Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-06-14

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All times shown according to UTC.

Time Nick Message
05:14 sneumann__ joined #bioclipse
05:42 egonw_ joined #bioclipse
05:48 annzi joined #bioclipse
07:01 olass joined #bioclipse
07:01 olass moin
07:02 * olass is back from a nice holiday
07:03 Gpox joined #bioclipse
07:04 egonw Gpox: when are you going on holiday again?
07:06 Gpox haven't set a date yet
07:08 * egonw is leaving at the end of this month, for three weeks
07:10 * olass has just come back
07:11 egonw no further holidays then?
07:13 * egonw is still working on the book chapters
07:13 egonw singular really...
07:14 egonw still working on Chapter 3: Representing Molecules in Computers
07:14 s_wolf joined #bioclipse
07:18 mgerlich joined #bioclipse
07:22 sneumann__ joined #bioclipse
07:22 egonw when jonalv gets in, we should have a 2.4 status meeting, I guess
07:23 egonw olass: Standard InChi + OS/X is commited, but sometimes seems to fail with class loading problems...
07:23 olass damn
07:23 egonw Gpox: is InChI generation still working on your machine?
07:23 olass egonw: status meeting < Yes, would be nice
07:24 Gpox I belive so
07:24 egonw olass: yeah, the cause is unclear
07:24 egonw Gpox: on jonalv's machine it was not...
07:24 egonw Gpox: did you also test the exported version?
07:25 Gpox Yes it works
07:26 egonw good
08:27 jonalv joined #bioclipse
08:28 jonalv moin
08:28 jonalv or something
08:28 * jonalv misses zarah
08:31 egonw http://github.com/bioscala/bioscala
08:34 Gpox joined #bioclipse
08:38 egonw @pz 1647
08:39 sneumann__ I miss zarah too, but what do you expect on a monday morning ?
08:44 jonalv ah true
09:00 zarah joined #bioclipse
09:02 egonw hi zarah
09:07 jonalv zarah: welcome back
09:07 zarah jonalv: are you making fun of me?
09:07 jonalv it sure is monday morning...
10:00 olass hi zarah
10:00 olass zarah: hi
10:00 zarah hello olass :)
10:22 mgerlich joined #bioclipse
10:26 sneumann joined #bioclipse
10:55 sneumann joined #bioclipse
11:09 egonw joined #bioclipse
11:20 * egonw is heading to his TV and tunes in on NL-DK
11:24 masak joined #bioclipse
11:24 ice9 joined #bioclipse
11:25 ice9 hi! Are there any "development from scratch" instructions for 2.4?
11:26 egonw mmm... no
11:26 egonw closest match: http://wiki.bioclipse.net/index.ph​p?title=Checking_out_Bioclipse_2.2
11:26 zarah egonw's link is also http://tinyurl.com/yaxkhfy
11:27 ice9 yeah. I'm kind of stuck at the "Apache Commons Codec" feature. Can't see it in Galileo. Maybe I'm looking at the wrong update site?
11:27 egonw Gpox: do you have time to copy/paste from this 2.2 page to describe the new target_platform approach?
11:27 egonw ice9: forget that...
11:28 egonw the 'new' way to do this, it is the target platform that will download the dependencies...
11:28 egonw but that is not explained in the wiki yet...
11:28 ice9 aha. So when I set the target platform all those nasty red flags will go away?
11:39 egonw yeah, it should
11:51 ice9 indeed they did go away :)
11:52 jonalv masak: didn't you work on a wiki page for 2.4?
11:53 jonalv masak: or did I dream that?
11:53 masak you dreamt that.
11:53 jonalv :(
11:56 ice9 do I need to set target platform again after importing cdk and chemoinformatics?
11:57 ice9 a bunch of bundles are unresolved after importing them
12:06 jonalv ice9: hm I don't think you should have to do that. Which ones?
12:10 egonw resetting target platform will seldomly hurt...
12:20 ice9 egonw: i showed the errors to janalv and was directed to you
12:20 ice9 do you have some sort of pastebin you prefer?
