Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-10-16

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All times shown according to UTC.

Time Nick Message
05:31 sneumann joined #bioclipse
06:56 Gpox joined #bioclipse
06:56 Gpoks joined #bioclipse
06:57 Gpox joined #bioclipse
06:58 sneumann joined #bioclipse
07:22 jonalv joined #bioclipse
07:23 jonalv oh hai
07:23 zarah oh hai jonalv
07:23 jonalv zarah: seen egonw?
07:23 zarah egonw was last seen 14 h 24 m 47 s ago in #cdk saying 'ok, bbl'
07:24 jonalv famous last words...
07:42 mgerlich joined #bioclipse
07:47 sneumann mgerlich: hier
07:48 sneumann http://www.weinelt.de/latex/hfill.html
07:48 zarah sneumann's link is also http://tinyurl.com/ykdhh5v
07:49 masak joined #bioclipse
07:55 egonw joined #bioclipse
08:08 egonw joined #bioclipse
08:08 egonw moin
08:08 zarah hello egonw, you fantastic person you
08:10 masak hello egonw, you fantastic person you
08:22 jonalv hello egonw, you fantastic person you
08:22 zarah hello egonw, you fantastic person you
08:23 masak zarah: you're the fantastic one!
08:23 zarah masak: no, YOU'RE the fantastic one! :)
08:25 egonw thanx guys! my bank account is with Nordea... 1801 ...
08:25 jonalv egonw: have you seen the review?
08:27 egonw review?
08:28 egonw oh, of the paper?
08:28 egonw no, not yet
08:28 jonalv egonw: okey
08:28 jonalv egonw: it was quite thorough
08:41 stain my project manager just installed Bioclipse
08:42 stain he got a bit excited, and then.. a bit disappointed :/
08:42 stain apparantly the help has lots of "Bla bla bla"
08:43 stain our boss is all onto this "Let's put Taverna inside Bioclipse" run right now, so we need to do some expectation management first
08:45 * jonalv thinks the putting Taverna inside Bioclispe thing has been talked about for a long time and he thinks that is an intresting project
08:46 egonw jonalv: nice blog!
08:46 jonalv egonw: you think? masak summed it up with one wrod: yagni
08:46 egonw yagni?
08:46 egonw what's that in English?
08:46 jonalv "You aint gonna need it"
08:47 egonw stain: let me know what we can do here
08:47 jonalv it's the philosphy about only implementing things that you 100% sure that you actually need
08:47 egonw stain: I'm eager to say file bug reports against the "bla bla" in the help, and in the luxurious situation of not having written too much of the help anyway :)
08:47 jonalv egonw: but, thanx I guess :)
08:48 egonw but clearly, she identifies areas where we should actually start writing proper docs
08:48 egonw jonalv: ah, ic
08:48 egonw yagni
08:48 egonw will remember that one
08:48 egonw did not do that so far, because I had not needed it yet :) hahahahha
08:58 masak :)
08:59 egonw "Darwin was mostly made of protein": http://bioinf.cs.ucl.ac.uk/tnugent/
08:59 zarah egonw's link is also http://tinyurl.com/yf6p2wn
09:19 samuell joined #bioclipse
09:29 egonw hi samuell
09:38 edrin joined #bioclipse
09:40 samuell Hi egon!
09:40 samuell ...and others
09:40 olass joined #bioclipse
09:41 edrin hi all
09:41 zarah oh hai edrin
09:46 egonw hi olass, edrin
10:03 samuell Anyone knows how to do LD_PRELOAD (of shared librariy files (.so) ) from Eclipse?
10:04 samuell (From commandline it is used like so:
10:05 samuell LD_PRELOAD=/usr/...path-to-library..so java ExampleClass
10:05 samuell or
10:05 samuell env LD_PRELOAD=/usr/...path-to-library..so java ExampleClass
10:05 samuell )
10:06 * egonw is looking how balloon is doing that sort of thing
10:06 egonw nope, that's not going to help
10:07 samuell It's not sure that balloon has to do it I think, because it's quite specific for java
10:07 egonw balloon seems to be using an executable
10:07 samuell Normally one can just use the -Djava.library.path= as an argument to the vm
10:08 samuell But when using jpl it seems one has to force the prolog libraries to be loaded before the jpl library. That's why.
10:08 egonw samuell: perhaps look at:
10:08 egonw https://jni-inchi.svn.source​forge.net/svnroot/jni-inchi
10:08 samuell Ok, thanks for tip
10:08 samuell Will check
10:10 egonw but in principle JPL should take care of this...
10:11 samuell Hmm, https://jni-inchi.svn.sourceforge.​net/svnroot/jni-inchi/trunk/README says:
10:11 samuell The Maven build system takes care of JNI InChI's dependencies, and runs Make to
10:11 samuell build the native code required.
10:11 samuell So it might be different.
10:11 egonw yes
10:11 egonw more target/native/jar/META-INF/jniin​chi/1.7/LINUX-AMD64/MANIFEST.xml
10:11 egonw <file library="true">libJniInchi​-1.7-LINUX-AMD64.so</file>
10:12 samuell Ah
10:12 samuell Interesting
10:12 egonw but still no clue if that will help here, though
10:12 samuell I'll try that soon!
10:12 samuell Thanks!
10:13 egonw it's not a osgi or eclipse manifest
10:13 samuell Ah, ok
10:13 samuell Any similarities to the plugin.xml ?
10:13 egonw perhaps ask on #eclipse
10:13 egonw if google does not help
10:13 egonw no, don't think so
10:14 samuell Ok. Yep, will just close some "threads" I have open
