Camelia, the Perl 6 bug

IRC log for #bioclipse, 2013-06-05

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
04:37 egonw joined #bioclipse
05:36 egonw joined #bioclipse
06:36 konditorn joined #bioclipse
06:37 egonw joined #bioclipse
06:59 egonw joined #bioclipse
07:02 zaetnick joined #bioclipse
07:27 sneumann joined #bioclipse
07:30 egonw joined #bioclipse
07:35 Gpox joined #bioclipse
07:46 egonw Gpox: ping
07:46 egonw Gpox: how does CDK 1.5 fit in the Bioclipse plans? In particular, I am seeing a need for CDK 1.5 OSGi bundles ...
07:47 egonw finally, after years and years, and in an unanticipated way, some more need for shared libraries...
08:09 Gpox egonw: I could create OSGi bundles for 1.5
08:09 egonw would be great
08:09 Gpox *I tried and it worked
08:10 egonw actually, it's become so stable now, that I would actually recommend a migration path for 2.6.x
08:10 egonw I am not sure what the current time line is...
08:10 egonw if already close to 2.6.1, then not...
08:10 egonw we want decent testing...
08:10 egonw but for 2.6.2 most certainly...
08:10 egonw John May is really doing excellent work
08:11 egonw Cytoscape/PathVisio can make use of the OSGi bundles too
08:11 Gpox we are planing a 2.6.1 relase realy soon(before summer)
08:11 egonw OK, then migration to 1.5 is certainly post 2.6.1
08:11 egonw OSGi bundles CDK 1.5 in August sound soon enough for me anyway
08:12 egonw but maybe it's just 15 minutes of Hudson config for you
08:12 egonw something else I wanted to ask...
08:12 egonw I am teaching RDF in a week or two...
08:12 egonw and for this I want to use Bioclipse
08:13 egonw and I was hoping you could rerun the Jenkins job to spit a cutting edge Bioclipse+OT+DS
08:13 egonw the job exists but last run was ages ago
08:13 egonw I can trigger it myself, but wanted to ping you first
08:15 Gpox http://pele.farmbio.uu.se/j​enkins/job/OpenTox_QSAR_DS right?
08:15 egonw right
08:16 Gpox updated to use cutting edge p2 site
08:16 egonw :)
08:16 Gpox hopefully it will build
08:17 egonw OK, one last thing, then...
08:17 egonw umm... make that two :)
08:17 egonw one is a notice
08:18 egonw the template stuff is working...
08:18 egonw Ola's code was wrong
08:18 egonw I send him updated code...
08:18 egonw not sure who will help him with templates drawing, but could you spread the info in the group?
08:19 egonw last thing is about CDK-JChemPaint
08:19 egonw you prob saw I released CDK-JCP 28
08:19 Gpox yes
08:19 egonw so, next up on that side is ensuring I really got all your patches, which I prob don't
08:19 egonw and clean up code (unit tests, JavaDoc) so that it can enter 1.5...
08:20 egonw I should be looking at your 2.6.x branch, right?
08:20 egonw this one?
08:21 egonw http://pele.farmbio.uu.se/cgi-bin/gitweb.cgi?p=​bioclipse-cdk.git;a=shortlog;h=refs/heads/2.6.x
08:22 egonw do you also have a rebased one?
08:22 egonw because it seems your patches are scattered in history...
08:22 Gpox http://pele.farmbio.uu.se/gitweb/?p=bioclips​e-cdk.git;a=shortlog;h=refs/heads/2.6.1-test
08:23 Gpox top 5 patches
08:24 Gpox I got some compile errors after applying klas's AtomTypeAwareSaturationChecker patch
08:24 egonw that also has older patches, or are those already in the cdk upstream, like this one? http://pele.farmbio.uu.se/gitweb/?p​=bioclipse-cdk.git;a=commit;h=96c94​2b60a6c65e659883d5658fe86251b400ca6
08:24 egonw [AtomTypeAwareSaturationChecker] yeah, I heard that...
08:24 egonw that I will have to look at too
08:25 egonw ok, thanx for the pointers!
08:31 Gpox 2.6.1-test should have all older patches it is based on cdk-jchecmpaint-28 witht he bioclipse specific patches re-applied on top
08:32 Gpox I can see no other patches from before cdk-jchempaint-26
08:33 egonw OK, well, may I miss an important patch, just ping me
08:51 Gpox egonw: cdk 1.5 OSGi bundles http://pele.farmbio.uu.se/bioclipse/cdk/1.5.x/
08:51 egonw super, thanx!
08:51 Gpox thre can be some issues with packages and classpath loading ( split packages)
08:52 egonw ack
08:53 egonw if you like, please send an email to cdk-devel about that...
08:53 egonw indicating the problem, and if the rest agrees (I do), we can mark these problems as genuine bugs
