Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-03-16

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All times shown according to UTC.

Time Nick Message
07:24 egonw joined #bioclipse
07:24 olass joined #bioclipse
07:25 egonw hi olass
07:25 olass moin
07:25 zarah saluton olass
07:33 egonw joined #bioclipse
07:44 edrin joined #bioclipse
07:44 edrin hi
07:44 zarah privet edrin
07:44 edrin sorry, late
07:45 olass hi edrin
07:49 egonw joined #bioclipse
08:00 Gpox joined #bioclipse
08:13 masak joined #bioclipse
08:24 jonalv joined #bioclipse
08:24 jonalv oh hai
08:24 zarah hi jonalv
08:24 olass hi jonalv
08:24 egonw hi jonalv
08:24 zarah hi jonalv
08:25 * jonalv is rebooting windows again...
08:26 jonalv that seems to happend each time one starts windows...
08:26 egonw Gpox: please have a look at that bug on JCP editor IDs....
08:26 egonw jonalv: yes, rebooting is a critical step in booting windows :)
08:26 jonalv so it seeems...
08:27 jonalv anyway, I am gonna try Bioclipse some more in windows I think...
08:27 olass yes, woudl be valuable
08:27 jonalv what the, it still has more updates
08:27 olass win has updates every time...
08:48 CIA-33 bioclipse: jonalv * r9313 /bioclipse2/trunk/plugins/net.bioclipse.jmol/sr​c/net/bioclipse/jmol/views/StatusListener.java: squeesed into 80 cols
08:48 CIA-33 bioclipse: jonalv * r9314 /bioclipse2/trunk/plugins/net.bioclipse.jmol/s​rc/net/bioclipse/jmol/editors/JmolEditor.java: activated select on click in jmol editor
08:49 CIA-33 bioclipse: jonalv * r9315 /bioclipse2/trunk/plugins/net.bioclipse.jmol/sr​c/net/bioclipse/jmol/views/StatusListener.java: removed superfluos whitespace
09:18 egonw olass: can you comment on bug #719 ?
09:18 egonw one sec... I'll post my question to you there...
09:18 olass ok
09:19 * olass is preparing his talk for KI today
09:20 egonw ok, questions commited
09:20 egonw -a
09:20 egonw -s
09:20 egonw just one question
09:20 olass ok
09:23 olass egonw: sorry, cannot help you with this. Please ask Gpox.
09:23 olass what is open-editor-with-certain-content-but-no-IFile' ?
09:23 egonw already talking to him on this...
09:23 CIA-33 bioclipse: goglepox * r9316 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/plugin.xml: Changed tooltip fixes bug #705
09:24 egonw olass: that's your feature request
09:24 zarah bug #705 | http://tinyurl.com/dg3tve
09:30 olass GAH
09:31 olass my bc2 workspace was wiped out!
09:32 olass what is this?
09:32 olass all projects deleted!?
09:32 egonw void?
09:32 egonw black hole?
09:32 olass moist
09:32 egonw maybe just $HOME/bioclipse kicking in?
09:32 olass grr
09:32 olass no not runtime WS
09:33 egonw ah, ic...
09:33 olass my checked out devel
09:33 olass hmm
09:33 olass something's wrong here
09:33 egonw yeah, now it would have been nice if your BC2 WS was in a (git) repository :)
09:33 olass well, I have time machine
09:33 olass probably even better
09:33 egonw you're sure not some eclipse update turned on 'clean'ws-before-start' ?
09:33 olass ?
09:36 olass I wonder how much is lost...
09:36 * egonw wonders what caused the wipe out
09:36 olass scary
09:37 olass very scary
09:38 olass hmm, two weeks work lost if not on SVN
09:38 olass luckily, most is
09:38 olass oh no
09:38 olass :(
09:38 olass oh NOOO
09:39 olass f*ck
09:41 egonw what?
09:41 egonw this does not sound good...
09:41 egonw you don't often catch ola using the f word
09:42 olass argh
09:42 olass *phew*
09:42 olass I have no idea what happened
09:42 olass but someone moved all my workspaces o tmp in the middle of a compilation
09:43 olass with very strange results
09:43 olass it was in the middle of a mylyn update
09:43 olass I most certainly hope this never happens again...
