
10:26 thomas_ku ;-(
10:27 thomas_ku a question where does the libinchi.so comes from?
10:27 thomas_ku does the cdk contains this lib?
10:27 masak` joined #cdk
10:29 egonw yes
11:05 CIA-31 blueobelisk: pansanel * r226 /structures/trunk/src/index.xml: Adding spanish translations
11:07 CIA-31 blueobelisk: pansanel * r227 /structures/trunk/xml/l10n.xml: Spanish translation added
11:10 egonw lunch time
11:20 steinbeck left #cdk
11:41 jpansanel moin
11:41 jpansanel egonw : could you tell me the dutch translation for macrocycles ?
11:42 egonw good one
11:42 egonw not sure
11:42 egonw refers to large ring system,  right?
11:43 jpansanel yes
11:43 egonw "Grote ringsystemen"
11:43 egonw is the best I can think of right now
11:43 jpansanel thanks
11:46 jpansanel ingvormig macromolecuul ?
11:46 jpansanel +r
11:46 egonw possibl
11:46 egonw y
11:47 egonw thoug ringvormig is uncmmon
11:47 egonw bbl
11:48 jpansanel ok
11:50 CIA-31 blueobelisk: pansanel * r228 /structures/trunk/src/ (34 files in 32 dirs):
11:50 CIA-31 blueobelisk: Spanish translation added
11:50 CIA-31 blueobelisk: Dutch translation added for Macrocycles
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13:54 CIA-31 bioclipse: biocoder * r4449 /trunk/plugins/net.bioclipse.statistics/sr​c/net/bioclipse/model/MatrixResource.java: Enforced using of US locale when parsing matrices with java.util.Scanner for uniform behaviour.
14:00 CIA-31 bioclipse: ospjuth * r4450 /branches/bioclipse2/chemoinformatics/net.biocl​ipse.jmol/src/net/bioclipse/jmol/views/outline/ (6 files): New model for the JmolContentOutline View wrapping Jmol model classes
14:05 CIA-31 bioclipse: ospjuth * r4451 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.jmol/ (10 files in 5 dirs): Implemented new object model in JmolOutlineView and started working on reverse selections in Jmol to propagate to Outline
14:10 CIA-31 bioclipse: carl_masak * r4452 /trunk/plugins/net.bioclipse.statistics/sr​c/net/bioclipse/model/MatrixResource.java:
14:10 CIA-31 bioclipse: [MatrixResource.java]
14:10 CIA-31 bioclipse: * extract method
14:23 CIA-31 bioclipse: biocoder * r4453 /trunk/plugins/net.bioclips​e.chart/src/net/bioclipse/ (chart/ChartUtils.java plugins/views/ChartView.java):
14:23 CIA-31 bioclipse: ChartUtils: Organized imports, made mouse event handling windows compatible (still have to re-test on mac)
14:23 CIA-31 bioclipse: ChartView: Organized imports.
14:31 CIA-31 bioclipse: ospjuth * r4454 /branches/bioclipse2/chemoinformatics/ne​t.bioclipse.jmol/src/net/bioclipse/jmol/ (2 files in 2 dirs): Only listen for selections in our selected ContentOultineAdapter and the other way around.
14:35 CIA-31 bioclipse: ospjuth * r4455 /branches/bioclipse2/chemoinformati​cs/net.bioclipse.jmol/src/net/biocl​ipse/jmol/editors/JmolEditor.java: Allowed for selections of multiple models (frames).
15:00 jpansanel egonw : did you saw this error :
15:00 jpansanel index.xml:8: element title: validity error : Value "nl" for attribute lang of title is not among the enumerated set
15:02 dleidert maybe you need to replace lang with xml:lang?
15:03 jpansanel I'm using xml:lang
15:03 dleidert which file are we talking about?
15:03 jpansanel <title xml:lang="nl">Aromaten</title>
15:03 jpansanel in chemical structure, each index.xml file
15:04 dleidert yupp
15:04 dleidert your index.dtd says:
15:04 dleidert <!-- Lang attribute value -->
15:04 dleidert <!ENTITY % Lang "(en|fr|de|es)">
15:05 dleidert there is no nl value
15:05 jpansanel ok
15:05 jpansanel is it a simple way to include value from ISO 3166 ?
15:05 jpansanel thanks
15:05 jpansanel for this fix
15:06 dleidert why do you define it yourself?
15:06 dleidert xml:lang is defined as part of XML (to my knowledge)
15:06 jpansanel ok
15:06 jpansanel I can simply remove the ENTITY line ?
15:07 dleidert mom
15:08 dleidert BTW: you should write a catalog.xml and deliver it
15:09 dleidert hm, no, you need to specify xml:lang as attribute
15:10 jpansanel ok
15:11 dleidert most common seems: xml:lang    NMTOKEN        #IMPLIED
15:11 jpansanel ok
15:37 CIA-31 bioclipse: biocoder * r4456 /trunk/plugins/net.bioclipse.chart/src​/net/bioclipse/chart/ChartUtils.java: ChartUtils is now making a decision based on which OS is running on where to put the mouse handler.
15:49 CIA-31 bioclipse: biocoder * r4457 /trunk/plugins/net.bioclipse.chart/src​/net/bioclipse/chart/ChartUtils.java: minor
16:06 CIA-31 bioclipse: ospjuth * r4458 /branches/bioclipse2/chemoinformatics/net.biocl​ipse.jmol/src/net/bioclipse/jmol/views/outline/ (4 files): Fixed selections from chains without ID
16:19 CIA-31 cdk: rajarshi * r9583 /trunk/cdk/tools/nightly.py: Updated to generate nightly build of jchempaint
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17:03 CIA-31 bioclipse: ospjuth * r4459 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.jmol/ (7 files in 3 dirs): Added propertysource for Chain and made only chains without ID appear if no other chains
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20:08 CIA-31 jmol: aherraez * r8763 /trunk/Jmol/src/org/jmol/translation/ (Jmol/es.po JmolApplet/es.po): Spanish
20:15 edrin joined #cdk
22:51 CIA-31 bioclipse: edrin_t * r4460 /trunk/xws-client/src/net/bioclipse/xws/client/ (9 files in 5 dirs): continue

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