Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-12-17

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All times shown according to UTC.

Time Nick Message
08:28 olass joined #bioclipse
08:28 olass moin
08:28 zarah hi olass
08:44 egonw joined #bioclipse
08:46 egonw moin
08:47 zarah hi egonw
08:47 masak joined #bioclipse
08:53 edrin joined #bioclipse
08:53 sneumann joined #bioclipse
09:13 edrin http://xkcd.com/518/
09:16 egonw flow charts are always funny
09:16 masak how meta.
09:19 egonw how's life over at Lenny's?
09:19 egonw running eclipse3.41 on OpenJDK?
09:19 egonw or IcedTea?
09:23 masak egonw: haven't gotten to eclipse yet.
09:23 masak going to try to switch from Gnome this morning.
09:23 egonw oh, and while at it... install apt-p2p
09:24 masak egonw: sounds nice.
09:25 jonalv joined #bioclipse
09:27 sneumann hi there
09:27 jonalv hi
09:27 zarah hi jonalv
09:28 egonw hi sneumann, jonalv
09:28 sneumann Last week I got around to fix some stuff in XCMS to export  CMLSpect
09:28 egonw oh, cool
09:28 sneumann but Bioclipse (1.2)  was unwilling to show spectra
09:28 egonw ok, let's try BC2 ...
09:28 egonw still in alpha...
09:28 masak or some other greek letter.
09:29 sneumann where do I find the minimum requirements for CMLSpect to show up in BC ?
09:29 egonw but Stefan has ported specmol already
09:29 egonw conventions implemented in schematron
09:29 sneumann And where do I find the CMLSpect for BC2 ?
09:29 egonw the CMLSpect paper should have them as SI
09:29 egonw mom...
09:29 egonw download BC2 from sf.net/projects/bioclipse
09:29 sneumann My stuff verifies against the schematron we hacked up here in Halle
09:30 sneumann I got BC2 fine,
09:30 egonw and CMLSpect is part of Speclipse:
09:30 sneumann but no CMLSpect stuff
09:30 sneumann Ah
09:30 egonw oh, well, please read: http://wiki.bioclipse.net/​index.php?title=Speclipse
09:30 zarah egonw's link is also http://tinyurl.com/5vumof
09:30 egonw ummm...no link to the update site...
09:30 egonw mom
09:31 egonw http://www.ebi.ac.uk/steinbeck-srv/specl​ipse/net.bioclipse.speclipse-updatesite/
09:31 zarah egonw's link is also http://tinyurl.com/5cvnvp
09:31 sneumann merci
09:32 egonw you'll need to add this update side once you booted BC2
09:32 egonw it's in the Prefs section
09:32 sneumann while at it, we only did MS1 spectra back then.
09:32 egonw yes
09:32 sneumann how would I proceed to export the xcmsFragments into CMLSpect
09:32 egonw as CML
09:32 sneumann Hack up an example and discuss here ?
09:33 egonw yes, sounds good
09:33 egonw then I finally get to some WUR left overs...
09:33 egonw will set up a MetWare instance here in Uppsala over the holidays...
09:34 egonw and really need to finish up that paper now :(
09:34 sneumann http://wiki.bioclipse.net/​index.php?title=Speclipse
09:34 zarah sneumann's link is also http://tinyurl.com/5vumof
09:34 sneumann An update site is available at EBI, which is maintained by the Steinbeck Group.
09:34 egonw sneumann: is the code up for download? then I can make a patch to export xcmsFragments
09:34 egonw sneumann: right
09:35 sneumann Code is the hacked playground/CML/... stuff from Mark,
09:35 egonw ok, good
09:35 sneumann I'll commit tonight
09:35 sneumann bbl
09:35 egonw ok
09:45 masak hm, is it evident enough that ui.exists() takes a filename as an argument?
09:49 egonw masak: good point...
09:50 egonw fileExists()?
09:57 masak I was thinking the same thing. it's clearer, I think.
