Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-05-14

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

All times shown according to UTC.

Time Nick Message
05:15 sneumann joined #bioclipse
05:51 egonw joined #bioclipse
07:58 s_wolf joined #bioclipse
08:11 s_wolf joined #bioclipse
08:38 sneumann joined #bioclipse
10:58 egonw joined #bioclipse
11:15 egonw joined #bioclipse
15:02 olass joined #bioclipse
15:37 olass hi egonw
15:38 CIA-61 bioclipse.core: Ola Spjuth 2.4.x * r7865737 / (25 files in 25 dirs): Set version to 2.4.0.RC1. - http://bit.ly/c7tPG1
15:38 CIA-61 bioclipse.core: Ola Spjuth 2.4.x * r87ae379 / (3 files in 3 dirs): Set version to 2.4.0.RC1. - http://bit.ly/aNp8XV
15:38 CIA-61 bioclipse.core: Ola Spjuth 2.4.x * rfeaecc7 / net.bioclipse.target.platf​orm/target-platform.target : Added logging dir to old target.platform - http://bit.ly/9TWeXu
15:39 olass egonw: would you like to set ID to 2.4.0.RC1 in cheminfo repo?
15:40 CIA-61 bioclipse.balloon: Ola Spjuth 2.4.x * r6dd730b / (8 files in 8 dirs): Set version to 2.4.0.RC1 - http://bit.ly/akgMgX
15:42 CIA-61 bioclipse.core: Ola Spjuth 2.4.x * r27d18f8 / plugins/net.bioclipse.ui/about.properties : Updated about text year to 2010 - http://bit.ly/9Zb3jz
16:16 CIA-61 bioclipse.statistics: Ola Spjuth master * r0d3e716 / (4 files in 4 dirs): Set version to 2.4.0.RC1 - http://bit.ly/bFyqP5
16:16 CIA-61 bioclipse.statistics: Ola Spjuth 2.4.x * r0d3e716 / (4 files in 4 dirs): Set version to 2.4.0.RC1 - http://bit.ly/bFyqP5
16:16 olass joined #bioclipse
17:45 samuell joined #bioclipse
17:46 samuell joined #bioclipse
17:58 egonw moin
17:58 zarah ni hao egonw
17:58 egonw hi olass, samuell
17:59 samuell egonw: Hi
17:59 samuell Just about to send you the final one, egonw, 1 min
17:59 egonw ok
17:59 egonw not sure if I will read it tonight
18:01 samuell Ok, should not be a problem
18:02 samuell I thought to send it to Mats late (24:00) saturday or so.
18:04 samuell For me, you don't need to read the whole thing. The extra changes I did were rather obvious ones, IMO.
18:04 egonw again, please indicate which parts I should read
18:04 egonw that's really important
18:04 samuell Yes
18:04 egonw I will not have time to read the full paper again
18:05 egonw thanx for the diff
18:05 egonw that's very useful
18:05 egonw samuell++
18:06 samuell Reg. the histogram btw, I really had a number of shifts at 578.3 or so
18:07 samuell And then a few spread out between 300 and 587
18:07 samuell I can give you a list if you want :)
18:07 egonw please blog them :)
18:08 egonw seriously, this is interesting...
18:08 samuell Guess one should try to locate the molecules ...
18:08 samuell (That's a nice sparql query of course :) )
18:09 egonw indeed! go for it!
18:10 samuell Maybe something for the report ... well anyway ...
18:10 samuell second report I mean
18:11 egonw yeah, in the report for Jarl, not this one
18:11 egonw ah, yes, second report :)
18:16 samuell Yep :)
18:18 CIA-61 bioclipse.cheminformatics: Egon Willighagen 2.4.x * r72e28f2 / (17 files in 17 dirs): Set version to 2.4.0.RC1 - http://bit.ly/cgJEkd
18:18 egonw samuell: btw, can you port the plugins for the second report to Bioclipse 2.4 perhaps?
18:19 samuell I guess that should be no problem
18:19 CIA-61 bioclipse.joelib: Egon Willighagen 2.4.x * ra3ee4c0 / (4 files in 3 dirs): Set version to 2.4.0.RC1 - http://bit.ly/akjp59
18:20 egonw olass: please put tags in place too
18:20 olass egonw: yes, when released
18:21 olass but there are some critical bugs left
18:21 egonw ah, ok... make sense
18:21 egonw for the RC1 ?
18:21 olass 1969?
18:21 olass did you see this?
18:21 olass just opening a mol throws exception...
18:22 olass it might be the inchi which gives trouble...
18:22 olass hard to tell from the trace
18:22 egonw no, not seen that yet
18:22 egonw will check
18:45 olass let me know if you manage to resolve it, would probably mean RC1 can be released
18:48 CIA-61 bioclipse.rdf: Egon Willighagen 2.4.x * r82ff6e7 / plugins/net.bioclipse.rdf.ui/src/net/b​ioclipse/rdf/ui/editors/RDFEditor.java : Removed Java6 @Overrides for interface methods - http://bit.ly/cCM320
18:48 CIA-61 bioclipse.rdf: Egon Willighagen master * raa41295 / (2 files in 2 dirs): Removed local files from repos: .settings folders - http://bit.ly/cXR9JV