10:14 samuell ("research threads", one per firefox tab :) )
10:34 samuell Nice thing is, now I at least got blip started when calling java from command line.
10:34 samuell Haven't even been able to do that.
11:21 sneumann joined #bioclipse
11:29 olass joined #bioclipse
11:37 olass_ joined #bioclipse
11:43 egonw olass: is it away?
11:43 olass_ sort of... final final is thursday next week
11:43 egonw ic
11:44 olass_ egonw: you are not at BMC
11:44 egonw no, I am not
11:44 * olass_ is in a meeting with jonalv
11:44 olass_ bbl
11:50 CIA-51 bioclipse.cheminformatics: Egon Willighagen 2.2.x * ra4fcb1e / (86 files in 65 dirs): Pushed in a new CDK 1.3.0.+ version plus updated JChemPaint-Primary: 0bioclipse5 - http://bit.ly/2oA41A
11:50 CIA-51 bioclipse.cheminformatics: Arvid Berg 2.2.x * rd035ed3 / cdk-externals/trunk/org.openscience.cdk.renderext​ra/src/org/openscience/cdk/renderer/Renderer.java : Added null check to avoid NPE when no model is present - http://bit.ly/14NWwh
11:50 CIA-51 bioclipse.cheminformatics: Egon Willighagen 2.2.x * rfe3a1c2 / cdk-externals/trunk/org.openscience.cdk.io/sr​c/org/openscience/cdk/io/MDLV2000Reader.java : Fixed reading of properties - http://bit.ly/1zwzXh
12:02 stain > Has anyone tried the latest bioeclipse ? - I did this morning - 2beta4
12:02 stain >
12:02 stain > I downloaded it - had to unzip to install and put a shortcut on the
12:02 stain desktop - it does not have an installer - Taverna 2.1 beta2 does
12:02 stain hm, it's too long to paste here
12:02 stain who should I forward my project manager's comments too?
12:03 stain I can summarize: No installer, command line/log window visible, Welcome documentation incomplete w/blablabla, Started a new file, but welcome screen stayed
12:04 stain don't know how to add more services in Workflow-mode. Tried to drag them into gray area, but nothing happened.
12:04 stain just little things, and we know from our own experince that each of these takes time to polish
12:04 stain and it is afterall a beta, I told him
12:05 stain but we're very keen on looking at doing a Taverna-workbench built on RCP and the gang.. but it would take time
12:05 stain which is what I have to convince our boss about! She thinks that if we're using OSGI then it's just a few minutes to hook up Taverna and Bioclipse :)
12:10 egonw stain: can you open a ticket on bugs.bioclipse.net ?
12:13 stain I can ask him to do it
12:14 egonw very much appreciated
12:14 egonw there is registration needed, with an email account
12:14 egonw stain: can you send me offline the email address used to register?
12:15 egonw with is particularly useful if a non manchester email address...
12:15 egonw though it should not be too hard to pick out which reports it are...
12:16 CIA-51 bioclipse.core: Ola Spjuth master * r72e38db / (7 files in 4 dirs):
12:16 CIA-51 bioclipse.core: Cleanup, plugins are added instead of features.
12:16 CIA-51 bioclipse.core: Also added brunn deps. Removed hardcoced versions.
12:16 CIA-51 bioclipse.core: Added feature branding. - http://bit.ly/1Ic3SR
12:17 egonw Gpox: the new 0bioclipse5 is in bioclipse.cheminformatics now
12:17 egonw Gpox: I see one 'regression'...
12:17 egonw it does not give the visual feedback for merging rings...
12:18 egonw the merging works fine, but the merge atoms are not marked/highlighted
12:18 Gpox that is a n.bc.cdk.jcp change
12:18 egonw yes, expected so
12:18 egonw do I have stuff in my fork queue I missed?
12:19 Gpox might not have pushed it yet
12:28 jonalv egonw: you pang?
13:09 samuell egonw: Managed to start blipkit from inside eclipse now as well, by starting eclipse with this custom script:
13:09 samuell export LD_LIBRARY_PATH="/usr/lib/jvm/java-1.5.0-s​un-1.5.0.19/jre/lib/i386/client/:/usr/lib/​jvm/java-1.5.0-sun-1.5.0.19/jre/lib/i386/"
13:09 samuell LD_PRELOAD=/usr/local/lib/pl-5​.7.15/lib/i686-linux/libjpl.so /home/samuel/program/eclipse/eclipse &
13:09 egonw cool
13:10 samuell Now gotta go for fika / "spikt�rta"
13:10 samuell bbl
13:10 egonw yeah, we sort out how that should be done platform independently
13:10 egonw yeah, fika here too
13:10 samuell Good :)
13:19 miguelrojasch joined #bioclipse
13:19 miguelrojasch hi everybody
13:20 miguelrojasch does someone know if exists some parser mzXML to cml?
13:25 egonw miguelrojasch: ask sneumann
13:29 miguelrojasch ok
14:00 jonalv @pz 1657
14:00 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1657
15:21 olass_ @pz 1662
15:21 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1662
15:42 CIA-51 bioclipse.core: jonalv master * re743091 / features/net.bioclipse.birt_feature/feature.xml :
15:42 CIA-51 bioclipse.core: updated version data since we made changes
15:42 CIA-51 bioclipse.core: Those changes are published on the brunn update site... - http://bit.ly/34lACf
16:25 sneumann joined #bioclipse
17:32 edrin left #bioclipse
20:24 egonw joined #bioclipse

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