09:44 olass scared the crap out of me
09:44 olass pardon my language
09:45 olass hmm, is there a bug in bug 719?
09:45 olass egonw: this happened when I read it...
09:45 egonw would be interesting...
09:45 egonw a virus spreading via Bugzilla
09:46 egonw targeting OS/X platforms
09:46 egonw olass: I think you just hit a gold mine... virus scanners for Bugzilla on OS/X :)
09:46 egonw olass: make sure to be quick with the patent
09:47 olass I'll probaby make a fortune
10:34 edrin joined #bioclipse
10:37 egonw masak: ping
10:37 masak egonw: you pang? :)
10:38 egonw masak: is Perl signing up for GSoC?
10:38 masak egonw: oh, definitely.
10:38 egonw if so... another idea could be in the Perl world...
10:38 masak both 5 and 6.
10:38 egonw not sure what kind of projects they will allow...
10:38 masak http://www.perlfoundation.org/per​l6/index.cgi?summer_of_code_ideas
10:38 zarah masak's link is also http://tinyurl.com/cqpf6m
10:38 egonw but was just thinking about XMPP support in Perl...
10:39 masak egonw: and you've hit CPAN on this, of course?
10:39 egonw well...
10:39 masak :)
10:39 egonw I was actually getting at IO-DATA support :)
10:39 egonw indeed... for example using Net::XMPP on CPAN
10:40 egonw well, just an idea :)
10:40 egonw did I tell you about the GSoC t-shirts already? :)
10:41 egonw oh, and I think you also get a book of your choice
10:41 masak that sounds familiar, somehow.
10:41 egonw at least, I think the students did last year...
10:41 masak I'm seriously considering applying.
10:41 egonw now for sometihng completely different...
10:41 masak but it'd have to be a project that motivates me at least as much as my hobbies. :)
10:42 egonw how can I access with an offline email client my UU mail?? (e.g. POP/IMAP)
10:42 egonw I cannot find the info
10:42 masak hold on.
10:42 egonw masak: yes... GSoC should be fun projects... (on top of paying rahter well...)
10:42 egonw that's why I bring in a new idea, around Perl...
10:42 egonw I thought that could align well with your hobbies...
10:43 olass egonw: I asked masak a while ago about this (it IS important for XMPP)
10:43 egonw olass: yes, indeed...
10:44 olass but it stranded on him having more urgent things in Bioclipse
10:44 masak egonw: http://www.it.uu.se/datordr​ift/faq/mail/installningar
10:44 egonw and a GSoC for this would be a win-win...
10:44 zarah masak's link is also http://tinyurl.com/cmewl5
10:44 egonw money for masak, code for us :)
10:44 olass egonw: indeed
10:44 egonw masak: tack!
10:44 olass code for us all
10:44 egonw masak++
10:44 masak olass, egonw: I'll look into applying for an XMPP GSoC job.
10:44 masak I am a bit curious about XMPP.
10:44 olass egonw: why is the pubchem not in release?
10:44 masak it seems a cool technology,
10:45 egonw olass: please put the Web Feature on the update site
10:45 egonw because not everyone want web integration...
10:45 * egonw thinks pharma
10:45 olass who cares at this poin t
10:45 egonw where you do not want to accidentally leak info to the web
10:45 olass we have webservices already
10:45 olass to get pdb
10:45 egonw yes, good point...
10:46 olass pharma will not use BC as it is now anyway
10:46 olass I suggest put it in cheminfo feature
10:46 olass it's a good showcase
10:46 egonw ok, please do
10:46 olass ok
10:46 olass one plugin only?
10:47 egonw at this moment
10:47 egonw pending plugins for chemspider, ...
10:47 * jonalv is beginning to think that Bioclipse is, well, well tested and sort of going towards stable
10:47 masak stable++
10:48 * jonalv doesn't know what to test now...
10:48 jonalv perhaps I should try some stuff with that 1GB sdf file... :)
10:53 egonw masak: which pwd?
10:53 egonw A does not seem to work...
10:53 egonw ok, found it...
10:53 egonw I need B
10:53 egonw point 36
10:53 egonw nicely hidden :)
10:54 masak egonw: not sure what you're talking about...
