Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-08-03

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All times shown according to UTC.

Time Nick Message
06:58 olass joined #bioclipse
07:00 egonw joined #bioclipse
07:01 egonw moin
07:01 zarah oh hai egonw
07:04 Gpox joined #bioclipse
07:04 egonw hi Gpox
07:04 egonw had a nice holiday?
07:04 Gpox yeah
07:05 jonalv joined #bioclipse
07:08 egonw Gpox: whenever you're done with breakfast, I like a short chat for updates...
07:09 egonw Gpox: btw, can you join me and Ola tomorrow at the BMC? for a longer catch up ... :)
07:09 Gpox yes
07:09 jonalv o/
07:09 zarah jonalv: You have new messages. Write '/msg zarah @messages' to read them.
07:11 egonw Gpox: yes, about being ready, or about tomorrow?
07:12 Gpox both :)
07:12 egonw ah, excellent :)
07:12 egonw I have fully ported jcpprim to CDK master now...
07:12 egonw and will this morning update Bioclipse master to use that branch
07:13 Gpox nice
07:13 egonw I would like to ask you to start using this branch too:
07:13 egonw bioclipse-2.1.x
07:13 egonw http://pele.farmbio.uu.se/cgi-bin/git​web.cgi?p=jchempaint-primary.git;a=sh​ortlog;h=refs/heads/bioclipse-2.1.x
07:13 zarah egonw's link is also http://tinyurl.com/l72447
07:13 egonw mind you, that this branch should be considered as patch...
07:14 egonw and that we'll have to frequently rebase to keep up with CDK master upstream...
07:14 olass egonw: why is that branch not on github?
07:14 egonw I've organized the jcpprim patches around the cdk modules they are in...
07:14 egonw numbering is following a historic pattern, not logical patch based error
07:15 egonw olass: because this is not actually what goes into your eclipse workspace
07:15 olass aha
07:15 egonw olass: instead, cdk-eclipse is run on this to update cdk-exports/trunk
07:15 olass so a bleeding-edge-patch
07:15 egonw yes
07:16 olass sounds bloody
07:16 egonw olass, Gpox: bioclipse-2.1.x is the place where we can put patches that have not made it into cdk upstream
07:16 egonw e.g. not passed the review process yet
07:16 olass ok
07:16 egonw e.g. that N atom type fix :)
07:17 * olass really want a bugfix out asap...
07:18 egonw yes
07:18 egonw same here
07:18 egonw will do good testing today
07:18 egonw after the bc2 master updating
07:19 olass super
07:19 jonalv so, who will be at bmc tomorrow? Can we have some sort of status meeting?
07:19 olass yes
07:19 olass sounds good
07:19 olass all except masak
07:20 egonw olass, Gpox: btw, there is a similar set up for bioclipse-2.0.x:
07:20 egonw http://pele.farmbio.uu.se/cgi-bin/gitweb.cgi?p=​cdk.git;a=shortlog;h=refs/heads/bioclipse-2.0.x
07:20 zarah egonw's link is also http://tinyurl.com/lv6czt
07:21 egonw olass, Gpox: you can see the tag for the most recent update with cdk-eclipse
07:21 mgerlich joined #bioclipse
07:21 egonw this branch too, will have to undergo frequent rebasing
07:31 sneumann joined #bioclipse
07:40 CIA-63 bioclipse.cheminformatics: Egon Willighagen master * r60abe4e / plugins/net.bioclipse.jmol/jars/Jmol.jar : Upgraded to bug fix release 11.8.RC4 - http://bit.ly/PJBaW
07:41 egonw ummm... crap
07:41 egonw wrong commit message :(
07:41 egonw 11.8.RC4 is *not* a mere bug fix...