09:57 masak whereas save() and open() are already quite clear.
10:03 masak joined #bioclipse
10:04 masak aah. ratpoison++
10:05 jonalv karma ratpoison
10:05 zarah ratpoison has a karma of 1
10:13 egonw masak: please file a short bug report, as reminder for me
10:14 masak egonw: ack.
10:14 egonw tack
10:14 masak @pz
10:14 zarah masak: Pelezilla is at http://pele.farmbio.uu.se/​cgi-bin/bugzilla/index.cgi
10:14 olass @pz ratpoison
10:14 zarah olass: Zarro boogs found.
10:37 egonw OMG... by a mac
10:37 egonw not a dell lattide...
10:38 egonw the l keyboard key just came off
10:38 egonw and I think the t is next...
10:39 egonw this really sucks
10:39 shk3 joined #bioclipse
10:40 egonw fortunatey I do not use the much
10:40 masak joined #bioclipse
10:46 jonalv egonw: is your new computer already falling apart?
10:47 egonw yes :(
10:47 egonw this is really bad
10:47 masak apart--
10:47 egonw I mean... it's not even a week old!
10:47 jonalv egonw: aouch
10:47 egonw the l key is off
10:47 masak must be a faulty manufacture or sump'n
10:47 egonw and cannot be reconnected
10:47 egonw the t is close
10:47 jonalv egonw: you should have bought an apple computer...
10:47 egonw to getting loose
10:48 egonw jonalv: yes, one would think so
10:48 egonw actually... I think the sound head phone connected is broken too
10:48 egonw but have to verify that under windows first
10:48 jonalv actually I think you can hand it in and get the isk back
10:48 jonalv oh I mean money
10:49 egonw nah... I'm happy with it otherwise
10:49 egonw like masak says...
10:49 egonw bad monday machine
10:49 egonw it happens
10:50 egonw annoying thing is...
10:51 egonw that the install over the weekend was all for nothing...
10:51 CIA-32 bioclipse: shk3 * r8067 /bioclipse2/trunk/plugins/net​.bioclipse.chemoinformatics/ (4 files in 3 dirs): added a molecule file content provider
10:51 egonw and that I have to take my heavier laptop on holiday :(
10:52 egonw and I was just getting used to a Swedish keyboard ayout
10:52 egonw +l
10:53 egonw well, on the bright side... they keyboard backlight for the l is very visible now :)
10:53 jonalv egonw: you have swedish keyboard layout? why oh why?
10:53 egonw becuase we are in swedish?
10:53 egonw becuase we are in sweden?
10:53 masak egonw: I'd agree with jonalv, the swedish layout is not good for much.
10:53 jonalv I am trying to unlearn it...
10:53 masak Swedish letters can be made by other means.
10:54 egonw paper/pen
10:54 masak no need to squander good keys to get to them.
10:54 egonw scan them
10:54 CIA-32 bioclipse: shk3 * r8068 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (4 files in 2 dirs): added some general file browsing classes
10:54 masak egonw: sure, whatever floats your boat.
10:54 CIA-32 bioclipse: shk3 * r8069 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui.sdfeditor/ (7 files in 3 dirs): using contentproviders from other plugins
10:55 masak wow, checking out all of bioclipse (incl. branches and tags) really isn't a good idea. aborting.
10:58 egonw well, any swedish keyboard is better with a l key than any US layout without...
10:58 egonw boy this sucks...
10:58 egonw typing speed is really lowering
10:59 masak egonw: don't be so squeamish. there are lots of English words without the letter 'l' in them.
10:59 egonw but the t is close to coming off too...
10:59 egonw and without l and t?
10:59 egonw nah...
11:00 CIA-32 bioclipse: shk3 * r8070 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): put all new wizards for spectra in one category
11:00 egonw if the t does come off... I'll get back on my old machine...
11:01 shk3 hi
11:01 zarah hi shk3
11:01 shk3 just saw that there are wizards for New MDL file etc.