10:54 egonw masak: nevermind
10:55 egonw it seems to work now :)
10:55 masak glad to hear that.
10:55 egonw yes, it does
10:55 * egonw is starting to use GPG again, so properly correspond to debian projects
10:56 egonw masak: I proofread/advice on a GSoC project proposal
10:56 egonw if needed
11:07 jonalv hm, I wonder if better Jmol support for Eclipse platforms is a worthy project...
11:07 masak egonw: ok, great. (took me a while to realize that was a suggestion.)
11:07 egonw masak :)
11:08 egonw jonalv: it's worth a shot, I'd say
11:08 egonw writing a proposal does take some time, but not overly much...
11:08 egonw jonalv: there should be an eclipse channel where you can get into contact with the (future) mentors...
11:08 egonw they will help you write the proposal
11:09 egonw and they will surely say so when they do not like it...
11:09 egonw the mentors pick the proposals...
11:09 egonw so, make use of that
11:09 egonw jonalv: maybe the Protopedia idea we had?
11:09 egonw that should be nice...
11:10 egonw as it will apply several RCP techniques...
11:10 jonalv yea but our Jmol solution needs some love as well..
11:10 egonw I'd say you would have a good chance with that proposal
11:10 jonalv I just have trouble finding any motivation for it at all...
11:10 egonw the Protopedia one involves Jmol-in-Bioclipse stuff, not?
11:10 jonalv I guess
11:10 egonw jonalv: 4500 is not enough motivations ? :)
11:11 egonw ummm
11:11 egonw 4500 motivations are not enough?
11:12 jonalv egonw: I don't know how it would work with my current job either...
11:12 egonw jonalv: that I do not know either...
11:12 jonalv it seems complicated..
11:12 egonw but since there is considerable overlap...
11:12 egonw I see that your day job activities and nite activities would coincide...
11:13 egonw but, correct: GSoC is a three month endavour a 40 hours per week...
11:13 egonw that said, combining with the first, and with your background... some 20 of them could easily coincide with your day job duties
11:14 jonalv yea and I can't really take out double salary for doing the same job, can I?
11:14 olass jonalv: why not?
11:14 jonalv olass: I can? I thought there where regualtions against such things...
11:14 olass if the results are what you would have done anyways...
11:14 olass well well
11:14 olass regulations
11:14 olass you know me :)
11:14 olass you could write it up on your spare time
11:15 olass no one wil lask you WHEN your spare time is
11:15 olass besides, we have not gotten the money yet
11:15 jonalv can someone tell me how to burn a disc on Mac OS X?
11:15 olass I use Toast
11:15 jonalv I am more and more considering installing buntu...
11:19 olass jonalv:
11:19 jonalv olass:
11:19 olass in finder, click more actions button
11:19 olass New Burn Folder
11:19 olass that gets you furthr?
11:19 jonalv olass: where is the more actions button?
11:19 olass egonw: can you explain the protopedia idea in 2 minutes?
11:20 olass jonalv: at the top
11:20 olass kugghjulet
11:20 jonalv okej
11:20 egonw olass: yes
11:20 jonalv ther alternative new buirn folder is not there
11:20 olass jonalv: never used it (I use Toast) but give it a try
11:20 olass click on your user home first
11:20 olass egonw: really fast please
11:21 * olass must run in a few minutes
11:21 egonw calm down...
11:21 egonw http://www.proteopedia.org​/wiki/index.php/Main_Page
11:21 zarah egonw's link is also http://tinyurl.com/5mafn3
11:21 olass yes, know about it
11:21 egonw olass: note the green links
11:21 olass yes
11:21 egonw which will cause Jmol to do stuff
11:21 olass yup
11:21 egonw idea: write a plugin to read a Protopedia page from p.org, create dynamically a cheat sheet
11:21 olass do this in the rich browser (=mozilloa in bioclipse)?
11:21 olass aah
11:21 egonw or indeed a rich browser
11:22 egonw with Jmol on the side
11:22 olass ok, got it
11:22 olass nice idea
11:22 jonalv olass: how do I then burn this burn folder?
11:22 olass after 2.0 I really really would like the rich browser...
11:22 egonw would make a perfect BC2.1 show case
11:22 olass yes
11:22 egonw indeed...