07:41 egonw but the whole brand new 11.8 series
07:42 egonw with a whole set of new goodies
08:07 CIA-63 bioclipse.cheminformatics: Ola Spjuth master * r73c838f / plugins/net.bioclipse.cdk.ui.sdfedit​or/src/net/bioclipse/cdk/ui/sdfedito​r/describer/MolTableDescriber.java : MolTableEditor is only preferred if list contains molecules, so check the first entry. - http://bit.ly/cBuCk
08:26 shk3 joined #bioclipse
09:02 CIA-63 bioclipse.cheminformatics: Egon Willighagen master * rb14df1a / (33 files): Added patches local to Bioclipse which may or may not be ported upstream yet - http://bit.ly/99N7Z
09:02 CIA-63 bioclipse.cheminformatics: Egon Willighagen master * r0bb28b8 / (20 files): Removed redundant patches - http://bit.ly/aQQen
09:26 CIA-63 bioclipse.cheminformatics: Egon Willighagen master * r308f4f4 / (6 files in 3 dirs): Updated for API changes from 11.6 to 11.8: added new interface methods and remove openFileError() - http://bit.ly/tVvfH
09:31 egonw Apple is just as worse as Microsoft, and only show interest in their profit :(
09:31 * egonw is happy to not have a mac
09:32 jonalv egonw: what has apple done now?
09:32 egonw http://tweakers.net/nieuws/61594/ap​ple-tracht-tienermeisje-met-ontplof​fende-ipod-monddood-te-maken.html
09:32 zarah egonw's link is also http://tinyurl.com/kw2yac
09:32 egonw they only wanted to refund a 11-year old girl's iPod if they would sign never to talk about the issue to anyone
09:32 * egonw thinks they call that a cover up
09:33 jonalv http://translate.google.com/translate?js=y&pr​ev=_t&hl=en&ie=UTF-8&u=http%3A%2F%2Ft​weakers.net%2Fnieuws%2F61594%2Fapple-tracht-tiene​rmeisje-met-ontploffende-ipod-monddood-te-maken.h​tml&sl=auto&tl=en&history_state0=
09:33 zarah jonalv's link is also http://tinyurl.com/m7o6nr
09:34 jonalv google++
09:37 egonw it's sad that succesful companies think they need practices like this...
09:38 jonalv egonw: yes
10:04 jonalv @pelezilla ui.open sequences
10:04 zarah jonalv: Zarro boogs found.
10:04 jonalv @pelezilla ui open
10:04 zarah [761] JsEditor edits a file backend, ... http://tinyurl.com/np3zzr
10:04 zarah [1454] Unable to parse PubchemXML wit... http://tinyurl.com/n5xm3o
10:04 zarah [222] Ability to cancel a JS call tha... http://tinyurl.com/cdg6w5
10:04 zarah [425] js console throws strange excpe... http://tinyurl.com/deomud
10:04 zarah [1421] Can not open ActionHistory view   http://tinyurl.com/lj7z35
10:04 zarah Entire list (34) at http://tinyurl.com/nc334w
10:04 jonalv @pelezilla ui open sequences
10:04 zarah jonalv: I couldn't find anything on 'ui open sequences' in the database.
11:14 jonalv egonw: around?
11:23 egonw in 10 minutes
12:26 egonw shk3: ping
12:26 egonw shk3: I'm going to update bioclipse.cheminformatics soon
12:26 egonw with cdk master + jcpprim patch
12:27 egonw which will require seneca plugins to be updated if you have those depend on bioclipse 2.1 instead of the 2.0.x branch
12:27 egonw affected are the plugins: .seneca and .specmol
13:44 zarah joined #bioclipse
13:51 CIA-63 bioclipse.structuredb: jonalv master * rc459a0b / plugins/net.bioclipse.structuredb/src/net/biocli​pse/structuredb/business/StructuredbManager.java : changed System.out.println to logger.debug call - http://bit.ly/9DD2w
13:51 CIA-63 bioclipse.structuredb: jonalv master * rcdd6b21 / plugins/net.bioclipse.structuredb/src/n​et/bioclipse/structuredb/Activator.java : tracker.getServices returns null instead of an empty array if no services are tracked so must check for null before iterating over it... - http://bit.ly/xE0Sl
13:51 CIA-63 bioclipse.structuredb: jonalv master * r3ed01ff / plugins/net.bioclipse.structuredb/src/net/bioclips​e/structuredb/viewer/DatabaseContentProvider.java : Labels never have childen - http://bit.ly/13hFpi
14:19 jonalv hm qsar.xml in a qsar project validates as correct cml. What's up with that?
