Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-10-08

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All times shown according to UTC.

Time Nick Message
05:40 Gpox joined #bioclipse
05:43 Gpox joined #bioclipse
06:49 egonw joined #bioclipse
07:51 egonw OK, here goes...
07:54 jonalv joined #bioclipse
07:55 jonalv hi
07:55 zarah hi jonalv
08:04 egonw jonalv: that patch is only about the annotation, right?
08:04 egonw no other changes I need to make, correct?
08:05 jonalv nope only those two annotations
08:08 * egonw wonders if he should dive into the Intrepid betas
08:09 egonw I've always upgrade about a month ahead of release...
08:09 jonalv haha
08:10 jonalv I am actually running HArdy at home. I feel like an early adopter... :)
08:10 jonalv *lol*
08:12 egonw http://feedproxy.google.com/~r/D​ilbertDailyStrip/~3/jc8hd5x-_hQ/
08:12 zarah egonw's link is also http://tinyurl.com/4gd6ff
08:14 CIA-30 bioclipse: egonw * r7253 /bioclipse2/trunk/ (395 files in 159 dirs): Merge branch 'add38cdkPlugins'
08:15 thomasku joined #bioclipse
08:15 egonw hi thomasku
08:16 egonw OK, that's it...
08:16 egonw one simple patch
08:16 egonw a day of work...
08:16 egonw yeah, check that commit line once more:
08:16 egonw "395 files in 159 dirs" !
08:17 egonw let me know about problems :)
08:19 thomasku moin
08:19 zarah hi thomasku
08:25 egonw and slowly I am waking up
08:47 jonalv egonw++
08:52 jonalv egonw: I just updated... things are not compiling... uhm what's the new world order? :)
08:54 egonw did you remove the org.openscience.cdk plugin, and add the 150 new ones?
08:54 egonw check the bioclipse/cdk-externals folder
08:54 jonalv uhm not removed no...
08:55 jonalv oh I think I got things to compile
08:55 jonalv nm
08:58 egonw are you at UU?
08:59 egonw oh, nm
08:59 olas joined #bioclipse
08:59 olas moin
08:59 zarah hi olas
09:01 egonw hi olas
09:01 egonw [10:14] <CIA-30> bioclipse: egonw * r7253 /bioclipse2/trunk/ (395 files in 159 dirs): Merge branch 'add38cdkPlugins'
09:01 * olas is scared
09:04 olas egonw: there's freshly brewed coffee available again...
09:04 egonw great
09:05 jonalv olas: COME HERE!
09:05 olas ?
09:05 jonalv uhm hang on
09:06 olas ?
09:06 * olas is confused
09:07 jonalv nvm is got a little confused there for a while
09:07 jonalv I thoought we had a problem...
09:07 jonalv we do but not as big as I though...
09:07 olas who is nvm and why did he get confused?
09:07 olas ok
09:08 jonalv s/is/I
09:08 egonw getting coffee
09:11 shk3 i will try to avoid updating my bioclipse checkout as long as possible
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09:20 edrin joined #bioclipse
09:20 edrin hi
09:21 zarah hi edrin
09:22 olas hi edrin
09:23 edrin hi olas
09:42 egonw shk3: why?
09:43 CIA-30 bioclipse: jonalv * r7254 /bioclipse2/trunk/ (7 files in 5 dirs): updated dependencies and switched jumbo jar in net.bioclipse.cml
09:44 gilleain joined #bioclipse
09:45 jonalv egonw: will you be removing org.openscence.cdk from svn?
09:47 gilleain Hello. Also let me get the steps right (if not their order):
09:47 gilleain 1) remove org.openscience.cdk project from bioclipse workspace
09:48 gilleain 2) download plugins from cdk-externals/trunk
09:48 egonw jonalv: yeah, thanx for the reminder
09:48 gilleain 3) also download the plugins like org.jama?
09:48 gilleain 4) profit
09:48 egonw re 3) -> which are available from cdk-externals/
09:49 gilleain Yup.
09:51 gilleain Hmm. It occurs to me that I should wait for the other 24 million pubchem compounds to download before checking out the 150 cdk plugins.
09:51 jonalv gilleain: hehe
09:59 * jonalv <- lunch
10:00 CIA-30 bioclipse: egonw * r7255 /bioclipse2/trunk/externals/: Removed svn:externals for CDK 1.2.x
10:21 shk3 egonw: jchempain-primary branch is from cdk 1.2, isn't it?