12:21 ice9 (resetting target platform made no difference)
12:32 egonw @google pastebin
12:32 zarah egonw: http://pastebin.com/
12:33 egonw http://bioclipse.pastebin.com/
12:33 zarah egonw's link is also http://tinyurl.com/7ckm92
12:38 ice9 http://bioclipse.pastebin.com/YR6ARUqg
12:38 zarah ice9's link is also http://tinyurl.com/327vnhh
12:40 ice9 put up the list of problems, let me know if you need more
12:41 ice9 (didn't include the type resolution issues)
13:00 egonw ice9: did you import the plugins from org.openscience.cdk/externals too?
13:00 egonw sorry for the delay... I'm hacking on book chapters for the pharmbio.org course
13:04 ice9 nah, probably not
13:04 ice9 not used to eclipse devel
13:05 ice9 actually, they seem to be imported
13:06 ice9 but if I remember correctly, when switching to 2.4.x in another workspace of mine, we had to remove them first and then import then
13:06 ice9 is there an order dependency for importing core, chemoinformatics and cdk?
13:07 egonw don't think it matters, but the order would be: core, cdk, chemoinformatics
13:08 ice9 ok. That's actually the order I imported them in
13:09 ice9 pulled core today from git, anything in chem and cdk I should catch up with perhaps?
13:09 egonw do you have 2.4.x branches for bioclipse.* all of them
13:09 egonw and the bioclipse2.4.x for org.openscience.cdk ?
13:09 ice9 should have, jonalv helped me set it up
13:10 ice9 yup
13:13 ice9 pulled/refresh/clean, problems remain
13:18 ice9 aha. this is starting to look familiar.
13:18 ice9 javax.vecmath was "empty"
13:19 ice9 removed and imported again from cdk/external -- _that_ problem went away
13:19 egonw ah...
13:23 ice9 same thing with cdk.core, and I'm guessing the rest as well.
13:23 ice9 I'll add the rest of them..
13:24 ice9 (brilliant feature of Eclipse showing the expansion arrow even if it's empty)
13:31 ice9 something is terribly wrong with my import. Most of org.openscience.cdk.* is empty
13:31 ice9 *sigh*
13:52 ice9 thanks for the input, I'm giving up for today now
13:59 egonw jonalv: ping
14:00 egonw jonalv: did you finish the bioclipse.requiresVersion() method?
14:00 jonalv egonw: oh right no
14:00 jonalv oops
14:00 jonalv there was something with that
14:00 egonw tests?
14:00 jonalv I needed something
14:00 egonw I think I said I would try the SDK
14:00 jonalv yea tests
14:00 jonalv that was it
14:00 egonw ok, I'm on it...
14:00 egonw Chapter 3 is done for now...
14:01 jonalv sounds good
14:01 egonw a whopping 28 pages...
14:01 egonw bit several Bioclipse Excursions
14:01 jonalv ah nice
14:10 CIA-71 bioclipse.core: jonalv 2.4.x * r14d543f / plugins/net.bioclipse.logback/src/logback.xml : Merge branch '2.4.x' of github.com:olas/bioclipse.core into 2.4.x - http://bit.ly/b1aVYO
14:11 CIA-71 bioclipse.core: jonalv 2.4.x * r1dd3aba / plugins/net.bioclipse.scripting/src/net​/bioclipse/scripting/JsEnvironment.java : removed old leftovers - http://bit.ly/ahtLHe
14:11 CIA-71 bioclipse.core: jonalv 2.4.x * r08e07b5 / plugins/net.bioclipse.scripting/src/net​/bioclipse/scripting/JsEnvironment.java : indentation and whitespace - http://bit.ly/9ImOR4
14:17 egonw masak-- (for messing with my agenda :)
14:20 jonalv masak: what did you do now?
14:20 masak I have not the slightest idea.
14:20 masak but some people enjoy randomly removing others' karma... :(
14:21 egonw blame jonalv... he pointed at you
14:21 jonalv blame blame blame
14:21 jonalv It's always my fault
14:21 egonw hehehehe
14:21 egonw no, only when we cannot blame someone else :)
14:21 masak egonw: I don't know what jonalv has said. so I can't defend myself.
14:22 masak in any case, probably not a topic for #farmbio.
14:22 * egonw feels jonalv is not self-confident enough
14:22 jonalv masak: this is #bioclipse
14:22 masak probably not a topic for #bioclipse either :)
14:22 masak jonalv-- # picky, picky, picky! :P
14:22 masak this won't end well... :)
14:22 * egonw noticed that ibg.uu.se was down
14:23 egonw that's where it started...