14:20 egonw file a bug report, please
14:25 egonw all: I am pushing CDK 1.3.0 + the JChemPaint-Primary patch to bioclipse.cheminformatics
14:26 jonalv sounds good
14:26 egonw Gpox: in cdk-externals/trunk/patches are patches that were in Bioclipse SVN only, and not in upstream
14:26 egonw or at least some...
14:26 egonw Gpox: we need to check those one by one for appropriateness...
14:26 CIA-63 bioclipse.cheminformatics: Egon Willighagen master * r09ed0e4 / (1062 files in 255 dirs): Uploaded CDK 1.3.0 with JChemPaint-Primary patch - http://bit.ly/kKPpv
14:26 CIA-63 bioclipse.cheminformatics: Egon Willighagen master * r0585e82 / (8 files in 8 dirs): Updates for JChemPaint-Primary based on CDK 1.3.0: 1. added new dependencies; 2. updates due to a few API changes. - http://bit.ly/irhqV
14:26 egonw all: this brings in new plugins...
14:26 egonw which you need to add to your workspace
14:33 olass egonw: ack
14:38 jonalv olass: I am trying to reproduce you trouble with the qsar plugin but I am afraid that you will have to shedule some time to help me tomorrow... :(
14:38 olass ok
14:38 olass it's ok
14:39 olass autobuild is turned off by default now
14:39 olass makes it much better
14:39 olass but users can still turn it on...
14:39 jonalv it seems that abort is not working in situations wither
14:39 jonalv |in all situations
14:39 olass hmm, possibly
14:54 * egonw still cannot run the Plugin unit tests...
14:55 olass egonw: 32 bits?
14:55 egonw 64 bit
14:55 egonw this really sucks
15:13 CIA-63 bioclipse: shk3 * r11710 /bioclipse2/trunk/plugins/net.biocli​pse.seneca/src/net/bioclipse/seneca/ (3 files in 2 dirs): the ga is making progress
15:45 CIA-63 bioclipse.structuredb: jonalv master * r99413d5 / (4 files in 3 dirs):
15:45 CIA-63 bioclipse.structuredb: make it possible to get number of molcules not only with a certain Label but any
15:45 CIA-63 bioclipse.structuredb: Annotation and use that call for doing progress reporting when deleting all
15:45 CIA-63 bioclipse.structuredb: molecules with a certain annotation. However it doesn't seem to work and the
15:45 CIA-63 bioclipse.structuredb: whole thing should probably be done with one big SQL statement... -
15:45 CIA-63 bioclipse.structuredb: http://bit.ly/2Y3Ive
16:03 steinbeck joined #bioclipse
16:03 egonw hi steinbeck
17:53 sneumann joined #bioclipse
18:08 egonw ok, that does it...
18:08 egonw bloody 64 bit...
18:08 egonw org.eclipse.core.runtime not satisfied ???!?!
18:45 thomasku joined #bioclipse
18:45 egonw hi thomasku!
18:45 thomasku hi egonw
18:46 thomasku just looking at the article...
18:46 egonw I was hoping to do the same tonie
18:46 egonw but Eclipse is acting up...
18:47 egonw and needed to do some unit test runs :(
18:48 thomasku yeah this week I have also not much time
18:48 thomasku :-(
18:48 thomasku but will do the best :-)
18:49 egonw yeah, saw your email
18:49 egonw I'm sure it will work out fine...
18:50 egonw we need to identify the problems in the argument first...
18:50 egonw I think Chris copied in all the examples ?
18:50 egonw from your thesis?
18:50 egonw OK, I need to take son to bed now...
18:50 egonw will be back in about 30 minutes
18:53 egonw olass: reinstalled Eclipse 3.4.2
18:53 egonw and I can now run the unit tests again
18:53 egonw bbl
18:53 thomasku ok
18:53 thomasku cu
19:19 egonw back
19:21 thomasku hi
19:21 zarah hello thomasku, you fantastic person you
19:21 thomasku egon
19:21 thomasku I had written the examples
19:22 thomasku and these are currently not all which were in my phd thesis
19:22 egonw but all from your thesis are in the paper too now?