10:21 egonw yes
10:22 shk3 and the next jcp release will be based on that
10:22 shk3 (next meaning not the one from 1.0 i am going to do)
10:24 egonw yes, let's hope so...
10:24 egonw this next would be JCP 3.0 or 2.6
10:24 egonw you are working on JCP 2.4
10:24 egonw of which the development releases are 2.3.x
10:25 egonw btw, don't worry about releasing 2.3.4, 2.3.5, ...
10:25 egonw I'd rather see that, than new releases all named 2.3.3
10:34 shk3 i didn't do development releases
10:34 shk3 shall I do one?
10:34 gilleain shk3, egonw: http://gilleain.blogspot.com/20​08/10/cdk-renderer-forest.html
10:34 zarah gilleain's link is also http://tinyurl.com/4ngg28
10:34 shk3 nice
10:34 shk3 thanks
10:36 egonw shk3: well, you did put 2.3.3 version up for download, not?
10:36 egonw gilleain: hand made or with a tool?
10:36 egonw ah, nvm
10:36 egonw hand made
10:36 gilleain hand made with software?
10:36 egonw I see some merges that have not happedn yet
10:36 egonw gilleain: yeah, that kind
10:36 egonw the future 'head' made
10:36 gilleain I was tempted to label that side "THE FUTURE!"
10:37 egonw where we think, adn the software acts
10:37 shk3 egonw: just put it on wiki.cubic, not a formal release
10:37 egonw shk3: to me, any release counts
10:37 shk3 hm, but then I should have renamed it
10:37 egonw yes
10:37 shk3 where does the release number come from?
10:38 egonw that's what 2.3.x is for
10:38 egonw history
10:39 shk3 I meant: where do i tell the output file to have 2.3.4 or 2.3.4 in the name?
10:39 shk3 is it directly in build.xml?
10:40 egonw build.props I think
10:40 egonw mom
10:42 egonw $ more build.props
10:42 egonw version=1.0.4
10:42 egonw jcp.version=2.3.3
10:43 shk3 ok
10:43 shk3 another question:
10:43 shk3 what to do with this builder3d-tools module?
10:45 egonw can you be more specific?
10:49 shk3 remember the discussion on the list?
10:49 egonw no
10:49 egonw (sorry)
10:50 shk3 there is a module cdk-builder3d-tools in svn
10:51 shk3 this seems to be a duplication of a class in the builder3d package of cdk itself.
10:51 shk3 I used the one in cdk and it works.
10:51 shk3 this module has never been touched after checkin
10:51 shk3 and for me, it is unclear how to use it.
10:52 Gpox joined #bioclipse
10:52 shk3 module here really means project
10:52 shk3 same level in svn as cdk
10:53 egonw ah, ok, ic
10:53 egonw umm... it has no code that the builder3dtools module does not have too?
10:53 egonw if not, then I guess you could remove the project from SVN
10:54 shk3 no new code in there
10:55 gilleain this is a problem with branches and projects. Once created, they are rarely removed for fear of losing something...
10:56 gilleain Also, on a completely different topic : I give up - what do I do about the org.apache.log4j bundle dependency?
10:56 shk3 the class HandleRingSystemsFromFile in there is a copy of templateextractor
10:56 shk3 and was never changed after checkin
10:56 egonw gilleain: see this bug report:
10:57 egonw ...
10:57 gilleain ...
10:57 egonw https://sourceforge.net/tracker2/?func=detail&amp​;aid=2152883&amp;group_id=150681&amp;atid=778609
10:59 shk3 I think we can remove that project/module/whatever
10:59 shk3 since even you have no idea what it is about, it will never be used again
11:01 egonw check the log who added it and when
11:01 egonw then you know why it is there
11:02 gilleain thanks, those changes worked.
11:04 shk3 you did
11:04 egonw when?
11:04 egonw I guess at the last CDK workshop in Cologne
11:04 shk3 15.3.9´08
11:04 egonw when Christoph worked on the reindexing
11:04 shk3 comments:
11:04 shk3 More infrastructure
11:04 egonw 15.3.9´08 ??
11:04 shk3 and
11:05 shk3 Moved into new hierarchy
11:05 shk3 sorry
11:05 egonw that would be the move, I guess...
11:05 shk3 15.3.08
11:05 egonw older log
11:05 egonw SVN does not do that well..
11:05 egonw where was it moved from, and when was that original location created...
11:06 shk3 thee more instrastructure is the first commit message
11:06 shk3 that must to the initial checkin, no?