14:23 masak it's down, yes.
14:23 masak not by my making.
14:24 jonalv yea and that was masak-- fault. Or maybe not fault but.. uhm osmething I don't know. I think pwople expect masak++ to solve it. Anyway I think masak-- could have done it duirng the weekd, and after all so tdoes he it appears
14:25 masak I'm being accused for something by a person who can't spell. great.
14:25 jonalv lol +1
14:26 * jonalv can splel ist' jsut taht his figners hist the kyes in the worng odrer
14:27 jonalv masak: at leas my keyboard is silent
14:28 masak jonalv: yes, and see what good that does you. :P
14:32 egonw masak++ (just randomly)
14:32 jonalv masak++
14:33 masak :P
14:35 * egonw is installing the Bioclipse SDK
14:35 egonw 1.1.10
14:37 * egonw is restarting eclipse
14:39 * olass is restarting his brain
14:40 * jonalv wonder if his brain has a restart button somehwere
14:40 jonalv or perhaps a start button?
14:44 masak for those who are interested, it seems the IBG server had a failed hard drive, which was causing database corruption, causing some pages to produce internal server errors.
14:44 jonalv oh
14:44 jonalv really?
14:44 masak YA RLY
14:45 jonalv so when can we haz it again?
14:45 masak I feel it's no longer my domain. I'm not a hardware guy. :)
14:45 jonalv good point
14:46 jonalv who is?
14:46 masak jonalv: Olle. I'd send you an URL, but... you know... :)
14:46 jonalv *lol*
14:46 masak ...it's on the site, which is down...
14:47 jonalv @pz SMARTS
14:48 zarah [1333] 70 source files without copyri... http://tinyurl.com/nz9aff
14:48 zarah [1326] Fix serialization/deserializat... http://tinyurl.com/msm3ak
14:48 zarah [1787] Cancel SMARTS file editing thr... http://tinyurl.com/38se9eo
14:48 zarah [1788] Add individual smarts always i... http://tinyurl.com/2wals8v
14:48 zarah [680] Run SmartsMatching on files fro... http://tinyurl.com/2udxxup
14:48 zarah Entire list (13) at http://tinyurl.com/33dyuwz
15:11 jonalv egonw: do we have a SMARTS object of some kind?
15:12 egonw olass: do we?
15:12 olass no
15:12 olass just a String
15:13 olass wel..
15:13 olass maybe there is an internal object in SMARTS plugin for showing it in the UI
15:13 * jonalv found bug 1197
15:13 jonalv @pz 1197
15:13 olass don't remember
15:13 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1197
15:13 jonalv I was just wondering if we had something like cdk.newSMARTS or so
15:14 olass nope
15:14 olass that does not exist
15:19 CIA-71 bioclipse.ds: Arvid Berg 2.4.x * rb576445 / (7 files in 5 dirs): Fix for changes of RendererParameters and builders in cdk - http://bit.ly/arzToJ
15:20 CIA-71 bioclipse.ds: Arvid Berg 2.4.x * rdc42d09 / (2 files): Changes for renderer parameters form cdk - http://bit.ly/dx3CSA
15:20 CIA-71 bioclipse.ds: jonalv 2.4.x * ra5867f5 / (2 files in 2 dirs): Set version to 2.4.0.RC2 - http://bit.ly/bbuRRq
15:23 CIA-71 bioclipse.balloon: jonalv 2.4.x * re956f68 / features/net.bioclipse.balloon_feature/feature.xml : Set version to 2.4.0.RC2 - http://bit.ly/clDpBR
15:25 CIA-71 bioclipse.balloon: Ola Spjuth 2.4.x * r7f53b3c / plugins/net.bioclipse.balloon.business/src/n​et/bioclipse/balloon/business/Activator.java : Set timeout for manager to 30 secs instead of 10. - http://bit.ly/9Azosh
15:27 olass egonw: ping
15:28 egonw pong
15:28 olass please have a look at my bioclipse.experimental git repo fork queue:
15:28 olass http://github.com/olas/bioc​lipse.statistics/forkqueue
15:28 olass it seems many commits by you are not applied
15:29 olass no idea how I have missed that
15:29 olass but you have write access now to stats repo
15:29 olass can you maybe look at sorting this out?