18:48 CIA-61 bioclipse.rdf: Egon Willighagen master * r8112b83 / (15 files in 10 dirs): Set version to 2.4.0.RC1 - http://bit.ly/bBFwZ1
18:48 CIA-61 bioclipse.rdf: Egon Willighagen master * r05ba349 / (5 files in 5 dirs): Some log4j removals to make it work nicely with Bioclipse 2.4 - http://bit.ly/9um1Bo
18:48 egonw oh fuck
18:48 olass ?
18:49 egonw that was the wrong branch
18:49 CIA-61 bioclipse.rdf: Egon Willighagen 2.4.x * refd77ff / (2 files in 2 dirs): Removed local files from repos: .settings folders - http://bit.ly/azlUrt
18:49 CIA-61 bioclipse.rdf: Egon Willighagen 2.4.x * r517e124 / (15 files in 10 dirs): Set version to 2.4.0.RC1 - http://bit.ly/8XsvaX
18:49 CIA-61 bioclipse.rdf: Egon Willighagen 2.4.x * r6aa1fc4 / (5 files in 5 dirs): Some log4j removals to make it work nicely with Bioclipse 2.4 - http://bit.ly/crj1iw
18:49 egonw long live git :)
18:49 egonw git cherrypick to the rescue
18:49 olass hehe
18:49 olass my favorite
18:51 egonw bioclipse.social on the experimental update site?
18:52 CIA-61 bioclipse.social: Egon Willighagen 2.4.x * r8d7af13 / (2 files): Set version to 2.4.0.RC1 - http://bit.ly/aqgTay
18:57 egonw and the features int he bioclipse.metabolomics repository on the experimental update site too please...
18:59 egonw samuell: ping
18:59 samuell egonw: pong
18:59 egonw the 7 Ack is still empty
18:59 egonw not that I need to check that...
18:59 egonw but something you should not forget :)
19:00 samuell Indeed
19:01 egonw samuell: lovely pink :)
19:01 egonw otherwise, good image!
19:01 samuell thx :)
19:01 egonw you could add the last missing layer
19:01 egonw the one with your performance testing scripts
19:02 samuell Ah, true
19:02 egonw and I could suggest to add an extension of the RDF Manager (dashed) with "TDB support"
19:02 egonw that's what got you your co-author on the paper :)
19:03 egonw would add some more dashes to the story
19:03 samuell True
19:03 egonw oh... and the first page of a chapter (4 Results) should be the caption of the chapter, not a Table
19:03 egonw try using [b!]
19:03 egonw ! for force
19:03 egonw b for bottom
19:04 samuell Indeed
19:04 egonw ok, all in all... 9 pages of results now... that sounds much more in balance now
19:04 egonw also 2.5 discussion looks good
19:05 egonw oh, and you are insisting on the 3.5 header?
19:05 egonw :)
19:05 samuell Ah, no, have missed to fix
19:05 egonw about Fig 8
19:05 egonw you can still opt to make to horizontal go up to 30
19:05 egonw you can still opt to make to horizontal go up to 300
19:06 egonw so that the rest shows up nicely...
19:06 egonw and then mention in the caption that an extra XX peaks are observed between 300 and 548.7 or so
19:06 samuell Yes
19:06 egonw samuell++ (for a much better Fig7)
19:07 egonw neat
19:07 samuell Went back to the original :)
19:07 egonw regarding the reference section
19:07 egonw you can opt to make the font size a tid bit smaller
19:08 samuell Ah
19:08 egonw and remove the empty lines between entries
19:08 samuell Hmm, know the latex command for that? :)
19:08 samuell (I can google otherwise)
19:08 egonw yeah, I'm looking it up
19:10 egonw \usepackage{bibspacing}
19:10 egonw \begin{footnotesize}
19:10 egonw \bibliographystyle{unsrt}
19:10 egonw \bibliography{book}
19:10 egonw \end{footnotesize}
19:10 egonw that's what I used
19:11 egonw I think
19:11 samuell Ok, will try
19:11 egonw google for bibspacing
19:11 zarah egonw: http://cnmat.berkeley.edu/user/andy_schmeder/b​log/2009/01/16/useful_latex_tips_tricks_hacks
19:11 egonw zarah++
19:11 samuell :)
19:13 egonw ok, will check the changed sections in more detail tomorrow
19:13 egonw got some CDK / JCP hacking to do
19:13 samuell Yep
19:28 egonw joined #bioclipse
19:40 samuell egonw: The bibspacing.sty doesn't compile on my Ubuntu ... (something about the \z command). Would you mind mailing your bibspacing.sty?
19:40 egonw mom
19:42 egonw sent
19:45 samuell Thanks!
19:46 samuell No improvement though. Maybe have to stick with only smaller font size for now.
19:47 samuell (Still didn't work, I mean)
21:03 CIA-61 bioclipse.core: Ola Spjuth 2.4.x * r7eb61d7 / plugins/net.bioclipse.ui/plugin.xml : Added a Predict popup menu. - http://bit.ly/bp6pfJ
21:34 olass joined #bioclipse
22:04 olass joined #bioclipse
22:51 sneumann joined #bioclipse
22:58 sneumann joined #bioclipse

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