11:01 egonw hi shk3
11:01 shk3 but they are in other
11:01 shk3 I made a chemistry file category
11:02 shk3 for sdf
11:02 shk3 shouldn't the other chemistry files go in there as well?
11:02 egonw sure
11:02 egonw file a bug report, or just add them
11:03 egonw thanx for adding the cat
11:05 shk3 ok, now I am going put the right icons in...
11:05 CIA-32 bioclipse: shk3 * r8071 /bioclipse2/trunk/plugins/net.bioc​lipse.chemoinformatics/plugin.xml: put new wizards into a chemestry files category
11:19 CIA-32 bioclipse: egonw * r8072 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Renamed method to make it more clear it applies to files
11:21 gilleain joined #bioclipse
11:22 CIA-32 bioclipse: shk3 * r8073 /bioclipse2/trunk/plugins/net.bioclip​se.nmrshiftdb/src/net/bioclipse/nmrsh​iftdb/wizards/DisplayWizardPage.java: using content and label providers from other plugins
11:22 CIA-32 bioclipse: shk3 * r8074 /bioclipse2/trunk/plugins/net.bioclipse.specmol/ (5 files in 2 dirs): using content and label providers from other plugins
11:23 CIA-32 bioclipse: shk3 * r8075 /bioclipse2/trunk/plugins/net.bioclipse.spectrum/ (4 files in 2 dirs): using content and label providers from other plugins
11:31 shk3 some questions:
11:31 shk3 there is a 2D-Structure view in net.bioclipse.cdk.ui
11:32 shk3 it seems to be broken (for me at least) and what is this supposed to do?
11:32 shk3 there is also a JChemPaintView (which is not the editor, right?)
11:32 shk3 only showing an empty window for me.
11:32 shk3 what is this for?
11:39 egonw showing content
11:39 egonw I think arvid showed it in action last week
11:40 shk3 which one?
11:58 egonw not sure
12:01 egonw file a bug report brining up the problem you found
12:35 jonalv is there a folder in Bioclipse SVN for documentation?
12:35 egonw depends on the type of docs
12:36 egonw several plugins have a docs/ folder
12:36 jonalv class diagrams?
12:36 egonw no, don't think so
12:39 jonalv egonw: help:
12:39 jonalv git svn rebase
12:39 jonalv plugins/net.bioclipse.ui/bioclipse.product: needs update
12:39 jonalv update-index --refresh: command returned error: 1
12:39 jonalv
12:39 jonalv I thought that was what I was trying to do...
12:39 egonw git stash
12:39 egonw git svn rebase
12:40 jonalv and then unstash?
12:40 egonw yes
12:40 egonw git stash apply
12:40 jonalv how do I do that?
12:40 jonalv aha
12:40 masak cool
12:40 * masak hasn't used stash so far
12:40 masak seems useful.
12:41 jonalv that seemed to woek. thanks egonw++
12:41 egonw <masak> *is* usefull
12:42 * masak feels useful
12:48 egonw gilleain: ping
12:49 gilleain 'lo
12:49 egonw hej, #cdk please
12:49 egonw I picked the wrong channel
13:02 masak the directory bioclipse2/trunk/outdated, could someone explain why we have that?
13:02 masak there are 1328 .java files in the plugins directory, FYI. :)
13:03 shk3 to keep outdated stuff (=cdk10) somewhere
13:04 masak shk3: so no-one is using it, but we want to keep it around?
13:04 shk3 that was my understanding, yes
13:04 masak I see.
13:05 masak there are several approaches to keeping stuff around, of course. one alternative way is to use svn.
13:05 masak but maybe that was impractical in this case.
13:07 shk3 but this uses svn?
13:07 gilleain my preferred method to keeping old code that I am never going to look at again, let alone use, is to not keep it. By throwing it out.
13:08 masak gilleain: aye.
13:09 masak shk3: no, this does not use svn in any reasonable sense of the word "use".
13:09 masak using svn means trusting that things are there even when you've removed them from HEAD.