11:22 olass [12:23] < olass> jonalv: never used it (I use Toast) but give it a try
11:22 egonw so, the GSoC would make a lot of sense
11:23 olass you are starting to convince even me...
11:23 olass ok, I'm off
11:23 olass see you later
11:23 * jonalv installs toast...
11:24 jonalv hey it's $80
11:24 jonalv he left off course...
11:24 jonalv this is silly
11:42 * jonalv should probably start thinking about food...
11:45 masak heh, when you install R you must "agree to" the terms of the GNU GPL...
11:46 masak whereas the entire point of the GPL is that if you don't agree to it (which you are certainly free to do), you're stuck with the much more draconian copyright restrictions.
11:49 jonalv masak: so, what are you saying?
11:50 masak jonalv: that the GPL has been fit into a mold in the installation which doesn't really suit it.
11:50 jonalv masak: and what are you suggesting we do about it?
11:50 edrin http://xkcd.com/556/
11:50 masak jonalv: nothing.
11:51 masak edrin: heh. :)
11:51 jonalv edrin: lol
11:59 egonw masak: good point
11:59 egonw not sure how that can be fixed, though...
12:19 masak no, it's difficult.
12:19 masak but I think there is a fundamental difference between an everyday EULA and the GPL.
12:19 masak and the installation processes on Mac OS X fudge that distincion.
12:27 shk3 joined #bioclipse
12:28 egonw hi shk3
12:28 masak hi shk3
12:28 shk3 hi all
12:28 zarah ni hao shk3
12:29 shk3 I forgot the new files in my commit on friday
12:29 shk3 committing again now
12:30 egonw shk3: thanx
12:32 CIA-33 bioclipse: shk3 * r9317 /bioclipse2/trunk/plugins/net.bioclip​se.specmol/src/net/bioclipse/specmol/ (3 files in 2 dirs): very basic child editing
13:07 masak ladies and germs, we can haz working R console.
13:07 masak stand by for commits.
13:07 egonw masak++
13:07 egonw gist, gist, gist...
13:08 masak egonw: sure, but of what?
13:08 egonw (supportive, encouraging, enthousastics cheering)
13:08 jonalv je avec
13:08 egonw moi aussi?
13:08 egonw is that what you mean?
13:08 jonalv egonw: yes it's a joke good damn it
13:08 egonw ah, ic...
13:09 egonw nice reply...
13:09 jonalv :)
13:09 egonw should remember that whenever I make a stupid english typo and get kicked by masak :)
13:09 jonalv :)
13:09 egonw btw, jonalv++ for the french dude trying to swear English
13:09 egonw "good damn it"
13:10 jonalv :)
13:10 egonw masak: ummm... try this:
13:10 egonw take 5 SMILES
13:10 egonw COC, CCO, CCCO, CCOC, CC(O)C
13:10 egonw and calculate XLogP
13:10 egonw and mass
13:10 egonw and plot that against each other?
13:10 masak I don't kick. I just ridicule.
13:11 masak egonw: not sure I know R well enough for that...
13:12 CIA-33 bioclipse: carl_masak * r9318 /bioclipse2/trunk/plugins/net.bioclipse.r/src​/net/bioclipse/r/ui/views/RConsoleView.java:
13:12 CIA-33 bioclipse: [RConsoleView] added a layer of async to avoid thread trouble
13:12 CIA-33 bioclipse: the R console view now works on my box. it does not warn, however, if the
13:12 CIA-33 bioclipse: computer does not already have R installed.
13:12 masak but you are welcome to try, and see if you get R working with the new commit.
13:12 egonw ack
13:12 egonw but not now...
13:12 masak np.
13:12 egonw doing home work for pharma bioinformatics :)
13:14 egonw masak: ok, better idea
13:14 egonw say I have something in the matrix editor opened...
13:14 egonw have access to that data
13:14 masak egonw: I like the sound of this.
13:17 masak "very basic child editing" -- I nominate this the commit comment of the day. it sounds like a GUI especially targeted for children.
13:18 masak shk3++
13:19 shk3 well, it's a bit of a workaround
13:19 shk3 I will finish it and everybody can comment
13:24 jonalv` joined #bioclipse
13:59 jonalv egonw: ping
14:00 jonalv egonw: are you familiar with the jmol application?