08:53 egonw it enforce that one java package only be in one cdk module
08:54 Gpox I don't know how common the sharing of packages by cdk-moduels
08:54 egonw neither do I :)
08:54 egonw it's not general, but certainly exists...
08:54 egonw e.g. for molecular descriptors...
08:55 egonw but now that OSGi is becoming so mainstream, we have to solve this
08:56 Gpox I belive it is true for jigsaw too. When ever that will come out
09:10 egonw :)
09:10 egonw OK, 1/5 patch in
09:10 egonw the oldest of the top 5 is just a merge patch
09:10 egonw so, 3 to go
09:11 egonw oh... cool... the next one is for the CDK itself... not the CDK-JChemPaint patch :)
09:20 egonw ok, third down
09:31 egonw Gpox: want to fix this message? "Ypdated radical spacing" -> http://pele.farmbio.uu.se/gitweb/?p​=bioclipse-cdk.git;a=commit;h=2a5f3​9cef293c9158dffd4d89ec68185bae0a2e2
09:31 egonw if not, I'll just apply :)
09:33 egonw and for this patch I have a suggestion:
09:33 egonw http://pele.farmbio.uu.se/gitweb/?p​=bioclipse-cdk.git;a=patch;h=14075d​cfa74589e3f6578c0a851a22f23a60188a
09:34 egonw it seems to be just about the mass number
09:34 egonw and then you can you use much more light weight (and faster):
09:34 egonw ... well, periodic table stuf...
09:34 egonw looking up the proper class
09:35 egonw PeriodicTable
09:36 egonw ummm... it's probably about the atomic number? or really the most common mass number, thus isotope?
09:38 jonalv joined #bioclipse
09:38 Gpox I belive it was a problem with atom number and coloring in jcp when changing symbol
09:38 egonw ok, good
09:38 egonw than please use the PeriodicTable class
09:39 egonw getAtomicNumber(String) method
09:39 egonw and let me know what you want me to do with that patch with the typo in the commit message
09:39 Gpox the setMAssNumber was because the configure method do not update the stuff if the mass number is set
09:40 egonw wait for a fixed commit message, or apply with type
09:40 egonw yeah, but mass number != atomic number
09:40 egonw mass number is which isotope...
09:40 egonw but when you change the symbol, you do not know what isotope to use
09:40 egonw and should be unset...
09:40 egonw so, nulling the mass number makes sense
09:41 Gpox I will fix those two patches then
09:41 egonw but it would not be configured by the isotope factory anyway
09:41 egonw OK, please just email them...
09:41 egonw one will go into CDK 1.4.19 and the other into the CDK-JChemPaint 29 patch
09:41 egonw (I think)
09:41 egonw depends on the modules they're in :)
09:42 egonw yeah, one is in renderbasic, the other in controlbasic
09:48 egonw BTW, got trouble running the Win64 bit Bioclipse binary...
09:49 egonw despite me having Java installed, it cannot find it...
09:50 egonw well, I indeed cannot start javaw.exe from the command line either...
09:50 egonw so, WT* did I just install??
09:51 egonw did I just install the plugin... ??
09:52 egonw did I just install the browser plugin... ??
09:55 egonw OK, the Linux version does not really work either :(
09:56 egonw java.lang.NoSuchMethodError: org.slf4j.spi.LocationAwareLogger.log(L​org/slf4j/Marker;Ljava/lang/String;ILja​va/lang/String;Ljava/lang/Throwable;)V
09:56 egonw ok, windows has javaw.exe now
09:57 egonw OK, same stacktrace on windows
11:07 Gpox egonw: try it now, it should be fixed
11:07 egonw testing
11:10 egonw ok, confirmed on Linux
11:11 egonw unzipping on win64
11:43 egonw yeah, win64 seems to work too
13:11 sneumann_ joined #bioclipse
13:27 cruttkie_ joined #bioclipse
13:34 zarah joined #bioclipse
13:47 ChanServ joined #bioclipse
14:28 cruttkie__ joined #bioclipse
14:44 sneumann_ joined #bioclipse
15:00 mgerlich__ joined #bioclipse
15:02 zaetnick joined #bioclipse
15:25 sneumann__ joined #bioclipse
15:42 sneumann joined #bioclipse
16:08 mgerlich__ joined #bioclipse
16:13 zaetnick joined #bioclipse
16:13 zarah joined #bioclipse
17:08 mgerlich__ joined #bioclipse
17:08 sneumann joined #bioclipse
17:11 mgerlich_ joined #bioclipse
18:30 egonw joined #bioclipse
22:05 sneumann joined #bioclipse

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary