Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-05-27

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All times shown according to UTC.

Time Nick Message
04:16 egonw joined #bioclipse
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08:26 jonalv egonw: around?
08:26 * jonalv and olas need your help
08:33 * egonw will have a meeting shortly, and just got back from one...
08:33 egonw what's up?
08:33 egonw you got my email this morning?
08:33 jonalv did you get an stacktrace?
08:33 egonw I can confirm JCP tab in SDF editor working...
08:33 egonw yes
08:34 jonalv could you share?
08:34 jonalv I don't seem to get one...
08:34 jonalv it's working once, as soon as you change and change back it's grey for me
08:34 egonw http://cdk.pastebin.com/d27ebeb62
08:34 egonw jonalv: yes, I have that too...
08:35 egonw have been debugging that this weekend, without success :(
08:35 egonw let me see which of the traces belongs to the greying...
08:35 egonw or at least happens around that time...
08:35 egonw (if time permits...)
08:39 egonw oi, an exception deep inside Swing code:
08:39 egonw http://cdk.pastebin.com/m7e7b097f
08:39 egonw that's when I get when getting the grey tab
08:42 jonalv aouch
08:46 egonw my guest has arrived
08:46 egonw will go offline to another room for a meeting...
08:46 egonw but with a bit of luck, I'll be online...
08:46 jonalv cya
08:57 egonw joined #bioclipse
09:16 CIA-46 bioclipse: jonalv * r5703 /bioclipse2/trunk/plugins/net.bioclips​e.cdk10.sdfeditor/src/net/bioclipse/cd​k10/sdfeditor/editor/SDFEditor.java: added some whitespace and fixed some indentation
09:28 jonalv egonw, how do you get to see that stack trace?
09:32 egonw int he eclipse console
09:32 egonw got to go offline for a while
09:32 egonw bbl
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09:46 CIA-46 bioclipse: Annzi * r5704 /bioclipse2/trunk/plugins/net.bioclipse.logg​er/src/net/bioclipse/logger/Activator.java: Created a workaround for reading OSGI properties on logger startup. It seems on windows we need to look up some paths via URL.
09:46 CIA-46 bioclipse: jonalv * r5705 /bioclipse2/trunk/plugins/net.bioclips​e.cdk10.sdfeditor/src/net/bioclipse/cd​k10/sdfeditor/editor/SDFEditor.java: SDF-editor. Fixed cashed swap between tabs with the same mol selected
09:48 * jonalv thinks olas might be using Annzis computer... :)
09:54 * egonw will have lunch now
10:41 egonw joined #bioclipse
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11:35 olas joined #bioclipse
11:36 olas egonw: around?
11:36 olas I get: DEBUG - javax.xml.parsers.FactoryConfigurationError: Provider org.apache.xerces.jaxp.SAXParserFactoryImpl not found
11:36 olas when parsing an SDF using cdk (not cdk10)
11:37 olas In fact, I get it for trying to parse all sdfiles in bioclipse
11:38 olas egonw: let me know when you get back
11:38 jonalv I can't get org.openscience.sdk to compile at all. It compiles for you?
11:38 olas yes
11:38 olas will do update classpath
11:38 olas yes
11:39 olas did you foloow the wiki page?
11:39 olas run ant task javacc?
11:39 olas then hit refresh
11:39 jonalv huh?
11:39 olas then update CP
11:39 olas see wiki page
11:39 olas by egon
11:39 jonalv nope the wiki must have been updated since I last checked it...
11:40 olas ok
11:41 olas what jar is: org.apache.xerces.jaxp.SAXParserFactoryImpl in?
11:41 olas hmm
11:41 olas xml-apis.jar
11:41 olas which is included
11:41 olas damn
11:42 olas indeed a strange error
11:42 jonalv hhat is a havacc ask and how do I find it?
11:42 jonalv hm one more time
11:42 jonalv what is a javacc task and how do I find it?
11:43 olas right-click build.xml, choode Run ant task...
11:43 olas select javacc
11:47 olas egonw: HELP
11:55 olas egonw: problem resolved (but you will not like the answer)
11:55 olas ping me when back
11:56 egonw olas: sorry... in the middle of a meeting...
11:56 egonw will ping you when done...
12:03 olas ok
12:05 CIA-46 bioclipse: jonalv * r5706 /bioclipse2/trunk/plugins/net.bioclipse.​structuredb.tests/META-INF/MANIFEST.MF: updated structuredb tests to use the new cdk solution
12:05 CIA-46 bioclipse: ospjuth * r5707 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui.tests/src/ (2 files in 2 dirs): Added new test file (SDF) and test for getChildren().
12:05 CIA-46 bioclipse: ospjuth * r5708 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui/plugin.xml: Removed obsolete ref to JCP from cdk.ui.
12:09 olas egonw: can we update the MDLReader of CDK10 to the version in cdk trunk?
12:10 olas seems it's been updated to support more files
12:10 olas now cdk10 dies on certain SDF that passes in cdk
12:10 olas egonw: please advice when you can
12:21 CIA-46 bioclipse: ospjuth * r5709 /bioclipse2/trunk/plugins/net.bioclipse.logg​er/src/net/bioclipse/logger/Activator.java: Corrected case when OSGI property ends in slash (valid only on Mac it seems).
12:59 CIA-46 bioclipse: ospjuth * r5710 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui.tests/src/ (3 files in 2 dirs): Updated test file mal.sdf.
13:29 olas left #bioclipse
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14:05 CIA-46 bioclipse: ospjuth * r5711 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.ui.tests/src/net/bioclipse/cdk/ui/​tests/MoleculeContentProviderTest.java: Updated test to reflect latest testfile mal.sdf.
14:25 egonw olas: ping
14:27 olas pong
14:28 egonw using the cdk-trunk MDLReader with cdk10 is a problem
14:28 egonw back we could backport patches to the cdk1.0.x/ branch
14:29 olas as you like
14:30 olas did you get my email?
14:30 egonw reading my email now...
14:32 egonw about xercesImpl?
14:33 egonw ok, noted
14:33 egonw please file a bug report for CDK on that
14:33 egonw so that I won't forget...
14:33 * egonw is abuot to go home
14:33 egonw had a busy day
14:35 olas ok
14:35 olas see you tomorrow
14:35 olas Gpox is working hard on the JCP in SDF problem
14:35 olas oh, egonw:
14:35 olas JCP is not set dirty
14:35 olas even in MDLEditor
14:35 olas and we can't see where it is
14:35 olas anyway
14:35 olas talk tomorrow
14:36 egonw olas: that used to be working...
14:36 egonw not sure what broke that bit...
14:36 egonw or why, but will explore...
14:36 olas ok
14:36 olas good
14:36 egonw please do file the xercesImpl bug report...
14:41 olas ok
14:54 malick left #bioclipse
15:30 CIA-46 bioclipse: ospjuth * r5712 /bioclipse2/trunk/plugins/net.bioclipse.qsar/ (5 files in 4 dirs): MoleculesPage now asks for molecules using new WSFileDialog.
15:31 CIA-46 bioclipse: ospjuth * r5713 /bioclipse2/trunk/plugins/net.bioclipse.ui/sr​c/net/bioclipse/ui/dialogs/WSFileDialog.java: Updated dialog with ability to filter out unwanted IResources.
16:27 CIA-46 bioclipse: jonalv * r5714 /bioclipse2/trunk/plugins/ne​t.bioclipse.structuredb/src/ (3 files in 3 dirs): Swapped fingerprintrepresentation in database from VARCHAR to BINARY as a first step in moving the fingerprint matching to the database layer
16:47 CIA-46 bioclipse: jonalv * r5715 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Wrote DAO test for fingerprint substructure search query. Moving this to the database should speed things up a bit.
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