13:09 masak among other things.
13:10 shk3 ok. I didn't do it
13:10 shk3 so this time I cannot be blamed
13:10 masak shk3: not blaming you. :)
13:10 egonw masak: it's not unused yet
13:10 masak egonw: ah. I see.
13:10 egonw the rdfeditor makes use of it
13:11 egonw it's just outdated...
13:11 egonw which should explain the name :)
13:11 egonw or you prefer needsupdates?
13:11 egonw but then we can better put everything in there :)
13:14 jonalv shk3: is there some way to test the behavior of that MoleculeFileContentProvider?
13:19 masak egonw: I'm fine with the name. just wondering if we were keeping it around for sentimental reasons.
13:19 masak I tend not to like keeping things around for sentimental reasons. that's like using svn and still making file backups.
13:20 masak no, that _is_ using svn and still making file backups.
13:21 shk3 jonalv: use the new sdf wizard
13:21 jonalv shk3: oki thanks
13:22 shk3 there is one problem
13:22 shk3 I would like it to use file extensions from plugin.xml
13:22 shk3 in net.bc.cdk.ui
13:22 egonw masak: agreed with that
13:22 shk3 defined there for moleculeType
13:22 shk3 I try to find out if I can do that
13:23 shk3 make the contentprovider to show all files of moleculeType
13:23 egonw shk3: doesn't bc2 move away from using file extensions?
13:23 shk3 parsing everything is even worse
13:23 shk3 I think would be ok here to use extensions
13:24 jonalv shk3: okey, I wasn't totally happy with the result of your refactoring so I have taken the liberty to refactor it again. Now I just want to test that it still does what it is supposed to do...
13:24 egonw ummm...
13:24 egonw shk3: why rely on extensions if bc2 would already detect file types?
13:25 egonw and the latter does not parse the complete file at all
13:25 masak jonalv++ # renegade cleanups
13:27 jonalv shk3: do you have som use case example using sample data that you know works?
13:27 shk3 don't know how to do that
13:27 shk3 reusing contenttypes
13:27 shk3 I think about it
13:27 egonw ask on the mailing list
13:27 laca69 joined #bioclipse
13:27 masak laca69: greetings.
13:27 shk3 btw, stuff like net.bioclipse.contenttypes.mdlMolFile2D is still defined via file extensions
13:27 olass hi laca69
13:28 laca69 tjena
13:28 egonw hi laca69
13:28 shk3 looking into files is only done for cml
13:28 jonalv hi laca69
13:28 shk3 at least that's my understanding
13:28 masak hi laca69
13:28 laca69 just got introduced by olass
13:28 egonw shk3: ok, so please reuse those net.bioclipse.contenttypes
13:28 egonw instead of writing some custom code
13:28 masak laca69: meet zarah, our housekeeper bot.
13:29 masak zarah: you're a smart girl.
13:29 zarah masak: Then why did you turn me down for that raise?
13:29 masak uhm.
13:29 jonalv zarah: meet laca69
13:29 zarah jonalv: excuse me?
13:29 masak zarah: he's making fun of you.
13:29 zarah masak: excuse me?
13:29 masak bah, forget it.
13:29 olass @karma olass
13:29 zarah olass has a karma of 2
13:30 olass @google bioclipse
13:30 masak @karma olas
13:30 zarah olass: http://www.bioclipse.net/
13:30 zarah olas has a karma of 46
13:30 olass @pz jcp
13:30 zarah [155] File not working in new jcp        http://tinyurl.com/5hlk8o
13:30 zarah [165] Color atoms and bonds in JCP fr... http://tinyurl.com/5q4sks
13:30 zarah [15] JCPView based on CDK does not di... http://tinyurl.com/5nrsdv
13:30 zarah [172] Custom tooltips for atoms/bonds... http://tinyurl.com/5ejuya
13:30 zarah [173] Set custom font in new JCP rend... http://tinyurl.com/5pk76x
13:30 zarah Entire list (16) at http://tinyurl.com/65hbv9
13:30 egonw olass: did you get the cc on the broken keyboard of my no-longer fancy laptop?