14:02 egonw pong
14:02 egonw yes, a bit
14:02 egonw it changed somewhat over time...
14:02 jonalv there are icons for doing measuremnts and selections
14:02 egonw but not too much since I last hacked on it...
14:03 jonalv egonw: do you know what jmol script commands taht are hidden beneth those toolbar items?
14:03 egonw mom
14:03 jonalv we should probably copy that behavior...
14:04 * masak looks at #78 and #628, and chooses the latter
14:04 masak anything to avoid starting Windows... :)
14:04 jonalv @pz 78
14:04 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=78
14:04 jonalv masak: 78 is important
14:05 jonalv @pz 628
14:05 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=628
14:05 masak so is 628.
14:05 egonw jonalv: searching
14:05 jonalv uhm and 628 is probably even more important
14:05 masak they are currently my only two P1 tickets.
14:08 egonw jonalv:
14:08 egonw http://jmol.svn.sf.net/viewvc/jmol/trunk/Jmol/​src/org/openscience/jmol/Properties/Jmol-resou​rces.properties?revision=10685&amp;view=markup
14:08 zarah egonw's link is also http://tinyurl.com/d5jprh
14:09 jonalv egonw: thanks
14:10 egonw de rien
14:10 jonalv egonw: all this stuff works in our Jmol. If we just get the selection listener to work and make a context menu and some toolbars then we have a full feathered Jmol application inside Bioclipse I think!
14:11 jonalv we should be able to have the exact same behavior in our editor!
14:11 egonw ack
14:11 egonw jonalv: talk to Gpox on how to define menu's from the plugin.xml
14:12 egonw I think he has just some stuff in the plugin.xml without any Java code to match it...
14:12 egonw which sounds the best way to use these scripts
14:12 egonw btw, did you see the 'select thisModel'
14:12 jonalv egonw: nope
14:13 jonalv egonw: what's "thisModel"?
14:13 egonw not entirely sure what it does, but looks important :)
14:18 olass joined #bioclipse
14:18 olass hi all happy guys
14:18 CIA-33 bioclipse: ospjuth * r9319 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.smartsmatching/build.properties: Added icons to build.props. Solves 727.
14:22 olass egonw: what view group should I use foor chemoinfo views?
14:22 olass the plugin net.bioclipse.chemoinformatics defines teh view category net.bioclipse.chemoinformatics.views.category
14:22 olass and I use that one
14:22 olass IMO that is correct
14:23 olass egonw: please advice
14:24 egonw where is the other one defined?
14:24 egonw it sounds good
14:24 olass good
14:24 olass marking jonalvs bug 728 as invalid.
14:25 jonalv uhu
14:25 jonalv @pz 728
14:25 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=728
14:26 jonalv olass: okey, could you perhaps see who is doing something wrong?
14:26 olass jonalv: report the other view as wrong
14:26 jonalv olass: or are you telling me that you want two chemoinfoamtis groups?
14:26 olass no
14:26 olass only one
14:26 olass and I use the correct one
14:26 olass according to egon
14:27 olass so if you see other views using another, file a bug for those
14:28 olass or even better: just fix it
14:31 Gpox fixed
14:31 CIA-33 bioclipse: goglepox * r9320 /bioclipse2/trunk/plugins/net.biocli​pse.cdk.jchempaint.view/plugin.xml: Removed category fixes bug #728
14:31 zarah bug #728 | http://tinyurl.com/den9c3
14:32 olass Gpox++
14:33 olass hmm
14:33 olass masak,jonalv: We need an attack plan for the console errors...
14:33 masak tell me about it.
14:33 jonalv olass: huh?
14:33 olass could we maybe talk tomorrow about this?
14:33 masak sure.
14:33 olass gr8
14:34 jonalv is this the errors that occur in the gui thread again?
14:34 olass sort of
14:34 olass jonalv: is there a solution?
14:34 masak olass: no.
14:34 jonalv olass: if taht is only sort of the problem then I have not understood the problem...
14:35 olass there could be more problems
14:35 jonalv I think there are solutions for everything though
14:35 olass I like that idea
14:35 masak I want you to note that the only reason we ended the meeting about this last week is because we convinced ourselves there is a solution. there isn't.