19:23 thomasku no I need to add them
19:23 egonw would be great if you could do that
19:23 thomasku missing is the validation of atom typing
19:24 thomasku the diversity analysis
19:24 thomasku and the reaction enumeration
19:25 thomasku I will try to copy paste a bit... :-)
19:26 egonw thanx
19:45 thomasku egonw: would I only mention the example workflow of my thesis or should I also mention the results of the workflows?
19:45 egonw leave that as comment in the text
19:45 egonw using the markup suggested by Chris
19:46 egonw \remark{Should workflow results also be discussed?}
19:47 thomasku good point
20:20 CIA-63 bioclipse.cheminformatics: Egon Willighagen master * r6278840 / plugins/net.bioclipse.cdk.business/src/ne​t/bioclipse/cdk/business/CDKManager.java : Fixed inconsistency between loadMolecule() and loadMolecules(): both should sanatize the input - http://bit.ly/q78Y0
20:20 CIA-63 bioclipse.cheminformatics: Egon Willighagen master * rc23b1c1 / plugins/net.bioclipse.cdk.business.te​st/src/net/bioclipse/cdk/business/tes​t/AbstractCDKManagerPluginTest.java : Updated for implicit hydrogens now being added by loadMolecule[s]() - http://bit.ly/1KOzjD
20:20 CIA-63 bioclipse.cheminformatics: Egon Willighagen master * r2cf3117 / plugins/net.bioclipse.cdk.business.te​st/src/net/bioclipse/cdk/business/tes​t/AbstractCDKManagerPluginTest.java : No need to perceive aromaticity twice: loadMolecule() already does this for MDL molfiles - http://bit.ly/38KdTD
20:21 CIA-63 bioclipse.cheminformatics: Egon Willighagen 2.0.x * r2951663 / plugins/net.bioclipse.cdk.business/src/ne​t/bioclipse/cdk/business/CDKManager.java : Fixed inconsistency between loadMolecule() and loadMolecules(): both should sanatize the input - http://bit.ly/8EK6J
20:21 CIA-63 bioclipse.cheminformatics: Egon Willighagen 2.0.x * r5a86279 / plugins/net.bioclipse.cdk.business.te​st/src/net/bioclipse/cdk/business/tes​t/AbstractCDKManagerPluginTest.java : Updated for implicit hydrogens now being added by loadMolecule[s]() - http://bit.ly/129sgb
20:21 CIA-63 bioclipse.cheminformatics: Egon Willighagen 2.0.x * r42a8fe2 / plugins/net.bioclipse.cdk.business.te​st/src/net/bioclipse/cdk/business/tes​t/AbstractCDKManagerPluginTest.java : No need to perceive aromaticity twice: loadMolecule() already does this for MDL molfiles - http://bit.ly/120Bsa
20:22 olass egonw: you seem to be on track with unit testing! Excellent!
20:22 egonw yeah...
20:22 egonw I just had to reinstall Eclipse
20:22 egonw and left with a messed up grouping into working sets...
20:22 egonw that's all
20:23 thomasku egon have to leave now
20:23 olass so 3.5 is problematic when it comes to unit tests...
20:23 olass hi thomasku
20:23 egonw no, this is 3.4
20:23 olass is all well?
20:23 thomasku will be online tomorrow or on wed. again
20:23 thomasku hi olass
20:23 egonw bioclipse2 does not run in 3.5 at all
20:23 egonw thomasku: ack
20:23 olass oh
20:23 egonw thomasku: I plan to take a day off on Wed and go to Stockholm
20:23 olass egonw: will go to bed now
20:24 egonw olass: ack
20:24 olass see you tomorrow at BMC
20:24 olass will be there at 9
20:24 egonw thomasku: thanx for the commits!
20:24 olass g'night
20:24 thomasku ok than we will see
20:24 egonw olass: I think I'll be there at 10
20:24 thomasku no prob
20:24 thomasku cu

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