13:30 olass yes
13:31 egonw ok
13:31 masak zarah: you're the many-talented one!
13:31 zarah masak: no, YOU are the many-talented one!
13:31 * shk3 and glleain are for a meeting
13:31 egonw @gg bioclipse
13:31 masak egonw: adding @gg as a synonym for @google.
13:31 olass zarah: you are the stupid one
13:31 zarah olass: no, YOU are the stupid one!
13:31 egonw @google bioclipse
13:31 zarah egonw: http://www.bioclipse.net/
13:31 egonw masak: :)
13:35 masak egonw: I'm not my usual fast self, due to missing modules on this new computer.
13:35 jonalv shk3: I can not read the sdf file with the sdf file ditor...
13:36 egonw masak: no worries
13:36 olass egonw: help
13:36 olass atom type fails for this:
13:36 olass DEBUG - AT null for atom: Atom(3136286, S:C, 2D:[(0.0, 0.0)], AtomType(3136286, FC:0, NC:0, EV:0, Isotope(3136286, MN:12, EM:12.0, AB:98.93, Element(3136286, S:C, AN:6))))
13:36 olass Arom: false
13:36 olass how could that be?
13:36 egonw context?
13:37 olass trying to percieve atom types
13:37 olass sybyl atom types
13:37 egonw sure
13:37 olass one atom type gets null
13:37 egonw need some code snippet, or so
13:37 egonw oh...
13:37 olass ok, so you can't depict from atom?
13:37 egonw a single atom?
13:38 egonw no neigbors?
13:38 olass no
13:38 olass that's just the atom that fails...
13:38 egonw umm...
13:38 olass I could hack up a junit test for you
13:38 olass it's from an SDFile with 232 mols
13:38 egonw an atom type is depending on the bonded atoms too
13:38 olass yup
13:38 olass guess you need that unit test?
13:39 egonw that would very much help indeed
13:39 olass ok, will do so
13:47 CIA-32 bioclipse: jonalv * r8076 /bioclipse2/trunk/plugins/net.bioclipse.chemoinfo​rmatics/src/net/bioclipse/chemoinformatics/conten​tlabelproviders/MoleculeFileContentProvider.java: Cleaned up code in MoleculeFileContentProvider. I will close bug #182 now.
13:47 zarah bug #182 | http://tinyurl.com/5zu73w
13:57 laca69 bye bye
13:57 egonw laca69: bye!
13:57 olass bye lac69
13:57 olass hope to see you soon again
14:21 CIA-32 bioclipse: carl_masak * r8077 /bot/trunk/zarah.pl: [zarah] @gg now synonym for @google
14:23 jonalv @gg synonym for google
14:23 jonalv zarah: ping
14:23 zarah jonalv: pong
14:23 masak jonalv: she needs a reboot.
14:23 jonalv zarah: boo!
14:23 zarah jonalv: eh... wha'?
14:23 masak jonalv: deprecated.
14:23 jonalv zarah: restart
14:24 zarah joined #bioclipse
14:24 jonalv @gg synonym for google
14:24 zarah jonalv: http://google.blogspace.com/archives/001019.html
14:27 CIA-32 bioclipse: carl_masak * r8078 /bot/trunk/zarah.pl:
14:27 CIA-32 bioclipse: [zarah] now only gives URLs on bug numbers on the #bioclipse and
14:27 CIA-32 bioclipse: #farmbio channels
14:27 jonalv zarah: restart
14:27 zarah joined #bioclipse
14:28 gilleain joined #bioclipse
15:10 CIA-32 bioclipse: jonalv * r8079 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java:
15:10 CIA-32 bioclipse: During drop into JS/console view replace \ with /
15:10 CIA-32 bioclipse: Fixes bug: #77
15:12 masak \with/ :)
15:13 masak gilleain: that's your bug, so you might want to have a look.