14:35 olass ok...
14:35 masak but feel free to prove me wrong on this one.
14:35 jonalv masak: so you have new proof claiming that there is no solution?
14:36 olass let's talk tomorrow
14:36 olass not now
14:36 olass IRC is limiting
14:36 jonalv yes
14:36 masak jonalv: no, I just haven't found anything besides the two impossibilities between us and the solution.
14:36 olass let's talk tomorrow
14:36 masak :)
14:36 jonalv afk
14:37 masak afk
15:17 CIA-33 bioclipse: shk3 * r9321 /bioclipse2/trunk/plugins/n​et.bioclipse.spectrum/src/ (2 files in 2 dirs): corrected a bug
15:17 egonw shk3: can you please describe what bug you fixed and how you fixed it?
15:17 egonw in the commit message
15:18 egonw shk3: it's much easier to learn that habit now
15:19 CIA-33 bioclipse: shk3 * r9322 /bioclipse2/trunk/plugins/net.bioclipse.specmol/ (2 files in 2 dirs): worked on the child editing
15:49 olass egonw: did you just close my reported bug 451?
15:49 olass :)
15:49 * olass is just wondering how to get rid of it in his query
15:50 olass mylyn is too poerful sometimes...
15:50 egonw oh, sorry...
15:50 egonw was not paying attention...
15:50 egonw though I got it email because I was owner...
15:50 egonw sorry about that...
15:50 egonw so why did it get assigned to me??
15:51 egonw so you want me to reopen?
15:51 olass no
15:51 olass just wondered what happened
15:51 olass I got it in my "close" query, but the bug was closed :)
15:51 olass resolved now
15:51 olass and updated my query
16:21 * jonalv just closed a bunch of fixed bugs. That is a nice feeling. The ebst part of doing testing actually :)
16:21 egonw :)
16:23 jonalv okey
16:23 jonalv egonw, olass, Gpox, masak: shk3 needs to know where the log files end up. Who knows?
16:23 egonw home folder?
16:24 masak Bermuda triabgle?
16:24 olass it's written to stdout on startup
16:24 jonalv oh and it's different on the different OSs I know that much
16:24 egonw shk3: I think mine end up in $HOME
16:24 olass log4j.configuration = file:/Users/ola/Workspaces/bioclipse2_1​/net.bioclipse.logger/log4j.properties
16:24 olass bioclipse.defaultLogDir = /Users/ola/Library/Logs/Bioclipse
16:24 olass INFO - Probable log file location: /Users/ola/Library/Logs/Bioclipse/bioclipse.log
16:24 olass !SESSION 2009-03-16 17:21:32.611 -----------------------------------------------
16:24 masak olass++
16:24 olass check the code that outputs this
16:24 jonalv shk3: did you get that?
16:24 olass that piece of code should know
16:25 shk3 mom
16:25 jonalv let's fix this know. And then whenever anyone feels that they have ended up in a situatiuon where they have caught an exception and don't know what to tell the user. Use this dialog!
16:26 jonalv so that we get some consistency in the behavior of Bioclipse
16:26 jonalv uhm btw, shk3: how do I use it? :)  is there a wiki page about it? :)
16:27 shk3 mom
16:27 shk3 telefoning
16:28 jonalv k
16:29 olass jonalv: please write this up on wiki for developers to know what to do in this case
16:30 CIA-33 bioclipse: ospjuth * r9323 /bioclipse2/trunk/plugins/net.​bioclipse.cdk.smartsmatching/ (11 files in 6 dirs): Added Help topics and dynamic help for smartsmatching plugin and view.
16:30 olass for all: I have written up how to use dynamic help in Bclipse on: http://wiki.bioclipse.net/index.php?t​itle=Adding_dynamic_help_to_a_plugin
16:30 zarah olass's link is also http://tinyurl.com/ct5s7p
16:30 olass olass++ //for documenting new things on wiki
16:30 zarah shame on you, olass, giving yourself karma like that
16:30 olass zarah: well, I felt like I deserved it
16:30 zarah olass: you've just exceeded my capabilities :/
16:31 olass zarah: it takes time to document things, but you win in the long run
16:31 zarah olass: are you talking to *me*?