11:06 shk3 on the same day, there was moved into new hierarchy
11:06 shk3 and that's it
11:07 egonw oh... :)
11:07 egonw well, remove it
11:07 egonw thanx for checking these things
11:07 egonw WTF?!?!
11:08 shk3 just want to avoid too much stuff hang around
11:08 egonw I've been spending a couple of hours now trying to upload a presentation to slideshare.net :(
11:08 egonw without success :(
11:08 shk3 confuses and doesn't help
11:09 egonw true
11:13 gilleain Does the presentation rely on the many new cdk plugins? That might be why it's taking so long :-p
11:13 gilleain Oh, and I wrote up the steps to migrate here:
11:13 gilleain http://gilleain.blogspot.com/2008/10/s​teps-to-move-bioclipse-to-new-cdk.html
11:14 zarah gilleain's link is also http://tinyurl.com/3rzxh4
11:14 gilleain Might be better on the wiki, I suppose.
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11:18 egonw jonalv: did you commit those fixes to SVN?
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11:33 jonalv egonw: yes
11:33 egonw jonalv: tack
11:34 * gilleain <- lunch
11:43 jonalv egonw: ping me when you and Magnus are done :)
11:54 CIA-30 bioclipse: egonw * r7256 /bioclipse2/trunk/.gitignore: Git should also ignore all those autogenerated bin/ folders
11:55 jonalv shk3: cdk10 is not compiling for me for the moment...
11:55 jonalv shk3: Do you know anything about that?
11:56 CIA-30 bioclipse: egonw * r7257 /bioclipse2/trunk/cdk-externals/trunk/ (12 files in 12 dirs): Fixed log4j Require-Bundle/Import-Package problem (closes #2152883)
12:02 olas joined #bioclipse
12:27 shk3 jonalv: please update
12:34 egonw jonalv: ping
12:34 egonw jonalv: if you got a sec, might you come over?
12:34 jonalv egonw: k
12:50 egonw olas: please do send me the details for that EMBRACE workshop, so that I can register
12:51 olas got no yet
12:51 olas will do when I get it
13:01 egonw ah, OK
13:02 jonalv olas: me too :)
13:02 jonalv olas: but shouldn\t that be soon?
13:04 olas egonw: coffee here
13:05 jonalv hm tea...
13:13 egonw jonalv: btw, your fix was not working, it seems:
13:13 egonw Testcase: testCML(org.openscience.cdk.​io.ReaderFactoryTest):Caused an ERROR
13:13 egonw Resetting to invalid mark
13:13 egonw java.io.IOException: Resetting to invalid mark
13:13 egonw at java.io.BufferedInputStream.rese​t(BufferedInputStream.java:408)
13:13 egonw as found on:
13:13 egonw http://cheminfo.informatics.indiana.edu/~rguh​a/code/java/nightly-1.2.x/test/result-io.html
13:13 zarah egonw's link is also http://tinyurl.com/53jjtq
13:14 jonalv egonw: oh, it was working for our purposes...
13:14 egonw :)
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14:22 CIA-30 bioclipse: goglepox * r7258 /bioclipse2/trunk/plugins/ (6 files in 5 dirs): Fixed support for StructuredDB annotations in molecules editor and added text indicating generated coordinates in 2D editor.
14:33 olas joined #bioclipse
14:33 egonw olas: opentox.org
14:34 olas yes?
14:35 olas same as AMBIT
14:35 olas what's new here?
14:36 egonw larger consortium
14:36 egonw and no mention of Bioclipse (yet)
14:36 egonw anyway... no point, just a link
14:37 olas ack
14:38 * egonw is going home
14:38 egonw maybe I reach home today befor the sun sets
14:40 CIA-30 bioclipse: goglepox * r7259 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jche​mpaint/src/net/bioclipse/cdk/jchempaint/widgets/ (JChemPaintSWTWidget.java SWTRenderer.java): Moved 'generated' text to top left corner
14:40 egonw bye!
14:43 masak egonw++ # poetic: "reach home before the sun sets"
15:18 CIA-30 bioclipse: jonalv * r7260 /bioclipse2/trunk/plugins/net.bioclip​se.structuredb/src/net/bioclipse/stru​cturedb/DBMoleculesEditorModel.java: Implemented adapter for dbmolecule from sdfelement and slimed related code
15:48 olas bye
15:53 gilleain joined #bioclipse
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16:18 CIA-30 bioclipse: carl_masak * r7261 /bot/trunk/zarah.pl: [zarah] attempt at fixing death bug when stopping nonexistent task
16:19 zarah joined #bioclipse
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