15:13 gilleain \o/
15:13 gilleain (will do)
15:13 masak :)
15:14 masak xargs++
15:14 gilleain users | xargs karma
15:15 gilleain er...anyway.
15:15 masak yes.
15:15 masak zarah has no concept of users, unfortunately.
15:15 masak she just talks to people indiscriminately.
15:15 masak zarah: you're the indiscriminate one!
15:15 zarah masak: no, YOU are the indiscriminate one! :)
15:15 egonw @karma
15:15 masak see?
15:15 zarah egonw has a karma of 31
15:16 egonw @karma all
15:16 zarah all has a karma of 0
15:16 masak all++
15:16 egonw @karma *
15:16 zarah * has a karma of 0
15:16 masak me++
15:16 jonalv *++
15:16 jonalv +++
15:16 masak jonalv: looks a bit like Perl 6. :)
15:16 jonalv ++++
15:17 jonalv karma ++
15:17 zarah ++ has a karma of 0
15:17 masak no, it's (++)++
15:17 jonalv :(
15:17 masak karma ++
15:17 zarah ++ has a karma of 1
15:17 gilleain users >>++<<
15:17 masak the rules are very clear. :)
15:17 masak gilleain: oh, an initiate. :)
15:17 jonalv (masak)++
15:17 gilleain hyper operators are very scary
15:17 masak gilleain: in a good way.
15:18 gilleain not as bad as junctions, of course.
15:18 masak full ack.
15:18 masak never combine junctions and negated comparison ops, f'rex.
15:18 masak that makes my brain curdle.
15:19 jonalv How do I credate a mylun query showing bugs that are assigned to me?
15:19 egonw owner == <your email>
15:19 jonalv egonw: yea I thought so too but it doesn't seem to work...
15:21 egonw mmm
15:21 egonw I will be @ bmc tomorrow
15:21 jonalv oh there was some strange things going on with resolved states...
15:21 egonw we can compare your settings with mine then
15:21 jonalv noit works better
15:21 jonalv |now
15:21 masak I'm about to make a commit involving 1289 .java files.
15:21 masak anyone foresee any problems? :)
15:22 * masak cackles evilly
15:23 egonw hehehe
15:23 masak I'm glad you're with me on this.
15:24 gilleain well /\//\\/ seems to work, but it's difficult to test, as tab completion is throwing string out of bounds errors.
15:24 * jonalv agrees
15:24 masak gilleain: yes, sorry about that.
15:25 masak I don't know why it's doing that.
15:25 gilleain what's an easy test I can do on a path? jcp.load(path)?
15:25 jonalv cdk.loadMolecule
15:25 gilleain okey
15:26 gilleain great. that does things and stuff.
15:27 jonalv yup :)
15:27 CIA-32 bioclipse: carl_masak * r8080 /bioclipse2/trunk/keep-clean.pl: [keep-clean.pl] script to remove unnecessary whitespace
15:29 gilleain hah. lol @ the comment below "Point oldSelection = text.getSelection()" in ScriptingConsoleView :)
15:30 masak some design decisions are historically bad.
15:30 jonalv hehe
15:30 * masak chickens out and decides not to commit yet
15:31 masak there might be destructive changes made. have to check for that.
15:31 masak I remember last time I did this. there were some nasty uses of tabs, for example.
15:31 egonw yeah, where's that CLI compile of BC2 when you need it
15:32 masak well, I guess I _could_ fire up Eclipse and see if everything compiles...
15:32 masak ...but then I'd need to install Eclipse...
15:33 egonw nah, you don't want to do that
15:36 * masak doesn't
15:37 jonalv egonw: what install Eclipse?
15:37 masak jonalv: ...just to see if everything compiles.
15:37 jonalv masak: oh well it would be so like you to not check that...
15:38 masak jonalv: aye.
15:38 masak jonalv: but for other people's code, I feel a larger... responsibility...