16:31 olass zrah: YES!!
16:31 olass zarah: YES!!
16:31 zarah olass: I see.
16:31 olass @botsmack
16:31 olass ;)
16:32 shk3 ok, here i am
16:33 shk3 looking for the log4j stuff
16:35 jonalv @botbeer
16:35 zarah ;)
16:35 jonalv olass: it would be even beter if shk3 wrote it on the wiki. He wrote the dialog. And honestly I don't know how to use it either :)
16:36 shk3 will write
16:36 shk3 mom
16:38 jonalv shk3++
16:42 shk3 looks like I need to make core depend on logger
16:43 shk3 is that ok?
16:44 shk3 and where to write best on wiki about this dialog method?
16:44 olass shk3: I am not sure if core can depend on logger
16:44 olass is import not enough?
16:45 olass in wiki: please write where you find it appropriate, with other similar messages
16:45 CIA-33 bioclipse: shk3 * r9324 /bioclipse2/trunk/plugins/net.bioclipse.logger/ (META-INF/MANIFEST.MF src/net/bioclipse/logger/Activator.java): added exports, made a method public
16:46 CIA-33 bioclipse: shk3 * r9325 /bioclipse2/trunk/plugins/net.bioclipse.core/ (2 files in 2 dirs): the error dialog gives log file name
16:46 olass shk3: please run ALL tests after a change in the core and logger
16:46 olass I really don't like changes there at this time
16:47 shk3 not sure about the import/depends stuff
16:47 olass so you must must run all tests now
16:47 shk3 sorry
16:47 shk3 the log method is in core
16:47 shk3 so I have to change this
16:47 olass shk3: no worries, just confirm by running all tests
16:47 shk3 will try to test everything I can
16:47 olass good
16:47 olass only plugin junit tests need testing
16:48 olass since standalone junit does not need OSGI
16:48 shk3 import works as well
16:49 shk3 shall I do that instead of a dependency?
16:57 shk3 tests look good
16:58 CIA-33 bioclipse: shk3 * r9326 /bioclipse2/trunk/plugins/net.bio​clipse.core/META-INF/MANIFEST.MF: import instead of dependency
17:03 olass shk3: was that a revert or a new commit?
17:03 olass was there no import from before?
17:03 shk3 new commit
17:03 shk3 yous uggested import
17:03 olass and there was no import previously?
17:04 olass shk3: right?
17:04 shk3 yes
17:04 shk3 not of that package
17:04 olass ok
17:04 * olass suspect we will run into trouble if this is not handled with cafre
17:08 shk3 well, not sure
17:08 shk3 I warned you ;-)
17:13 olass did you warn me?
17:14 * olass never heard that
17:14 olass import should not do any harm
17:14 olass dependency is much worse
17:15 shk3 http://wiki.bioclipse.net/index.php?​title=General_Issues_with_Logging_in​_Bioclipse2#How_to_handle_an_error
17:15 zarah shk3's link is also http://tinyurl.com/c5jrfs
17:20 masak @pz console
17:20 zarah [695] Give jmoloutput to jmol console    http://tinyurl.com/d6afq4
17:21 zarah [729] Remove the Eclipse Console from... http://tinyurl.com/ccq4d7
17:21 zarah [605] Drag and drop of IBioObjects fr... http://tinyurl.com/czwcze
17:21 zarah [268] Failing test for spectrum          http://tinyurl.com/ccczo6
17:21 zarah [706] The error message about Bioclip... http://tinyurl.com/ddrg8t
17:21 zarah Entire list (39) at http://tinyurl.com/6pke5y
17:39 egonw olass: OK
17:39 olass gut gut
17:40 * olass is away for dinner
17:40 edrin egonw: did you finish the editing of the doc?
17:40 egonw yes, emailed about that
17:40 edrin ok
17:40 egonw around 14:00 or so
17:40 egonw at least for today
17:40 edrin so i will start editing it, ok?
17:41 egonw discussion and conclusion are now full english sentences
17:41 egonw yes
17:41 edrin k
17:43 shk3 is anybody willing to have a look at bug 268?