15:29 egonw [06/14/10 17:28] <olass> please have a look at my bioclipse.experimental git repo fork queue:
15:29 egonw [06/14/10 17:28] <olass> http://github.com/olas/bioc​lipse.statistics/forkqueue
15:29 egonw stats, not experimental, right?
15:29 olass yes
15:29 olass sry
15:29 olass link is correct
15:30 egonw sorry, I might have pushed to the wrong upstream perhaps
15:30 CIA-71 bioclipse.statistics: jonalv 2.4.x * rfea3dcd / features/net.bioclipse.stat​istics_feature/feature.xml : Set version to 2.4.0.RC2 - http://bit.ly/d4TYAL
15:30 olass no idea what problem is
15:30 olass but please confirm fixes are in 2.4.x and master please
15:30 egonw olass: these are really old
15:30 egonw are you sure they are not yet in your copy too?
15:31 olass mom
15:31 egonw olass: as far as I can see, they are
15:31 egonw I see quite a few commits in your branch dated Dec 16
15:31 olass yes, looks like it
15:31 egonw merged in on 02-07
15:31 olass ok, then I will delete the pull requests
15:32 olass no idea why they are still here
15:32 olass done
15:32 egonw ok, good
15:32 egonw I love it when a plans comes together
15:32 olass a plans?
15:33 egonw yes, that's the problem with cheap rip offs
15:33 egonw they are never quite right :)
15:33 egonw oh no...
15:33 egonw can you access pele?
15:33 olass yes
15:34 olass well
15:34 egonw mmm...
15:34 olass ?
15:34 olass no
15:34 olass seems down
15:34 olass damn
15:34 egonw damn
15:34 egonw cannot log in either
15:34 egonw yes, pele is down
15:34 egonw bugger
15:35 egonw and only barely...
15:35 egonw [06/14/10 17:31] <-- zarah has left this server (Ping timeout: 252 seconds).
15:35 olass egonw: will you be at bmc tomorrow? Someone at BMC data need to push the rest button...
15:35 * olass will be in italy
15:35 egonw yes, I will be at BMC tomorrow
15:35 olass maybe ask Anders at BMC data?
15:36 olass tomorrow=
15:36 olass ?
15:36 egonw or Magnus?
15:36 CIA-71 bioclipse.qsar: jonalv 2.4.x * r1cea025 / (2 files in 2 dirs): Set version to 2.4.0.RC2 (+5 more commits...) - http://bit.ly/c8chz9
15:38 olass @tell jonalv please send pull requests for RDF and cheminfo repo to egonw and not to me
15:39 olass Magnus might not have key to that server room
15:39 olass but feel free to ask
15:39 olass BMC data hosts that server
15:40 egonw olass: no worries about those... jonalv send them to everyone :)
15:40 olass why?
15:40 olass ok, good to know..
15:41 egonw ok, will email anders lovgren
15:43 egonw dinner, bbl
15:46 egonw_ joined #bioclipse
15:53 egonw_ joined #bioclipse
15:59 egonw__ joined #bioclipse
16:28 egonw pele is back online
16:29 egonw and has not been down either:
16:29 egonw $ uptime
16:29 egonw 17:25:45 up 138 days,  3:12,  2 users,  load average: 0.08, 0.13, 0.16
16:29 egonw so, must have been a network problem
16:31 olass I see
16:31 olass good
16:55 CIA-71 bioclipse.sdk: Egon Willighagen master * rc48fcd4 / (2 files in 2 dirs): Removed code that created a scripting contribution for the test plugin (fixes #1737) - http://bit.ly/9nqVQQ
16:55 CIA-71 bioclipse.sdk: Egon Willighagen master * r9d9ba13 / (3 files in 3 dirs): Release Bioclipse SDK 1.1.10 (available from the update site) - http://bit.ly/dCBFFo
16:55 egonw @tell jonalv the Bioclipse SDK is working for me...
16:56 egonw @tell jonalv use the New Plug-In Project wizard
16:56 egonw @tell jonalv a new Bioclipse SDK 1.1.10 is released and online on the update site
17:17 CIA-71 bioclipse.core: Egon Willighagen 2.4.x * r54ba504 / (13 files in 3 dirs): Added a missing test plugin - http://bit.ly/94IpMB
18:52 sneumann joined #bioclipse
20:07 sneumann joined #bioclipse

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