15:38 masak or something.
15:38 jonalv yea "or something"
15:38 masak don't want to just indiscriminately destroy someone's code.
15:38 masak yeah. "or something".
15:39 jonalv no better to do it discriminately :)
15:39 masak exactly.
15:39 egonw masak: file patch reports for the differnt plugins
15:39 egonw so that the plugin owners can review the patch
15:39 masak uh.
15:39 egonw oh, you mean you do not have a script for that yet?
15:39 masak egonw: hm. :)
15:40 masak fear the power of Perl!
15:40 * masak goes back to hacking
15:40 egonw oh no...
15:40 egonw what have I done??
15:40 egonw :)
15:40 jonalv a monster?
15:40 jonalv :)
15:41 masak jonalv: 'create a monster', not 'do a monster'.
15:41 * masak doesn't know what the latter would mean
15:41 jonalv btw do we have a list of plugin owners?
15:41 * jonalv feels that could be very usefull...
15:50 CIA-32 bioclipse: carl_masak * r8081 /bioclipse2/trunk/keep-clean.pl: [keep-clean] now lists files that might need review
16:00 CIA-32 bioclipse: carl_masak * r8082 /bioclipse2/trunk/keep-clean.pl:
16:00 CIA-32 bioclipse: [keep-clean] disabled possibly destructive changes to whitespace for now
16:00 CIA-32 bioclipse: also cleared up misunderstanding about newlines
16:02 CIA-32 bioclipse: carl_masak * r8083 /bioclipse2/trunk/keep-clean.pl: [keep-clean] corrected last commit
16:03 masak ok, here it comes!
16:04 masak 1291 files.
16:04 * gilleain braces for impact
16:04 masak I decided to only make the safe changes now, until I figure out how to get an overview of the possible unsafe ones.
16:05 masak awk++ xargs++ svn++ perl++
16:05 egonw :)
16:05 egonw next time, please in Java...
16:06 egonw so we can make it proper unit tests
16:06 masak egonw: all programming languages are in some sense equivalent. but this kind of task is definitely more Perl-centric than Java-centric.
16:07 masak egonw: also, how do you propose to do unit tests on source files? I'd like to see a proof-of-concept of that.
16:16 masak still transmitting...
16:17 masak keep still, everyone! don't make any commits. :)
16:19 egonw http://www.aegisub.net/2008/12/if-prog​ramming-languages-were-religions.html
16:19 zarah egonw's link is also http://tinyurl.com/67tpdf
16:19 egonw ok, this is what happens if you do:
16:19 egonw RA layer request failed: Server sent unexpected return value (500 Internal Server Error) in response to PUT request for '/svnroot/cdk/!svn/wrk/8c331b88-30f9-47bf​-b034-d42085d96010/cdk/branches/cdk-1.2.x​/src/test/org/openscience/cdk/reaction/ty​pe/RadicalSiteRrAlphaReactionTest.java' at /usr/bin/git-svn line 461
16:20 egonw or something like that
16:20 masak egonw: I can't believe you actually tried. :)
16:20 egonw masak: this is CDK
16:20 egonw I commited to a completely different branch!
16:20 egonw different files, what ever
16:21 masak egonw: oh.
16:21 masak svn isn't very distributed, I guess.
16:22 masak egonw: but it was still in the bc repo, yes?
16:23 * masak is on the 'Transmitting file data' state now
16:24 egonw masak: no, cdk repos
16:24 masak egonw: then I don't think it's my fault...