17:44 shk3 I am probably missing something, but I can't see what's wrong
17:44 egonw @pz 268
17:44 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=268
17:45 egonw no idea when I have time for it, but if you're really stuck you can assign to me
17:59 CIA-33 bioclipse: ospjuth * r9327 /bioclipse2/trunk/plugins/net.bioclipse.jmol/doc/ (15 files in 2 dirs): Added minimal docu pages for Jmol.
18:00 CIA-33 bioclipse: ospjuth * r9328 /bioclipse2/trunk/plugins/net.bioclipse.jmol/ (5 files in 3 dirs): Hooked in jmol help in dynamic help + TOC.
18:04 CIA-33 bioclipse: ospjuth * r9329 /bioclipse2/trunk/plugins/net.bioclipse.jmol/doc/ (jmolScriptEditor.html jmolScriptEditor.png): Added creenshot of JmolScriptEditor.
18:18 CIA-33 bioclipse: ospjuth * r9330 /bioclipse2/trunk/plugins/net.biocli​pse.ui/html/workbench/wb_menus.html: Updated docs for general Bioclipse menu.
19:00 edrin egonw: around?
19:00 egonw yes
19:00 egonw but really busy
19:00 egonw what's up?
19:02 edrin i was just wondering about the text you wrote, my english is not really the best but do you think the red marked letters in the first paragraph are wrong in grammar, too?
19:03 egonw no sure who made it red... but agreed, that's not good english
19:03 egonw at least, erally diificult to read
19:03 egonw (did I write that? if so, sorry about that)
19:04 edrin i think so ;)
19:04 edrin i will fix it ok?
19:04 egonw yes
19:13 olass I made it red
19:14 olass I think it's wrong
19:14 edrin me too
19:21 edrin regarding the word "web", isn't this http?
19:22 edrin egonw: isn't web http?
19:23 egonw olass: there actually are a two things in the course that are new to me: rough sets, and statistical molecular design
19:23 egonw the latter combines things I already know
19:23 egonw but never really seen this application
19:23 egonw edrin: yes, I think so: http := web
19:24 egonw olass: in particular how the ED is set up...
19:24 edrin egonw: ok, should we replace the web in the first sentence of background with internet
19:24 egonw mom
19:25 egonw I would not start using HTTP just yet in the first paragraph
19:25 egonw but loosly introduce the transport layer, not to loose the readers in the first paragraph already
19:25 egonw as you said, http == web, so synonyms
19:26 edrin ok, you want to restrict current bioinfo usage to web = http then
19:27 egonw you don't?
19:27 edrin is biomoby http based?
19:27 egonw yes, biomoby is on top of soap
19:27 edrin ah
19:27 edrin ok
19:27 edrin thus, all current bioinfo internet services use http
19:28 edrin that's what we say here, right?
19:28 egonw yes
19:41 egonw olass: ping
19:41 egonw olass: nevermind
20:20 * olass is neverminding to the best of his ability
20:21 egonw (there was also GRIND and MoRSE which was new :)
20:40 egonw olass: ping
20:40 egonw (now for real...)
20:40 olass pong
20:40 egonw pele only has 2GB memory
20:40 * olass is sort of around
20:40 olass ok?
20:40 egonw with all things running there now...
20:40 egonw it needs more
20:41 olass ok
20:41 olass you at BMC tomorrow?
20:41 egonw it's using 1GB+ swap now
20:41 egonw yes, think so
20:41 olass lets investigate then
20:41 egonw memory is cheap, so can't be the problem
20:41 egonw ok
20:42 olass we should really run services on ws1
20:42 olass it isMUCH more powerful
20:43 egonw ok...
20:43 egonw will try to move them there tomorrow...
20:45 olass I had problems running them on ws1
20:45 olass could not get them to connect with ejabberd
20:45 olass please try you too
20:45 egonw yes will I
20:46 egonw ha, git svn speeds @ SF are nice... ~1MB/sec
20:48 rajarshi joined #bioclipse
20:56 egonw rajarshi: welcome :)
21:04 edrin cu later
21:04 edrin left #bioclipse
21:27 egonw olass: btw, I will be somewhat later tomorrow
21:27 olass ok
21:27 egonw not before 11, I think
21:27 egonw meeting at Lars' school first
21:27 olass hi rajarshi
21:27 olass ok
21:27 olass see you when you get there

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