16:25 egonw no, it's not
16:25 egonw only wanted to back up your statement 'please don't commit' :)
16:26 egonw ok, second 'git svn dcommit' attempt
16:26 egonw to cdk repos again
16:27 egonw http://www.mygrid.org.uk/tools/taver​na/taverna-2-0/download-taverna-2-0/
16:27 egonw Taverna 2.0 released
16:27 zarah egonw's link is also http://tinyurl.com/5dxqro
16:34 CIA-32 bioclipse: carl_masak * r8084 /bioclipse2/trunk/plugins/ (1291 files in 290 dirs):
16:34 CIA-32 bioclipse: [plugins/] turned line-initial tab chars into spaces, and removed whitespace
16:34 CIA-32 bioclipse: from otherwise empty lines
16:38 laca joined #bioclipse
17:23 masak left #bioclipse
18:48 edrin left #bioclipse
18:52 sneumann_ joined #bioclipse
18:52 sneumann_ zarah: tell shk3 to give http://msbi.ipb-halle.de/~sneumann/xset3.cmlspect a try
18:52 zarah sneumann_'s link is also http://tinyurl.com/5k6h3c
18:52 zarah Consider it noted.
19:35 egonw sneumann: so, what fragment info do we get from XCMS?
19:35 egonw MF's, or better?
19:38 sneumann_ From xcms not even that
19:38 egonw right
19:39 sneumann_ But Leiden assigned MF to fragments
19:39 sneumann_ as on their boston poster
19:39 egonw r
19:39 egonw indeed
19:39 sneumann_ Just Tried Specclipse
19:39 sneumann_ getting NPE
19:39 sneumann_ at net.bioclipse.spectrum.editor.SpectrumE​ditor.addPages(SpectrumEditor.java:163)
19:39 egonw :(
19:40 sneumann_ I probably need to get stuff from SVN ?
19:40 sneumann_ I have a 20081022 version
19:40 sneumann_ from the update site
19:40 egonw well, particularly what you downloaded should have worked...
19:40 egonw could you please file a bug report?
19:40 sneumann_ Hm.
19:40 egonw pelezilla.farmbio.uu.se
19:40 egonw and assign to Stefan
19:41 egonw weird NPE place, btw...
19:41 egonw did not have that one for the download version
19:44 sneumann_ Please mention this bugzilla somewhere
19:44 egonw in BC2 itself?
19:44 sneumann_ Firefox can't find the server at pelezilla.farmbio.uu.se
19:45 egonw sorry...
19:45 egonw pele.farmbio.uu.se
19:45 egonw @pz
19:45 zarah egonw: Pelezilla is at http://pele.farmbio.uu.se/​cgi-bin/bugzilla/index.cgi
19:45 sneumann_ Please report bugs in the sourceforge bug tracking system, see http://sourceforge.net/tracker/?​group_id=150681&amp;atid=778609. Click "Sumbit New"
19:45 sneumann_ http://wiki.bioclipse.net/index​.php?title=Contribute_feedback
19:46 zarah sneumann_'s link is also http://tinyurl.com/4fwvgt
19:46 zarah sneumann_'s link is also http://tinyurl.com/3e7tax
19:47 egonw :(
19:47 egonw will change that immediately
19:50 egonw updated
19:50 egonw thanx for letting me know
20:04 sneumann_ OpenID for bugzillas ?
20:06 egonw @gg openid bugzilla
20:06 zarah egonw: https://wiki.mozilla.org/B​ugzilla:OpenID_Auth_Plugin
20:09 egonw not released it seems
20:24 sneumann_ Never mind.
20:24 sneumann_ I tried reinstalling bc2
20:24 sneumann_ using the alpha2
20:24 sneumann_ and updating to 20081028
20:24 sneumann_ and got
20:24 sneumann_ !MESSAGE UpdateManagerUtils copy() at offset:1176210 [InputStream ended after 1176210 bytes (expected 1677664 )]
20:25 sneumann_ retry did not report a problem, though
20:26 sneumann_ and another one in chemoinformatics feature 20081028.jar
20:26 sneumann_ java.io.IOException: InputStream ended after 2251392 bytes (expected 4688151 )
20:31 sneumann_ So same NPE in Speclipse with freshly installed BC2 :-(
20:32 sneumann_ Lets see what shk3 finds out
20:49 egonw mmm...
20:49 egonw those inputstream exception don't look good
20:50 egonw looks like rcp internals...

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